Lecture 1

LIF101AA
Biology
Instructors:
Dr. Saravanan Matheshwaran (BSBE, IIT K)
Dr. Pradip Sinha (BSBE, IIT K)
 Course Structure
wednesdays and Fridays : 2 to 3 PM
Course Contents:

Part I:
Principles of Cellular Life - 12 lectures

Dr.Saravanan Matheshwaran

Part II:
Principles of Inheritance: Information
processing in living systems - 14 lectures

Dr. Pradip Sinha

 Principles of Cellular Life

Molecules of Life Cell: structural and functional

unit of life
( 7 lectures)
(5 lectures)
 Text book :

Biology: Concepts and Applications without

Physiology
International Edition, 8th Edition
By Cecie Starr, Christine Evers & Lisa Starr
ISBN-10: 0538736186
ISBN-13: 9780538736183
2011

50 copies available in the reference section of the library

 Mid-Semester Exam: 50%
Portion: Part-I (Principles of Cellular life)

End-Semester Exam: 50%

Syllabus: Part II (Principles of inheritance:
Information processing in living systems)
 What is Biology?
• It is the study of life.
• Branch of science
– A way of understanding nature.
• A human endeavor
– An attempt to understand, explain, integrate and
describe the world of living things.
 What is Life?
• Living organisms:
– Highly organized and
complex.
– Are composed of one or
more cells.
– Contain a blueprint of
their characteristics.
– Acquire and use energy.
– Carry out and control
numerous reactions.
 What is Life?
• Living organisms:
– Grow. Insert F01_03b
– Maintain constant
internal environment.
– Produce offspring.
– Respond to
environmental changes.
– May evolve.
 Life is based on many structural levels
Levels of biological organization:

Atoms
Molecules
Subcellular organelles
Cells
Tissues*
Organs*
Organ systems*
Organism: May consist of a single cell or a complex
multicellular organism.

* Level of organization not found in all organisms

 Common features of all organisms:

1. Cells: Basic structural and functional unit of life. Genetic

information contained in DNA.

2. Growth and Development:

Growth: Occurs by an increase in cell size, cell number, or both.
Development: Changes that take place during an organism’s life.
3. Energy use and metabolism:
All organisms must take in and transform energy to do work, to live.

Metabolism: All chemical reactions and energy transformations essential

for growth, maintenance, and reproduction.
4. Regulation
External environment may change, but internal environment
remains fairly constant.
Homeostasis: Organisms constantly strive to maintain a “steady
state” (e.g.: constant body temperature or blood pH) despite
changes in the internal and external environment. Metabolism
is regulated by homeostatic mechanisms.

5. Movement:
Internal movement: Characteristic of all life.
Locomotion: Self-propelled movement from point A to point B.
Not observed in all life forms.

6. Respond to environmental stimuli: Organisms respond to

internal and external changes (visual stimuli, temperature, light,
sound, pressure, etc.).
7. Order: Organisms are highly organized, when compared to nonliving
environment.

8. Reproduction: Organisms come from other organisms. Reproduction

may be sexual or asexual.

9. Evolutionary adaptation: Populations, not individuals, “evolve” or

change over many generations so they can survive in a changing
world.
All life can be classified taxonomically
– Taxonomy: The branch of biology concerned with naming and
classifying organisms
– Most Biologists Recognize Five Kingdoms: Monera, Protista,
Plantae, Fungi, and Animalia
1. Kingdom Monera (Procaryotae): Most widespread organisms.
• Procaryotes (“Before nucleus”):
– Lack nuclear membrane around DNA.
– Lack membrane bound organelles (mitochondria, chloroplast, golgi,
endoplasmic reticulum).
• Unicellular: Single celled organisms.
• Have a cell wall.
• Include: Bacteria.
Kingdom Prokaryotae: Bacteria lack nucleus and
membrane bound organelles
 “Typical” Animal Cell

http://web.jjay.cuny.edu/~acarpi/NSC/images/cell.gif
 “Typical” Plant Cell

http://waynesword.palomar.edu/images/plant3.gif
 Topics to be covered
Biomolecules (Proteins, DNA, RNA, lipids,
carbohydrates)

Cell and different cell organelles

Cell Metabolism

Photosynthesis

Release of stored energy from molecules

Biomolecules : Introduction
Monomers, polymers, and
macromolecules

There are 4 categories of macromolecules:

Carbohydrates
Proteins,
Lipids,
and Nucleic acids
• What is an • Compounds containing C, H, O
organic and often N, P, & S.
compound? • Organic compounds make up all
living things and are necessary
for life.
• What is so • It can combine to form long
special about chains which act as the
Carbon? backbone of large molecules.
• Macromolecules – giant
molecules.
• How does • Carbon needs to bond 4 times
carbon bond? to fill it’s outer shell.
• It can form single, double or
triple covalent bonds.

• Carbon can form straight chains,

rings or branched chains.
 Carbon is the central element
• All biomolecules contain a Carbon chain or ring
• Carbon has 4 outer shell electrons (valence = 4)
• Therefore it’s bonding capacity is great
• It forms covalent bonds –hence, has strong bonds
• Once bound to other elements (or to other Carbons),
it is very stable
 CH4 =
Carbon linkages
Propane
• Single chains
• Rings = C3H8

The 4 types of biomolecules often

consist of large carbon chains
 Carbon binds to more than just
hydrogen!!
• To OH groups in sugars
• To NH2 groups in amino
acids
• To H2PO4 groups of
nucleotides of DNA,
RNA, and ATP

Amino acid

OH, NH2, PO4 are called ‘functional groups’!

Functional groups:
 Isomers have the same molecular
formulas but different structures
• Structural isomer = difference in the C skeleton structure

• Stereoisomer = difference in location of functional groups

 Enantiomers are special types of
stereoisomers

Enantiomers are mirror

images of each other
One such enantiomer
contains C bound to 4
different molecules and is
called a chiral molecule
Chiral molecules rotate
polarized light to the right
(D form) or to the left (L
form) molecules
Examples: amino acids (L
form)
sugars (D form)
 Monomers and polymers
• Monomers are made into polymers via dehydration reactions
• Polymers are broken down into monomers via hydrolysis
reactions
• What are • Very large molecules.
macromolecules? • Carbon compounds can vary
greatly in size. Some contain
just one or two C atoms, others
can have 10 or even 1000 C
atoms.
• How are
macromolecules
formed? • Macromolecules form when
many smaller molecules bond
together.
• What is a • A molecule made up of many smaller
polymer? molecules.

• Formed by a reaction called

dehydration synthesis – which means
water must be removed to bond them
together.

• The building block of a polymer.

• What is a Varies depending on the type of
monomer? molecule being built
 Monomers and polymers
• Monomers are made into polymers via dehydration reactions
• Polymers are broken down into monomers via hydrolysis
reactions
• How are polymers • By a chemical reaction known as
broken down? hydrolysis. Water is added back in
and the monomers separate.

Monomers

• This is dehydration
synthesis
• What is a • Organic compound composed of
carbohydrate? C, H, & O in a 1:2:1 ratio
• C6H12O6
• 3 types – monosaccharides,
disaccharides and
polysaccharides.
• Function: main source of energy
for all living things.
• Some structure (ex plant cell
walls)
• What is a • Simple sugar – only one sugar.
monosaccharide? • Contains 3 – 7 carbon atoms in
their skeleton.
• Can take ring form or straight
chain form.
• ** monosaccharides are the
building blocks for all larger
carbs **
• What is a • Two monosaccharides combined
dissaccharide? minus water.
• Sucrose = glucose + fructose

• What is a • When many monosaccharides

combine to form a large
polysaccharide?
carbohydrate.
• Have no fixed size, but must be
broken down into simple sugars to
be used by the cell.
• Ex. Starch and cellulose
• Summary – 3 Types of Carbohydrates
• 1. monosaccharides – single sugar.
– Ex. Glucose, fructose, galactose
– Aka – simple sugars
• 2. Disaccharide: 2 simple sugars
– Ex. Sucrose (table sugar) maltose
• 3. polysaccharides: 3 or more sugars (complex
carbs)
– Ex. Cellulose – used in cell walls
– Starch stores energy in plants
– Glycogen – stored energy in animals
• What are lipids? • Organic compounds made up of
C, H, & O, but not in any fixed
ratio.
• The building blocks of lipids are
fatty acids.
• Usually 3 fatty acids combine
with one glycerol to form a
triglyceride.
• properties of fats and oils are
determined by the fatty acids
that make them up.
• What is a • All the carbon atoms are joined
saturated fat? by single bonds (usually solid
fats)
• What is an • The carbon chain contains
unsaturated double or triple bonds (usually
fat? oils)
• What is the • Lipids are often called fats or
function of oils, but are large
lipids? macromolecules with 2 primary
functions:
• 1. long term energy storage
• 2. building cell membranes.
• What are • Organic compounds that contain
proteins? C, H, O & N.
• Every cell contains protein.

