1.

2 Enzymes Enzymes are proteins:

-Enzymes are globular (spherical/ball-shaped) proteins with a specific tertiary structure
Proteins/Hydrolysis/Rate built to accelerate biochemical reactions.
-Primary sequence of amino acids leads to secondary structure of alpha helices and
beta sheets. This folds in 3D, forming ionic bonds, disulphide bridges, hydrogen bonds
O and salt bridges to bring about the tertiary structure.
-Often more than one polypeptide chain comes together to form a quaternary structure
N C (associations of multiple chains).
Enzymes have an active site:
H -The active site of the enzyme has a shape specific to its substrate.
-This specific shape is brought about due to the specific sequence of amino acids in the
enzymes structure.
-The substrate forms chemical bonds with the active site, and the enzyme then
Protease enzymes target undergoes a conformational change to better fit to the substrate.
peptide bonds in proteins for -The enzyme-substrate complex has now been formed thanks to the complementary
hydrolysis. This breaks the nature of the enzyme and substrate.
bonds holding amino acids -The enzyme will now carry out its catalysis dependent on what enzyme it is (some
together.
break things down, other build things up) often through hydrolysis.

Competitive Inhibition: Non- competitive Inhibition:

-The inhibitor has a similar, complementary shape to the
active site of the enzyme in question. It can therefore
compete with the substrate for the availability of the
active site. If the inhibitor is bound, the substrate cannot
bind with the active site as it is occupied. The substrate
cannot therefore be broken down as quickly, so the rate
of reaction decreases.
-The inhibitor does not have a complementary shape to
the active site, but binds to the enzyme all the same. This
time it binds at an allosteric site and through interactions
with the enzymes tertiary structure, it causes deformation
of the active site. This means that the enzymes active site
is no longer complementary to the substrate, so less
substrate can be broken down. The rate therefore
decreases.

Increasing the concentration of Non-competitive inhibitors

substrate could help increase the Enzyme Enzyme
typically cause an irreversible
rate in the presence of a competitive effect owing to the fact that they
inhibitor. This is because a higher Substrate distort the shape of the active Substrate
concentration will mean a higher site. Nonetheless, increasing
likelihood of substrate reaching the Competitive [substrate] right at the start of
active site. Non-Competitive
Inhibitor the inhibition could rescue some Inhibitor
rate.

How enzymes denature is explained in GCSE enzymes. This has Allosteric site: A site on the enzyme that is
detailed explanations for why temperature and pH changes cause NOT the active site.
the active site to lose its specificity.

Taq Pol: A polymerase taken

Factors affecting enzyme rates: Temperature from hydrothermal vents and
A very low temperature will mean that both the enzyme and the substrate molecules hot springs. It can withstand
will have a low KE (kinetic energy) and therefore will be less likely to successfully high temperatures of above
collide to form an ES-complex (enzyme-substrate). 90 degrees Celsius without
denaturing. It is therefore
As temperature is therefore increased, the enzyme and substrate molecules will used in PCR, which couples
begin to gain more kinetic energy. There will be an increased level of vibration as a high temperature and free-
well as increased frequent successful collisions between enzyme and substrate. floating nucleotides and
primers to exponential; DNA
As temperature is increased beyond the optimum, the bond vibrations become so amplification, with
kinetic that they begin to break. This begins to lower the rate of the enzyme, as its applications in CSI and
active site denatures, losing its shape and therefore specificity to its substrate. This paternity testing
is known as loss of complementarity.
Factors affecting enzyme rates: pH Bell-Shaped: Narrow
Enzymes are highly pH sensitive. Since pH is a measure of the hydrogen ion [H+] optimum with denaturation
concentration, pH is calculated using the equation: pH = -log[H+]

A acidic solution will therefore have a high H+ concentration, whereas an alkaline

solution will have a high OH- concentration. As either of these two ions is introduced
to a proteins tertiary structure, they begin to interfere with specific bonds. These

Rate
include ionic bonds/salt bridges as well as hydrogen bonds.

