1.

1 monomers polymers
Biological molecules refer to large chemical compounds that are found in living
(biological) organisms. Although there are approx 8.7 million species on earth, they
all contain variations of the same four bio molecules:

e
proteins

ti
lipids indirect evidence

Ka
carbohydrates of evolution

by
nucleic acids

gy
These biomolecules are referred to as polymers. They are made up of monomers

lo
o
many or multiple't v
Bi

single or alone
e

ahhh allyn allyn alkyd

ti

age
Ka

age
by

Building large polymer molecules from single monomer units is the result of
gy

condensation reactions
lo

monomers polymer
o
Bi

appt alum s appt alum

one moleculeof
H2O water is new bond
removed formed
 one molecule of water is released per new bond formed…

ahhh allyn allyn alkyd alkyd alkyd

e
u v u v u

ti
5 new bonds were formed to build this polymer

Ka
therefore 5 molecules of water must have been

by
released in the process

gy
The reverse reaction, breaking down polymers to restore the monomer units from
which it is built, is called hydrolysis
lo
o
Bi

hydro water
e

lysis to split
ti
Ka

polymer monomers
by

agginally alkyd adapt

gy
lo

one molecule of
o

water Ho used
Bi

to break bond

One molecule of water is required to break each bond

 adapt adapt noggin off nogginoff

e
this polymer is made up of 5 unique bonds

ti
as one H2o molecule is required to break

Ka
each bond 5 molecules of water are needed

by
to hydrolyse this molecule into monomers

gy
Organic: carbon-containing
Monomer: single unit
lo
o
Polymer: large molecule made up of repeating monomer units
Bi

Condensation: building polymers from monomers with the release of H2O

e

Hydrolysis: breaking down bonds using H2O

ti
Ka
by
gy
lo
o
Bi
 1 2
carbohydrates
• Monomer: monosaccharide
• Polymer(s): starch
glycogen cellulose

e
• Unique bond:
glycosidic

ti
Ka
Monosaccharides are single (mono) sugar (saccharide) units. They are the monomer

by
units of carbohydrates. We need to know about 3 monosaccharides:

gy
998 6918198
tryp
H O
co É on
lo
y
H C on H C ou c o
HO C H
o
Ho C H
H C on YE I H C on
Bi

H c on H C H H C on
H on H OH H OH
g E E
e

These three molecules are isomers of each other: they have the same chemical
ti
Ka

formula (C6H12O6) but the atoms of each molecule are arranged differently
by

We need to know the structure of the two glucose isomers: alpha and beta
gy

OCH OH OCH OH
lo

H s O H H O OH
o

s
Bi

4 I 4 1

3 2 3
140 OH 140
2
H
alpha glucose beta glucose
 Two monosaccharides bond together to form disaccharides…

AbsorbiRanYrEK
EEE

e
Glucose Galactose Fructose

ti
monosaccharides

Ka
by
t.EGB.AE iBaSPog
gBÉa

gy
maltose disaccharide

lo
t.azMN iINMI
o
FFD
Bi

lactose disaccharide
e
ti

at
Ka

MtBMMEMK
tgaaOK.x H2O
Mtwara Mohawk
tag
by

Fructose
sucrose disaccharide
gy

Polysaccharides are formed when multiple monosaccharide units come together to

lo

form a long chain. The first polysaccharide is starch. It is an alpha-glucose storage

o

molecule found in plant cells only

Bi

oasis
ii iiii i
 How starch is formed…
6CHOH 6CHOH
µ 5 O H y s O H
4 I 4 1

OH HO OH

e
HO

ti
alpha glucose alpha glucose

Ka
H2Oremoved c

by
condensation

gy
CHIH CHOH
H H H O H
lo
s 0 o 5
Bi

s 2 3
140 o
maltose
e

glycosidic
ti

bond formed
Ka

amylose
by

CHIH OCHOH
CHIH H H
H O H H s 0
s O H Holy
gy

H
s
who
s a O
g a
o s s
o
O H
lo

H t
2 s
2
o

O
HO 1-4 linkages: the glycosidic bond forms between
Bi

C-1 of one glucose, and C-4 of the other

tirIies tirexiso anarsiet

omaintitigiiansieaainiitigiiamsasoeesesiftiisYiiiiaaxixe.int

7i'iesaasaneeezi
 amylopectin
CHOH
Holy
action HH O HH
s 4 I y
O H
O t 1-6 linkages: glycosidic
s 7
bond bet ween C-1 and C-6

e
Ho
Eth

ti
CHOH H H Holt
H H H O

Ka
s 0 O
t
µ 4 y
t ly Holy
s
aits o
a O
s z O s z y o

by
O t
H 2 i s
a
0

gy
hiosaiifiomiiis

itite imresimiiiitiiminimrimiamirmmurimo

ooEt
xxx
i
tireithii lo teasigag IOsiogxxao
o
iii ii i
gii.EE iigii.be
i iiziiEmi
i oioigogg.io
Bi
xeii.EE igneous iguanas
again ignore
e

Starch…
ti
Ka

• Compact, coiled structure: a lot of glucose can be stored in a small space

• Large, insoluble: does not diffuse out of cells
by

• Large, insoluble: does not affect osmotic pressure within the cell
• Easily hydrolysed to glucose: valuable for respiration
gy

• Amylopectin branching: more sites for hydrolytic enzymes to work, therefore

lo

glucose can be released faster

o
Bi

The second polysaccharide is glycogen. This is a large polysaccharide also made up of

repeating alpha-glucose units. Glycogen is only found in animal cells, it has the
nickname ‘animal starch’ due to its similarities to starch
 How glycogen is formed…

6CHOH 6CHOH
µ s O H y s O H
4 I 4 1

e
3 2 3 2
OH 140 OH

ti
140

Ka
alpha glucose alpha glucose

by
H2Oremoved c
condensation

gy
CHOH OCHOH
H s O H H lo s O H
o
1
Bi

3 3 2
140
2 O OH
e

maltose
ti

glycosidic
Ka

bond formed
o
by
gy

1-6 linkages: glycosidic

lo

bond bet ween C-1 and C-6

tch
o

64204 HOH
H H O H H
Bi

H
H go
o s
s o
o O
µ 1-4 linkages: glycosidic 3
t
bond bet ween C-1 and C-4
 i
i i i ii.iiimi i
iiiii.im i.i.mn

ii
mii

oosidinga ieiasen tesEigp

mi

e
ismomooooomoooooiinimoooooiamainiiiimITlaaiaooooooini'tiiseis

iIi i
on

ti
Ka
iEBEtisiKis's
geighootoi
Eisai ggga

idgIiEIEargarasiiao

by
Glycogen is much more highly branched than starch (amylopectin). Glycogen has

gy
branching every 10-15 glucose, amylopectin has branching every 25 glucose
molecules
lo
o
Bi

Glycogen…
e

• Compact, coiled structure: a lot of glucose can be stored in a small space

ti
Ka

• Large, insoluble: does not diffuse out of cells

• Large, insoluble: does not affect osmotic pressure within the cell
by

• Easily hydrolysed to glucose: valuable for respiration

• Highly branched: more sites for hydrolytic enzymes to work, therefore glucose
gy

can be released faster. Needed in animals as they have a higher metabolic rate
lo
o

The final polysaccharide to learn about is cellulose. Cellulose differs from the other
Bi

two polysaccharides in that it is made up of beta-glucose molecules rather than

alpha-glucose. This affects its ultimate structure
How cellulose is formed…
 CHOH X OCHOH
H s 0 OH H s 0 OH
4 1

e
4 1
X

ti
3 2 3 2

Ka
140
beta glucose beta glucose

by
Glycosidic bond cannot form here, as once H2o is removed there will be
no atom left for the bond to form around. so, there is another version

gy
of beta-glucose: the inverted form. This is beta glucose that has been
rotated by 180°
lo
o
Bi
e
ti

CHOH
Ka

H s 0 OH HO s a H
by

4 I 4 1

S
HO
gy

3
140
2
H H O
lo

6CHzOH
beta glucose inverted beta glucose
o
Bi

inverted B glucose glycosidic bond

can form here
rotated by 1800
 H d o HH o s H

O O H O O
Hobetaigiucose
t beta glucose whom
inverted glucose inverted beta glucose

e
ti
Ka
In

by
o to s H

gy
j
I
s o H O O
lo
a
th
6 HOH
o
Bi

ftp
e

HOH
it
ti

o nothin o
Ka

a
th
II o s H
by
gy

tho
lo

gtfo
SEE
o

microfibril
Bi

to
fibril
 Cellulose…
Beta-glucose: inverted and normal glucose molecules form alternating glycosidic
bonds, forming straight, un-branched chains
Hydrogen bonding: H bonds form between hydroxyl groups, creating strong and

e
stable molecules of cellulose

ti
Microfibrils: Parallel chains group to form microfibrils

Ka
Fibrils: microfibrils group into fibrils that provide huge strength

by
Biochemical tests for carbohydrates…

gy
lo
All monosaccharides are reducing sugars. Maltose and lactose are also reducing
o
sugars. A reducing sugar is a sugar that will donate electron(s) to another chemical,
Bi

therefore reducing the other substance

e
ti

Oxidation oxidation is
Ka

1 the
Is gain of oxygen
by

2 the loss of electrons

3 the loss of
Loss hydrogen
gy
lo

Reduction reduction is
o

1 the loss of oxygen

Bi

Is 2 the gain of electrons

3 the
gain of hydrogen
Gain
 Benedict’s test for reducing sugars

Alkaline solution of copper 1 sulfate

e
ti
Ka
VI V

by
gy
1 add sample in
liquid form
2 add equal
volume of benedict'slo 3 heat in boiling
water bath for
o
5minutes
reagant
Bi
e
ti
Ka
by

VVVVV
gy
lo
o

increasing amount
Bi

The positive result (reducing sugars present) is a red precipitate. This is because the
copper || Sulfate has been reduced to copper | oxide, which is an insoluble red
precipitate. The more reducing sugar there is, the more Benedict’s is reduced
 For non-reducing sugars…

1 carry out benedicts test asabove

2 add dilute Hd and gently boil

e
3 add NAH 003

ti
4 re test with benedicts

Ka
by
• The dilute hydrochloride acid will hydrolyse any disaccharides into their
monosaccharide units, therefore showing a positive result the second time.

gy
lo
• The sodium hydrogen-carbonate neutralises the acid
o
Bi

Iodine test for starch…

e
ti

At
Ka
by
gy
lo

V.V
o

V
Bi

1 add sample 2 add iodine Positive

solution blue black
 13 lipids
Lipids refer to a diverse range of biomolecules including fats and oils. Lipids share
common chemistry in that they are comprised mainly of carbon, hydrogen and

e
oxygen atoms.

ti
Ka
There are two main types of lipids we must be aware of: triglycerides and

by
phospholipids

gy
1
triglycerides
lo
three
o
tri glyceride
Bi

three fatty acids glycerol

e
ti
Ka

• Glycerol: a simple triol molecule (three functional OH/ hydroxyl groups)

• Fatty acid: a hydrocarbon chain with a terminal carboxyl (COOH) group
by

H 0314803
gy

H OH
G
lo
o

H C OH
Bi

H d OH
I
 Fatty acids are classified as being ‘saturated’ or ‘unsaturated’.

Saturated hydrocarbon chains contain NO double carbon-carbon bonds, thus each

carbon has the maximum number of hydrogen atoms bonded

e
ti
Unsaturated fatty acids have hydrocarbon chains with at least one carbon-carbon

Ka
double bond (C=C). Consequently, they cannot form as many C-H bonds

by
1 saturated
d E EE
gy
to c c c H
H H H H H H lo
o
Bi
e
ti

É ÉÉÉ H 2 un saturated
Ka

Ho
E c H
by

H H H H H
H
gy
lo

d É É É É É É É É H 3 saturated
o
Bi

to
H H H H H H H H
 Three (tri) fatty acids form bonds with each of the hydroxyl groups on the glycerol
molecule (glyceride)

e
d d
I 4 4É fatty acid 1

ti
H
H onto

Ka
d d ftp.tcfcj
H OH Ho
I IIi c nfatyacid2

by
H d OH no d fatty acid

gy
I Egypt
H
lo
o
Drawing out the entire fatty acid chains is time consuming and often unnecessary.
Bi

We usually use the letter ‘R’ to represent variable groups and just show the atoms
e

that are directly involved in the bonding, like so…

ti
Ka

H
E
by

H C O r
1 O
gy

H C O d pl
lo

I o
o

11
Bi

H C O c pl
I
H
 Let’s look at how the final triglyceride is formed…

Y
H C OHHO
É R H C O É r

d f

e
I H o pl

ti
H C OHHO pl
nom

Ka
I
H C OH HO É pl H d o f pl

by
H H
3420

gy
Each of the new bonds is called an ester bond
lo
o
Bi
e

2 phospholipids
ti
Ka

phosphate
by

group
Phospholipids are similar in structure to a triglyceride, except one of the three fatty
gy

acids is replaced by a phosphate molecule.

lo

R
o

pop is a POLAR
Bi

9 molecule therefore
p o it is SOLUBLE in
d water
 The formation of a phospholipid molecule…
H
d I.ci
H
gouto t

e
d

ti
H onto
g EE

Ka
q
O P O HOH H
G

by
H

gy
lo
o
Bi

H
e

d d c'it
ti

H o ct E
cti E.tt
Ka

H H H H H H H H
1
É
by

It
H c o
9 I
gy

o p o C H
lo

l
d H hydrophobic
o

hydrophilic
Bi

Phospholipids are polar molecules, the two ends behave in two different ways. This
gives them unique properties that are important for cell membranes
 Hydrophilic head group will position

ma
itself close to water

e
ti
Hydrophobic tails will orientate

Ka
themselves away from water

by
In a water-based environment, a process of self-organisation takes place between

gy
phospholipids. The polar heads face water, and hydrocarbon tails face away. They

lo
arrange themselves in two layers, facing towards one another. This allows the
o
hydrophobic fatty acid chains to ‘shelter’ from water on the inside, and the two
Bi

layers of polar heads to interact with the water happily.

e
ti
Ka

AQUEOUS ENVIRONMENT
by
gy
lo
o
Bi

AQUEOUS ENVIRONMENT

This structure is referred to as the lipid bi-layer (two layers of lipids!)

 Functions of lipids…

• Monomer unit:
Waterproofing glycerol fatty acids
• Polymer (s):
Insulation
triglyceride phospholipid

e
Protection • Unique bond: ester bond

ti
Energy storage

Ka
by
The emulsion test for lipids…

gy
Ethanol cloudy Milky
lo white emulsion
o
Bi
e
ti
Ka

VVV
by
gy

1 Add 2cm 2 Add 5cm 3 Add 5cm

lo

sample ethanol watert

o

Shake gently
Bi

A positive result, suggesting lipids are present in the sample, would be the solution
having a milky/ cloudy white appearance
 1.4.1 general properties of proteins

Proteins are large, complex biomolecules that are responsible for the majority of the

e
characteristics and functions of living organisms. They are the most diverse group of

ti
biomolecules.

Ka
by
“Protein” —> derived from Greek term “proteios” meaning ‘holding first place’. The
use of this term outlines the importance of this group of molecules

gy
• Monomer unit:
amino acids lo
o
• Polymer (s): polypeptide protein
Bi

• Unique bond:
peptide
e
ti
Ka

Amino acids are the building blocks

(monomer units) of proteins
by

L V
gy

u v u v u
lo
o
Bi

There are 20 different amino acids that are used to build a variety of proteins
 The general structure of all amino acids is the same. They only differ in one area
that we identify as the ‘variable group.’ Similarly to with fatty acids, we use the
letter ‘R’ to show this group

e
H H

ti
theaminegroup

Ka
NHL
µ

by
gy
variable
the

H R lo group different
o
for each of the
Bi

20 amino acids
e
ti
Ka

the carboxyl
by

group COOH
carbonyl co
gy

H plus a hydroxyl
lo

OH group this
o

group is acidic
Bi

As with all other biomolecules, proteins are built via a series of condensation
reactions between their monomer units, amino acids
 Formation of a dipeptide…

two multiple amino acids

BEFORE AFTER

e
H H

ti
H H

Ka
H H

by
H G R

gy
H G R

lo
o
Bi

0
e
ti

H H H H
Ka

H newpeptide
by

G R
bondformed H
gy

H G R
lo

O
o

H2O
Bi

0 H

H
H
 As amino acids join together, they form a chain that we refer to as a ‘polypeptide
chain’ (remember poly=many). The unique sequence of amino acids that form the
polypeptide chain is coded for by DNA. The polypeptide chain is the primary structure
of a protein. The primary structure is the first step in building a fully functional

e
protein

ti
Ka
AAI AA

by
AAZ AA AAS AAG AAF AAS AAN AAN
Aaa

gy
This polypeptide chain is made up of 11 different amino acids. There are 10 peptide

lo
bonds, meaning 10 water molecules will have been released. This sequence of amino
o
acid will determine the overall structure of this protein
Bi
e

Next: secondary structure

ti
Ka

Hydrogen bonding
between amine and
by

Y
carboxyl groups that
gy

are amino acids

apart This pulls the
lo

chain into a coiled

o

structure
Bi

called the
alpha helix
Y
 mentortheamino
acid chain lineup parallel
i I
i to one another Hydrogen

e
bonds form between
ip

ti
adjacent strands

Ka
by
gy
Next: Tertiary structure

lo
o
charged'Efudup 888008
Bi

positivelygagged
e
ti

O CHz COO 43N H24

Ka
by

giantesses

8
gy

s's
valine
lo

É
088 8888
o

9 080000000000
Bi

008
hydrogen 000 Yacine
bonding
hydrophobic
interactions
 The tertiary structure of a protein is arguably the most important. It is this level of
structure that allows each protein to be distinctive, recognisable and fully-
functional. The tertiary structure is dictated by many different types of bonds,
depending on the sequence of amino acids.

e
ti
Finally: quaternary structure

Ka
d chain
p.cn

by
gy
lo
yfg
o
heme
Bi

group
e

DAP
ti
Ka

sp chain
by
gy

d chain
lo
o

The quaternary structure of proteins arises when two or more polypeptide chains
Bi

linked together to form one final protein. There may also be non-protein groups
associated. Not all proteins have a quaternary structure
 The Biuret test for proteins…

sodium hydroxide
copper sulphate

e
ti
Ka
by
gy
O

lo
o
Bi

Vvv
e
ti
Ka
by

1 Add sample 2 Add equal 3 Add a few

gy

solution to volume of drops of

lo

test tube NaOH sodium coppevilsulfa

o

hydroxide solution mix

Bi

If the solution turns purple, this indicates a positive result meaning that proteins,
specifically peptide bonds, are present in the solution
 1.4.2 many proteins are enzymes
Proteins can be globular or fibrous. Let’s look at some properties of each

e
FIBROUS GLOBULAR

ti
shape long thin spherical
largestructure

Ka
strands

by
Amino repetitive many irregular many
Acids of the same different

gy
function structural functional
components lo roles
o
example keratin collagen enzymes insulin
Bi

myosin fibrin haemoglobin

e

solubility insoluble in soluble in

ti

water water
Ka

fibrous globular
by
gy
lo

vs
o

ya
Bi
 In this topic we are interested in a particular type of globular protein: enzyme

enzymes are biological catalysts

e
Biological: relating to living cells or organisms

ti
Catalyst: a substance that increases the rate of a chemical reaction without

Ka
undergoing any permanent change itself

by
So how does a catalyst speed up a reaction ? Think about one of the hydrolysis

gy
reactions we have looked at so far:

maltose water
lo glucose
o
glucose
Bi

For this reaction to occur naturally we would need the following:

e
ti
Ka

• The two reactants (maltose and water) must collide with enough energy to
initiate a reaction between the two
by

• An minimum threshold of energy must be reached. This is called the activation

gy

energy sometimes represented as Ea

lo
o

The idea of the enzymes are that they lower the activation energy required to
Bi

initiate a reaction by offering an alternative pathway for the reaction to occur.