There are at least 7 functions of proteins

1. Enzyme catalysts – specific for 1 reaction
2. Defense – antibody proteins, other proteins
3. Transport- Hgb, Mgb, transferrins, etc
4. Support – keratin, fibrin, collagen
5. Motion – actin/myosin, cytoskeletal fibers
6. Regulation- some hormones, regulatory proteins
on DNA, cell receptors
7. Storage – Ca and Fe attached to storage proteins
• What are amino • Amino acids the building blocks
acids? of proteins!!
• They consist of a central carbon
atom with a H, a –COOH, a NH2
and a “R” group attached.
• The “R” group is different for
each of the 20 different amino
acids.
• What is a • The bond that holds together
peptide bond? amino acids into a large
macromolecule called a
polypeptide.
• Longer polypeptides are called
proteins and can be made up of
50 – 300 amino acids.
• How does a • The order of amino acids give a
protein get its protein its shape. The shape
shape? determines the protein’s
function.
• Even one amino acid out of
place will prevent a protein from
doing its job.
• Proteins that speed up the rate
• What is an of chemical reactions
enzyme?
• Without enzymes chemical
reactions would occur too
slowly for life to exist.
• What are nucleic • Organic molecule made up of
acids? C,H,O,N,& P
• Nucleic acids are passed from parent
to offspring, you get one copy from
each parent for a total of 2 complete
sets.
• Nucleic acids dictate amino acid
sequence in proteins which in turn
control all life processes.
• DNA forms the genes or units of
genetic material that determine your
characteristics.
• What is a • Nucleotides are the building
nucleotide? blocks of Nucleic acids.
• Each nucleotide is made up of 3
parts:
– A 5 Carbon sugar (deoxyribose or
ribose)
– A phosphate group
– A nitrogen base ( a ring containing
C, H, & N)
• What are the • Adenine, guanine, cytosine thymine,
different types and uracil.
of nucleotides? • Thymine is only in DNA, uracil is only
in RNA.
• Adenine pairs with thymine (uracil)
• Guanine pairs with cytosine.
• Nucleotides link together between
sugars and phosphates, nitrogen bases
stick out.
• What is DNA? • Deoxyribonucleic acid
• Contains the sugar deoxyribose.
• The molecule of heredity.
• Double stranded, sugar and
phosphates form the back bone,
paired nitrogen bases hold the two
strands together.
• The shape is called a double helix.
• What is RNA? • Ribonucleic acid
• Contains the sugar ribose, uracil
replaces thymine.
• Single stranded.
• 3 types each with a different
function
– Ribosomal
– Transfer
– messenger
The major classes of biological molecules that are important forall living things are
carbohydrates, lipids, proteins, and nucleic acids.

Large biological molecules are called macromolecules

Carbohydrates
 Introduction
• Carbohydrates are one of the three
major
classes of biological molecules.
• Carbohydrates are also the most
abundant biological molecules.
• Carbohydrates derive their name from
the
general formula Cn (H2O).
 functions
• Variety of important functions in living
systems:
– nutritional (energy storage, fuels, metabolic
intermediates)

– structural (components of nucleotides,

plant and bacterial cell walls, arthropod
exoskeletons, animal connective tissue)
–informational (cell surface of
eukaryotes -- molecular recognition,
cell-cell communication)
–osmotic pressure regulation (bacteria)
–Carbohydrates are carbon compounds
that contain large quantities of
hydroxyl groups.
 Carbohydrates are chemically
characterized as:

• Poly hydroxy aldehydes or

• Poly hydroxy ketones.

• Sugars that contain an aldehyde group
are called Aldoses.

• Sugars that contain a keto group are

called Ketoses.
 classification
All carbohydrates can be classified as
either:
• Monosaccharides
• Disaccharides
• oligosaccharides or Polysaccharides.
• Monosaccharides- one unit of carbohydrate
• Disaccharides- Two units of carbohydrates.
• Anywhere from two to ten monosaccharide
units, make up an oligosaccharide.
• Polysaccharides are much larger, containing
hundreds of monosaccharide units.
• Carbohydrates also can combine with
lipids to form glycolipids
OR
• With proteins to form glycoproteins.
 Isomers
• Isomers are molecules that have the
same molecular formula, but have a
different arrangement of the atoms in
space. (different structures).

• For example, a molecule with the

formula AB2C2, has two ways it can be
drawn:
Isomer 1
Isomer 2
Examples of isomers:
1. Glucose
2. Fructose
3. Galactose
4. Mannose

Same chemical formula C6 H12 O6

 EPIMERS
• EPIMERS are sugars that differ in
configuration at ONLY 1 POSITION.
 Examples of epimers :
 D-glucose & D-galactose (epimeric at C4)
 D-glucose & D-mannose (epimeric at C2)
 D-idose & L-glucose (epimeric at C5)
 ENANTIOMERS

Non-Superimposable COMPLETE mirror

image (differ in configuration at EVERY
CHIRAL CENTER.
The two members of the pair are designated as D
and L forms.

In D form the OH group on the asymmetric carbon is

on the right.

In L form the OH group is on the left side.

D-glucose and L-glucose are enantiomers:

 cyclization
• Less then 1%of CHO exist in an open chain
form.

• Predominantly found in ring form.

• involving reaction of C-5 OH group with the C-

1 aldehyde group or C-2 of keto group.
• Six membered ring structures are called
Pyranoses .

• five membered ring structures are called

Furanoses .
 Optical Activity
• When a plane polarized light is passed through a
solution containing monosaccharides the light
will either be rotated towards right or left.

• This rotation is because of the presence of

asymmetric carbon atom.

• If it is rotated towards left- levorotatory (-)

• If it is rotated towards right- dextrorotatory(+)

 Some hexose derivatives important in biology
• Amino
sugar—NH2 is
replaced –OH.
• deoxy sugar--
substitution
of –H for –OH.
The deoxy
sugars of
nature as the
L isomers

• The acidic sugars contain a carboxylate--- confer a negative

charge at neutral pH.
• D-glucono-d-lactone – formation of ester linkage between the
C-1 and C-5.
Monosaccharides are reducing agents - Fehling’s
reaction
• Reducing sugars:
glucose and other
sugars capable of
reducing ferric or
cupric ion (carbonyl
carbon is oxidized to
a carboxyl group
(Fe3+ , and Cu2+ to
Fe2+ and Cu+ --- red
cuprous oxide
precipitate).
Dissaccharides contain a glycosidic bond

• Disaccharides consist of two

mono-saccharide joined
covalently by an O-glycosidic
bond formed when a glydroxyl
of one sugar reacts with the
anomeric carbon of the other.
• Sugar (sucrose) containing the
anomeric carbon atom cannot
exist in linear form and no
longer acts as a reducing sugar.
• Nonreducing disaccharides
are named as glycosides
Dehydration Synthesis
of a Disaccharide
Formation of Disaccharides
Hydrolysis of a Disaccharide
Polysaccharides--glycans
• may compose of one,
two, or several
different
monosaccharide, in
straight or branched
chains of varying
length
• Homo- vs. hetero-
polysacchairdes.
• As fuel or structure
element
Starch and glycogen granules
• Polysaccharides do not have definite
molecular weight. (protein is on the
template of defined sequence and
length; no template of
polysaccharides)
• Starch– amylose (long and
unbranched chains of glucose) and
amylopectin (branched 24 to 30).
• Glycogen — more extensively
branched and more compact than
starch.
• Dextrans are bacterial and yeast
polysaccharides made up of (1 -
6)-linked poly-D-glucose; all have
(1 - 3) branches, and some also
have (1 - 2) or (1 - 4) branches.
Dental plaque, formed by
bacteria growing on the surface
of teeth, is rich in dextrans.
Amylose and amylopectin