Enzymes have a very narrow pH range, and therefore if their rate is plotted against
pH on a graph, a bell-shaped curve will appear. This means that even discrete
changes to the pH can cause the active site of the enzyme to denature and lose
complementarity, therefore decreasing the rate. pH

Factors affecting enzyme rates: [Enzyme]/[Substrate] Limiting factor: Something

If the concentration of substrate does not change, then increasing the [enzyme] will which constrains the rate of
cause the rate of reaction to increase. This is because there are more active sites something, or how quickly
available for the substrates to bind to and release the product. something happens. Usually it
is the variable that must be
changed in order to see a
Increasing the [enzyme] beyond a certain point will not cause the rate to increase. change in the rate.
This is because now there exist more enzymes (and therefore more active sites) than
substrate molecules. The [substrate] therefore becomes the limiting factor at this
stage, where increasing the [substrate] will have an effect on ROR. Examples in nature of limiting
factors include light, [CO2]
The same can be said for [substrate], whereby increasing its concentration will and temperature in
saturate enzymes active sites with substrate molecules. The [enzyme] will therefore photosynthesis. Limiting
become the limiting factor. factors can be biotic (living)
or abiotic (non-living).

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1.1Biological Molecules
Proteins/Lipids/Carbohydrates/Nucleic acids
Polymers and bond dynamics:
-Polymers are molecules which are made up out of
repeating units. These repeating units are called
monomers.
-Typically, bonds can form between monomers through
condensation (where water is excluded and a bond is
formed as a result).
-Bonds are broken by adding water to them. This type
of bond breaking is known as hydrolysis.
Monomer example: Nucleotide
Polymer example: DNA
Polysaccharides and carbohydrates:
-Polysaccharides are examples of polymerised
carbohydrates. The monomer, or repeating unit to a
polysaccharide is a single sugar, a monosaccharide.
-An example of a common monosaccharide is the
hexose sugar glucose. These join together through
condensation reactions, forming a glycosidic bond.
-Glucose has two isomers (alpha/beta glucose) which
differ simply by the orientation of a hydroxyl group.
Beta-glucose is used in cellulose, whilst alpha glucose
is used in starch (repeating unit)
Disaccharide:
A-Glucose + A-Glucose = Maltose
A-Glucose + Fructose = Sucrose
A-Glucose + Galactose = Lactose
Polysaccharides:
Glycogen = Highly branched form of starch, monomer
is A-glucose. Since it is branched, it has both 1,4 and
1,6 glycosidic bonds. Branching mean rapid enzyme
activity for rapid hydrolysis/release of glucose into
blood. Insoluble means it does not affect WP of the
cell.
Cellulose = Long straight chains of beta-glucose, which
run parallel to one another and form hydrogen bonds to
form microfibrils (strong threads, higher order
structure). The strong hydrogen bonds make it easy for
plant cell walls to cope with dramatic osmotic pressure
changes.
Roles of lipids:
-Lipids are used not only as storage and energy
molecules, but also as structural components of every
cell.
-The phospholipid bilayer is made up of many
phospholipids. It is the hydrophobic nature of the fatty
acid tails in these phospholipids which allows the
membrane to arrange itself properly in water.
-Glycolipids can be present in this membrane which act
as signalling molecules or binding sites for
hormones/signalling chemicals.
Importance of protein:
Proteins make up a huge proportion of structures within any
organism. They make up all of the enzyme component of
cells (as all enzymes are protein), as well as having distinct
structural roles in cells such as hair cells. They combine with
carbohydrates to form glycoproteins, which act as both
signalling molecules as well as binding sites for hormones or
chemical messengers.
Testing for reducing sugars:
-All monosaccharides as well as some disaccharides are
reducing sugars, and are therefore able to donate e- (reduce)
specific reagents.
-By using Benedict's reagent, a clear colour change from blue
to brick red can be seen as an insoluble ppt of copper oxide
is formed.
1. Add 2cm3 food sample that is being tested (liquid)
2. Add 2cm3 Benedict's reagent
3. Heat mixture in water bath for 5 mins
*You can also test for non-reducing sugars. The difference to
the experimental procedure here is that 2cm3 of dilute HCl
must be added to the food sample prior to the BR. This HCl
hydrolyses the glycosidic bonds, releasing reducing sugars in
the process. NaHCO3 will then be added to neutralise excess
acid, then the test is run again.
Test for starch: Iodine stains starch blue-black
Lipids and triglycerides:
-Lipids are made of carbon, hydrogen and oxygen, similar to
carbohydrates. However, they are structurally different and
carry differing functions.
FATTY ACID
GLYCEROL
FATTY ACID
FATTY ACID
Saturated: No double-bonds in fatty acid tail. Carbons
present are 'saturated' with hydrogen. Found in animal fats.
(solid as room temp)
Unsaturated: Double-bonds present in the fatty acid tail.
Carbons present are not 'saturated' with hydrogen. Found in
plants. (liquid at room temp)
Properties of triglycerides:
-Low mass:energy ratio makes them a good storage
molecule. Lots of energy stored in small volume.
-High ratio of C:H to C:C bonds, so large amount of energy
can be released.
-Large and non-polar means that lipids can be stored inside
cells without affecting the WP of the cell.
-Release water when hydrolysed, so important for animals
living in arid conditions.
Testing for lipids:
1. Add 2cm3 of sample to a test tube
2. Add 5cm3 ethanol to the sample
3. Add 5cm3 water and shake gently
4. Formation of white ppt indicates lipids present
*Repeat with a control group with no lipids to make sure
solution remain clear!
Primary Structure:
Amino acid monomers (lilac) linked together by
planar peptide bonds (dark grey)
Protein folding:
-The primary structure of a protein describes the sequence
of amino acids present. This primary structure will form the
basis for the folding of the protein.
-The secondary structure describes hydrogen-bond
interactions that occur when alpha helices and beta-
pleated sheets form from the primary structure.
-The tertiary structure describes the three-dimensional
folding of the secondary structure. This will result in the R-
groups from residues that are far away from interacting.
-The quaternary structure describes the association of
more than one individual polypeptide chain. For example,
haemoglobin (Hb) has four polypeptide chains in its
quaternary structure.
Protein amino-acid specific interactions:
-Disulphide bridges form between sulphur atoms present in
cysteine residues (an amino acid with sulphur present in
the R-Group)
-Ionic/salt bridges form between oppositely charged
residues such as aspartic acid (negative) and lysine
(positive)
Testing for proteins (biruet):
1. Place sample in tube and add equal volume of NaOH
(sodium hydroxide).
2. Add a few drops of dilute copper (II) sulphate and mix
gently at room temperature.
3. Orange to purple colour change indicates that a
protein is present in the sample.