This allows reactions to take place at lower energy conditions
 Ea activation energy

e
ti
É

Ka
s

by
Ianthe

gy
lo
o products

progress of reaction
Bi

So what is an enzyme?
e

the enzyme active site

ti

is an inward groove
Ka
by

images involves a small numbe

gy
lo

substrate
o

the enzyme active

Bi

entans
to a certain molecule
iMessage
 Products
MET
rainE

gaBT

e
Mpaa MMM

ti
PEE ÉMND

Ka
enzyme substrate enzyme ready
complex for next reaction

by
Enzymes are believed to be slightly flexible in their formation of an enzyme-

gy
substrate complex. The active site has a fixed shape (complementary to one

lo
substrate) but can mould slightly upon collision with the substrate
o
Bi

MMM
e

substrates
IIIs ite
ti

enzyme substrate
complexformed
2
Ka

tag Iiing
by
gy
lo

itopy
o
Bi

Aiaa
IIE
 This model of enzyme action is called the induced fit model. It is the most widely
accepted model of enzyme action at present time. Binding of the substrate to the
active site of the enzyme puts pressure on the substrate, causing intramolecular
bonds to weaken and require less energy to break (lower activation energy). Previous

e
model: lock & key model.

ti
Ka
Factors affecting enzyme action…

by
1 temperature

gy
n
b
lo
o
I
Bi
e
ti
Ka

a c
d
by
gy

d to do 30 40 to
lo

temperature oc
o

a= a positive correlation between temperature and rate of reaction. This is due to

Bi

the fact that as temperature increases, kinetic energy of molecules increases and
they collide more frequently, leading to more successful enzyme-substrate complexes
 b= the optimum temperature. This is the temperature at which the enzyme will
work the fastest. The optimum temperature of enzymes will differ depending on the
organism

e
c= above the optimum temperature, the bonds within the enzyme that are holding

ti
the tertiary structure together begin to alter. At this point, the enzyme is less

Ka
effective as the active site shape will change shape. If temperature continues to

by
increase, many bonds will break and the enzyme will stop working all together, as it
is no longer complementary to its substrate. We describe this enzyme as being

gy
denatured. This is an irreversible change

lo
o
2 PH
Bi

ftp.tff.bz
e

1 2 3 4 5 6 8 9 12 13 14
Gg
ti

193ns
ACIDS
Ka

pepsin amylase arginase

by

É
gy

E
lo

E
o
Bi

É
I z s 4 s 6 I s a lo ti iz
PH
 The endurable range of pH for an enzyme is much smaller than that of temperature.
pH alters the the charges of variable side chains of amino acids. This can alter the
bonds that they form. Therefore, any variation around the optimum pH will alter
function of the enzyme

e
ti
3 enzyme concentration

Ka
by
state
at soat soat
EiÉ8g ÉÉs
oEinstagagama
Yi i
MMotEadFEoooKEEEamEEEEAEgg

gy
substratesubstrate substratesubsea

lo
i o
substrate
substrate substrate substrate
Bi
1YÉggx.ptg g s
e
ti

g
Ka

substratesubstratesubstratesubstrate

ammonia mom
ragtag
by

enzyme concentration
At first, if enzyme concentration is increased rate of reaction also increased due to
gy

more active sites available for substrate binding which means more enzyme-
lo

substrate complexes can form. The graph levels off once the substrate concentration
o

becomes the limiting factor

Bi

4 Substrate concentration
 i i i s substrate substrate substrate substrate

substrate substrate
IEEEEEE
t
g.gg
iggygommam

MEDEEEPOEMAKERIA.int
against

in

e
ti
Ka
by
substrate

Miggy.tk
pmaM
MEMKEEEENNt.mn

gy
enzyme concentration
lo
At first, if substrate concentration is increased, rate of reaction also increased due
o
to more substrate being available to bind with the enzyme therefore more enzyme-
Bi

substrate complexes can form. The graph levels off once the enzyme concentration
e

becomes the limiting factor

ti
Ka
by
gy
lo
o
Bi
 1.5.1 structure of DNA tRNA
Nucleic acids are very important biomolecules within all living organisms.
There are t wo main types we must be familiar with: deoxyribonucleic acid
(DNA) and ribonucleic acid (RNA). You may remember the nucleotide structure
from GCSE

e
ti
Ka
• Monomer unit: nucleotide
• Polymer (s):
poly nucleotides nucleic acids

by
• Unique bond:

gy
lo
The nucleotide structure is common in all nucleic acids:
o
Phosphodiester­ase
Bi
e
ti

050
50.99
Ka

Mao
8tdo
by

hosphategrotup nitrogenous base

pentosesugar
gy
lo

Deoxyribonucleic acid and Ribonucleic acid both contain nucleotides with the
o
Bi

same general structure. However if we look at the structure in more detail,

there are noticeable differences that allow us to determine which type of
nucleic acid that any single nucleotide may belong to
 Let’s start with deoxyribonucleic acid, commonly referred to as DNA

Motors

e
ti
Ka
The phosphate group

by
Kis gy
lo
The specific pentose sugar molecule in DNA
is deoxyribose
o
Bi
e
ti

o ET TE Possible nitrogenous bases of DNA molecules are

Ka

adenine (A), thymine (T), cytosine (C) and Guanine (G)

by
gy

The nitrogenous bases form bonds bet ween one another that allows for a
lo

range of processes including DNA replication and mRNA transcription. The

bonds only form when certain bases come together, though. We call those that
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do form bonds ‘complementary base pairs.’

UBINESS ftp.aieaiamdn
 Adenine and Thymine are complementary to each other. They will be held
together by hydrogen bonds, forming a close relationship. Hydrogen bonds will
only form bet ween Adenine and Thymine and vice versa; they are a bonding
pair or base pair

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uanine

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Cytosine and Guanine are complementary to each other. They will be held

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together by hydrogen bonds, forming a close relationship. Hydrogen bonds will

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only form bet ween Cytosine and Guanine and vice versa; they are a bonding
pair or base pair
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forming DNA
e
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Ka

i i

Ito gig
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phosphodiester bond
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tooo
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Polynucleotides are formed by joining multiple single nucleotides together. Let’s

start with t wo. A bond forms bet ween the pentose sugar of one nucleotide,
and the phosphate group of another. The bond formed is a phosphodiester bond.
This structure is a dinucleotide (t wo). Let’s add more for a polynucleotide
 gtpase
traces

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giggabedead water

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phosphodiester bond t Molecules H2O
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This structure is made up of 5 nucleotide molecules bonded together, making

this a polynucleotide. Each nucleotide is bonded to the next via the unique
by

phosphodiester bond bet ween the pentose sugar and the phosphate group.
Remember, each time a new bond is formed bet ween monomer units, a water
gy

molecule is released as this is a condensation reaction

lo

This polynucleotide is single-stranded. It consists of only one chain of

o
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nucleotides. DNA is always made up of t wo adjacent strands (double stranded).

The t wo strands are held together by the hydrogen bonds bet ween the
complementary bases. This is where the term double helix comes from
 strand 1 strand 2
complementary base pair
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double stranded polynucleotide DNA

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Ok, let’s look now at ribonucleic acid, commonly referred to as RNA…

gy
lo

Hippert
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Baas
Bi

toad
The phosphate group
 rio
The specific pentose sugar molecule in RNA
is ribose

e
ti
Possible nitrogenous bases of RNA molecules are

Ka
o ET TE adenine (A), uracil (U), cytosine (C) and Guanine (G)

by
Two major differences bet ween DNA and RNA nucleotides: the pentose sugar is

gy
different. In DNA, it was deoxyribose, whereas in RNA it is simply ribose.

lo
Furthermore, one of the possible bases is different. Thymine will never appear
in an RNA molecule. Instead it is replaced by Uracil. Uracil is complementary to
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adenine
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RNA
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RNA is always single-stranded. It only consists of one chain of nucleotides
joined by phosphodiester bonds. RNA is usually much shorter than DNA
 tree

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complete strand of RNA

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DNA is an important information holding molecule within all living organisms.

by

It carries the genetic information unique to the individual. RNA is a temporary

molecule that carries information from the DNA to the ribosomes
gy
lo
o
Bi
 1 5.2 DNA replication
DNA replication is the process of copying existing genetic information to
produce more. This process allows for new cells and organisms to be produced.
Remember the double helix structure of DNA from the last topic.. it is

e
important here

ti
Ka
iF
by
gy
lo
DNA replication is an enzyme-controlled process. To be replicated, the DNA
must first be unwound. The enzyme responsible for this is DNA helicase
o
Bi
e
ti
Ka

ifs
by

y
gy

DNA Helicase
lo
o
Bi

DNA helicase works by breaking the hydrogen bonds that have formed bet ween
the complementary base pairs on each strand. Only a few bases are exposed at
once. The exposed area is called the replication fork
 G

e
É

ti
Ka
DNA Helicase
I

by
G At ut

gy
a to y
att o
lo
a
free nucleotides
Bi

Free nucleotides are present in the nucleus. They line up with a complementary
exposed bases on one of the template strands. Hydrogen bonds form bet ween
e

complementary base pairs

ti
Ka
by
gy
lo

q
hj
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DNApolymerase
É
 The next enzyme involved in replication is DNA polymerase. DNA polymerase
works by catalysing the condensation reaction bet ween t wo adjacent
nucleotides, so that a phosphodiester bond is formed. The action of DNA
polymerase causes the free nucleotides in each strand to be bound together,
forming t wo brand new strands of complementary DNA. DNA polymerase only

e
ti
works in one direction - 5’ to 3’ direction. This means that DNA polymerase

Ka
works in the opposite direction on each strand as they are anti parallel

result

by
final

gy
lo
o
Bi
e
ti
Ka

A
by
gy
lo
o
Bi

newinastrand
originality
ewDNastrand triginfang
 Each new molecule of DNA contains one strand of original (template) DNA, and
one new strand (formed by the condensation of free nucleotides). The method
of DNA replication is therefore said to be ‘s emi-conservative’.

e
Meselson Stant

ti
Ka
Before this experiment, it was unknown whether DNA replication was

by
conservative or semi-conservative

gy
DNA

lo parent
farentona
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Ka
by

9303
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daughter DNA daughter DNA

conservative semi conservative
replication replication
 Meselson and Stahl used t wo isotopes of nitrogen - one type of isotope had a
higher mass than the other, due to the presence of an extra neutron

14 mass number 15

protons neutrons

e
ti
Ka
nitrogen atomic number nitrogen
7
Number of protons

by
protons 7 protons 7
neutrons 7 neutrons 8

gy
total mass 14 total mass 15

lo
• Isotopes are forms of element that have the same number of protons (shown
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by the smaller number on the periodic table info) but will differ in their
number of neutrons. This means that the total mass number (shown by the
e

larger number on the element information) is also different

ti
Ka

1 Bacteria grownona 2 Bacteria grownona

by

medium containing medium containing

nitrogen is only nitrogen 14 only
gy
lo
o

N 14 if
Bi
 Meselson and Stahl started by culturing bacteria on t wo different mediums;
one containing N-15 only (the ‘heavier’ isotope) and the other with N-14 only
(the ‘lighter’ isotope). Bacteria will use and incorporate nitrogen to produce
new DNA when replicating (remember: nitrogenous bases a.k.a nitrogen-
containing bases)

e
ti
Ka
They centrifuged the DNA from each sample to determine the mass

by
The DNA produced by
bacteria that have

gy
been grown with N-15
V only appears to have a

lo
larger mass, and
separates at a higher
o
density
Bi
e
ti

The DNA produced by

Ka

bacteria that have

been grown with N-14
only appears to have a
by

V
lighter mass, and
separates at a lower
gy

density
lo

They then transferred some of the bacteria that was growing on N-15
o
Bi

originally, to a culture containing n-14 only. The idea was if DNA was replicated
conservatively then we would see the t wo bands of DNA as shown above, just
in the same sample. However, if DNA replicated semi-conservatively, we should
see a band that is bet ween the heavy and light ones, as the DNA would have a
mix of the isotopes
 i

e
ti
Ka
The sample they collected after one round of DNA replication had an

by
intermediate mass, meaning that the band was half way bet ween the heavier
and the lighter bands. This proved the mechanism of semi-conservative

gy
replication as it showed that the new DNA was half original and half made up

lo
of new lighter isotope o
Bi
e
ti

Y
Ka

Lintermediate
DNA
mass of
by
gy
lo

one heavy one

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chain lighter
chain
 1 6 Adenosine triphosphate Atp
Adenosine triphosphate, commonly referred to as ATP is the energy-carrying
molecule found in all living cells

e
ti
large amount of

Ka
energy stored in
one of the 4 nucleotide phosphate bonds
bases that is used to 7

by
build and RNA
DNF a pentose sugar
also in RNA
present phosphate

gy
molecules
adenine

BA lo mi
o
HAMMANN piggin p i.io p
Bi

Etzel
e
ti
Ka

ATP is very similar structurally to a single RNA nucleotide (see unit 1.5.1). It is
made up of a nitrogenous base (adenine), a ribose sugar molecule, and not one
by

but three (hence, “tri”) phosphate groups

gy

When ATP is hydrolysed, the terminal phosphate group is cleaved off, releasing
lo

a small, manageable quantity of energy. Releasing energy in this way means

that less is wasted. Energy is required for absolutely everything, so
o
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conservation is vital

meaning adenine
T HW
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 When a single phosphate group is removed from ATP, it is converted to ADP
(adenosine diphosphate). The phosphate group removed is referred to as an
inorganic phosphate molecule or Pi. The hydrolysis of ATP is catalysed by the
enzyme ATP Hydrolase

e
ATP H2O ADP pit energy

ti
released

Ka
n

ATPhydrolase

by
ATP can be re-synthesised from ADP and an inorganic phosphate molecule using

gy
the reverse reaction. This reaction is catalysed by ATP Synthase and is a

lo
condensation reaction o
ATP H2O
Bi

ADP t pi I
e
ti

ATP synthase
Ka

When ATP is hydrolysed into ADP and phosphates, the phosphates can be used
by

for another purpose. Adding phosphates to other molecules, such as enzymes,

in a process called phosphorylation can cause them to be converted from being
gy

‘inactive’ to ‘active’ or ‘more reactive’

lo

c c c c c e glucose
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Bi

pi c c c c o c pi phosphorylated
glucose
 1.7 water
Water is a molecular compound, made up of single molecules of H2O (2 hydrogen
atoms and 1 oxygen atom). The three atoms are held together by covalent
bonds, meaning that they share their outer shell electrons with each other

e
ti
o

Ka
Two shared pairs of electrons

by
= 2 covalent bonds present in
this molecule of water

gy
lo
o
Bi

Electrons are negatively charged. When covalent bonds are formed bet ween
oxygen and hydrogen, like in water molecules, the electrons tend to sit a lot
e

closer to the oxygen. This is because oxygen is more electronegative, meaning

ti
Ka

that is has more influence over the electrons. The water molecule looks a bit
like this
by
gy

electronpair
the electron pair is
O
lo

o
i pulledcloser to the
µ oxygen atom
o
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i
coat in
 As there are now extra electrons circulating around the oxygen atom, it
becomes ‘partially negative’. The hydrogen, on the other hand, becomes
‘partially positive’ as its atoms have moved away. This creates an uneven
distribution of charge within a water molecule. We say the molecule is polar

St partialpositivecharge

e
µ

ti
electronpair

Ka
g partialnegativecharge

by
cogent

gy
coffined

lo
St partialpositivecharge
H
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Due to these areas of partial negativity and partial positivity, water

e

molecules are attracted to each other. Hydrogen bonds form bet ween the
ti
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oxygen on one molecule and the hydrogen on another

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 Water is the predominant substance in all living organisms; it makes up about
2/3rds of the human body. It has some unique features that make it very
important in living organisms:

1. Water is a solvent - the polarity of water means that it will form

e
ti
hydrogen bonds with other polar molecules, such as charged ions

Ka
2. Water is a metabolite - water is used in hydrolysis reactions to break
polymers into their monomer units, such as the breakdown of starch into

by
glucose. Water is also produced in the reverse process of condensation,
where polymers are built from monomers, for example building proteins

gy
from amino acids. Hydrolysis and condensation are vital processes in living

lo
organisms
3. High specific heat capacity - a lot of energy is required to increase the
o
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temperature of water, as the hydrogen bonds absorb lots of energy. The

temperature of water therefore does not change too much. A very useful
e

feature in cells, water acts as a temperature buffer to prevent enzymes

ti
Ka

from denaturing
4. High latent heat of vaporisation - a lot of energy is required to convert
by

liquid water into water vapour. Particularly useful in offloading excess heat
energy during sweating
gy

5. Cohesion and surface tension - water molecules are bound together by

lo

many hydrogen bonds. The cohesion of water molecules means that water
can travel in a column. It also has surface tension, meaning it can resist
o
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external force and form a skin where water meets air. This allows some
objects to float on water
 1 8 inorganic ions
An inorganic ion is a charged particle that does not contain carbon. Inorganic
ions can be positively charged (cations) or negatively charged (anions).
Inorganic ions are found dissolved in solution in the cytoplasm of cells and

e
ti
tissue fluid, as they are polar.