•
The structure of cellulose
• β1-4 linkage –most
stable conformation
for the polymer is that
in which each chair is
turned 180o relative to
its neighbors, yielding
a straight, extended
chain. (inter and intra
H bonds)--- water can
not get in.
• Digested by cellulase
(termites, fungi,
bacteria, ruminants)
Cellulose breakdown by wood fungi
• All wood fungi have the enzyme
cellulase, which breaks the (1- 4)
glycosidic bonds in cellulose, such
that wood is a source of
metabolizable sugar (glucose) for
the fungus.
• The only vertebrates able to use
cellulose as food are cattle and
other ruminants (sheep, goats,
camels, giraffes). The extra stomach
compartment (rumen) of a
ruminant teems with bacteria
(symbiotic microorganism,
Trichonympha) and protists that
secrete cellulase
 Chitin — polymer of N-
acetylglucosamine in β linkage

• is a linear homopolysaccharide composed of N-acetylglucosamine

residues in linkage
• Indigested by most vertebrate animal.
• Exoskeletons of arthropods—insects, lobsters, and crabs.
Conformation at the glycosidic bonds of
cellulose, amylose and dextran
• The three-dimensional structures of
these molecules can be described in
terms of the dihedral angles, and ,
made with the glycosidic bond.
• Cellulose, the most stable conformation
is that in which each chair is turned 180
relative to its neighbors, yielding a
straight, extended chain.
• The most stable three-dimensional
structure for starch and glycogen is a
tightly coiled helix-Each residue along
the amylose chain forms a 60 angle with
the preceding residue, so the helical
structure has six residues per turn.
Bacterial cell walls contain peptidoglycans
proteoglycans
• Polymer of N-
actylglucosamide,
cross-linked with
short peptides
• Lysozyme (tear,
bacterial viruses)—
lyses the (β1-4)
glycosidic bonds.
• Penicillin prevents
synthesis of cross-
links leaving the cell
wall too weak to
resist osmotic lysis.
 The structure of agarose

• The repeating unit consists of D-galactose (1- 4)-linked to 3,6-anhydro-L-

galactose (in which an ether ring connects C-3 and C-6). These units are
joined by (1- 3) glycosidic links to form a polymer 600 to 700 residues long.
A small fraction of the 3,6-anhydrogalactose residues have a sulfate ester
at C-2.
• When a suspension of agarose in water is heated and cooled, the agarose
forms a double helix: two molecules in parallel orientation twist together
with a helix repeat of three residues; water molecules are trapped in the
central cavity. These structures in turn associate with each other to form a
gel—a three-dimensional matrix that traps large amounts of water.
 Repeating units of some common
glycosaminoglycans of extracellular
matrix

• extracellular matrix - a gel-like

material that fill between
multicellular organisms - composed
of an interlocking meshwork of
heteropolysaccharides and fibrous
proteins: collagen, elastin,
fibronectin, and laminin.
• One is N-acetylglucosamine or
galactosamine; the other is D-
glucuronic (most cases)
• Esterified with sulfate (negative
charge)--- assume extended
conformation in solution. Attaches to
proteins– proteoglycans. pliability
 Glycosaminoglycans
• Hyaluronic acid (Glass): lubricants in synovial fluid, eye,
cartilage and tendons; hyaluronidase secreted by bacteria —
bacteria invasion. Similar enzyme for sperm to penetrate ovum.
• Chondroitin sulfate (Cartilage): tensile strength pf cartilage,
tendons and ligament, aorta.
• Dermatan sulfate (Skin): skin, blood vessel and heart valves.
Pliability of skin.
• Keratan sulfates (horn): cornea, horn, hair, hoof, nails, claws,
no uronic acid.
• Heparin (liver): made in mast cell- a anticoagulant with highest
negative charge density, release to blood, inhibit blood clotting
by binding to antithrombin III - bind to and inhibit thrombin, a
protease essential to blood clotting.
Function of polysaccharides
 Proteoglycan structure, showing the trisaccharide bridge
• A typical trisaccharide
linker connects a
glycosaminoglycan— ex.
chondroitin sulfate
(orange)— to a Ser
residue (red) in the core
protein. The xylose
residue at the reducing
end of the linker is joined
by its anomeric carbon to
glycosaminoglycan the hydroxyl of the Ser
residue.
• Proteoglycan: macromolecules of cell surface or extracellular matrix in which
one or more glycosaminoglycan chain are jointed covalently to a membrane
protein or a secreted protein. Major components of cartilage.
• Glycoprotein: have one or several oligosaccharides of varying complexity
joined covalently to a protein– outer surface plasma membrane, extracellular
matrix and in the blood.
• Glycolipid: membrane lipid in which the hydrophilic head are oligosaccharides.
Proteoglycan structure of an integral
membrane protein -- syndecan
• A core protein of the plasma
membrane. The N terminal on
the extracellular side of the
membrane is covalently
attached to three heparan
sulfate and two chondroitin
sulfate chain.
• S domains - highly sulfated
domains alternate with
domains having unmodified
GlcNAc and GlcA residues (N-
acetylated, or NA domains). -
bind specifically to extracellular
proteins and signaling
molecules to alter their
activities.
 A proteoglycan aggregate of the extracellular matrix
• One very long
molecule of
hyaluronate is
associated
noncovalently with
about 100
molecules of the
core protein
aggrecan. Each
aggrecan molecule
contains many
covalently bound
chondroitin sulfate
and keratan sulfate
chains. Link proteins
situated at the
junction between
each core protein
and the hyaluronate
backbone mediate
the core protein–
hyaluronate
interaction.
Interactions between cells and extracellular matrix

• The associating
between cells and the
proteoglycan of
extracellular matrix is
mediated by a
membrane protein
(integrin) and by an
extracellular portein
(fibronectin) with
binding sites for both
integrin and the
proteoglycan
Oligosaccharide linkages in glycoproteins (secretion protein
and cell surface)

• O-linked
oligosaccharides–
glycosidic bond to
hydroxyl group of Ser or
Thr residues.
• N-linked have and N-
glycosyl bond to the
amide nitrogen of an
Asn
• Alter polarity and
solubility; protein
folding, protect proteins
from attack by
proteolytic enzymes,
increasing structural
complexity
• add in Golgi complex
Bacterial liposaccharides (glycolipid)
• Ganglioside- membrane lipids
of eukaryotic cells, the polar
group is a complex
oligosaccharide containing sialic
acid (determine human blood)
• Target of Ab. Serotype: strains
that are distinguished on the
basis of antigenic properties.
• Toxic to human (lowered blood
pressure toxic shock syndrome)---
Gram-negative bacteria infection.
 Oligosaccharide - lectin interactions mediated
many biological processes
• Lectins: proteins that bind
carbohydrates with high
affinity and specificity (H
bonds…) --- cell-cell
interaction and adhesion. -
useful reagents for detecting
• sialidase (neuraminidase) remove sialic acid –
and separating glycoproteins
asialoglycoprotein receptors binds => triggers with different
endocytosis and destruction of the protein, oligosaccharide moieties.
another i.e. RBC • Sialic acid residues situated
• The lectin of the influenza virus (HA) - binding of at the ends of the
the virus to a sialic acid–containing
oligosaccharide on the host surface, a viral
oligosaccharide chains of
sialidase removes the terminal sialic acid residue, many plasma
triggering the entry of the virus into the cell. glycoproteins — protect the
Inhibitors of this enzyme are used clinically in the proteins from uptake and
treatment of influenza. degradation.
Role of lectin-ligand interactions in lymphocye
movement to the site of and infection or injury
• An infection site, P-selectin on
the surface of capillary
endothelial cells interacts with a
specific oligosaccharide of the
gluycoproteins of circulating T
lymphocytes --- integrin interact
with E-selectin (endothelial cell,
L-selectin on the T cell)
• Cholera toxin molecule entering
intestinal cells (oligosaccharide
of ganglioside GM1).
• another i.e. Pertussis toxin
Helicobacter pylori adhering to
the gastric surface
• Helicobacter pylori (bacterial
membrance lectin), adheres
to the inner surface of the
stomach.
 The Genetic Code
Deciphering the genetic code required
determining how 4 nucleotides (A, T, G, C)
could encode more than 20 amino acids.
Francis Crick and Sydney Brenner determined
that the DNA is read in sets of 3 nucleotides
for each amino acid.