Globular vs Fibrous proteins

Proteins can either fold to form structural components or fold to form GLOBULAR
shapes which participate in reactions. Two distinct classes of
proteins can therefore be brought to light: Globular and Fibrous.

-Globular proteins fold to a more spherical orientation, and therefore

form specific binding sites through their tertiary structure shape
specificity. These globular proteins therefore typically form enzymes
(which are globular and have an active site)

-Fibrous proteins fold to form more long/sheet like structures.

Collagen is a triple helix of protein cross-linked to give a high tensile
strength. Keratin is another example of a tough protein which folds
for strength/structural reasons.
FIBROUS

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 1.3 Lungs & Ventilation
Exchange/Structures/Functions/Fish/Insects/Practical
Exchange surface: The Lungs
The lungs are organs located in the chest cavity. They are
responsible for removing carbon dioxide and introducing oxygen to
the bloodstream. The carbon dioxide is a respiratory product, and
oxygen is a respiratory requirement (mitochondria). The lungs are
surrounded by the ribcage, which protects the organs as well as
assisting in ventilation with the diaphragm and intercostal muscles.
The trachea, bronchi and bronchioles aid in getting the air into and
out of the lungs.
Structures and functions:
-Cartilage offers structural support to the trachea and stops collapse
of the airway due to the large pressure changes caused by
ventilation.
-Ciliated epithelial cells are cells with small hairs that waft mucus,
helping to prevent infections from occurring.
-Goblet cells are specialised, mucus secreting cells which make the
mucus which the cilia move.
-Smooth muscle fibres allow constriction and relaxation of the airway,
helping to control the air which reaches the alveoli.
-Elastic fibres help to deal by stretching and recoiling, offering
structural support.
-Diaphragm and intercostal muscles are two muscles which contract
and relax during breathing.
Exchange surfaces adaptations:
-Surface area e.g. RHC (root hair cells or
forms of folded membranes)
-Thin (one cell thick) short diffusion pathway
so distance travelled is short.
-Good blood supply in order to maintain a
strong concentration gradient (e.g. alveoli in
the lungs).
Spirometer practical (measuring volume):
-Vital capacity describes the maximum volume
of air that can be inhaled/exhaled in one
breath.
-Tidal volume describes the volume of air we
breath in and out when we are resting.
-Breathing rate is how many times a breath is
taken per unit time (breaths per minute)
-Residual volume is the volume of air always
present in the lungs.
*Know how to answer questions which
address how each of these change between
resting/exercise etc.