Ka
Ht hydrogen ions Ht ion concentration

by
of a solution determines the pH the
higher the concentration of Ht ions the

gy
more acidic a solution is lower pH valve

Acids lo
neutral BASES
o
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Bi

1 2 3 4 5 6 7 8 9 10 11 12 13 14
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ti

increasing Ht concentration
Ka

Maintaining a stable concentration of H+ ions in cells and organisms is vital,

by

as pH can affect the tertiary structure of proteins, including enzymes

Nat sodium ions Nations

gy

are vital
in the transmission of an electrical impulse
lo

in neurons Nations are necessary for

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the co transport of glucose and amino

Bi

acids across lipid membranes this is the

only way glucose and amino acids can
enter cells
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oxygen molecules to bind there are 4 Felt lo
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8043 phosphate'lons pop ions makeup

the phosphate groups of nucleotides
and ATP the phosphate ions allow for the
 formation of phosphodiester bonds to form
nucleic acids phosphate phosphate bonds
store energy in Atp that is released
when ATP is hydrolysed phosphate ions are
used in the formation of phospholipids too

e
ti
Ka
1 ATP 3 phospholipid
Phosphate
adenine

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 unit 1 glossary
You need to be able to recognise, remember and use all these key terms in the
correct context in exams…

e
ti
Ka
• Monomer: a small single unit of which polymers are made
• Polymer: molecules made up of multiple repeating monomer units

by
• Condensation: the reaction bet ween t wo monomers to form a polymer, a
water molecule is released, and a new bond formed

gy
• Hydrolysis: the breakdown of a bond using water. Polymers are broken down

lo
into monomers using hydrolysis
• Monosaccharides: single sugars (glucose, fructose, galactose)
o
Bi

• Disaccharide: t wo monosaccharides joined together by a glycosidic bond

(maltose, lactose, fructose)
e

• Polysaccharide: multiple polysaccharides joined together by glycosidic

ti
Ka

bonds (starch, glycogen, cellulose)

• Starch: alpha-glucose storage molecule in plant cells
by

• Glycogen: alpha-glucose storage molecule in animal cells

• Cellulose: beta-glucose polysaccharide, the structural component of plant
gy

cell walls
• Triglyceride: a lipid molecule made up of a glycerol and 3 fatty acids
lo

• Phospholipid: a lipid molecule made up of a glycerol, 2 fatty acids and a

o
Bi

phosphate group
• Fatty acid: hydrocarbon chains with a functional carboxyl group
• Amino Acid: the monomer unit from which proteins are made
• Dipeptide: 2 amino acids joined together by a peptide bond
 • Polypeptide: multiple amino acids joined together by peptide bond
• Enzyme: a biological catalyst
• Catalyst: a substance that speeds up a reaction without being used up
• Activation energy: the minimum amount of energy required for a reaction
to occur

e
• Nucleotide: the monomer unit of DNA and RNA, made up of a phosphate,

ti
Ka
sugar and base
• Nucleic acid: molecules such as RNA and DNA that are made up of multiple

by
repeating nucleotide units
• Semi-conservative replication: the method of DNA replication where one

gy
strand acts as a template, and a new strand is synthesised from free

lo
nucleotides
• Inorganic ions: charged particles that do not contain carbon (E.g., Na+, K+,
o
Bi

Cl-)
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ti
Ka
by
gy
lo
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2.1 structure of Eukaryotic cells

All cellular life is classi ed into t wo groups : eukaryotic cells and prokaryotic
cells. Eukaryotic cells are cells that contain a distinct nucleus, as well as other
membrane-bound organelles. On the contrary, prokaryotic cells lack both a
nucleus and any other membrane-bound organelles.

Eukaryotic cells: plant vs animal cells

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animal cell plant cell

Plant and animal cells are the most familiar types of eukaryotic cell. There is
also fungal cells and protist cells, which you might remember from GCSE
‘infection & response’.

The ultrastructure of a cell is the ne structure of specialised structures

(a.k.a. organelles) within a cell. The ultrastructure of a cell is only visible
when viewed through a high-resolution microscope, such as an electron
microscope
the nucleus
The nucleus contains all of the cells genetic information in the form of DNA.
The nucleus therefore controls all cell activities

chromatin
7 DNA molecules + associated
proteins to form chromosomes

nucleoplasm

0,8 aka-'karyoplasm' is the jelly-like

uid that lls the nucleus,
enclosed by the nuclear envelope

money J
nucleolus
small spherical structure
within the nucleus. it is the
site of ribosome synthesis

u v u

nuclear pores
large openings in the nuclear J nuclear envelope
envelope that allow movement
the double membrane that
of large molecules, such as
surrounds the nucleus. it has
mRNA during protein synthesis
nuclear pores
 the mitochondria
The mitochondria are a membrane- bound cell organelle that are the site of
aerobic respiration in eukaryotic cells. They are responsible for the release of
large amounts of ATP

mitochondrial DNA
small circular DNA that
allows mitochondria to
assemble its own proteins

i
ATP synthase
the protein responsible
for mass generation
of Atp during oxidative

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cristae o phosphorylation
ATP synthase the
components of the
electron transport chain
are embedded in the
membrane
Ribosome

you
the site of
protein synthesis

matrix
viscous component within
the inner membrane. the
matrix is the site of the link
reaction and Krebs cycle in
respiration
 the ribosome
Found both free in the cytoplasm and on the rough endoplasmic reticulum,
ribosomes are the site of protein synthesis in living cells. They are not
membrane-bound
large sub-unit
the larger section of the
ribosome is responsible for
catalysing peptide bond
formation bet ween amino
acids

messenger RNA
MRNA is transcribed
in the nucleus. it is a small sub-unit
short, single-stranded the smaller section of
molecule that carries the ribosome is responsible
information from the DNA for decoding the information
to the ribosome on the mRNA strand
the golgi apparatus
The Golgi apparatus receives proteins and lipids that have been synthesised by
the endoplasmic reticulum. The Golgi then modi es and packages the substances
into vesicles in which they are sent to their nal targeted destination

incoming vesicle
vesicles are used to
cisternae transport substances
a series of from the endoplasmic
attened sacs reticulum to the golgi
that contain a apparatus

Y
variety of
enzymes needed
for modi cation
of substances

1
lumen
the area enclosed
by the golgi
membrane

0
secretory vesicle
the golgi apparatus
uses a net work of
vesicles to transport
the substances it has
modi ed out of the cell
the phospholipid membrane
The phospholipid membrane that is common in all living cells is responsible for
the regulation of movement of substances both into and out of the cell

Extrinsic proteins
these proteins do not
Phospholipids extend through the whole
lipid structures made up of a membrane, instead they
phosphate head a t wo fatty sit at the top and act as
acid tails - the unique support molecules
structure of phospholipids
allows the lipid bi-layer to
form

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Intrinsic proteins
L
Other wise known as
transmembrane proteins,
intrinsic proteins are embedded V
in the membrane and usually Cholesterol
provide a pathway through the A type of naturally occurring fat
lipid bilayer, such as a channel produced by the liver, cholesterol
protein molecules are embedded
intermittently in the membrane,
adding to its overal strength and
impermeability
 the endoplasmic reticulum
The endoplasmic reticulum are a series of attened membrane sacs that are
continuous with the nuclear membrane. There are t wo types: the rough
endoplasmic reticulum and the smooth endoplasmic reticulum

The smooth ER
Nucleus the smooth endoplasmic reticulum has
no ribosomes on its surfaces. It is
responsible for the synthesis of lipids,

Is
such as cholesterol

The rough ER
the rough endoplasmic reticulum is
named so due to the presence of
ribosomes on the surfaces of the
membranes. The ribosomes are
responsible for the synthesis of
proteins. The rough ER also synthesises
glycoproteins
lysosomes
Lysosomes contain hydrolytic enzymes, and are responsible for the breakdown
of old and worn-out materials within the cell
membrane
phospholipid so
c
bilayer encloses
the lysosomal uid
fr At i transport proteins
facilitate the
and the enzymes
movement of
s substances across
th the lipid bilayer

hydrolytic enzymes C BE
produced originally in my
the rough endoplasmic
reticulum, hydrolytic
enzymes digest large
molecules

plant cell wall vacuole

Plant cells have a few features that are not common with animal cells: the
chloroplasts, cell wall and the permanent vacuole

Cell wall
a structural
component of plant Vacuole
cells made of a permanent vesicle
within the cell
polysaccharide aiming
im
cellulose. The cell wall cytoplasm containing
helps to keep plant cell sap. The vacuole
cells rigid provides support for

i
o the plant cell and keeps
it turgid
the chloroplast
The chloroplasts play a very important role in plant cells due to the fact that
they are the site of photosynthesis. Photosynthesis is the conversion of
carbon dioxide and water into glucose and oxygen using light energy

Thylakoids
the thylakoid membranes
contain chlorophyll and enzymes
that are necessary for the rst
stage of photosynthesis: the
light-dependent reaction

ii

Stroma
much like the cytoplasm of the
wider cell, the stroma is the
uid that lls the inner space Grana
of the chloroplast and thylakoid membrane discs
surrounds the grana. The stack on top of one another
stroma is the site of the to form structures known
second stage of as the grana
photosynthesis: the light-
independent reaction
Cells are the smallest functional unit of life. Cells are often referred to as
‘building blocks of life’. In order for complex, multi-cellular organisms (such as
animals and plants) to be formed, cells must work together.

1. Cell - the most basic unit of all

living organisms

2. Tissue - a group of similar cells

o o working together as a functional
unit. E.g. muscle tissue, nervous
tissue, connective tissue

3. Organ - different types of

tissue come together to form a
t.IT single functional unit with a
speci c function. For example the
heart is made up of cardiac tissue,
epithelial tissue and connective
tissue

brain C
4. Organ system - t wo or more
u n organs can work together to
perform a speci c function in
the body, such as the
t.EE circulatory system. The

E f
circulatory system is made up
of the heart and blood vessels,
and it’s role is to pump blood all
liver c around the body
c kidneys
intestine
2.1.2 structure of prokaryotic cells viruses
As mentioned before, prokaryotic cells are those that lack a distinct nucleus or
any membrane-bound organelles. Prokaryotic organisms are always single-
celled or unicellular. They cannot form multicellular organism. A prokaryotic
cell we are all familiar with is a bacteria cell

see

prokaryotic cell us eukaryotic cell

• The rst, most obvious
difference is the lack of a
nucleus
• Prokaryotes still have DNA,
but it is found free- oating
in the cytoplasm
• The DNA is a small, circular
(but still double-stranded)
molecule. The DNA is not
associated with histone
proteins
• Prokaryotic ribosomes are
smaller than those found in
eukaryotic cells.
Prokaryotic ribosomes are
70S
• Prokaryotic cell walls are
made from murein
• Prokaryotic cells are much
smaller than eukaryotic
cells
• The rst, most obvious
difference is the presence of
a nucleus
• Eukaryotic DNA is contained
within the nucleus,
surrounded by the nuclear
envelope
• Eukaryotic DNA is linear, and
is wrapped around histone
proteins to form
chromosomes
• Eukaryotic ribosomes are
larger, they are 80S
• Some eukaryotic cells (plant
and fungus) have cell walls,
but not all. The cell walls are
made of cellulose or chitin
• Eukaryotic cells are larger
than prokaryotic cells
 Let’s have a look at a general prokaryotic cell and identify any extra
structures that we haven’t seen thus far

Flagella
prokaryotes can have multiple
agella. agella allow the cell to
move through a process called cell
locomotion

v
Plasmid
small, circular strands of DNA found in Capsule
prokaryotic cells that are separate some prokaryotes have a
from the main strand of DNA. plasmids slime capsule that
often carry genes that help bacteria protects the cell from the
adapt to their environment host immune system

Viruses are abiotic, meaning they are non- living. They do not meet the
criteria to be considered living organisms. They are not made of cells
Attachment
glycoprotein

a
This image is of a HIV virus. Viruses
a o contain genetic material, usually in

j 3
o o
the form of viral RNA (however they
oo
o oo
o
o foo
D
RITE o o 0 o8,90 can have viral DNA) that is injected
o
o
o
o
oo
D
o
pooooo into a host nucleus. Attachment
agr oD
o

II
o A
o pooooo proteins allow viruses to lock onto
oo Dooo host cell receptors and in ltrate the
oo f p oo
host cell. The viral capsid is a protein
‘shell’ that protects the genetic
60 information
To
 2 13 methods of studying cells
On average, eukaryotic cells have a diameter of somewhere bet ween 10 and
100 micrometers. A micrometer is one millionth of a meter, so very small! This
means that cells are not visible to the naked human eye - we must use
microscopes to see them!

the light microscope

Ez
ke Ndaa
eyepiece
objective lens

i
stages
s
adjustment knob
for focus
light sources

The light microscope uses visible light passing through a sample to create a
magni ed image through the eyepiece lens. Light microscopes are inexpensive
and easy to operate, thus they are the popular option in school and university
laboratories. However, their resolution is limited, so smaller organelles are not
visible. The maximum magni cation is approximately 2000x normal size
the electron microscope
The electron microscope uses beams of electrons to create an image of a sample
specimen. There are t wo types of electron microscope that we must be familiar
with, along with their advantages and limitations

ogelectron source

bedmorelectrons condenser lens

J L

t
objective lens

i era sample

SCANNING ELECTRON MICROSCOPE

the scanning electron microscope (SEM) uses a beam of electrons directed at
the surface to ‘s can’ the surface of the sample. The electrons are scattered by
the surface of the sample and are used to create a detailed image of the sample
exterior. This creates a 3-D image of the sample based on its external topology

TRANSMISSION ELECTRON MICROSCOPE

the transmission electron microscope (TEM) also uses a beam of electrons,
however they are passed through the sample, not just directed at the surface.
The sample must be very thin. The TEM generates a very detailed 2-D image of
the internal structure of a specimen
microscope light SEM TEM
magnification 20001 5001000 100010004

resolution 0.2mm Inm Inm

image 2 D 3 D Z D

live sample
yes not not

internal structures
visible limited no yes

thin sample dehydrate dehydrate

sample prep
stain for coat with cut ultra
visibility metal layer thin sample
glass slide vacuum stain
dropof water seal vacuum
cover slip seal

the use of a beam of electrons in both SEM and TEM’s means that they
must operate using a vacuum environment (no air). This is because air particles
could scatter or absorb the electrons and affect the image results. The lack of
oxygen means that live samples cannot be used. Furthermore, sample
dehydration is required so that water vapour is not formed in the electron
tower by evaporation. Live samples would not sur vive dehydration. The lack of
ability to view live samples is a limitation of light microscopes
 magnification formula
I M X A

image size

ÉE magni cation
actual size I
M A

SO Image size magnification x actual size

magnification Image size

actual size

actual size Image size

magnification
For example…

i Ii
The actual size of this
mitochondria is 1.2
micrometers. Calculate
the magni cation of this
i.am image
1. We know that the image size is 3mm and the actual size is 1.2 micrometers.
We must rst convert these data so that they are in the same units

unit abbreviation conversiontometre

Kilometre km 4103

metre m Xl
centimetre cm x 10 1
millimetre mm x 10 3
micrometre MM x 10 6
nanometer nm x 10 9

So, to convert micrometers to milimeters, we would do (sample x 10^-3) or

divide the number by 1000.