2
3
 The Genetic Code
codon: set of 3 nucleotides that specifies a
particular amino acid

reading frame: the series of nucleotides read in

sets of 3 (codon)
– only 1 reading frame is correct for encoding the
correct sequence of amino acids

4
 The Genetic Code
Marshall Nirenberg identified the codons that
specify each amino acid.
RNA molecules of only 1 nucleotide and of
specific 3-base sequences were used to
determine the amino acid encoded by each
codon.
The amino acids encoded by all 64 possible
codons were determined.

5
6
 Putting It All Together

Once again, sickle cell anemia

illustrates the gene – protein -
biological character connection.

normal
A single base (DNA “letter”) change in red blood
the gene for the protein β-globin cell
changes one amino acid for another
in this greater than 300 amino acid sickled red
blood cell
protein.
 Amino Acids:
The building blocks of proteins

pK2 pK1

α amino acids because of the α carboxylic and α amino groups

pK1 and pK2 respectively pKR is for R group pK’s

pK1 ≈ 2.2 while pK2 ≈ 9.4

In the physiological pH range, both carboxylic and

amino groups are completely ionized
 Amino acids are Ampholytes

They can act as either an acid or a base

They are Zwitterions or molecules that have both

a positive and a negative charge
 Acid - Base properties of amino acids
 [A - ] 
pH = pK + log 
 [HA] 

Isoelectric point: the pH where a

molecule carries no net electrical charge
 Amino acids are the building blocks of
proteins
• Three major parts: carboxyl
group, amino group, and side
chain.
• Central C atom called alpha
carbon.
• Amino acids can differ in their
side chains (R).
• The alpha carbon is a chiral
center. (except for one amino
acid)
• L-form found almost exclusively
in proteins
 Peptide bonds
• Proteins are sometimes called polypeptides since they contain many peptide bonds

R1 O H R2 O
+
H3N C C OH +
H N C C O-
H H

R1 O R2 O
+ + H2O
H3N C C N C C O-
H H H
 Amino acids can form peptide bonds
Amino acid residue Proteins are
molecules that consist
peptide units of one or more
polypeptide chains
dipeptides
tripeptides
oligopeptides
polypeptides

Peptides are linear polymers that range from ~8 to 4000

amino acid residues
How many different naturally occurring amino acids
are there in most species encoded by the genome?
 Linear arrays of amino acids can
make a huge number of molecules
Consider a peptide with two amino acids

AA1 AA2
20 x 20 = 400 different molecules

AA1 AA2 AA3

20 x 20 x 20 = 8000 different molecules

For 100 amino acid protein the # of possibilities are:

20100 = 1.27 x10130

The total number of atoms in the universe is estimated at
Polar, non-charged amino acids
Cystine consists of two disulfide-linked
cysteine residues

Important
In Protein
Folding
And
Structure
 Nucleic acids
• Principle information molecule in the
cell.

• All the genetic codes are carried out on

the nucleic acids.

• Nucleic acid is a linear polymer of

nucleotides
 Nucleotides
• Nucleotides are the unit structure of
nucleic acids.
• Nucleotides composed of 3
components:
– Nitrogenous base (A, C, G, T or U)
– Pentose sugar
– Phosphate
 Nitrogenous bases
• There are 2 types:
– Purines:
• Two ring structure
• Adenine (A) and Guanine (G)

– Pyrimidines:
• Single ring structure
• Cytosine (C) and Thymine (T) or Uracil (U).
Nucleotide bases
 Types of Nucleic acids
There are 2 types of nucleic acids:
1. Deoxy-ribonucleic acid (DNA)
• Pentose Sugar is deoxyribose (no OH at 2’ position)
• Bases are Purines (A, G) and Pyrimidine (C, T).
2. Ribonucleic acid (RNA)
• Pentose Sugar is Ribose.
• Bases are Purines (A, G) and Pyrimidines (C, U).
 Linear Polymerization of Nucleotides
• Nucleic acids are
formed of nucleotide
polymers.
• Nucleotides
polymerize together by
phospho-diester
bonds via
condensation reaction.
• The phospho-diester
bond is formed
between:
– Hydroxyl (OH) group
of the sugar of one
nucleotide.
– Phosphate group of
other nucleotide
 Polymerization of Nucleotides
• The formed polynucleotide
chain is formed of:
– Negative (-ve) charged
Sugar-Phosphate backbone.
• Free 5’ phosphate on one
end (5’ end)
• Free 3’ hydroxyl on other
end (3’ end)
– Nitrogenous bases are not
in the backbone
• Attached to the backbone
• Free to pair with
nitrogenous bases of other
polynucleotide chain
 Polymerization of Nucleotides
• Nucleic acids are polymers of nucleotides.
• The nucleotides formed of purine or
pyrimedine bases linked to phosphorylated
sugars (nucleotide back bone).
• The bases are linked to the pentose sugar to
form Nucleoside.
• The nucleotides contain one phosphate
group linked to the 5’ carbon of the
nucleoside.
Nucleotide = Nucleoside + Phosphate group
• The polymerization of nucleotides to form
nucleic acids occur by condensation
reaction by making phospho-diester bond
between 5’ phosphate group of one
nucleotide and 3’ hydroxyl group of another
nucleotide.

• Polynucleotide chains are always

synthesized in the 5’ to 3’ direction, with a
free nucleotide being added to the 3’ OH
group of a growing chain.
 Complementary base pairing
• It is the most important structural feature of
nucleic acids
• It connects bases of one polynucleotide
chain (nucleotide polymer) with
complementary bases of other chain
• Complementary bases are bonded together
via:
– Double hydrogen bond between A and T (DNA), A
and U (RNA) (A═T or A═U)
– Triple H-bond between G and C in both DNA or
RNA (G≡C)
Base pairing
 Significance of complementary base
pairing
• The importance of such complementary base
pairing is that each strand of DNA can act as
template to direct the synthesis of other
strand similar to its complementary one.

• Thus nucleic acids are uniquely capable of

directing their own self replication.

• The information carried by DNA and RNA

direct the synthesis of specific proteins
which control most cellular activities.
 DNA structure
• DNA is a double stranded molecule consists of 2
polynucleotide chains running in opposite
directions.
• Both strands are complementary to each other.
• The bases are on the inside of the molecules and the
2 chains are joined together by double H-bond
between A and T and triple H-bond between C and G.
• The base pairing is very specific which make the 2
strands complementary to each other.
• So each strand contain all the required information
for synthesis (replication) of a new copy to its
complementary.
 Forms of DNA
1- B-form helix:
– It is the most common form of DNA in
cells.
• Right-handed helix
• Turn every 3.4 nm.
• Each turn contain 10 base pairs (the distance
between each 2 successive bases is 0.34 nm)
• Contain 2 grooves;
– Major groove (wide): provide easy access to bases
– Minor groove (narrow): provide poor access.
2- A-form DNA:
– Less common form of DNA , more common in
RNA
• Right handed helix
• Each turn contain 11 b.p/turn
• Contain 2 different grooves:
– Major groove: very deep and narrow
– Minor groove: very shallow and wide (binding site for RNA)

3- Z-form DNA:
 Radical change of B-form
 Left handed helix, very extended
 It is GC rich DNA regions.
 The sugar base backbone form Zig-Zag shape
 The B to Z transition of DNA molecule may play a role in
gene regulation.
Denaturing and Annealing of DNA
• The DNA double strands can denatured if
heated (95ºC) or treated with chemicals.
• AT regions denature first (2 H bonds)
• GC regions denature last (3 H bonds)

• DNA denaturation is a reversible process, as

denatured strands can re-annealed again if
cooled.

• This process can be monitored using the

hyperchromicity (melting profile).
 Hyperchromicity (melting profile)
• It is used to monitor the DNA denaturation and
annealing.

• It is based on the fact that single stranded (SS)

DNA gives higher absorbtion reading than
double stranded (DS) at wavelength 260º.

• Using melting profile we can differentiate

between single stranded and double stranded
DNA.
 Hyperchromicity (melting profile)
Using melting profile we can differentiate between SS DNA and DS
DNA

SS

SS
Ab260

DS

Tm
Temperature

Tm (melting temp.): temp. at which 50% of DS DNA denatured to SS

•Heating of SS DNA: little rise of Ab reading
• Heating of DS DNA: high rise of Ab reading
 Melting profile continue…..
• Melting profile can be also used to give
an idea about the type of base pair rich
areas using the fact that:
– A═T rich regions: denatured first (low melting point)
– G≡C rich regions: denatured last (higher melting
point)
SS
AT rich DNA
Tm1: Small melting temp. of AT rich
GC/AT DNA
DNA
GC rich DNA
Tm2: higher melting temp. of AT/GC
equal DNA

Tm3: Highest melting temp. of GC rich DS

DNA

Tm1 Tm2 Tm3

 RNA structure
• It is formed of linear polynucleotide
• It is generally single stranded
• The pentose sugar is Ribose
• Uracile (U) replace Thymine (T) in the
pyrimidine bases.