Inspiration:
-External intercostal muscles contract
-Internal IC muscles relax.
-Ribs are raised upwards and outwards.
-Diaphragm contracts and flattens.
Expiration:
-Internal IC muscles contract
-External IC muscles
-Rib cage lowers
-Diaphragm relaxes and rises up
-Abdominal muscles contract
Inspiration:
Bony fish rely on a counter current principle in order to exchange gas.
They have four pairs of gills and distinct apparatus set up for this gas
exchange. The apparatus is held apart by the flow of water, explaining
why fish cannot survive out of water for very long.
-Fish opens mouth and buccal cavity lowers, enabling the flow of water
into it.
-Fish closes mouth and buccal cavity rises, increasing pressure and
forcing water over the gills.
-The operculum acts as a valve and pump, letting water out as well as
pumping it in.
-The blood meeting the water will always have a gradient for exchange.

Insects and breathing Practical element:

-Insects have pores in their skin which open. They are called
spiracles. The pores lead to a system of tracheoles which control
the exchange of gases through diffusion (constant gradient
maintained). The end of the tracheoles contain water.
Tracheoles and water:
-The ends of the tracheoles are filled with water. This means when
cells are anaerobically respiring, they will produce lactic acid. The
lactic acid draws in the water from the tracheole ends by osmosis.
This creates a pressure difference which helps to bring in more
oxygen through the spiracles.
OD curves and ppO2 further:
-The partial pressure at which oxygen binds to haemoglobin is
also dependent on other factors, such as the concentration of
carbon dioxide or whether the haemoglobin is fetal haemoglobin.
The Bohr effect: When cells respire they release carbon dioxide,
which dissolves in solution to form carbonic acid. This causes a
low pH to arise, changing the shape of the haemoglobin protein,
decreasing the Hb affinity for CO2.
Fetal Hb: Has a higher affinity for oxygen as it must be able to
cope with surviving at a low ppO2, so O2 moves across placenta.
Decreased affinity: OD curve shifts right.
Increased affinity: OD curve shifts left.
-You will be expected to outline a practical
measuring the breathing rate of insects.
-This practical involves gently sealing a locust in a
syringe then counting how many times its
abdomen moves.
-You then calculate spiracle activity based on how
active the abdomen is.
Haemoglobin structure/function:
-Quaternary structure of 4 polypeptide chains (2 x
alpha chains and 2 x beta chains. Forms a
globular tertiary + quaternary structure.
-Haem group contains a coordinated Fe2+ ion
using in binding oxygen and carbon dioxide.
-Hb combines with oxygen to form
oxyhaemoglobin.
-Carbon monoxide is poisonous as it binds
irreversibly with the haemoglobin.
-The way in which oxygen molecules bind is
known as positive cooperativity- the idea that by
binding more oxygen molecules, Hb undergoes a
conformational change to make the next binding
easier.
-This type of behaviour is explained in an oxygen
dissociation curve, which shows how the partial
pressure of oxygen affects the binding affinity of
oxygen to haemoglobin.
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1.4 The Heart Arteries, veins and capillaries