Actual size in mm= (1.2/1000) = 0.0012mm

2. Now that we have the data in the correct units, we can use the formula to
calculate magni cation. Remember from above…

magnification Image size

actual size

Let’s incorporate our values into the formula by doing

magnification 3mm 2500

0.0012mm

Therefore, the mitochondria has been magni ed by 2500

 cell centrifugation
fractionation
Cell fractionation is a technique used to separate the contents of a cell. It
allows us to extract and study speci c organelles, such as the nucleus,
chloroplast and mitochondria. Before cell fractionation takes place, we
suspend the sample in a cold, isotonic, buffer solution. Here’s why:

1 cold placing a sample in a cold solution reduces enzyme activity due to

low kinetic energy of the particles. we want to inhibit enzyme activity to
preser ve the integrity of the organelles that we want to isolate

it
temferantec.jo to

2 Isotonic an isotonic solution is one where the concentration of the

solution produced is the same as the concentration of the solution it is being
compared to. So here we would place a cell into a solution that is the same
concentration. This means that there is no difference in water potential and
there will be no net movement of water by osmosis. We want to avoid
movement of water by osmosis to prevent the cell from shrinking or bursting

o water molecule solute

 o o o
o o o
o o o o o

t.EEB
o 0
o o o o o
ifb o o 0 o

o
o

insidecell solution insidecell solution insidecell solution

hypertonicsolution hypotonic solution isotonic solution

higherconc insolution lower conc insolution sameconc in both
watermoves out of cell watermovesintocell solutions no movement

3 buffer buffer solutions prevent any uctuation in the pH value of the

sample so that the organelles are not damaged

There are three main stages to cell fractionation: homogenisation, ltration

and centrifugation

Homogenisation is the process of using a piece of laboratory equipment similar

to a blender that breaks down the phospholipid membranes of cells. This
releases the contents of the cells (the organelles) into the solution. Once
homogenisation has taken place, we refer to the solution as the homogenate

an
go.io.TKidW8g
homogenisation
_jB t.o To
yyiy.gs
i É i Xt
M Hh
homogenate
Mj
Filtration is the process of passing the solution through a selectively
permeable lter to remove any large, complete cells or large particles of debris

Centrifugation is the process of isolating cell organelles based on their

density. It involves spinning the homogenate at high speeds using a piece of
equipment called a centrifuge. The spinning motion generates a force referred
to as the centrifugal force that causes the denser organelles to be forced to
the bottom of the solution. Centrifugation is a multi-step process: you
increase the speed of the centrifuge each time and isolate the organelles that
have been removed

centrifuge
lowspeed
centrifuge
faster
mediumspeed

page
highspeed

homogenate
thesolution
formedafterhomogenisation Magoo q
Of cellsample sediment

1 nucleus kanaka

Mess 2 mitochondria
8868
Umass 3lysosomes
The sediment is isolated and removed each time, whilst the supernatant is re-
centrifuged at a higher speed. In order of decreasing mass, the organelles are:

nucleus -> chloroplast -> mitochondria -> lysosome -> endoplasmic reticulum -> ribosomes
2.2 all cells arise from other cells
The basic principles of cell theory are that all living organisms are made up of
cells, with multi-cellular organisms having levels of organisation such as
tissues, organs and organ systems. Secondly, this idea that all cells come from
pre-existing cells by some mechanism of cell division

the cell cycle

The cell cycle is a highly regulated process that allows cells to replicate in a
safe and controlled way

M mitosis

GI gap I

GE gap 2

S synthesis

Interphase is the longest stage of the cycle, and is the stage in which a
eukaryotic cell will spend most of its time. The average duration of the cell
cycle of a human cell is 24 hours, with 18-20 of those hours being spent in
interphase
 cell growth & organelle replication
Gap 1

synthesis :duplicated
semi-conservative replication of DNA. all chromosomes are
and consist of t wo identical 's ister' chromatids,
attached at the centromere

93
To'É

centromere
chromatids chromatid2

DNA duplicatedDNA

the cell continues to grow in preparation for mitosis. DNA checks

Gap 2 are carried out to ensure no mistakes have been made during
replication

a multi-step process in which the chromosomes are split into 2

mitosis new daughter cells
 mitosis
Mitosis is the stage of the cell cycle in which the original cell or ‘parent cell’ is
split into t wo genetically identical ‘daughter cells’. Mitosis is a vital process
for growth, repair and asexual development. It consists of 4 stages: prophase,
anaphase, metaphase and telophase. Mitosis is then followed by cytokinesis.
Let’s go through each of these stages in detail

I prophase
the chromosomes
first becomevisible
i as short condense
structures
Yo i
i

think's'aisappears
completely breaks

centrosomes
he two
igrateto opposite
olesorthecell spindle 18 nuclearenvelope
bresstarttoform breaks down the
romeachone chromosomes are
now freely present
in the cytoplasm
 2 metaphase
M
i

spindle fibres from

the centrosomes
continue to extend
until they attach to
centromeres W chromosomes lineup
at the equator of the
cell attached to the
spindle apparatus by
theirgentromere
each of the sister
chromatids is
attached to spindle
fibre extending from
opposite centrosomes
at opposite poles ready
be pulled apart

3 anaphase the two sister

Chromatids begin
to separate from
the centre the
8 centromere

w
the spindle fibres
g contract and begin
contraction of spindle to shorten moving
ibres requiresenergy back towards their
tis obtained from the original polesof the
cell
hydrolysisof ATP provided
by nearby mitochondria
4 telophase

the chromosomes TT
Iger made it to
oppositepoles
1
two new nuclear l
envelopes reform
around them 1 I
I 1
spindle fibres begin to
y disintegrate and will
eventually disappear
completely
1 y
I 1
l l
s two new nucleolus are
formed one within
each new nuclear
envelope
Mitosis ends after telophase, however there is one more process that must
happen: cytokinesis. Cytokinesis is the separation of the cytoplasm, creating
t wo new daughter cells with their own complete set of genetic information

Mitotic index is a gure that gives an indication of how many cells within a
tissue sample are actively undergoing mitosis

mitotic number of cells undergoing mitosis

index
total number of cells in sample
 there are 4 cells that are
AM undergoing mitosis in this
sample-we know this as the
chromosomes are visible in
man s these cells, not the others.
There are 9 cells in the
sample in total
iii

mitotic cells in mitosis 0

index g total cells in sample
Mitotic index is only expressed as a percentage if speci ed

division 1

division

a Ig
divisions divisions divisions divisions
Whilst mitosis is an extremely important process in the growth and
development of organisms, it is just as important that mitosis is tightly
regulated. Uncontrolled cell division can lead to the formation of tumours,
some of which can become cancerous

binary fission
Binary ssion is the mechanism of cell division carried out by single-celled
organisms, such as bacteria

the main strand of

circular DNA replicates,
then the plasmids. Any
agella and internal
structures such as
ribosomes replicate, too

The cytoplasm
splits into t wo

ÉTÉE Each new cell receives a

single copy of the circular
DNA, as well as a variable
number of plasmids. Each
cell must receive at least
one plasmid, or it will die
 2.3 transport across cell membranes
We identi ed the cell membrane back in unit 2.1.1. In this unit, we will be looking
at it in great detail to include the intrinsic structure and how it’s structural
components relate to its function

The cell membrane is universal. All cell and organelle membranes have a very
similar structure that is based around the phospholipid bilayer. Let’s rst talk
about the phospholipid

s
MmM
É phosphate head
hydrophilic

eats acid rain

hydrophobic fly
hey
The phospholipid is a type of lipid made up of a glycerol molecule, t wo fatty
acid chains and a phosphate group. The phosphate group is negatively charged -
it is polar and will interact with water. Therefore we describe it as being
hydrophilic (‘water loving’). The fatty acid chains are long hydrocarbon chains
and non- polar. They will actively avoid interacting with water and are
therefore described as ‘hydrophobic’ (water repelling)
The unique properties of the phospholipid result in the formation of the
universal membrane structure, a structure we refer to as the ‘phospholipid
bilayer’

AQUEOUSENVIRONMENT The fatty acid chains

seek ‘shelter’ from
their aqueous
surroundings and
arrange themselves
like so; t wo layers
facing toward each
other protected by
the hydrophilic layer
on either side

AQUEOUS ENVIRONMENT On the other hand, the hydrophilic

phosphate heads will happily interact
with the water-based environments that
surround them, such as the cell cytoplasm
or extra cellular uid. The result is this bi-
layer formation in which all properties of
the phospholipid are satis ed

However, the cell membrane structure is not as simple as this… it looks a little
bit more like the diagram below

glycolipid intrinsicprotein i

glycoprotein
0i iodineio

All AHAHAHA
iPOis.OEIOOEIE'EM'BOisainiooooisooE
igg.isopiggepgagqq

titled
ioffesignsiosos
Eison.io
60
ismsxies
H
io
8
cholesterol
Hilton
i
mines
iii
iisiosIIEEominoaloooiidzooiidaodosimIsoioana
toooo

extrinsic protein
Let’s have a look at each of these structures and their speci c roles within the
overall membrane:

Glycolipids - these are phospholipid glycolipid

molecules with a carbohydrate chain
attached to it. The carbohydrate chains
are hydrophilic and stretch out into the
i E
iffy i
aqueous environment. Glycolipids act as
cell recognition sites and antigens, playing
a vital role in cell signalling and
0pYO 0OOtg

communication

i Glycoproteins: very similar

both structurally and
glycoprotein functionally to glycolipids.

é i
É i.BE
Rather than a carbohydrate
chain attached to a membrane-
909 bound protein. Glycoproteins are
also involved in cell-signalling
and the immune response

Cholesterol: an amphipathic lipid, 0i i000ia igloo ideal

HALL
much like phospholipids and is
synthesised in the liver. Cholesterol
molecules in the membrane act as

H TH
‘s pacers’ to stabilise the membrane.
Cholesterol also regulates
membrane uidity and ensures it is
kept at an optimum – not too rigid M
i i8 é
0i mo
but not too exible, either
cholesterol
 Intrinsic proteins: proteins that span the
whole membrane – they start outside of the
intrinsic protein cell and extend inside. They act as channels
or carriers, facilitating the transport of
large or polar molecules such as inorganic
ions and glucose across the membrane. They
i
É00
I ii.I
i.EE 90 E000 i
0i also act as receptor sites for hormones and
neurotransmitters and are involved in

MIHA
crucial cell adhesion mechanisms. Intrinsic
proteins can be channels – hydrophilic pores

too
in the membrane that create direct channels
for molecules to travel through, or carriers –
i0B I wigged.io
0300
proteins that bind to speci c molecules,
undergo a conformational change, and
release them on the other side of the
membrane.

Extrinsic proteins: these proteins do oi iight

MA iBNK
not extend through the entire 0Y
membrane and usually act as
membrane-bound enzymes. They are

iII ii
more loosely associated with the
membrane and can be easily removed 0ID II0ioo.si
00
0003in.io

extrinsic protein

So, why the ‘ uid mosaic model?’. Well – the term ‘ uid’ because the membrane
is exactly that. It is not a xed, rigid shape but instead slightly exible and
‘ uid’ in nature. The term ‘mosaic’ is a nod to the artistic technique of using lots
of patterned tiles. The different components that make up the membrane
leave the whole thing resembling a mosaic pattern
The membrane’s role is to provide shape and structure whilst maintaining
control over what goes into and out of a cell. It is important that cells can
exchange substances with their external environment. There are several ways
that substances can cross the cell membrane:

1. Simple diffusion: diffusion is the movement of particles from an area

of high concentration to an area of low concentration, down a concentration
gradient. It is a passive process and does not require energy. Simple diffusion
refers to movement of particles through the membrane without the need for
the help of protein channels or carriers. Only small, non-polar molecules such
as oxygen, carbon dioxide and steroid hormones can pass via simple diffusion

06
6
988
gig highconcoxygen
at
oooo
at
go 0008
ooooo

at i
at
Ba ooooo

i What
go
8 0ii i.im
0 Di iiEBOEEDIBisiEO.ogassiooooeasooEO
0 EE iDOE iDEN

igg.io NNdIN
ÉÉ
HAHAHAHAHAHA
0 D iIDi
ÉD.É
Big
igÉ Éoo
a
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i
AH
11tHHH7
08 o ai oi oi oi 0aioooooosida.io0d
0Ed
misasagi.in
i oaa.e

8
9.0 txg8 wi
lowconc oxygen
2. Facilitated diffusion: this process is still a movement of high to low
concentration, but it requires the help of membrane proteins. This type of
membrane transport is used by molecules that cannot simply pass through the
lipid bilayer, such as charged ions (e.g. Na+, K+ and Cl-) and larger molecules,
such as glucose.

The rate of diffusion depends on several factors. Fick’s law of diffusion is a

good way to remember the conditions that may alter rate of diffusion

• The higher the concentration gradient (difference bet ween concentration of

substance on one side of the membrane compared to the other), the faster
the rate of diffusion
• The larger the surface area of the exchange surface, the faster the rate of
diffusion
• The thicker the membrane/ longer the diffusion distance, the slower the
rate of diffusion
• The more intrinsic channel proteins there are (if necessary for facilitated
diffusion), the faster the rate of diffusion

3. Osmosis: much like diffusion, but for water molecules only. Osmosis is
the passive movement of water molecules from an area of high water
potential (low solute concentration) to an area of lower water potential
(higher solute concentration) across a selectively permeable membrane. Pure
water (absolutely nothing dissolved into it) has the highest possible water
potential (0 KPa). Any other solution will have a lower water potential – the
more solute, the lower the water potential gets o water molecule
i
Solute

O O
g
g
higher o lowery

In
opt
o
o
O
O
O O
4. Active transport – unlike any other process so far, active transport
requires energy to move substances across a membrane. This is because active
transport is the movement of particles from an area of low concentration to
an area of high concentration, against the gradient. Active transport requires
the use of a carrier protein

highconc sodium
MA Mk wat
ya qq qq
0
At what wat wat
Wat

iO0o
i i i10i0o
iI0 00 O 00
i.ie 6i 0i
E0
AAAAA ID d HAA
78 7 7 1 an
7 7 71
É O iOO
I0i É0 OiÉ eiO
i IOi Oi
t
wat at AMenergy
ya ya low conc sodium
my

5. Co-transport: this method moves t wo ‘coupled’ substances across the

membrane at once, via an intrinsic carrier membrane protein. The
electrochemical gradient of one of the substances (usually Na+) drives the
movement. Active transport is also used alongside co-transport to maintain a
favourable gradient of Na+
 iepEoomEEEooEEMaEEEMaBEoomEEEBaBraaETam

digestion
aPREFENeaga

NOOtago image team a lumenofthe

ileum

microvilli
MN hdd
d
cotransport
membrane
protein

epithelial
cell

glucoseprotein
channel
sodium
potassium 1 blood
pump
Mongkut
3 capillary

1. Na+ ions are actively transported OUT of the epithelial cell. This creates
an electrochemical gradient bet ween the lumen and the epithelial cell
2. Na+ Ions then diffuse into the epithelial cell from the lumen. They do so via
a special carrier protein called a co-transport protein. This means that as
a Na+ ion passes through, so does a glucose molecule
3. Glucose then passes into the blood via a channel protein, down a
concentration gradient
24 cell recognition and the immune system
The human immune system is a network of cells and organs that work collectively
to defend the body against pathogens. Pathogens are microorganisms of various
types that cause disease. Pathogens can be…

1 Bacteria e.g salmonella or gonorrhea

2 viruses e.g HIV or influenza
3 funghi e.g athlete's foot or ringworm
A protists e.g malaria

The immune system is made up of a number of different mechanisms, both specific

and non-specific. Each has its advantages and disadvantages

the human immune system

specific non specific

lymphocytes B lymphocytes physicalbarriers phagocytosis

Physical barriers:
• Skin - the skin is the body’s largest organ and acts as an external barrier,
preventing the entry of pathogens into the body
• Hairs - inside the nose and ling the eyes, external body hairs help to trap
pathogens before they can enter the body. The cells in the nose also produce
 mucous, trapping pathogens and guiding them into the stomach
• Stomach acid - the low pH of the stomach due to secretion of strong hydrochloric
acid makes for a very hostile environment for pathogens. This means most
ingested pathogens are killed in the stomach

self recognition
• It is of vital importance that the body is able to actively distinguish between its
own cells (‘self’ material) and anything else (‘non-self’ or ‘foreign’) material,
otherwise the body would be constantly launching immune attacks on itself. So
how does it know?
na

are
glycoprotein glycoprotein
i
0
self cell non selfcell
or

1 or
y yo

Remember from unit 2.3 that glycoproteins

are formed when a carbohydrate chain is
attached to a membrane-bound protein. All i
cells, whether they are considered to be ‘s elf’
or ‘non-self’ have different, speci c glycoprotein

i 8i i.IE
molecules attached to the membranes. A lot
of the time, these molecules are i 0i
glycoproteins. They allow the cell to be
recognised as friendly or harmful by the
immune system cells.
If the specific molecule on the surface of a cell is not recognised by the immune
system, it is considered to be ‘foreign’. A foreign membrane molecule is referred to as
an ‘antigen’. Antigens are defined as being non-self cell membrane molecules that
will initiate an immune response.

no
0
an antigen
glycoprotein glycoprotein
t
0
self cell me
non selfcell

or

no action taken by the immune responses are activated

immunesystem to remove non self material

So, how does the body come to recognise its own cells ? This happens very early on
in life, during foetal development. A process called ‘self-tolerance’ or ‘immune
tolerance’ occurs, whereby any self-reactive T or B lymphocytes are removed and do
not mature. Therefore, as we develop and grow, the immune system will not
recognise our own cells as being a threat.