Although RNA is generally single stranded,

intra-molecular H-bond base pairing occur
between complementary bases on the same
molecule (secondary structure)
 Types of RNA
• Messenger RNA (mRNA):
– Carries genetic information copied from DNA in the form of
a series of 3-base code, each of which specifies a particular
amino acid.
• Transfer RNA (tRNA):
– It is the key that read the code on the mRNA.
– Each amino acid has its own tRNA, which binds to it and
carries it to the growing end of a polypeptide chain.
• Ribosomal RNA (rRNA):
– Associated with a set of proteins to form the ribosomes.
– These complex structures, which physically move along the
mRNA molecule, catalyze the assembly of amino acids into
protein chain.
– They also bind tRNAs that have the specific amino acids
according to the code.
 RNA structure
• RNA is a single stranded
polynucleotide molecule.

• It can take 3 levels of structure;

– Primary: sequence of nucleotides
– Secondary: hairpin loops (base pairing)
– Tertiary: motifs and 3D foldings
RNA structure

Transfer RNA (tRNA) structure

 Central Dogma
DNA ---------→ RNA---------→Protein.
• This unidirectional flow equation represents the
Central Dogma (fundamental law) of molecular
biology.
• This is the mechanism whereby inherited
information is used to create actual objects, namely
enzymes and structural proteins.

• An exception to the central dogma is that certain

viruses (retroviruses) make DNA from RNA using the
enzyme reverse transcriptase.
 Gene Expression
• Genes are DNA sequences that encode
proteins (the gene product)

• Gene expression refers to the process

whereby the information contained in genes
begins to have effects in the cell.

• DNA encodes and transmits the genetic

information passed down from parents to
offspring.
 Genetic code
• The alphabet of the genetic code contains
only four letters (A,T,G,C).

• A number of experiments confirmed that the

genetic code is written in 3-letter words, each
of which codes for particular amino acid.

• A nucleic acid word (3 nucleotide letters) is

referred to as a codon.
 Central Dogma of Molecular Biology

RNA molecules carry out protein synthesis

•Each cell starts out life with DNA inherited from a parent cell
•DNA contains all the information necessary to build a new cell
•In the case of multicelled organisms, DNA contains information to
build an entire individual
•Parts of the sequences (DNA, RNA or protein) are identical or nearly
so in all organisms
•Most is unique to a species or an individual
 DNA unwinding during transcription

http://www.mun.ca/biology/desmid/brian/BIOL2060/BIOL2060-21/21_09.jpg
 DNA Replication
• Replication of the DNA molecule is semi-conservative,
which means that each parent strand serves as a
template for a new strand and that the two (2) new
DNA molecules each have one old and one new
strand.

• DNA replication requires:

– A strand of DNA to serve as a template
– Substrates - deoxyribonucleoside triphosphates
(dATP, dGTP, dCTP, dTTP).
– DNA polymerase - an enzyme that brings the
substrates to the DNA strand template
– A source of chemical energy to drive this synthesis
reaction.
 DNA Replication
• Nucleotides are always added to the growing strand
at the 3' end (end with free -OH group).

• The hydroxyl group reacts with the phosphate group

on the 5' C of the deoxyribose so the chain grows

• Energy is released when the bound linking 2 of the 3

phosphate groups to the deoxyribonucleoside
triphosphate breaks

• Remaining phosphate group becomes part of the

sugar-phosphate backbone
 Step 1 - Unwinding and Exposing
Strands
– DNA strands are unwound and opened by
enzymes called HELICASES

– Helicases act at specific places called

ORIGINS OF REPLICATION

– Synthesis of new DNA strands proceeds in

both directions from an origin of replication
resulting in a bubble with REPLICATION
FORKS at each growing point.
Step 2 - Priming the Strand
– In order to begin making a new strand, a helper
strand called a PRIMER is needed to start the
strand.

– DNA polymerase, an enzyme, can then add

nucleotides to the 3' end of the primer.

– Primer is a short, single strand of RNA (ribonucleic

acid) and is complimentary to the DNA template
strand.

– Primers are formed by enzymes called PRIMASES.

 Step 3 - Strand Elongation
– DNA Polymerase III catalyses elongation of new
DNA strands in prokaryotes

– Two molecules of DNA polymerase III clamp

together at the replication forks, each acting on 1
of the strands

– One strand exposed at its 3' end produces a

daughter strand which elongates from its 5' to 3'
end and is called the LEADING STRAND. This
strand is synthesized continuously and grows
from 5' to 3'.
Step 3 - Strand Elongation
– The second daughter strand is called the
LAGGING STRAND and is antiparallel to the
leading strand. It’s template is exposed from the
5' to 3' end but it must direct the 5' to 3' synthesis
of the lagging strands, since nucleotides are
added at the 3' end of the chain.

– The lagging strand is constructed in small,

backward directed bits consisting of
discontinuous sections of 100-200 nucleotides in
eukaryotes and 1000-2000 nucleotides in
prokaryotes, called OKAZAKI FRAGMENTS.
Step 3 - Strand Elongation
– When an Okazaki fragment forms:
DNA polymerase I removes the RNA primer and
replaces it with DNA adjacent to the fragment.

– leaving 1 bond between adjacent fragments

missing.

– A second enzyme called a DNA LIGASE

catalyses the formation of the final bond.
 Telomerase
• Telomerase is a reverse transcriptase that contain
an RNA template, adds nucleotides to the 3’end of
the lagging-strand template and thus prevents
shortening of lagging strands during replication of
linear DNA molecules such as those of eukaryotic
chromosomes.
Lipids
Lipids
 Structure: Greasy or oily nonpolar compounds
 Functions:
 Energy storage
 membrane structure
 Protecting against desiccation (drying out).
 Insulating against cold.
 Absorbing shocks.
 Regulating cell activities by hormone actions.
 1. Structure of Fatty Acids
 Long chains of mostly carbon and hydrogen atoms with a
-COOH group at one end.
 When they are part of lipids, the fatty acids resemble
long flexible tails.
 Saturated and Unsaturated Fats
 Unsaturated fats :
 liquid at room temp
 one or more double bonds between carbons in the fatty acids
allows for “kinks” in the tails
 most plant fats
 Saturated fats:
 have only single C-C bonds in fatty acid tails
 solid at room temp
 most animal fats
Saturated fatty
acid
Saturated fatty
acid

Unsaturated
fatty acid
 Solid Vs Liquid

Saturated Vs Unsaturated

Simplest fatty acids are

unbranched, linear chains of
CH2 groups linked by carbon-
carbon single bonds with one
terminal carboxylic acid group.
Saturated indicates that the
maximum possible number of
hydrogen atoms are bonded to
each carbon.
An unsaturated fat is a fatty acid in which there is

at least one double bond within the fatty acid chain.

Monounsaturated contains one double bond, and

polyunsaturated contains more than one double bond.

2. Structure of Triglycerides
 Glycerol + 3 fatty acids
 3 ester linkages are formed between a hydroxyl group of the
glycerol and a carboxyl group of the fatty acid.
 3. Phospholipids
 Structure: Glycerol + 2 fatty acids + phosphate group.
 Function: Main structural component of membranes, where they arrange
in bilayers.
Phospholipids in Water
 4. Waxes

 Function:
 Lipids that serve as coatings for plant parts and as animal
coverings.
 5. Steroids
 Structure: Four carbon rings with no fatty acid tails
 Functions:
 Component of animal cell membranes
 Modified to form sex hormones
TriGlycerides

The simplest lipids

constructed from fatty acids
are the triacylglycerols.

These are also called

triglycerides, fats or neutral
fats.