Arteries/Veins/Cardiac cycle
Red Blood Cells:
-No nucleus so have a large
volume inside cell for storing
oxygen.
-Biconcave shape for
maximised surface area for
exchange of gas.
-Filled with oxygen transporting
pigment Hb or haemoglobin.
Arteries: Move oxygenated blood away from the heart and to respiring tissue.
Arteries are thicker walled, with elastic structures for stretch and recoil, and blood
held under a high pressure (narrow lumen)
Veins: Move deoxygenated blood from the respiring tissue to the heart, so that the
blood can be pumped back to the lungs and be oxygenated. Veins carry blood at a
lower pressure and therefore have valves to stop backflow of blood.
Capillaries: The smallest type of blood vessel, capillaries are typically 1 cell thick and
are therefore suitable sites for exchange to occur. Their lumen is big enough to
accommodate the width of a red blood cell, but only just!

Main blood vessels in the heart:

Simplified diagram: -aorta: Main artery leaving the heart. Left ventricle powerful contraction causes high
blood pressure in aorta as blood is squeezed around the body.

-vena cava: Returns the deoxygenated blood from respiring tissues to the right
atrium.
-pulmonary artery: The only artery in the heart to contain deoxygenated blood, the
RA LA pulmonary artery carries the deoxygenated blood from respiring tissue to the lungs
RHS LHS to be oxygenated.

-pulmonary vein: Returns the oxygenated blood from the lungs to the heart into the
left atrium before a second contraction event pumps the blood through the aorta.

RV LV -coronary artery: The artery which supplies the heart myogenic muscle with oxygen
so it can respire/make ATP/contract.

The Cardiac Cycle: Tissue fluid formation:

1. The RA contains special tissue called the SA
(sinoatrial) node which releases a wave of excitation,
causing atria to contract simultaneously.
2. Pause before ventricles contract as they fill up with
blood (septum at bottom of heart cannot conduct wave
of excitation)
3. The wave of excitation passes to the AV node
(atrioventricular) which causes the impulse to move
along the purkinje fibres and eventually the bundle of
His, causing the ventricles to contract.
Diastole: The relaxation of heart tissue (i.e in cardiac
diastole, where the heart relaxes and begins filling with
blood.
Systole: The contraction of heart tissue (ventricular
systole forces blood out of the aorta)
The coronary artery: This artery runs on the outside of
the heart and supplies the myogenic heart muscle tissue
with oxygen and glucose for respiration (contraction ATP
demanding)
-A high hydrostatic pressure is generated in the capillaries
as the contraction of the ventricles occurs.
-This increased pressure squeezes components out of the
blood such as glucose, oxygen and nutrients.
-This lowers the WP of the newly formed tissue fluid, so
water moves back into the blood due to the osmotic
gradient.
-Remaining tissue fluid drains into the lymph and is carried
in the lymphatic system. The lymphatic system contains
many lymphocytes, so clears out any pathogens.
-Lymph contains less oxygen and dissolved nutrients than
tissue fluid.
Features of a circulatory system:
​Atria (thin walled with elastic tissue for stretch and
recoil) which stretch as they fill with blood.
Ventricle (thick, muscular wall for strong contraction
and high pressure)
Left AV valve is bicuspid
Left AV valve is tricuspid

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1.5 Immunity
Types of immune response/Vaccines
Primary defence system:
-Skin composed of dead cells containing an
indigestible protein keratin. The skin also
produces sebum, which lowers pH inhibiting
pathogenic growth.
-Lysozymes in tears, saliva, sweat are
antibacterial agents and can kill pathogens.
-Respiratory tract has mucus which traps
pathogens, whilst cilia waft mucus towards the
stomach, protecting gas exchange surfaces
that are important.
-Bacteria are destroyed in the stomach by the
low pH HCl (hydrochloric acid).
Antigens and recognition:
Inflammatory response:
-Histamine is released into the wound by white blood cells
(lymphoctyes), increasing vasodilation events as well as vascular
permeability.
-Vasodilation (much like the response against heat) and the area
becomes warm and red.
-Increased vascular permeability means that more tissue fluid
(containing plasma proteins and antibodies) can move into the
tissues, causing swelling.
Phagocytosis (non-specific):
-Phagocytes are examples of immune cells that destroy pathogens.
The most notable example here is the macrophage ('large eater')
-Phagocyte is attracted to pathogen by chemotaxis (pathogen gives
off chemicals, phagocyte attracted to pathogen along chemical
gradient.
-Antibodies cause opsonisation of bacteria/pathogen (fully coated)
increasing the binding efficiency between the bacteria and
phagocyte.
-Phagocyte forms psuedopodia around pathogen (extending sleeve
of cytoplasm) encasing pathogen in phagosome.
-Vesicles containing hydrolytic enzymes (lysosomes) move towards
the newly formed phagosome and fuse with it, killing the pathogen
with digestive enzymes.
-Phagocyte may become APC once this process is complete.