T
B q T
T
00
selfcell B
B
T ha B B
T z
B These t wo white blood cells are self- T
reactive, so they must be destroyed
phagocytosis
Phagocytosis is considered to be a non-specific response within the immune system,
due to the fact that it does not recognise precise antigens on the cell-surface
membranes of pathogens. Instead, is launches a common attack on any pathogen it
encounters, without having to have been exposed to the pathogen previously

lysosome vesicle
containing lysozyme
nucleus
lysozyme hydrolytic
enzymes that can destroy
pathogens bydigestion

• Pathogen recognition - phagocytes are able to detect pathogens in the blood. They
do this using receptors that are able to identify pathogenic features, or by
chemotaxis (moving towards a chemical trail produced by a pathogen)
• Engulfing - the phagocyte engulfs the pathogen by extending its membrane
temporarily around the pathogen, before enclosing it within an intracellular
vesicle. This process is called endocytosis. A vesicle containing a pathogen is a
‘phagosome’

phone
• Digestion - the phagocyte lysosomes migrate towards the phagosome and fuse
with it, releasing their digestive enzymes into the vesicle where the pathogen is
being held. The pathogen is broken down and therefore destroyed

•
phone
• Antigen presentation - once the phagocyte has digested the pathogen, it will
present the pathogenic antigens on its own cell surface membrane, becoming
what we call an ‘antigen-presenting cell’ or ‘APC’. This process helps to alert the
T-lymphocytes

pathogenic
antigen

Whilst we most commonly associate antigens with invading pathogens, an immune

response can be activated by other means, too. For example, transplanted cells - if
somebody receives a donor organ. Furthermore, abnormal body cells such as cancer
cells can alter their membrane proteins to alert the immune system that they are
under duress. Toxins produced by cells can also be recognised by the immune system

lymphocytes Lymphocytes are a type of

white blood cell. There are
t wo main types: T-cells and
bonemarrow B- cells. Both are produced
B
stem B matureBlymphocyte in the bone marrow from
hematopoietic stem cells.
B-cells stay and mature in
maturerlymphocyte the bone marrow, whereas
T T-cells move to and mature
thymus in the thymus
 cell mediated immunity t cellsa.k.at lymphocytes
T-lymphocytes are involved in a specific type of immunity called cell-mediated
immunity. This means that they will respond to antigen-presenting body cells only.
If a T-lymphocyte encounters a self-cell that is presenting a non-self antigen, such
as a phagocyte after it has completed phagocytosis, it will respond. T-lymphocytes
are specific immune cells, so they have receptors that will be complementary to a
specific shape of antigen. Once the complementary T-cell binds to the pathogenic
antigen, this specific T-cell is ‘activated’

Aka

activated T cell

presentingcell
t
complementary

T
T
non complementary
non complementary

The activated T-cell then starts to divide rapidly by mitosis to produce many copies
of the same cell
7 T T
T T
s t
T T

i
T
T
t
T T
T J T
These cloned T-cells are allocated one of 3 roles

activation of other immune cells, such as B-lymphocytes and

TH
phagocytes. These are ‘T-helper’ cells

activation of cytotoxic (killer) T-cells. These cells reproduce

Te
perforin, a protein that forms pores or holes in cell membranes,
causing them to become permeable and die

develop into memory cells - some T-cells become memory cells to

Tm
enable a more efficient secondary response in the future

Remember, cell-mediated immunity needs to involve an antigen-presenting human

body cell. It can be a phagocyte, an abnormal body cell or a transplanted cell

humoral immunity B cells a.k.a B lymphocytes

The word ‘humour’ is an old -fashioned term that describes the fluids in the body,
such as the blood and the tissue fluid. The type of immune response that B-
lymphocytes are involved in is humoral immunity, named so as they produce
‘antibodies’. Antibodies are proteins produced by plasma B-cells that are soluble in
body fluids. There are many different B-cells in the body, each with a different
shape antibody on its cell surface membrane. As with T-cells, the complementary
antibody must bind to the pathogen in order to activate
Unlike T-lymphocytes, B-lymphocytes can respond directly to a pathogen in the
blood. It doesn’t need to wait for an antigen-presenting body cell

B bacteria
non complementary B
complementary

B
non complementary
B-lymphocytes will take in a pathogenic antigen by endocytosis, before presenting it
on its own cell surface membrane. The B-lymphocyte has now become an antigen-
presenting body cell and will therefore stimulate T-lymphocyte activation

on a
ganja's
in M B Y
byaconnagey

B B
B
complementary

A complementary T-helper lymphocyte will bind to the antigen being presented by

the B cell. The B cell then becomes activated

B T
Once a B-lymphocyte has been activated, it is stimulated to divide and multiply by
mitosis. This process is referred to as ‘clonal expansion’, resulting in many copies of
the same B-lymphocyte. They will then differentiate into one of two types: memory
B-cells or plasma B-cells

B T

B
B
B B B
B
B B
B B B
B

u v
Bp Bm
Bp Bm
Bn
Bp Bp
Bp Bm Bm

plasmacells memory cells

Plasma B-cells circulate in
the blood for a short amount
of time, mass-producing
antibodies that are to the
pathogen in order to fight it.
This is the primary immune
response
Memory B-cells do not produce
antibodies. They lie dormant in the
blood for many years, and can
‘remember’ the antigen so a response is
launched faster should the pathogen
invade the body again. If this happens,
memory cells will divide to form
plasma cells and secrete the
appropriate antibody. This is the
secondary immune response
 antibodies
An antibody is a globular protein with a quaternary protein structure (made up of
more than one polypeptide chain). They are produced by plasma B-cells during the
specific immune response. The general structure of an antibody is as below

disulfide bridges
antigenbinding site

A variable region
ahh 1mm
if slight chain
Lennon
constant region
h

The antibody is made up of 4 polypeptide chains, all held together in a final

quaternary structure by multiple disulfide bridges (a covalent bond formed between
two sulfur atoms). The constant regions stay the same, whereas the variable
regions have a unique shape that allows them to bind to a specific antigen. There are
two antigen binding sites at the ends of each antibody
 su su a
a

Once activated, plasma B- lymphocytes can produce up to 2000 antibodies per

second. When an antibody binds to a complementary antigen on a pathogen or
antigen-presenting cell, an antigen-antibody complex is formed. Remember that each
antibody has two binding sites

antigen antibody
complex ÉÉÉ tangy antigen antibody
complex

The formation of the antigen-antibody complex can directly neutralise a pathogen

by disrupting its function, or it can act as a marker for other immune cells such as
phagocytes to come and destroy the pathogen

The presence of t wo binding sites allow

antibodies to bind to more than one
if
hacienda

agist pathogen or cell at once. This often leads

to the pathogens becoming clustered
iigno together, almost herded up by the
io
s i antibodies. This process is called

i K agglutination. It makes phagocytosis more

ef cient as the phagocytes will engulf
clusters of pathogen at once, speeding up
the process
 monoclonal antibodies
Monoclonal antibodies are lab-produced antibodies that are derived from a single
immune cell (hence “monoclonal”). The process of producing monoclonal antibodies
involves injecting a mouse with the antigen for which the antibody is desired,
stimulating the humoral immune response and the production of complementary B-
cell antibodies. These B-cells are extracted from the spleen and fused with a tumour
cell (fast cell division), forming a “hybridoma”. Rapid division of the hybridoma leads
to rapid production of the desired antibody, which can then be collected

antigen

mouse B

plasma tumour hybridoma

B cell cell

mass production of
cloned plasma desired antibody
B cell
 monoclonal antibodies for diagnosis
Monoclonal antibodies can be used in diagnostic testing such as pregnancy tests.
Firstly, monoclonal antibodies are produced (via the above process) that are
complementary to the human chorionic gonadotropin (hCG) hormone that is found in
the urine during pregnancy only

s s s

Q
q

hCG hormone hCGantibody with antibody that willbind

fluorescentdye to any free antibody
not attached to hCG

positive result u negative result

If a woman is If a woman is not
pregnant, there will be pregnant, there will
hCG in the urine be no hCG in the urine
sample. The hCG will sample. Therefore, no
bind to the free antigen will bind to
r antibodies in the test the free antibodies.
strip, and move as the The antibodies will
urine absorbs up the move as the urine
strip. The antibodies absorbs but they will
will bind to another not bind to the

1 set of anchored
antibodies in the
result window,
anchored antibodies,
so there will be no
colour change in the
a showing a coloured line result window
 The control window has anchored antibodies that will initiate a colour change if the
free antibodies have moved, indicating the test has been successful whether it is
negative or positive. This type of diagnostic test is called an Enzyme-linked
immunosorbent assay (ELISA) test and can also be used to diagnose HIV

monoclonal antibodies for treatment

As antibody binding sites are specific, we can use them to deliver a drug or
radioactive substance to specific cells. For example, cancer cells. An antibody that
has a complementary binding site to a certain tumour cell will have a radioactive
drug attached to it in a lab. Once it finds a tumour cell, it will bind, deliver the drug
and subsequently kill the cell

O o

nodal
nodal normal

noggal normal 919

antibodyapplied
Yen
arekined
leavingonly the
mtgmog.ee

antibodyattaches
to tumour cells

Monoclonal antibodies are specific, so they can be used in smaller doses, making
them a generally cheaper treatment. It also reduces risk of potential side effects.
However, they are generally more difficult and expensive to produce initially
 vaccination
Vaccinations are lab-made preventative treatments that work by administering a
weak or inactive version of the antigen for which we want to build immunity
against. This triggers a specific immune response, ultimately leading to the
production of memory B-cells

B
B B
B B
B
B
B

Bp BP Bm
Bm

Bp Bp Bm
Bm

memory cells
The presenceplasma
of the memory
cells cells will decrease the immune response time and
increase its effectiveness should the person be infected with a live version of the
pathogen
 vaccine advantages vaccine disadvantages
protectagainst outbreaks side effects are possible
can completely eradicate
may not be effective due
diseases e.g smallpox to antigenic variability
can reduce costs and may be difficult to stove
stressof healthcare systems eg very low temperatures

herd immunity protects must be tested on humans

to ensure safety
those who cannot be
vaccinated can be expensive

vaccinated unvaccinated

80% of this population are

vaccinated against a particular
disease. The other 20% cannot be
vaccinated due to age, allergies or
immunosuppression. However, disease
rates remain low due to high uptake
of the vaccine, meaning that those
who are unvaccinated are generally
safe against the disease, too. This is
called ‘herd immunity’. The
percentage of the population that
needs to be vaccinated for herd
immunity differs with the disease
but generally it is 80% and above
 human
The
immunodeficiency virus of bodily
HIV virus is a deadly virus that is transmitted through exchange HIV fluids
with an infected individual e.g. via sexual intercourse or sharing of needles to
administer intravenous drugs. It can also be passed from mother to baby via
placenta, during birth or breastfeeding
Attachment
glycoprotein
gooo

capsid

Oooo
o Nooooo
8
00 D oo
888
viral o o p
o o
o oo
0 o 8,0
RNA
X
ooo o
oo f
o
ooo o f8 o
o
o
06 oo o
j
e'inriedore

11
o D
8o
o
0
088
oo

jj siriptase
Ireverse
EE do enzyme
Homatrix
proteins

replication of HIV on the outer surface of HIV virus

• Attachment - the attachment glycoproteins
particles are complementary to human helper T-lymphocytes. This means that
HIV will bind to helper T-lymphocytes whenever it enters the blood stream
• Injection of genetic information - a single strand of viral RNA is injected into
the host cell, along with the enzyme reverse transcriptase
• Conversion to DNA - the reverse transcriptase enzyme has the ability to produce
a double-stranded fragment of DNA from the original single stranded viral RNA
• Insertion - the viral DNA is then inserted into the host DNA. The DNA takes a
while to activate, so symptoms of infection are delayed
• Protein synthesis - as the viral DNA has been incorporated into the host DNA, it
will now be transcribed into functional mRNA before being translated into
polypeptides by the host cell ribosomes. The host cell has effectively become a
factory for production of viral proteins
• Host cell death - as more and more viral proteins and particles are produced
within the host cell, the cells becomes overloaded and dies

TH q
TH
TH i o0

i
o
o.o o TH
TH oo
o
ooo
o
or O
o
o
O o

TH
TH

TH
TH of T- lymphocytes by theo OHIV viruso causes an infected persoIH
The destruction n to
TH
become extremely TH Br oka

THimmunodeficient, as the T-lymphocytes play a vital role in

activating B-lymphocytes to produce antibodies. Somebody infected with HIV finds it
very difficult to fight off even almost harmless diseases. Antibiotics will not work
on HIV as it is a virus and is therefore abiotic. There is currently no cure for HIV,
although there are treatments available to reduce the effect of infection
 unit 2 glossary
You need to be able to recognise, remember and use all these key terms in the
correct context in exams…

• Eukaryotic cell: a cell containing a nucleus and membrane-bound organelles

• Prokaryotic cell: a cell that does not contain a nucleus or membrane-bound
organelles
• Virus: acellular pathogen
• Microscope: specialised laboratory equipment used to view cells
• Resolution: the minimum distance t wo objects can be apart and still be
viewed as separate objects
• Magnification: how many times bigger an image of an object is in
comparison to the actual size of the object
• Cell fractionation: a lab technique used to separate cell components
• Ultracentrifugation: the use of a fast-spinning centrifuge to separate cell
components based on their mass
• Interphase: the ‘resting’ phase of the cell cycle in which the cell is not
dividing
• Mitosis: a process of cell division resulting in the production of 2
genetically identical daughter cells
• Cytokinesis: a process of cytoplasmic division that occurs at the end of
mitosis or meiosis
• Organelle: the sub-cellular structures within a cell such as the nucleus,
mitochondria, Golgi body etc
• Diffusion: the movement of a substance from an area of high concentration
to an area of lower concentration, down a concentration gradient
• Active transport: the movement of a substance from an area of low
 concentration to an area of higher concentration, against a concentration
gradient. This process requires energy
• Osmosis: the movement of water molecules from an area of high water
potential (more dilute) to an area of lower water potential (more
concentrated) through a selectively permeable membrane
• Co-transport: the coupled transport of substances across a membrane
through via a specialised membrane co-transporter protein
• Pathogen: a micro-organism that can cause disease
• Toxin: a type of poisonous substance that can be produced by pathogens
• Lymphocyte: a type of white blood cell involved in the speci c immune
response
• Phagocyte: a type of white blood cell that carries out phagocytosis
• Antibody: a protein structure produced by B-lymphocytes that will bind to
a speci c pathogen
• Monoclonal: a cloned cell(s) that is derived from asexual division of a single
cell
3.1 surface area to volume ratio
The surface area to volume ratio of a 3-D surface is a gure that is used to
determine how effective it is as an exchange surface. To be an effective
exchange surface, the surface area must be high in comparison to the volume

SURFACEAREAOFA CUBE Length X Width X Number of sides

length g
8cm
Width 8
8cm noOfsides 6

u surface area 8 8 6 384cm

VOLUME OF A CUBE Length X Width X Height

s
length g
i som
Width 8
8cm Height 8

Volume 8 8 X8 512cm

To gure out the ratio with the volume as 1, we divide the area by the volume

384 512 0.75

Therefore, the surface area to volume ratio of this cube is
0.75
The surface area of this cube is small in comparison to its volume, meaning
that it would be an inef cient exchange surface. Let’s look at some smaller
cubes to compare the nal value

i si 4cm
som
im Imam
6cm
u

SA 6 6 6 216 SA 4 4 6 96 SA 1 1 6 6
V01 6 6 6 216 V01 4 4 4 64 VOL 1 1 1 1
216 216 1 96764 1.5 61 6
SAVOL 1 I SAVOL 1.5 SAVOL 6

As you can see from the results, the surface area to volume ratio increases as
the overall size of the cube decreases. The t wo factors are negatively
correlated. From this information, we can deduce that larger organisms (like
humans) are ineffective as exchange surfaces in comparison to smaller
organisms (such as insects) due to the differences in their surface area to
volume ratio

Organisms with a high surface area to volume ratio (smaller organisms) tend to
have a higher metabolic rate
32 Gas exchange
The exchange of gases in living organisms is vital for survival. Primarily, we
must acquire oxygen for aerobic respiration, and we must remove the carbon
dioxide that is produced as a result

Humans, being large organisms, have a small surface area to volume ratio (see
topic 3.1). This means the outer surface of a human (the skin) does not make for
an ef cient exchange surface. Humans have a dedicated exchange system: the
lungs

Trachea - also known as

Intercostal muscles the windpipe, the
- muscles bet ween trachea funnels air that
the ribs that assist is inhaled through the
with ventilation mouth/ nose to the lungs

Bronchioles - the
bronchi split further
into smaller air
passages called
bronchioles
Mogg
i
Bronchi - passages
that split off from
D the trachea in t wo
o
directions - one into
a 00 the left lung, one
into the right. Each
is called a bronchus

Alveoli - at the end of

Diaphragm - a dome-shaped
bronchioles are
muscle at the bottom of the
microscopic air sacs
thoracic cavity that assists
called alveoli. These
with ventilation
are the site of gas
exchange in humans
Gas exchange in humans happens at the alveolar surface. Here’s how alveoli are
adapted to be an effective exchange surface

capillaries

Thin alveolar walls - the walls of the alveoli contain only one single layer of
epithelial cells. We say they are ‘one cell thick’. This minimises the diffusion
distance for gases, allowing it to occur faster. The alveolar membrane is also
very permeable to gases

Large surface area - alveolar sacs contain around 30 alveoli each; there are
millions of alveoli within the human lungs, generating a huge collective
surface area. Such a large surface area means that more gas exchange can
occur simultaneously throughout the system
Extensive capillary network - the alveoli are surrounded by a vast net work
of the smallest blood vessel, the capillaries. As well as keeping the diffusion
distance short, the constant ow of deoxygenated blood across the alveoli
maintains a concentration gradient, promoting movement of oxygen into the
blood

Elasticated surfaces - the elasticity of alveoli facilitates ventilation by

allowing them to expand during inhalation and recoil during exhalation.
Elasticity facilitates gas exchange by allowing the alveoli to expand and move
closer to the capillaries during inhalation

Inhalation external
intercostalmuscles
f contract

ribcagemoves ribcagemoves
and't supandout
giggggfgIgg
a ly
or
a

L r v
diaphragmcontractsandflattens
As a result, the volume of the lungs is increased, therefore the pressure inside
the lungs decreases. This causes air to be drawn into the lungs (inhalation)
 external
intercostalmuscles
Exhalation f relax

ribcagemoves ribcagemoves
and downand in

Joe ÉYY o
of

i n go

diaphragmrelaxesand domes
As a result, the volume of the lungs is decreased, therefore the pressure inside
increases. This causes air to be forced out of the lungs (exhalation)

Lung disease can occur whereby the function of the lungs is compromised by
onset of disease. Let’s discuss t wo common diseases of the lungs

1. Emphysema - this disease causes the walls of the alveoli to become

damaged, lose their elasticity and break down all together. This decreases
the surface area of the alveoli and makes gas exchange less ef cient. It
also leads to ‘a ir trapping’ where, due to the loss of recoil, stale air remains
in the lungs and doesn’t get expelled. The most prominent risk factor for
emphysema is smoking, as the tar in cigarettes is what causes the
breakdown of the alveolar walls. Emphysema is incurable
2. Fibrosis - this disease causes permanent scar tissue to form in the lungs.
Scar tissue is thick and rigid, therefore interferes with the alveoli as an
exchange surface by increasing the diffusion pathway, as well as
decreasing the elasticity. Risk factors for pulmonary brosis include the
inhalation of environmental toxins such as asbestos or dust. It is an
incurable disease

Some important information that we must know for human gas exchange:

tidal volume the volume of air that enters

the lungsduring one innate

breathing rate number of breaths taken per

minute

pulmonary tidal volume x breathing rate

ventilation rate
PVR

forced viral the volume of air that can be

capacity frc forcefully exhaled following a
deep breath in
gas exchange in fish
For this topic, we must also be aware of a few non-human gas exchange
systems and be able to appreciate the differences and similarities. The next
organism we will look at is sh. Of course, sh exist in aquatic environments
and therefore do not ‘breathe’, however they still require oxygen for cellular
aerobic respiration. The trouble is, the oxygen content of water is much lower
(around half as much) than that of atmospheric air, so the sh gas exchange
system is much more effective at extracting oxygen

the gills of fish The

i i

Gill filament - thin

ÉÉ
plates that make up the
gills of the sh,
arranged in stacks

É
Lamellae - the lamellae are
small disc-like structures that
stand at a right angle to the
surface of the laments. They
increase the surface area of
the gills and have a net work
of capillaries running through
them
Fish carry out a very specialised mechanism of water movement called buccal
pumping. They draw water (containing dissolved oxygen) into their mouths,
and force it back out over the gills. They expel the water over the gills in the
opposite direction to the ow of blood through the capillaries.