Triacylglycerols are composed

of 3 fatty acids, each in an
ester linkage with a single
glycerol group. They are
nonpolar - and hence water-
insoluble - and have lower
specific gravity than water.
(This is why oil and water don’t
mix, and why oil floats on the
surface of water)
Most abundant lipids in cell membranes Phospholipids
A phospholipid has two fatty acid tail and a
head that contains a phosphate group.
The opposing properties (hydrophobic and
hydrophilic) give rise to cell membrane
structure
Cell membranes have two layers of lipid

Heads dissolved in the

cell’s watery interior
Hydrophobic
tails sandwiched
between the
hydrophilic
heads

Heads dissolved in the fluid surroundings

 Waxes: a complex, varying mixture of lipids
Long chain fatty acids tightly packed and linked to long-
chain alcohols or to carbon rings.
Molecules pack tightly; resulting substance is firm and
water-repellent
Help to restrict water loss and keep out parasites and
other pests in plants
Others protect, lubricate, and soften skin and hair

Waxes, together with fats

and fatty acids, make feather Honeycomb is made from wax
waterproof that bees secrete
Health Problems
 Energy Intake > Energy needed = Lipids
overtaking
 Develop medical problem
 Cancer
 Heart disease
 Diabetes
 Obesity
 High blood pressure
 High blood cholesterol
 Cholesterol
 Plant and animal food contain sterols but only animal
food contain cholesterol
 Why? Cholesterol is made in the liver and plants do no
have a liver
 Cholesterol is needed to make bile, sex hormones,
steroids and vitamin D.
 It is the constituent of cell membrane structure
 Dietary recommendation - <300 mg/d
 Sources – egg yolks, liver, shellfish, organ foods
 Lipoproteins
 Low Density Lipoproteins (LDL) – is made by
the liver and is comprised of cholesterol that is
delivered to the cells in the body
 High levels of LDL is strongly correlated with
heart disease
 High Density Lipoproteins (HDL) - made by
the liver and picks up cholesterol from the
cells fro recycling or excretion
 High levels of HDL is inversely correlated
with heart disease
 It is protective
 Blood levels for Lipids
 Total Cholesterol:
 <200 mg/dl = desirable
 200-239 mg/dl = borderline hyperlipidemia
 >240 mg/dl = hyperlipidemia
 LDL < 130 mg/dl is favorable
 HDL > 35 mg/dl is favorable
 Prevention of Lipid Disorder
 Reduce fat
 Cut down on high fat foods
 E.g. butter, margarine, oil, mayonnaise
 Consume small amounts of
unsaturated fats
 Do not eliminate fat completely since it
is high in calories
Prevention of Lipid Disorder
 Limit added sugar and alcohol
 Added sugar and alcohol are ‘empty
calories’
 Watch portions of all food
 ‘fat free’ ≠ ‘calorie-free’
 Drink at least 8 glasses of water everyday
 Water is calorie-free, refreshing, and filling
 Prevention of Lipid Disorder
 Increase intake of vegetables, fruits,
and whole grains
 Loaded with fiber
 Contain high amounts of vitamins,
minerals, and phytonutrients
 Include low-fat protein-rich food
with every meal
 E.g. tofu, beans, eggs, and fish
 Prevention of Lipid Disorder

 Slow down when eating

 Too fast eating will exceed calorie needs
before realizing we are full
 Cell Membranes

Yeast – Transmission Electron Micrograph

http://163.178.103.176/Fisiologia/general/activ_bas_3/Membrane%20Structure%20and%20Function.htm
http://php.med.unsw.edu.au/cellbiology/index.php?title=2009_Lecture_3
 Cell Membrane

Fluid Mosaic Model

Membrane lipids, properties and their

function

Membrane proteins and their function

 Membrane proteins
oMany types of proteins are associated with a cell membrane
oEach type adds a specific function to the membrane

oDifferent cell membranes can have different characteristics depending on

which proteins are associated with them

oExample: A plasma membrane has certain proteins that no internal cell

membrane has.

oTypes of membrane proteins: Enzymes, adhesion proteins, recognition

proteins, receptor proteins, transport proteins

Membrane proteins constitute more

than 30% of human proteins
 Types of membrane proteins
Bind to a
particular
substance
outside of the
cell. Binding
triggers a change
in cell’s activities
that may involve
metabolism,
movement,
division or even
cell death

Function as identity Fasten cells together in

tags for a cell type, animal tissues
individual or specieshttp://faculty.southwest.tn.edu/rburkett/Menbranes%20&%20cell%20function.htm
 Transporter proteins

oThey move specific

substances across a membrane

oThese proteins are

important because lipid
bilayers are impermeable to
ions and polar molecules

oSome transport proteins are open channels through which a substance

moves on its own across a membrane

oOthers use energy to actively pump a substance across

Diffusion through Cell Boundaries
• Particles move from an area of high
concentration to an area of lower
concentration
• No energy is required
Osmosis
 Diffusion of water through a selectively
permeable membrane
onic
means the same

 Concentration of
solutes (salts) is the
same inside and
outside of cell.
 Water flows in and
out in equal amounts
 No effect on cell
ertonic
” means more
 Concentration of solutes is more
outside the cell than inside
 Water flows out of cell
 The cell shrivels and may die.

 This is why it is dangerous to

drink sea water
 This is also why "salting fields"
was a common tactic during war,
it would kill the crops in the field,
thus causing food shortages.
ypotonic
YPO" means less

 Concentration of solutes
is less outside the cell
than in.

 Water flows in

 The cell swell with water

and becomes “turgid”
Active Transport
 Carried our by protein pumps found in the
membrane
 Energy is required
Facilitated Diffusion
 Molecules move through protein channels.
 No energy required
 Endocytosis
 Cell takes material into cell by infolding of the cell membrane
 Phagocytosis – eating – cell engulfs large particles
 Pinocytosis – drinking – cell takes in liquid
 www.endocyte.com/ animation/animation.htm
Exocytosis
 Cell releases large
amounts of material
 Cell Specialization
 The cells in multicellular organisms can develop in different
ways to perform different tasks.
Levels of Biological
Organization

 Organism
 Organ system
 Organ
 Tissue
 Cell
 Organelle
 DNA
 Atoms
Cell Structure and Function: Topics to be discussed
Where are the “Molecules of Life” located in the cells?

What are common between different types of cells?

Are there differences between cells of different

organisms?

Why is cell size so small?

What are the experimental techniques that help us to

understand the cell structure and organization?

What are the different cellular organelles?

 E. Coli O157:H7 strain is harmful to humans

oIntestinal bacteria that

live in cattle, deer, goats,
sheep and humans

oSeverely damage the

lining of human intestine
http://everything-pr.com/ecoli-germany-spain/228647/

oComplications: Bloody oWhat makes bacteria sticky?

diarrhea, kidney failure,
blindness, paralysis and
oWhy do people but not cows get sick
death
with E. coli O157:H7?

oWe need to learn about cells and how

they work?
Cell is the smallest unit that shows properties of life
oCells vary dramatically in shape and function
oHowever, all cells share certain organizational and functional
features

Examples of cells
Traits common to all cells
1665: Antoni van Leeuwenhoek first
observed tiny moving organisms in rainwater,
insects, fabric, sperm and other samples
Robert Hooke coined the term cell

Robert Brown first identified

a cell nucleus in 1820s

Matthias Schleiden first hypothesized

that a plant cell is an independent living
unit even when it is part of a plant
Theodor Schwann together with Schleiden
concluded that tissues of animals and plants
are composed of cells and their products

Rudolf Virchow realized that all cells

descended from another living cell
Cell Theory

• 1. All living things are made of cells.

• 3. New cells are produced from existing cells
• 2. Cells are the basic unit of structure and function in
living things.
Surface-to-volume limits also affect the
body plan of multicelled species

http://voer.edu.vn/c/comparing-prokaryotic-and-eukaryotic-cells/a64457a4/6b98166e
 A sense of scale

https://www.jic.ac.uk/microscopy/scale.html
 Prokaryotes vs. Eukaryotes
• Prokaryotes
(bacteria)
have no nucleus
and very few
organelles. DNA is
not contained

• Eukaryotes
(protists, fungi, plants and
animals) larger,more
complex,DNA is inside the
nucleus
Eukaryotic Cell : Animal Cell
 Plant Cell

Smooth endoplasmic
Vacuole reticulum
Ribosome
(free)
Chloroplast
Ribosome
(attached)
Cell
Membrane
Nuclear
Cell wall envelope

Nucleolus

Golgi apparatus
Nucleus

Mitochondrion Rough endoplasmic reticulum

 Compare and Contrast

Animal Cells Plant Cells

Cell membrane
Ribosomes
Nucleus
Endoplasmic reticulum
Cell Wall
Centrioles Golgi apparatus
Chloroplasts
Lysosomes
Vacuoles
Mitochondria
Cytoskeleton
Internal Organization
• Cells contain
ORGANELLES.
• Cell Components that
PERFORMS SPECIFIC
FUNCTIONS FOR THE
CELL.
 Cellular Organelles
• The Plasma
membrane
– The boundary of the
cell.
– Composed of three
distinct layers.
– Two layers of fat and
one layer of protein.
 The Nucleus
• Brain of Cell
• Bordered by a porous
membrane - nuclear envelope.
• Contains thin fibers of DNA
and protein called Chromatin.
• Rod Shaped Chromosomes
• Contains a small round
nucleolus
– produces ribosomal RNA which
makes ribosomes.