As the water ows over the lamellae in the opposite direction to the ow of
blood, it will come into contact with the most oxygenated blood rst. However,
it is likely that oxygen concentration will still be slightly higher in the water,
so a small amount of oxygen will move into the blood via diffusion

IÉGÉGIES
As the water ows over the lamellae and oxygen diffuses into the blood, the
oxygen concentration of the water is depleting. However, as the water is
owing opposite to the ow of blood, the oxygen concentration of the blood is
also decreasing. This means that a concentration gradient is always
maintained where oxygen concentration is always higher in the water than in
the blood. Therefore, oxygen will always diffuse into the blood. This mechanism
is called the counter-current ow and allows the gills to maximise their oxygen
absorption

water

dissusionoroxygen
down a concentratio
gradient

blood
*the numbers are an arbitrary unit representing the quantity of oxygen in the
water or the blood

The counter-current ow mechanism ensures that the concentration gradient

always favours the movement of oxygen into the blood

gas exchange in insects

Insects also have a specialised system for gas exchange, called the tracheal
system. A lot of insects have hard exoskeletons that are impermeable to gas
Spiracles are C Insect trachea are very
pores in the similar in function to
exoskeleton that human trachea in that it
allow gas to enter acts as a passage for air to
and leave enter into the body

Muscle cells Tracheoles provide

are highly smaller passages for
metabolically air to be exchanged
active cells in with cells within the
all organisms body

Insects will carry out rhythmic abdominal movements in order to draw air
into the trachea through the spiracles

gas exchange in single celled organisms

Due to their large surface area to volume ratio, single celled organisms lack the
need for a dedicated gas exchange system. Instead, they use simple diffusion of
gases through the phospholipid membrane

oxygen in carbonydioxideout

t
t
gas exchange in dicotyledonous plants
Gas exchange in plants occurs in the leaves. Similar to insects, plants have
pores in their leaves that allow air to diffuse in and out. These pores are called
the stomata. The stomata can be open or closed depending on the conditions.
The opening and closing of stomata is controlled by surrounding guard cells

0 epidermis

É É É É ÉO palisade
mesophyll

of
00 spongy
mesophyll

000000 epidermis
guard cells stomata v02

Plants need to open their stomata to allow for the exchange of gases.
However, when the stomata are open, water is also lost via evaporation from
the leaves through the stomata. There must be a balance established bet ween
the rate of gas exchange, and the rate of water loss
 Here, the stomata are open. They allow for oxygen
and carbon dioxide to diffuse in and out. However,
when the stomata are open, water is being lost by

oxtail is
evaporation. The stomata generally open during the
daytime for wild plants, as the availability of light
energy favours photosynthesis, for which carbon
dioxide diffusion is essential

Here, the stomata are closed. They do not allow

for gas exchange or water loss by evaporation
to occur. The stomata generally close at night,
where no light energy is available and therefore
exchange of gases is not essential. Closing the
jaeger
stomata when gas exchange is not needed helps
to limit water loss

Some plants have evolved even more specialised mechanisms of preser ving
water, as they live in dry, barren environment. These plants are called
xerophytes
A thick, waxy cuticle
forms a waterproof
barrier on the surface
of the plant
Smaller leaves
reduce the surface
area to volume ratio Sunken stomata
of the plant, that are found in
helping to limit grooves of the leaf
water loss trap moist air. This
reduces the
moisture gradient
and limits water
loss by
evaporation
3.3 digestion and absorption
The digestive system is another one of the 11 body systems within the human
body that carries out essential roles for survival. The digestive system is
responsible for the breakdown of large food molecules into their monomer
units for simple absorption and transport

The three major macromolecules consumed in the diet and their monomer
nutrients are as follows

ii
again

iii.ir'oisiitainisittiismisanimaramimi

hydrolysis
ix iii ix
t
ÉÉ
Y tii
tiii.it
again
tiii
Y inioniY
iam i tii.it'iiiiMazaramisisentiniiiiiiennigiousian
EÉI
ggx.jp
again

Starch glucose

i
hydrolysis
protein amino acids

near
hydrolysis
lipids monoglyceridestfatty acids

The breakdown of polymers into monomers is carried out by hydrolysis

reactions (see topic 1.1), where water molecules are used to break bonds
The hydrolysis of these large molecules is carried out by speci c hydrolytic
digestive enzymes. Enzymes have a speci c active site that is complementary
to the shape of one speci c substrate. Therefore, there are many different
digestive enzymes found in the digestive system, each with its own role

Starch
Starch is the glucose storage molecule found in plant cells. When ingested by
humans, it must be hydrolysed into glucose that can then be used for
respiration. Starch digestion begins in the mouth

IggyÉT

Salivary amylase is secreted from the salivary glands. Amylase is a type of

carbohydrase that breaks starch down into maltose (disaccharide of 2 glucose
molecules)

hydrolysis
Food then passes into the stomach via the oesophagus, where salivary
amylase is denatured. There is no further digestion of starch until the food
reaches the small intestine. Digestive enzymes, including pancreatic amylase
are secreted into the small intestine from the pancreas, allowing further
digestion of starch into maltose. Furthermore, an enzyme (maltase) that
hydrolyses maltose into glucose is found embedded in the membrane of the
epithelial cells of the small intestine
glucose

glucose

i
maltose

i
ipspiiOsiOEIideJpoisoiigEIBooissaooigooi p iio.PE PEDOÉEI.io
00 y
IioK
ee.I ioaiaG oiseios oiIi.osimisoaisioooi oi si ro
isidiooiosriIasile tooooo
oogonia

epithelial membrane
Protein
Proteins are broken down into amino acids by protease enzymes. Amino acids
are then used to build different proteins that are needed by the body. There are
three different types of protease

• Endopeptidase - these are protease enzymes that only break internal bonds
of the polypeptide chain. They do not break terminal bonds (e.g. an
endopeptidase will break a chain in half, rather than break an amino acid
off the end of the chain)
i
i

i
hydrolysis
• Exopeptidase - these proteases only break terminal (end) peptide bonds. This
process releases single amino acids

i
hydrolysis

i
• Dipeptidase - these protease enzymes are a type of exopeptidase that
hydrolyse the nal peptide bond holding t wo amino acids together, breaking a
dipeptide into t wo amino acids

hydrolysis

Pepsin is a type of endopeptidase enzyme and one of the few digestive enzymes
that are present in the stomach. Most enzymes are denatured by the low
(acidic) pH of the stomach. Proteins can therefore be digested in the stomach.
Protein is also digested in the small intestine by pancreatic peptidases

Stomach pH2
I
marousis
i i
Lipids
Lipids (fats and oils) are broken down into monoglycerides (glycerol molecule
bonded to one fatty acid) and separate fatty acids. Lipid digestion more
complex than the others, as it involves help from the bile salts of the liver

Bile salts released by the liver travel into the small intestine and emulsify
large lipid droplets (break the large droplets down into smaller ones to increase
the surface area for enzyme action)

liver gallbladder

emulsification

bilesalts large fat droplet triglycerides

Once large fats have been emulsi ed, they can be further digested by lipases
that are produced in the pancreas and secreted into the small intestine

hydrolysis
 absorption
Digestion of large molecules is only half of the process. The next stage is to
move the resultant nutrients into the bloodstream. That way, they can be
transported all throughout the body and utilised as required. Glucose and
amino acids, once broken down are absorbed from the ileum of the small
intestine into the blood stream by a process called co-transport

Starch is broken down

into glucose molecules
by digestion
aiggEooEEEoomEEMaEEEMAEEMaEEEogamogamETam
Sodium ions are actively
transported out of the
epithelial cells via a
sodium/potassium pump.
As a result, sodium ions
move into the epithelial
cell from the ileum down a
ASEEITNaga concentration gradient.
They move through a
temEamaggg a toga wa special protein carrier
called a co-transporter.
This requires a second

always a lower
concentration of sodium
AntaraM
This ensures that there is
molecule, either a glucose
or amino acid to be carried
through at the same time

in the epithelial cell that Na

in the ileum

It
those

L
Glucose then moves into a nearby capillary by
facilitated diffusion. Glucose is then transported
to cells that need in the ow of blood

Remember - this co-transport method of absorption is the same for both

glucose and amino acid molecules
Absorption of fat molecules is a little different to absorption of glucose and
amino acids. After the emulsi cation of large droplets, lipases break lipids down
into monoglycerides and fatty acids. These then combine with bile salts and
phospholipids to form small droplets called micelles
bile
say
ymonoglycerides

micelle

T
phospholipids

Éacids
The purpose of micelles are to facilitate the movement of monoglycerides and
fatty acids through the ileum into the space surrounding the epithelial cells
where they will be released and diffuse into the epithelial cell

micelle
mine mine
lumenof the
micelle

ileum

f
endoplasmic
microvilli reticulum

1
epithelial
cell triglyceride
 Once the monoglycerides and fatty acids reach the endoplasmic reticulum
within the epithelial cell, they are converted back into triglyceride molecules.
These triglycerides then combine with cholesterol and phospholipids to form a
structure called a ‘chylomicron.’ These chylomicrons then enter the
bloodstream via lymph vessels called lacteals. The monomer units of lipids have
therefore made their way successfully into the blood

micelle

lumen of the
micelle micelle micelle

ileum

f
endoplasmi
microvilli reticulum

t
epithelial
triglyceride

of lacteal

into bloodstream
3.4.1 mass transport in animals
Due to the small surface area to volume ratio of humans, we have specially
adapted mechanisms of transporting important substances around the body,
such as oxygen. Oxygen is transported in the blood by a protein called
Haemoglobin
beta chain alpha chain

Haemoglobin also
has four non- Haemoglobin is made
protein units up of four
go
attached - four polypeptide chains:
haem groups, 2 alpha chains and
each containing a 2 beta chains. This
ferrous (Fe 2+) means that
Mr
ion that can bind Haemoglobin has a
to oxygen quaternary protein
structure

alphatchain betachain

Haemoglobin is a globular protein (see topic 1.4.2 - many proteins are enzymes).
Haemoglobin has a unique characteristic in that it’s af nity for oxygen can
alter. ‘Af nity’ describes how likely substances are to bind to one another

highaffinity lowaffinity

039
09186
oxyget 8Y oxygten

If af nity of Haemoglobin is high, oxygen will bind. If af nity is low, oxygen will
not bind and may even dissociate from the Haemoglobin
 When discussing the amount of oxygen in a given area, we use the term ‘partial
pressure’. Partial pressure refers to the amount of pressure exerted by a
certain gas in a mixture of gases. The higher the percentage of oxygen in a
given mixture of gas, the higher the partial pressure

partialpressure ofoxygen HIGH partialpressure ofoxygenLOW

partialpressure of carbondioxide LOW partialpressure of carbondioxide HIGH

At the alveoli, partial pressure of oxygen (pO2) is high, due to the constant
in ux of oxygen through inhalation. Partial pressure of carbon dioxide (pCO2) is
low, due to the constant removal of carbon dioxide via exhalation

At respiring cells, pO2 is low due to the occurrence of aerobic respiration within
the mitochondria - using up the available oxygen. Furthermore, pCO2 is high at
respiring cells as carbon dioxide is released as a waste produce of aerobic
respiration

Partial pressure is measured in Millimeters of Mercury (mmHg)

oxygen dissociation curve
The oxygen dissociation cur ve is a distinctive graph that depicts the
relationship bet ween the percentage oxygen saturation of Haemoglobin and
the partial pressure of oxygen

to
poammt
1: the 4 polypeptide sub-units (2 alpha, 2 beta) are shaped in a way that makes
binding of the rst oxygen molecule dif cult, hence the shallow curve

2: the binding of the rst oxygen molecule causes the Haemoglobin to change
shape slightly, becoming less tightly wound. This makes it easier for the second
and third oxygen molecules to bind, hence the steeper curve

3: it is again dif cult for the fourth and nal oxygen molecule to bind due to the
lack of vacant binding sites (there is now only one available out of the original
four)
the bohr shift
As we have seen, the af nity of Haemoglobin for oxygen can change. Another
factor that can affect af nity of Haemoglobin for oxygen, is the partial
pressure of carbon dioxide (pCO2) in the environment

partialpressureofoxygenHIGH fd.ioiae
19111ft

HIG jE

É É É

t t t t t 10
pfammHg poambmHg

A high partial pressure of carbon dioxide causes a decrease in the pH level of

the blood. This causes the Haemoglobin to change shape slightly, decreasing the
af nity for oxygen and making it easier for oxygen to of oad

The way that high pO2 increases af nity and pCO2 decreases af nity allows
oxygen to be loaded at the lungs then transported and of oaded at the
respiring cells
The type of Haemoglobin found in the blood of different animals is not always
the same. Different animals have different types of Haemoglobin depending on
the environment in with they live

mountaingoathaemoglobin

adulthaemoglobin

É Nj

o 1 to
poantmHg's
Haemoglobin with a higher af nity for oxygen is a survival advantage for
organisms living in areas of lower pressures of oxygen (for example high
altitudes) as it allows them to extract suf cient oxygen from the air

the circulatory system

As aforementioned, humans have a small surface area to volume ratio. This
makes them inadequate at natural exchange of important substances. We have
looked at how the structure of the lungs facilitate exchange of gases. Let’s
now look at how the heart, blood and blood vessels (the circulatory system)
facilitate the transport and exchange of other substances, too.

First up, the heart…

The mammalian heart uses a ‘double pump’ system. There are t wo sides of the
heart: left and right. The left side deals with oxygenated blood, whilst the
right side deals with deoxygenated blood

de oxygenated

The separation of oxygenated and deoxygenated blood ensures that oxygen is

effectively delivered to respiring cells. It also means that a high
concentration gradient is maintained bet ween deoxygenated blood and the
alveoli so oxygen will always be adequately loaded into the blood

Blood always enters the heart through the atria

Blood always exits the heart through the ventricles

Blood is moved through opposite sites simultaneously e.g. both the left atrium
and the right atrium ll with blood at the same time
 lungs

vena cava
iii

Order of blood ow through the heart

1: deoxygenated blood enters the right atrium via the vena cava
2: deoxygenated blood moves from the right atrium into the right ventricle
3: deoxygenated blood exits the heart from the right ventricle and travels to
the lungs via the pulmonary artery
4: blood is oxygenated at the lungs
5: oxygenated blood is transported back to the heart via the pulmonary vein.
It re-enters the heart through the left atrium
6: oxygenated blood moves from the left atrium into the left ventricle
7: oxygenated blood exits the heart from the left ventricle and is transported
into the wider arterial system through the aorta
Blood ow is maintained in the heart by a sequence of co-ordinated
contractions carried out by the heart muscle. We call this, ‘the cardiac cycle’

Systole = muscle contraction

Diastole = muscle relaxation

IY

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1 Iii
1L

atrial systole ventricularsystole diastole

The left and right The left and right Both atria and
atria contract ventricles contract ventricles relax.
simultaneously, simultaneously, Blood starts to re-
increasing atrial increasing enter the heart via
pressure and ventricular pressure both of the atria
forcing the blood and forcing blood before the cycle
down into the out of the heart starts again
ventricles through the arteries

It is very important to maintain a uni-directional ow of blood in the heart to

avoid the mixture of oxygenated and deoxygenated blood. Another adaptation
of the heart to do so is the presence of valves. Valves are specialised
structures made of connective tissue that prevent the back ow of blood as
pressure changes occur thoughout the cardiac cycle
 ifaY

pts off
and

and the arteries the semi lunarvalveswill open

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when ventricularpressure is higherthanarteria
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ventricular
pressure during systole

yYj
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As for the wider circulatory system, blood is transported around the entire
body through a net work of arteries, veins and capillaries

Arteries carry blood away from the heart and

mostly (except for the pulmonary artery) carry
oxygenated blood. The arteries are specially adapted

q .si
for fast, high-pressure blood ow generated by the
contraction of the heart muscle. They have a thick
muscular lining with lots of elastic tissue, making
them more resilient to pressure damage. Arteries
have a small lumen to maintain high pressure
Veins carry blood back to the heart and mostly
(except for the pulmonary vein) carry deoxygenated
blood. Blood is owing at a much lower pressure as it

Ms
returns to the heart, as it has been passed through

wifi
capillaries along the way. Veins have thinner walls
with less muscle and elastic tissue. They have a larger
lumen than arteries. Veins also contain valves (they
are the only blood vessel with valves) as the reduced
pressure puts blood at risk of back ow

Blood passes from arteries to veins through capillaries. Capillaries are

extremely thin - just one cell thick - to facilitate exchange. The capillaries are
where substances like oxygen and glucose will move out of the blood into the
tissues. Waste products such as carbon dioxide will move back into the blood to
be removed. The surfaces of capillaries are very porous to facilitate the
movement of substances further

vein capillaries

e ta a artery
I Gaucose

C BRAIN

The arterial net work runs on the left side of the

body, carrying blood away from the heart and

iiis
branching off into vast net works of capillaries. At
the capillaries, exchange will take place bet ween
the blood and the surrounding cells, tissues and
organs. The capillaries then rejoin larger blood
n
stomach vessels on the venous system, on the right side of
the body. Blood will then be returned to the heart
T Kinney
 tissue fluid formation
Tissue uid is a liquid substance that surrounds all tissues in the body, supplying
them with their much- needed x of glucose, amino acids, oxygen and more.
When arteries branch off into net works of thinner vessels (arterioles and
capillaries), there is a high hydrostatic pressure due to the change in diameter
of the lumen. As a result, blood plasma (a mixture of water and dissolved
substances) is forced out of the blood vessel and into the surrounding space.
This is the tissue uid

highhydrostatic
Pff pressure

88
Inlymphatic vessel
As a lot of water is forced out at the arteriole end, the water potential of the
blood is lowered towards the venule end. The water potential of the
surrounding tissue uid is higher in comparison. Therefore, some water moves
back into the blood via osmosis at the venule end, taking with it waste
products such as carbon dioxide

highhydrostatic
pressure

potentates

ÉJLymphatic
vessel
Any excess tissue uid is returned to circulation via the lymphatic system
3.4.2 mass transport in plants
Plants also have specially adapted transport tissues to help them deliver
water and nutrients throughout

In plants, photosynthesis takes place at the leaves. Photosynthesis requires

water as one of the reactants. Water is absorbed by the root hair cells in the
roots of plants. Therefore, water must be transported from the roots to the
leaves
76002 6420 16641206 602

water

The xylem are the specialised transport tissues that are responsible for the
transport of water and dissolved mineral ions in a plant

Xylem walls are Xylem vessels are made

ligni ed (contain up of dead cells with no
lignin) to provide end walls to give them a
structural strength hollow route through
and rigidity

Xylem walls have ˋpitś -

areas of the wall that
There are no organelles are not ligni ed. These
within the xylem vessels, pits allow water and
leaving more space for the nutrients to move in and
transport of water and out of the xylem
mineral ions
Water moves up the xylem in one direction only. Water is pulled against the
force of gravity. A tension force is created and maintained as water
evaporates from the surface of the leaf through the stomata

Factors affecting the rate of

D transpiration:

OO Temperature - higher temperature will

increase the rate of evaporation due to
increase in kinetic energy

00
000
Light intensity - higher light intensity
increases rate of transpiration as the
stomata are open longer to facilitate
A
extra photosynthesis
Humidity - the lower the humidity, the
faster the rate of evaporation as the
0000000000 water potential gradient bet ween the
stomata
I v02 leaf and the environment is greater

Yutaka IEEE.IEeataasit

So, tension force builds as the loss of water creates the pull. But it is the
cohesion of water molecules (the way they stick together) that allows water
to be pulled up through the xylem in a continuous column that we call the
transpiration stream

I É
o tÉ c
ya
a
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o 11114
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1111111 hydrogenbond It
There is a nal factor involved in the movement of water. It is a force called
‘adhesion’, whereby water molecules are attracted to other substances around
them. For example, the walls of the xylem. This can also help with the upwards
movement of water

Important points about the xylem vessels:

• No end walls - dead cells

• Forti ed with lignin
• Responsible for transport of water and mineral ions
• One way movement within the xylem only
• Tension creates pulling force
• Cohesion creates column of water
• Adhesion occurs bet ween water and xylem walls

There is a second specialised transport tissue within plants - the phloem. The
phloem are responsible for the transport of sugar from the cells that produce
it to the cells that need it

The sieve plates of Phloem are made up of cells

phloem are perforated to called sieve tube elements. They
allow substances to still are living cells and are joined
pass through end-to-end by sieve plates

Like xylem, the cells of

the phloem contain no
Pjs
401
It Sieve tube elements are
associated with

Giri
organelles to leave more companion cells. The
space for the companion cells provide
transportation of
substances that lots of energy, needed to
load sugar into the phloem
The liquid within phloem is not limited to uni-directional movement. Sugars are
moved both up and down the plant. They are transported from source cells (the
photosynthetic cells that produce sugar) to the sink cells (the cells that need
the sugar for respiration). The process of moving the sugar is called
translocation
PHLOEM XYLEM

i
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Ili
g
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ToiIIio

1
is
Firstly, hydrogen ions are actively transported from the companion cells into
the source cell. This creates a concentration gradient where there are more
hydrogen ions in the source cell than in the companion cell

SOIREE COMPANION

Hydrogen ions then move back into the companion cell, down a concentration
gradient. They move through a specialised membrane protein called a co-
transport carrier. Each time a hydrogen ion is relocated into the companion
cell, a molecule of sucrose (sugar) is taken, too
COMPANION
SOIREE CELL

Ht Ht
ooooo

00

it

The sucrose molecules are actively transported into the sieve tube elements by
active transport. As sucrose is moved into the sieve tube element, the water
potential of that area of the phloem is decreased, as the solution has become
more concentrated. This causes water to move into the phloem from the
nearby xylem vessels
 SOFIE COMPLEXION

i.IQ

YI
Mili
passed
Volume of water in the phloem near the source cell increases due to movement
of water in from the xylem via osmosis. This increases the amount of pressure
in this area (pressure exerted by a liquid is called hydrostatic pressure). An
increase in hydrostatic pressure causes the liquid (containing the sucrose) to be
forced to an area of lower pressure, towards the sink cell

That
nigh
pressure
Tgif
movement f

or solution
ÉIEILTILE ly

low
hydrostatic
x
The sucrose then moves into the sink cell, through the companion cell via
facilitated diffusion. This increases the water potential of the phloem as the
solution has become more dilute once again. Therefore, water moves back into
the xylem via osmosis

O i m

iPiigig.im
H

i
Io.to I

As a result, sucrose has been transported from source to sink. This whole
process is described as the ‘mass ow hypothesis’. It is the most widely
accepted theory into how sucrose is transported within plants
 unit 3 glossary
You need to be able to recognise, remember and use all these key terms in the
correct context in exams…

• Adaptation: a change that occurs in which an organism becomes better

suited to its environment
• Ventilation: the mechanism of breathing
• Gas exchange: the exchange of gases across an exchange surface of an
organism
• Digestion: the breakdown of large food molecules into smaller molecules by
hydrolysis
• Carbohydrase: enzymes that hydrolyse carbohydrates into
monosaccharides
• Amylase: a speci c type of carbohydrase secreted by the salivary glands
and the pancreas that hydrolyses starch into maltose
• Maltase: a speci c type of carbohydrase that hydrolyses maltose into
glucose
• Lipases: enzymes that hydrolyse lipids into monoglycerides and fatty acids
• Proteases: enzymes that hydrolyse proteins into amino acids
• Endopeptidases: proteases that only hydrolyse internal peptide bonds
• Exopeptidase: proteases that only hydrolyse terminal peptide bonds
• Dipeptidase: proteases that hydrolyse the peptide bond holding t wo amino
acids together as a dipeptide
• Bile salts: acidic substance produced by the liver that emulsify lipids
• Emulsification: the breakdown of large fat molecules into smaller fat
molecules to increase surface area for enzyme digestion
• Absorption: the process of absorbing digested nutrients from the small
 intestine into the bloodstream
• Micelle: monoglycerides, fatty acids and phospholipids associated with bile
salts to form small droplets called micelles
• Surface area: the total area that the surface of an object occupies
• Volume: a measure of the 3-dimensional space that an object occupies
• Haemoglobin: a globular protein found in red blood cells that can bind to
oxygen
• Affinity: how likely t wo substances are to bind to one another
• Partial pressure: the amount of pressure exerted by a particular gas within
a mixture of gases
• Bohr shift: a lower af nity for oxygen of haemoglobin caused by a high
partial pressure of carbon dioxide
• Oxygenated blood: blood that is rich in oxygen
• Deoxygenated blood: blood that has a very low concentration of oxygen
• Arteries: blood vessels that carry blood away from the heart
• Veins: blood vessels that carry blood towards the heart
• Capillaries: thin blood vessels that connect the arteries and veins
• Atria: the top chambers of the heart through which blood enters
• Ventricles: the bottom chambers of the heart through which blood leaves
• Valves: connective tissue that prevents the back ow of blood in the heart
and the veins
• Systole: cardiac muscle contraction
• Diastole: cardiac muscle relaxation
• Tissue fluid: uid forced out of the blood that bathes the cells and is rich in
nutrients
• Xylem: plant transport tissues that transport water and dissolved minerals
• Phloem: plant transport tissues that transport organic products of
photosynthesis
• Mass flow hypothesis: the process that described how sucrose is
transported from the source cell of a plant, through the phloem vessels to
the sink cell via companion cells
• Translocation: the movement of substance from one place to another
• Transpiration: the process of water movement through a plant driven by
the evaporation of water through the stomata
41 DNA genes chromosomes
Before we delve into the role of DNA and how the genetic code governs
organisms, it is important to have a comprehensive understanding of DNA
structure. We have previously learnt about how DNA is built from nucleotides
(see topic 1.5.1- structure of DNA and RNA)

DNA is stored differently in prokaryotes than eukaryotes

Prokaryotic genetic information is stored as a single molecule of circular DNA.

prokaryotes have much less genetic information and therefore much less DNA
than eukaryotes. Prokaryotic DNA is not associated with histone proteins

We already know that eukaryotic DNA is stored in the nucleus. Eukaryotic DNA
is wrapped around packaging proteins called histones. Histones are positively
charged proteins, attracting the negatively-charged phosphate groups of DNA
molecules and allowing them to closely associate with one another

histone
During stages of the cell cycle that the cell is not dividing, the DNA-histone
complex is stored in a more exible, dynamic way. This structure is known as
chromatin. When DNA is stored as chromatin, the genes can be accessed easily
by transcription factors

chromatin

During times that the cell is dividing, either during mitosis or meiosis, the DNA
condenses into a more organised structure called a chromosome. Once
condensed into these chromosome structures, DNA is visible through a
microscope. Condensing into chromosomes allows the DNA to be accurately
allocated into daughter cells without any damage

centromere
chromosome

Chromatin and chromosomes hold lots of genes (anywhere bet ween 200-2000
genes lie on each chromosome). A gene is a short section of a DNA molecule that
codes for a particular characteristic

t thespecificposition
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32
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located on a
chromosome is
mmmm caneathenous
Remember from topic 1.5.1, we learnt how all DNA nucleotides had a
nitrogenous base, either A, T, C or G

atte
ABBÉ
phosphategrotup 8tdo nitrogenous base
pentosesugar

A, T, C and G came in t wo sets of complementary pairs. The bases of DNA

nucleotides are hugely important, as they carry the genetic code.

DNA is used to build proteins by rst copying complementary strands of RNA,

before using the sequence of RNA bases to build a speci c sequence of amino
acids. Let’s have a look at a table known as the genetic code table
As you can see, there are 64 different 3-letter combinations present on this
table, all with the code to a speci c amino acid associated. The genetic code is
read in sets of 3. We call the 3 bases a ‘triplet codon’. Each codon codes for a
speci c amino acid

I t t ttt t t t t tt t tt ttt ttt

RNA
Ah Eh
1 todonzhodonts
ant IIs code Yodonttodonstodona

This strand of mRNA is made up of 27 nucleotides with 27 bases. Therefore,

this strand contains 9 separate codons (groups of 3 bases) and will code for 9
amino acids in total. Let’s look at how we read the table to understand how the
base sequence is translated. Let’s start with codon 1: CUA

The rst letter is C, so we nd C on the vertical list of letters. The second letter
is U, so we nd U on the horizontal list of letters. We look in the box where the
t wo meet, and nd the combination CUA

We can see from the table that the codon CUA codes for the amino acid ‘Leu’.
We do not need to know the name of individual amino acids
Let’s do one more, the next codon - AGC

I 1 I

IET

The table shows that the codon AGC codes for the amino acid ‘Ser’

• The genetic code is always read in sets of 3. Codons are always made up of 3
bases - no more, no less.
• The genetic code is universal. This means that the triplet codon ‘CUA’ codes
for Leu in all living organisms - not just humans
• The genetic code is non-overlapping. Each base will only be read once. If a
strand of RNA has 9 bases, it will produce 3 amino acids only. If the strand
has 12 bases, it will produce 4 amino acids only
• The genetic code is degenerate. This means that more than one combination
of 3 bases can code for the same amino acid. For example, amino acid ‘Ala’ is
coded for by GCU, GCC, GCA and GCG. This is due to the fact that there are 64
possible different base combinations, yet there are only 20 amino acids in
existence within cells
4 2 DNA 3
protein synthesis
We have established that eukaryotic DNA is held within the nucleus, whereas
prokaryotic DNA simply lies within the cytoplasm. What we need to gure out
next, is how the information held within said DNA ends up as a fully-
functional polypeptide.

First up, a new term - genome. The term ‘genome’ describes the complete set of
genetic information present within an organism. In humans, the genome
consists of 23 pairs of chromosomes, holding approximately 20’000 genes
maternal copy from mother
E paternal copy from father

63 ES E
CHR
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CHR2 CHR22 CHR23

Throughout the process of protein synthesis, there are t wo types of RNA

involved - messenger RNA and transfer RNA

mRNA is a short, single-

stranded form of nucleic
acid. The role of mRNA is to
carry a ‘message’ from the
DNA in the nucleus to the
MRNA ribosomes
 tRNA molecules are tRNA is still a single
associated with a 7 stranded nucleic acid,
speci c amino acid. but it has adopted a 3D
The amino acid structure due to base
depends on the pairing. We liken the
anticodon sequence shape to a cloverleaf

tRNA molecules have an

anticodon at one end that
t
pairs with an mRNA codon
at the ribosome

The rst stage of protein synthesis is transcription. This happens within the
nucleus and results in the production of functional mRNA. RNA polymerase is
involved in the process of transcription

polyhidrase
DNA s

nuclearenvelope
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nubs 1
s nuclear pores
Transcription is the process of copying a short section of DNA into a molecule
of RNA, so that the code can be transferred to the ribosome and a protein
assembled. First, the genetic code must be made more accessible (right now it is
protected within the double helix). RNA polymerase binds to a promoter region
on a gene and starts to ‘unwind’ the double helix

Promoter region: a section of non-coding DNA located just before a gene. The
role of a promoter region is to signal cell machinery to start copying the
following DNA into RNA. The promoter region is like a start button

RNA polymerase
dthkadhdhdtthddddltttihdathtdth.in a'chittattilittanadatht

iii iaiii.in iiaiiiiiiiiaiiitiiiiiaiiaii iii.it ttiiiaiiit

promoterregion

RNA polymerase unwinds a short section of the DNA, exposing the DNA bases.
The double helix is made up of t wo strands of DNA - the sense strand and the
anti-sense strand (the template strand). The anti-sense strand, or template
strand is the strand that will be copied into an RNA molecule
sensestrand

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7 anti sense strand
7997 templatestrand
Free RNA nucleotides in the nucleus begin to line up with their complementary
exposed DNA bases. Remember with RNA, thymine (T) is replaced by uracil (U)

hittin'ata'd't't't't
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free RNAnucleotides
ftp
jgg.jggg.g.g.g.gg.gg

yg
As RNA polymerase moves along the template strand, it catalyses the
condensation reaction bet ween adjacent RNA nucleotides, forming a new
phosphodiester bond bet ween each. The end result is a single, continuous
strand of RNA that is complementary to the template strand of DNA

hittin'ata'd't't't't
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917,444,4
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This molecule is referred to as ‘pre-mRNA’ as it is not quite ready to leave the
nucleus. It has been previously mentioned that eukaryotic DNA contains non-
coding regions, called introns. These introns are copied into RNA, and must be
removed before RNA is translated at the ribosome. The removal of introns
from a strand of pre-mRNA is called ‘s plicing’ and occurs in the nucleus

inti im into tin into iion initiation intiin

C U A AGO A CA C U U AGG CCC UUG AAC GAU Pre MRNA

É'd dit dit'd mrna

Once it has been spliced (introns removed), the functional, coding strand of
mRNA is ready to leave the nucleus. It will diffuse out of the nucleus, into the
cytoplasm via gaps in the nuclear envelope called nuclear pores

ear pore

Mogg 86
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The next stage of protein synthesis is translation, and occurs at the ribosome.
Ribosomes can be found free- oating in the cytoplasm, or associated with the
rough endoplasmic reticulum. When the mRNA enters the nucleus, the ribosome
attaches and begins to ‘read’ the code

td
man

As the mRNA sequence is read by the ribosome, the correct tRNA molecules
(with anti-codons that are complementary to the mRNA codons) bind to the
mRNA strand. The tRNA molecules are carrying a speci c amino acid that
corresponds to the mRNA codon

it it it it
The tRNA molecule ‘drops off’ the amino acid and returns to the cytoplasm,
where it will re-associate with another copy of the same amino acid.
Meanwhile, the ribosome moves onto the next codon, and the next
complementary tRNA molecule binds

it iii iii i
The same process occurs. The ribosome catalyses a condensation bet ween the
t wo amino acids, forming a peptide bond bet ween the t wo

Bu

Mi iii iii i
This process repeats until the entire mRNA strand has been read, and the
correct amino acids have been assembled, all connected by peptide bonds. This
speci c sequence of amino acids forms the primary structure of a complex
protein

oa
It is important to recognise the role of the energy molecule, ATP, in the
translation process. Firstly, the hydrolysis of ATP provides the energy required
by the ribosome to ‘move along’ the strand of mRNA. ATP is also required by the
tRNA molecules to help them deliver their speci c amino acids to the ribosome.
Finally, energy provided by ATP allows the ribosome to ‘detach’ from the mRNA
once it reaches the terminal codon, releasing the nished polypeptide

adenine

MtDNA P iii p iii P ATP

Etat V

ADP Pit energy released

oedonianoea

RiMAMm p iii p
East gigot
4.3 Genetic diversity as a result of mutation or meiosis
Genetic diversity is a measure of genetic variation within a population or
species. Genetic variation refers to the differences that are present among
individuals within a species or population. Variation is measurable by
sequencing and comparing the genetic information of individuals. Genetic
variation can be caused by a genetic mutation

Mutation: a permanent change that occurs in the sequence of DNA within an

organisms genome. A mutation is transcribed into the mRNA sequence during
transcription

I 11 111 I 11 1 11 111 111 111 111 111

CTA AGC ACA CTT AGG CCC TTG AAC GAT template strand ofDNA
7,49994949119999991199999 complementaryRNA

Let’s use the genetic code table to work out the sequence of amino acids coded
for by this complementary strand of RNA

5,499,999179999 TIME
Asp Ser Cys Glu set Gly Asn Leu Leu
So let’s see what happens if one of those bases were to change in the DNA,
resulting also in a change in the sequence of RNA bases. This rst type of
mutation is a ‘s ubstitution mutation’ meaning that one base is removed and
replaced by another, different base

I 11 111 111 111

111 111 111 111 111
CTA AGC ACA CTT AGT CCC TTGAAC GAT
GAU UCG UGH GAA UCA GGG AAC HUG CUA
111 111 111 111 111 111 111 111 111