The nucleus controls access to DNA and permits easier

packing of DNA during cell division.
 Ribosomes
• Small non-membrane
bound organelles.
• Contain two sub units
• Site of protein synthesis.
• Protein factory of the cell
• Either free floating or
attached to the Endoplasmic
Reticulum.

Cells also contain non-membranous structures:

Ribosomes, "free" or attached to membranes, participate in assembly of
polypeptide chains.
 Endoplasmic Reticulum
• Complex network of
transport channels.
• Two types:
1. Smooth- ribosome free
and functions in poison
detoxification.
2. Rough - contains
ribosomes and releases
newly made protein from
the cell.

The endoplasmic reticulum (ER) modifies newly formed

polypeptide chains and is also involved with lipid synthesis.
 Golgi Apparatus
• A series of flattened
sacs that modifies,
packages, stores, and
transports materials
out of the cell.
• Works with the
ribosomes and
Endoplasmic
Reticulum.

The Golgi body modifies, sorts, and ships proteins; they also play a role
in the synthesis of lipids for secretion or internal use.
Lysosomes
• Recycling Center
– Recycle cellular debris
• Membrane bound
organelle containing a
variety of enzymes.
• Internal pH is 5.
• Help digest food particles
inside or out side the cell.
 Centrioles
• Found only in animal cells
• Paired organelles found
together near the
nucleus, at right angles to
each other.
• Role in building cilia and
flagella
• Play a role in cellular
reproduction
 Cell membrane

Endoplasmic
reticulum
Cytoskeleton Microtubule

Microfilament

Ribosomes Mitochondrion
Main Components

1. The cytoskeleton is an interconnected system of fibers, threads, and lattices that

extends between the nucleus and the plasma membrane.

2. It gives cells their internal organization, overall shape, and capacity to move.

3. The main components are microtubules, microfilaments, and intermediate

filaments: all assembled from protein subunits.

4. Some portions are transient, such as the "spindle" microtubules used in

chromosome movement during cell division; others are permanent, such as filaments
operational in muscle contraction.
 Cytoskeleton
B. The Structural Basis of Cell Movements

1. Through the controlled assembly and disassembly of their subunits,

microtubules and microfilaments grow or shrink in length (example:
movement of chromosomes).

2. Microfilaments or microtubules actively slide past one another (example:

muscle movement).

3. Microtubules or microfilaments shunt organelles from one location to

another (example: cytoplasmic streaming).
 Cytoskeleton

C. Flagella and Cilia

1. Flagella are quite long, are usually not numerous, and are found on one-celled
protistans and animal sperm cells.
2. Cilia are shorter and more numerous and can provide locomotion for free-living cells
or may move surrounding water and particles if the ciliated cell is anchored.

3. Both of these extensions of the plasma membrane have a 9 + 2 cross-sectional array

(arising from centrioles) and are useful in propulsion.
 Mitochondrion
A. Mitochondria are the primary organelles for
transferring the energy in carbohydrates to ATP
under oxygen-plentiful conditions.

B. Hundreds of thousands of mitochondria occur in

cells.

1. It has two membranes, an inner folded

membrane (cristae) surrounded by a smooth
outer membrane.

2. Inner and outer compartments formed by the

membranes are important in energy
transformations.

3. Mitochondria have their own DNA and some

ribosomes, a fact which points to the possibility that
they were once independent entities.

Mitochondria are efficient factories of ATP production.

The Chloroplast
• Double membrane
• Center section contains
grana
• Thylakoid (coins) make up
the grana.
• Stroma - gel-like material
surrounding grana
• Found in plants and algae.
A. Chloroplasts and Other Plastids

1. Chloroplasts are oval or disk shaped, bounded by a double membrane, and

critical to the process of photosynthesis.
a. In the stacked disks (grana), pigments and enzymes trap sunlight
energy to form ATP.
b. Sugars are formed in the fluid substance (stroma) surrounding the
stacks.
c. Pigments such as chlorophyll (green) confer distinctive colors to the
chloroplasts.

2. Chromoplasts have carotenoids, which impart red-to-yellow colors to plant parts,

but no chlorophyll.

3. Amyloplasts have no pigments; they store starch grains in plant parts such as
potato tubers.
 Mitochondria vs.
Chloroplasts

• Mitochondria make energy from

chemicals (food molecules)
• Chloroplasts make energy
from light through
photosynthesis
 The Vacuole
• Sacs that help in food
digestion or helping
the cell maintain its
water balance.
• Found mostly in plants
and protists.

1. In the mature plant, the central vacuole may occupy 50 to 90% of the cell interior!
a. stores amino acids, sugars, ions, and wastes.
b. enlarges during growth and greatly increases the cell’s outer surface area.

2. The cytoplasm is forced into a very narrow zone between the central vacuole and the plasma
membrane.
 Cell Wall

• Extra structure surrounding its plasma

membrane in plants, algae, fungi, and
bacteria.
• Cellulose – Plants
• Chitin – Fungi
• Peptidoglycan - Bacteria
 Smooth ER vs. Rough ER
• Rough ER - ribosomes on the ER make proteins,
the ER modifies the proteins
• Smooth ER - makes lipids
 Cytoskeleton
• Network of
protein filaments

• Maintains shape

• Involved in cell
movement
 Prokaryotes Eukaryotes

Nucleus
Endoplasmic reticulum
DNA is Golgi apparatus
Cell membrane
free Lysosomes
Contain DNA
floating Vacuoles
Mitochondria
Cytoskeleton
 Cell Wall
• Provides support and
protection for plant cell
walls
• Made of porous cellulose
so it does not regulate
what enters and leaves
Eukaryotic Cell Walls

1. Many single-celled eukaryotes have a cell wall, a supportive

and protective structure outside the plasma membrane

2. Microscopic pores allow water and solute passage to and

from underlying plasma membrane.

3. In plants, bundles of cellulose strands form the primary cell

wall, which is more pliable than the more rigid secondary
wall that is laid down inside it later.
 Cell Membrane
• Regulates what enters and leaves the cell and
provides support and protection
• Structure – lipid bilayer with embedded
proteins
 Diffusion through Cell Boundaries
• Particles move from an area of high
concentration to an area of lower
concentration
• No energy is required
 Osmosis
• Diffusion of water through a selectively
permeable membrane
 Isotonic
"ISO" means the same

• Concentration of
solutes (salts) is the
same inside and
outside of cell.
• Water flows in and
out in equal amounts
• No effect on cell
 Hypertonic
“Hyper” means more
• Concentration of solutes is more
outside the cell than inside
• Water flows out of cell
• The cell shrivels and may die.

• This is why it is dangerous to drink

sea water
• This is also why "salting fields"
was a common tactic during war, it
would kill the crops in the field,
thus causing food shortages.
 Hypotonic
"HYPO" means less

• Concentration of solutes
is less outside the cell
than in.

• Water flows in

• The cell swell with water

and becomes “turgid”
 Active Transport
• Carried our by protein pumps found in
the membrane
• Energy is required
 Facilitated Diffusion
• Molecules move through protein
channels.
• No energy required
 Endocytosis

• Cell takes material into cell by infolding of the cell

membrane
• Phagocytosis – eating – cell engulfs large particles
• Pinocytosis – drinking – cell takes in liquid
• www.endocyte.com/ animation/animation.htm
 Exocytosis
• Cell releases large
amounts of material
 Cell Specialization
• The cells in multicellular organisms can develop in
different ways to perform different tasks.
Levels of Biological
Organization

• Organism
• Organ system
• Organ
• Tissue
• Cell
• Organelle
• DNA
• Atoms
LIF101a : Basics of Immunity
In Living system
Think why?
• Why do organisms contract diseases?
• What happens when an organism contracts a
disease?
• What factors can help (or hinder) the likelihood that
we will contract a disease?
• What happens when an organism is injured?
• What factors can help (or hinder) the likelihood that
we will recover from an injury?
What is immunity?