In this case, the ‘G’ has been swapped for a ‘T’ in the 5th codon on the template
DNA strand. Therefore, the ‘C’ has been swapped for an ‘A’ in the
complementary RNA strand. On the original strand (see above to the rst
example) the 5th codon UCC coded for the amino acid ‘Ser’. Let’s see how the
mutation has changed this, if at all…

494 ser

In this case, even though a change in the sequence of bases has occurred, the
amino acid coded for remains the same. This is due to the degenerate nature of
the code (more than one codon coding for the same amino acid). This mutation is
‘s ilent’ as it does not affect the primary structure of the protein
Let’s try another substitution mutation…

I 11 111 111 111 111 111 111 111 111

CTA AGC ACA CTT AGG CTC TTGAAC GAT
GAU UCG UGA GAA UCC GAG AAC HUG CUA
111 111 111 111 111 111 111 111 111
This time, the ‘C’ has been substituted for a ‘T’ in the 6th codon of the
template DNA strand. Therefore, ‘G’ has been substituted for an ‘A’ in the
complementary RNA strand. Originally, the 6th codon GGG coded for amino
acid ‘Gly’

919 saw

This time, the mutation has resulted in a different amino acid being coded for.
This means that the primary structure of the protein will be different.
Although a change of one amino acid seems small, it can affect the bonding
structure of the whole protein, and ultimately cause the protein to become
non-functional

The next type of mutation is called a ‘deletion mutation’ and involves the
complete removal of a DNA nucleotide & base
 dthfadhdkdtthdd ddlttd hhdat.tt original DNA
itYYi9 999917,9999917949 in original RNA
Asp Ser cys Glu ser aly Asn Leu Leu originalsequenceof
amino acids

dthhdhkdtth dd ddlttd hhdat.tt mutated Dna

119999999119999951,99999 mutated Riva

As you can see, the ‘C’ has been removed from position 2 in the 3rd codon of
the DNA sequence. That also means that ‘G’ will not be copied into the
complementary RNA strand. The new sequence, without the deleted base,
looks like this

9,49999991199999519999
Remember that the genetic code is always read in groups of 3 (triplet codon).
Now, instead of 9 complete codons there will be 8 with 2 bases left over

GAU UCG YUK GAA UCC GGG AAC HUG CUA

GAU UCG HUG AAU CCG GGA ACU UGC UA

These types of mutations (involving the deletion or addition of a base) are
referred to as ‘frame-shift’ mutations, as the whole reading frame of the gene
is shifted either one to the left or one to the right. In this case, a base has been
deleted so the frame has shifted one to the left
How has this ‘frame-shift’ affected the amino acid sequence?

mutation occurred here

GAU UCG HUG AAU CCG GGA ACU UGC UA

ASP Ser Leu Asn pro Gly Thr Cys

Let’s compare the sequence of amino acids coded for by the mutated RNA with
the original sequence

Asp Ser cys a laser Gly Asn Leu Leu original

Asp Ser Leu Asn pro Gly Thr Cys mutated
SAME SAMECHANGECHANGECHANGE SAME CHANGECHANGE

There have been 5 changes to this 9-amino acid sequence. This will have a huge
impact on the tertiary structure of the protein and will make it non-
functional. Frame shift mutations are very disruptive to protein synthesis
Mutations generally happen spontaneously, although the incidence of
mutation can be increased by exposure to mutagenic agents such as smoking,
obesity, viral infections and radiation exposure

meiosis
Topic 2.2 covered the process of one type of cell division - mitosis. There is a
second type of cell division - meiosis. This sub-topic will cover the process of
meiosis and how it can lead to genetic variation in offspring

Meiosis: a type of cell division that produces 4 daughter cells that are
genetically different to one another. Meiosis is a mechanism of cell division
that is only used to produce gametes (sex cells)

Egg cell - female gamete Sperm cell - male gamete

In order for successful fertilisation to occur and an embryo to develop, both

the egg and sperm cell must contain a haploid nucleus. A haploid nucleus is a
nucleus that contains only one set of 23 chromosomes - they are not paired.
Haploid nuclei contain 50% of the human genome. When sperm and egg fuse
together, they share their genetic information to produce a new cell (zygote)
that has 100% genetic information of a human. This is a diploid nucleus

Meiosis produces haploid cells. Mitosis produces diploid cells

A brief overview of the mechanism of meiosis… remember that before any type
of division occurs, the cell undergoes a period of ‘interphase’. By the end of
interphase, the DNA has been duplicated, and the cell contains 200% of its
normal information. The chromosomes are ‘double-armed’ - made up of t wo
identical chromatids attached at the centromere
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Meiosis consists of t wo separate stages of division, aptly named ‘meiosis 1’ and

‘meiosis 2’. Meiosis requires t wo cycles of division, as the end goal is to produce
haploid cells with 50% DNA. Considering we start off with a cell that has
duplicate (200%) DNA, just one cycle of division would not be adequate

meiosis

meiosis Il

gamete gamete 2 gametes gamete4

 g g g
Independent assortment occurs during meiosis 1 and is responsible for the
genetic variation bet ween gametes. During independent assortment, one
chromosome from each homologous pair is allocated into each of the t wo
daughter cells. The assortment is random, so there are many different
combinations of maternal and paternal chromosomes that a daughter cell
could potentially receive

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From each homologous pair, one copy of the chromosomes is passed into each
daughter cell. For example daughter cell 1 received the maternal copy of
chromosome 1, whilst daughter cell 2 received the paternal copy.

Daughter cell 1 received the paternal copy of chromosome 3, whereas daughter

cell 2 received the maternal copy
There is a formula that helps us to recognise exactly how much variation can
be accredited to the process of independent assortment:

2n where n the number of homologous

chromosome pairs in the genome of
an
organism
Humans have 23 homologous pairs of chromosomes in their genome…

223 813881608
This means that there are over 8 million different combinations of maternal
and paternal chromosomes possible when meiosis occurs in humans. In theory,
each human being can produce 8.3 million gametes and have not one of them be
genetically identical to another

Dogs have 39 pairs of homologous chromosomes…

239
5491755 8131888
There are over 500 billion different combinations of chromosomes possible in
the gametes of dogs

Fruit ies have 4 pairs of homologous chromosomes…

24 16
Independent assortment in fruit ies can only produce 16 different
combinations of chromosomes - there is much less genetic variation within
fruit ies
Another way that meiosis contributes to variation within sexually-
reproductive organisms is through crossing over. Crossing over occurs during
prophase in meiosis 1, where homologous pairs of chromosomes line up next to
each other. Sometimes, they may swap a small section of their DNA with one
another

There are t wo genes outlined on this chromosome: eye colour and blood group.

The paternal
The maternal chromosome
chromosome carries the
carries the dominant B allele
recessive b allele
for blue eyes, and
the recessive Io
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and the dominant
Be Gene Ia allele for blood
allele for blood wooageneIA
group A
group o boggy

Without any changes, there would be 2 possible combinations of these genes

that a gamete could receive

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Io
blood
gene dgeney IA gene
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b Io b Io B IA B IA
When crossing over occurs, the chromosomes swap small sections of their DNA
with each other (it has to be the same section on each)

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gene
gene
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When crossing over does happen, new allele combinations are formed that can
then be passed on into the gametes

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b Io b IA BIA B I

As a result, there are an extra t wo combinations that can now be passed onto
gametes, further increasing the scope for variation through meiosis. Crossing
over during meiosis 1 is common, but it does not occur every time a cell
undergoes a cycle of meiosis

Furthermore, errors can sometimes occur during the process of meiosis that
lead to differences in the number of chromosomes of gametes
Normal meiosis progresses as below (the illustration shows the behaviour of
just 2 homologous pairs - remember a human cell would actually have 23 pairs)

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During meiosis 1, the homologous chromosomes are separated and allocated

into one of the 2 daughter cells. During meiosis 2, the identical chromatids
that make up the homologous chromosomes are separated at the centromere.
Only one copy of each chromatid ends up in each of the 4 gametes

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During non-disjunction meiosis, a pair of homologous chromosomes fail to

separate during meiosis 1. This results in t wo of the gametes having 2 copies of
the same chromosome, whereas t wo of the gametes don’t receive a single copy.
A well known condition caused by a non- disjunction error is Down’s syndrome
4 4 genetic diversity adaptation
As mentioned in the previous sub-topic, genetic diversity is a measure of the
variation within a population. Diversity measures how many different alleles
of genes there are within a population. New alleles can arise as a result of
mutations. Some alleles are disadvantageous so they are not passed on. Some
alleles may provide a sur vival advantage and therefore the frequency of the
allele increases over time. This is called natural selection and occurs as below:

Prior to the Industrial Revolution, peppered moths in the UK had a light,

speckled appearance, allowing them to be camou aged on trees and avoid
predation. Due to genetic variation, a small percentage of the population had a
darker appearance

During the Industrial Revolution, soot pollution caused the trunks of trees to
appear black. This is an environmental change

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was no longer able to camou age. It became more visible to predators against
the black tree trunks. The darker moth, however, was able to camou age well

Fix

The lighter moth had a sur vival advantage when the tree trunks were lighter,
so the lighter appearance characteristic appeared more frequently within the
population. However, when the trees changed, the darker moths had the
survival advantage. Over time, a change occurred in the population so that
the darker moths were more common

The allele for dark appearance in the moths became more common in the
population. This is an example of evolution by natural selection
directional vs stabilising selection
The case of the peppered moth is an example of directional selection. This
means that environmental changes cause a change in what characteristics are
considered to be advantageous. Over time the frequency of the newly
advantageous allele increases
Population after
8
selection occurs
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a population before

É selection occurs

phenotype

Another example of directional selection is the development of antibiotic

resistance in bacteria. Firstly, a mutation in the DNA causes a single/ few
bacterial cells to develop antibiotic resistance
antibioticresistant

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Once the antibiotic is applied to treat a bacterial infection/ growth, only the
single cell with resistance will sur vive. Bacteria cells reproduce using an
asexual method called binary ssion - when this single cell replicates the
offspring are guaranteed to possess the allele for antibiotic resistance

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The entire new population will be resistant to the antibiotic

Natural selection can also cause a trend of stabilisation. This is where the
average phenotype is the most advantageous as the environmental factors
are stable. This is known as stabilising selection and is the case in the birth
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phenotype

Human birth mass is a perfect example of stabilising selection. Extreme low

birth mass is associated with higher rates of mortality. Extreme high birth
mass is associated with birth complications and higher rates of mortality. The
average birth mass is selected for and remains the most popular within the
population

Evolution occurs by natural selection and enables organisms to be as successful

at sur vival within an environment as possible, even if the environment alters

Adaptations may be…

• Anatomical - the development of a long neck from a short neck in giraffes
to enable them to access better nutrition and thermoregulation
• Behavioural - the migration behaviour of birds allows them to cope with
seasonal changes in their environment
• Physiological - the ability of camels to store large volumes of water in their
blood to avoid dehydration in their dry desert environment
 4.5 species taxonomy
There are over a million different species of organism that have been
discovered and registered to be living on planet earth. It is estimated that
there are actually over 8 million different species living on earth. It is
important that we are able to classify these organisms with accuracy and
agreement. The classi cation of organisms according to their characteristics is
called taxonomy. The taxonomic hierarchy is organised into 8 groups

TAXONOMIC CLASSIFICATION OF HUMANS

domain eukarya
Kingdom animalia

phylum chordata

crass mammalia

order primates

family hominidae

genus nomo

species sapiens

The of cial binomial name of the human species is ‘Homo Sapiens’

1. Domain - the highest category in which all life on earth is classi ed into 3
groups: bacteria, archaea and eukarya. The domain separates species
based on the most fundamental principles of cell structure
2. Kingdom - the next highest rank has 5 categories: animal, plant, fungi,
protist and monera. All living organisms are classi ed into one of these
kingdoms. Each domain has at least one kingdom
3. Phylum - as the classi cation gets more speci c, the phylum taxon is used
to group together organisms that have similar fundamental
characteristics, as well as shared evolutionary relationships
4. Class - organisms in the same class share more similarities than those in
the same phylum
5. Order - organisms in the same order share more similarities than those in
the same class
6. Family - family is the taxon that ranks just above genus and species.
Members of the same taxonomic family are closely related and share a lot
of similar characteristics
7. Genus - the genus is the second most exclusive taxon and is used in the
binomial name of all living organisms
8. Species - the nal level of classi cation is species. There is only one type of
organism that belongs to each species. Members of the same species have
the same genome and are able to reproduce to produce fertile offspring

There is no overlap bet ween the different groups of each taxonomic level - an
organism can only be classi ed into one de nitive group

The binomial name of an organism is the genus name followed by the species
name. Use of binomial naming allows for easy correspondence worldwide
TAXONOMIC CLASSIFICATION OF BOTTLENOSE DOLPHIN
domain eukarya
Kingdom animalia
phylum chordata
crass mammalia
order cetacea

family delphinidae
genus tursiops
species truncactus

Binomial name: Tursiops Truncactus

TAXONOMIC CLASSIFICATION OF SUNFLOWER

domain eukarya
Kingdom plantae

phylum tracheophyta
class magnoliopsida

order asterates

family asteraceae

genus helianthus
species annus

Binomial name: Helianthus Annus

phylogeny
Phylogeny is the study of evolutionary relationships within groups of
organisms. Phylogeny allows us to identify how closely related t wo species
are, and how close of a common ancestor they have

Phylogenetic trees are used to illustrate these relationships, and help us to

identify how closely related certain species are. Let’s look at a simple
phylogenetic tree for humans

most recent common ancestors human

chimpanzee
8mamspeciestor
gorilla
orangutan

macaque

This phylogenetic tree shows that humans share the most recent common
ancestor with a chimpanzee. The macaque was the rst to become a separate
species. Species that are more closely related on the tree became separate
species much later
4 6 Biodiversity within a community
Biodiversity (biological diversity) is de ned as the variety of living organisms
within a particular habitat

A habitat is the environment in which a particular organism or community of

organisms live

A community is a group of species that inhabit a shared environment and

interact with each other

Species richness is the number of different species that are present within a
particular habitat

The index of diversity (D) is a mathematical tool used to quantify the the
biodiversity within a habitat

D
NIN 1

En n 1

where
E means sum of or total of
N the total number of individuals of all of the
species combined
n the number of individuals of each separate
species
Let’s do a worked example to calculate the index of diversity of a rock pool
habitat

species number of
n t n n 1
individuals n

shore crab 4 3 4 3 12

hermit crab 2 I 2 1 2

7 6 7 6 42
prawn

Starfish 2 I 2 1 2

anemone 2 I 2 1 2

Limpet 5 4 5 4 20

419 22 Intent 80

NCN 1 N 22
D NCN 1 22 21 462
En n 1

With all values calculated, our equation would be

D 462 SO D 5.775
80
Our calculated D value of 5.775 suggests a relatively high level of diversity
within this rock pool habitat. A D value of 1 means that there is no diversity
at all, and after that there is a positive correlation bet ween the D value and
the biodiversity

factors affecting biodiversity

• Pesticides - chemicals used in the agricultural industry kill insects and other
organisms that feed on crops. By reducing the number of such insects, the
food source becomes limited to those that feed on them
• Deforestation - areas of woodland/ forest are often cut down to make
space for more farmland. This land is then used to grow a limited amount of
crop, or to rear cattle. Deforestation hugely reduces biodiversity by direct
removal of plants, and the loss of habitat to the animals that live there
• Herbicides - another chemical used frequently in agricultural practices to
kill weeds. Herbicides reduce the diversity of plants, thus reducing food
sources and insect habitats
 unit 4 glossary
You need to be able to recognise, remember and use all these key terms in the
correct context in exams…

• DNA: a form of nucleic acid that holds the genetic information of an

organism
• Histone: a positively charged packaging protein commonly associated with
DNA in eukaryotic cells
• Chromatin: the DNA-histone complex within the nucleus of a eukaryotic cell
during interphase stages of the cell cycle
• Chromosome: tight, condensed structures of DNA and histones within the
nucleus of a eukaryotic cell during cell division (mitosis or meiosis)
• Centromere: the central region of a chromosome to which spindle bres
attach
• mRNA: messenger RNA is a copy of a short section of DNA that is carried
from the nucleus to the ribosome
• tRNA: transfer RNA molecules are folded strands of RNA in a clover-leaf
shape with an anticodon and associated with a speci c amino acid
• genetic code: the instructions contained within a section of DNA that
contains the information for a protein
• Degenerate: the nature of the genetic code meaning that more than one
codon code for the same amino acid
• Genome: the complete set of genetic information present within a cell or
organism
• Protein synthesis: the process of converting the information held within
DNA to a functional polypeptide
• Transcription: the process of production of mRNA from a short section of
 DNA in the nucleus
• Translation: the process of converting mRNA to a polypeptide chain in the
ribosome using tRNA molecules
• Splicing: the removal of non-coding DNA (introns) from pre-mRNA
• Codon: a sequence of 3 bases that codes for a single amino acid
• Genetic variation: the number of different alleles within a population
• Mutation: a permanent change in the sequence of DNA of an organism
• Meiosis: the process of cell division that results in 4 haploid daughter cells
• Haploid nucleus: a nucleus that contains 50% of the genome of an organism
• Diploid nucleus: a nucleus that contains 100% of the genome of an organism
• Independent assortment: the random allocation of one chromosome from
each homologous pair into each of the t wo daughter cells during meiosis 1
• Crossing over: the swapping of genetic information bet ween t wo
chromosomes during prophase of meiosis 1
• Recessive allele: an allele that must appear t wice in the genotype to show
up in the phenotype
• Dominant allele: an allele that only must appear once in the genotype to
appear in the phenotype
• Non-disjunction meiosis: a type of mutation in meiosis 1 where the
chromosomes fail to separate
• Directional selection: selection that favours extreme characteristics and
results in a shift in number of alleles over time
• Stabilising selection: selection that favours the average characteristics
• Taxonomy: the classi cation of all living organisms into groups based on
their characteristics
• Binomial name: the of cial taxonomic name of a species, the combination of
the genus and species titles
• Phylogeny: the study of evolutionary relationships bet ween organisms
• Biodiversity: the variety of living organisms within a habitat
• Habitat: the environment in which a particular organism lives
• Community: a group of interacting species that inhabit a shared
environment
• Species richness: the number of different species that are present within a
habitat