•“Protection” from infection, tumors, etc.

•Innate immunity is always available
•Adaptive immunity distinguishes “self” from
“non-self” and involves immune system
“education”
•Responses that may result from host tissue
damage
 Two types of immunity
• Innate immunity (not antigen-specific)
• Anatomical barriers
• Mechanical
• Biochemical
• Non-specific (eg. Low pH in stomach)
• Receptor-driven (eg. PAMP-recognition)
• Adaptive immunity (antigen-specific)
• Receptor-driven
• Pre-existing clones programmed to make a specific immune
response (humoral/cellular)
 Antigen
• A substance (antigen) that is capable of reacting with the
products of a specific immune response, e.g., antibody or
specific sensitized T-lymphocytes.

• A “self” component may be considered an antigen

even though one does not generally make immune responses
against those components.
Basic Organization and Function of the
Immune System

The immune system is

the body’s response to
disease and injury
• Nonspecific response
(innate immunity)
• Specific response
(acquired immunity)

T-cell (part of the specific

immune response)
Innate Immunity : The first barrier to foreign pathogen

Innate Immunity Barriers

Nonspecific response (Innate immunity)
Exterior barriers
• Skin
• Mucous membranes
• Secretions
Nonspecific response (Innate immunity)
• Involves myeloid leukocytes (including all phagocytic
cells) such as macrophages
• Participate in the inflammatory response to injury or
disease
• Mast cells also involved
• Proteins (cytokines) signal between cells

inflammation mast cell protein

Specific Response (Adaptive immunity)
• Antigen-antibody
relationship (acquired
immunity)
• Vaccinations depend on this
• Involves lymphocytes (B, T
and plasma cells)
Model of an antibody

T-cells, made visible by fluorescent dye

B Cells and T cells
Differentiation into
Originates in lymphoid stem cells
bone marrow in the bone marrow
• Rich supply of
hematopoietic stem – General B cells
cells mature in the bone
• Asymmetric cell marrow
division (one
daughter stays in
bone marrow ) Differentiation into
• Lymphoid and lymphoid stem cells
Myeloid lineage
cells begin and are in the thymus
released from here – General T cells
mature in the
thymus
• Bacteria are of
immense importance
because of their rapid
growth, reproduction,
and mutation rates, as
well as, their ability to
exist under adverse
conditions.
• The oldest fossils
known, nearly 3.5
billion years old, are
fossils of bacteria-like
organisms.
• Bacteria can be autotrophs or hetertrophs.

• Those that are classified as autotrophs are

either photosynthetic, obtaining energy from
sunlight or chemosynthetic, breaking down
inorganic substances for energy .
• Bacteria classified as
heterotrophs derive energy
from breaking down complex
organic compounds in the
environment. This includes
saprobes, bacteria that feed
on decaying material and
organic wastes, as well as
those that live as parasites,
absorbing nutrients from
living organisms.
• Depending on the
species, bacteria can be
aerobic which means
they require oxygen to
live
or

• anaerobic which means

oxygen is deadly to
them.
Green patches are green sulfur
bacteria. The rust patches are
colonies of purple non sulfur
bacteria. The red patches are purple
sulfur bacteria.
Archaebacteria
Methanogens
These Archebacteria are
anaerobes. They make
methane (natural gas) as
a waste product. They are
found in swamp
sediments, sewage, and
in buried landfills. In the
future, they could be
used to produce methane
as a byproduct of sewage
treatment or landfill
operation.
Halophiles
These are salt-loving Archaebacteria that grow in
salt. Large numbers of certain halophiles can turn
these waters a dark pink. Pink halophiles contain a
pigment very similar to the rhodopsin in the human
retina. They use this visual pigment for a type of
photosynthesis that does not produce oxygen.
Halophiles are aerobes, however, and perform
aerobic respiration.
Extreme halophiles can live in extremely salty environments. Most
are photosynthetic autotrophs. The photosynthesizers in this
category are purple because instead of using chlorophyll to
photosynthesize, they use a similar pigment called
bacteriorhodopsin that uses all light except for purple light,
making the cells appear purple.
Thermophiles
These are Archaebacteria from hot springs and other
high temperature environments. Some can grow
above the boiling temperature of water. They are
anaerobes, performing anaerobic respiration.

Thermophiles are interesting because they contain

genes for heat-stable enzymes that may be of great
value in industry and medicine. An example is taq
polymerase, the gene for which was isolated from a
collection of Thermus aquaticus in a Yellowstone
Park hot spring. Taq polymerase is used to make
large numbers of copies of DNA sequences in a DNA
sample. It is invaluable to medicine, biotechnology,
and biological research. Annual sales of taq
polymerase are roughly half a billion dollars.
Eubacteria
Cyanobacteria
This is a group of bacteria that
includes some that are single
cells and some that are chains
of cells. You may have seen
them as "green slime" in your
aquarium or in a pond.

Cyanobacteria can do "modern

photosynthesis", which is the
kind that makes oxygen from
water. All plants do this kind of
photosynthesis and inherited
the ability from the
cyanobacteria.
Cyanobacteria were the first organisms on Earth to
do modern photosynthesis and they made the first
oxygen in the Earth's atmosphere.
• Bacteria are often
maligned as the causes
of human and animal
disease. However,
certain bacteria, the
actinomycetes, produce
antibiotics such as
streptomycin and
nocardicin.
• Other Bacteria live symbiotically in the guts of
animals or elsewhere in their bodies.

• For example, bacteria in your gut produce

vitamin K which is essential to blood clot
formation.
• Still other Bacteria live
on the roots of certain
plants, converting
nitrogen into a usable
form.
• Bacteria put the tang in
yogurt and the sour in
sourdough bread.

• Saprobes help to break

down dead organic
matter.

• Bacteria make up the

base of the food web in
many environments.

Streptococcus thermophilus in yogurt

• Bacteria are prokaryotic and unicellular.

• Bacteria have cell walls.

• Bacteria have circular DNA called plasmids

• Bacteria can be anaerobes or aerobes.

• Bacteria are heterotrophs or autotrophs.

• Bacteria are awesome!

• Bacteria can reproduce sexually by conjugation or
asexually by binary fission.
 Endospore
• Bacteria can survive
unfavorable conditions
by producing an
endospore.
Shapes of Bacteria
Penicillin, an antibiotic, comes from molds of the
genus Penicillium Notice the area of inhibition
around the Penicillium.
• Penicillin kills bacteria by making holes in their cell
walls. Unfortunately, many bacteria have developed
resistance to this antibiotic.
• The Gram stain, which divides most clinically
significant bacteria into two main groups, is
the first step in bacterial identification.

• Bacteria stained purple are Gram + - their cell

walls have thick petidoglycan and teichoic
acid.

• Bacteria stained pink are Gram – their cell

walls have have thin peptidoglycan and
lipopolysaccharides with no teichoic acid.
In Gram-positive bacteria, the purple crystal violet stain is
trapped by the layer of peptidoglycan which forms the outer
layer of the cell. In Gram-negative bacteria, the outer
membrane of lipopolysaccharides prevents the stain from
reaching the peptidoglycan layer. The outer membrane is then
permeabilized by acetone treatment, and the pink safranin
counterstain is trapped by the peptidoglycan layer.
The Gram stain has four steps:
• 1. crystal violet, the primary stain: followed by

• 2. iodine, which acts as a mordant by forming

a crystal violet-iodine complex, then

• 3. alcohol, which decolorizes, followed by

•
4. safranin, the counterstain.
Is this gram stain positive or negative?
Identify the bacteria.
Is this gram stain positive or negative?
Identify the bacteria.
• Gram staining tests the bacterial cell wall's ability to
retain crystal violet dye during solvent treatment.
• Safranin is added as a mordant to form the crystal
violet/safranin complex in order to render the dye
impossible to remove.
• Ethyl-alcohol solvent acts as a decolorizer and
dissolves the lipid layer from gram-negative cells.
This enhances leaching of the primary stain from the
cells into the surrounding solvent.
• Ethyl-alcohol will dehydrate the thicker gram-
positive cell walls, closing the pores as the cell wall
shrinks.
• For this reason, the diffusion of the crystal violet-
safranin staining is inhibited, so the bacteria remain
stained.