Antigen: Surface
protein/glycoprotein/glycolipid which
gives cellular recognition for
bacteria/viruses/cells. Stimulate
antibody production.
Antibody function:
-Antibodies are immune proteins made by plasma cells. Their
function is to attach by complementary protein interactions to their
antigen (each antibody is specific to an antigen).
-Antibodies help mark pathogens as foreign invaders by attaching to
their surface antigens.
-Antibodies are responsible for agglutination (the clumping together
of multiple pathogenic entities) to allow for rapid en masse
degradation using phagocytes.
-Antibodies are also responsible for carrying out opsonisation
(coating the pathogen fully).

Antibody structure vs function: Antibody structure:

-Variable region: Specific tertiary structure adopted in order to bind
antigen with high specificity and complementarity. Similar to enzyme Variable
active site idea. region

-Disulphide bridge: Strong bonds holding the heavy chains together.

Disulphide bridges typically arise from cysteine residues, which Light chain
contain sulphur.

-Fc region: Conserved across antibodies, the Fc region adopts a

constant tertiary structure. This allows immune cells (lymphocytes) Disulphide Bridge
to bind to the Fc region of any antibody.
Heavy chain
The Humoral Response:
-Pathogen ingested by a macrophage and antigen is displayed on
the surface (antigen presenting cell-APC).
-Th cells (T-helper) bind to antigen by complementary protein- Fc region (constant)
protein interactions and release cytokines to activate b-cells. This is
known as clonal selection.
-Rapid clonal selection and expansion (production of antibodies)
occurs to strengthen the response.
-Th cells also divide by mitosis to form clones, whilst plasma cells Vaccination:
are also formed, which produce large amounts of the specific -The word vaccine comes from the Latin
antibody. vacca, for cow. This is because the earliest
-Immunological memory is stored within memory cells, which can forms of inoculation and vaccination involved
rapidly differentiate upon 2nd encounter with disease. using cowpox to generate immunity against
smallpox.
The Cell-Mediated Response: -Vaccines contain weak or inactive forms of a
-Cell becomes an APC through viral infection/cell takeover. MHC given pathogen. When exposed to this
proteins are expressed normally, but interact with the non-self pathogen, our bodies carry out the cell
antigen. mediated and humoral response in order to
generate immunological memory.
-Specific T-lymphocyte recognises MHC abnormality and
differentiate into different types of cell.
-Cytotoxic T-cells destroy pathogens and infected cells by secreting
damaging enzymes into them (perforins + granzymes).
-Helper T-cells release cytokines to stimulate other immune t-
lymphocytes. These are destroyed by HIV.
-Memory T-cells are formed to retain immunological memory.
HIV: Human Immunodeficiency Virus
AIDS: Acquired Immunodeficiency Syndrome
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-The next time someone encounters the
antigen from the vaccine, they will be able to
rapidly generate more antibodies as well as
other immune cells to help clear the infection
faster.
-Modern vaccines e.g the Pfizer vaccine is
different in the sense that is uses the mRNA
instead of a protein component. This means
our bodies endogenously produce the spike
proteins found on the coronaviruses lipid coat.
 1.6 Biodiversity Niche: The role of an organism within its habitat or ecosystem. Species
which occupy the same niche will compete with each other for resources
Classification/Adaptations/Genetics such as food/shelter.

Keep- Kingdom Adaptations in ecosystems:

Pond- Phylum -Anatomical adaptations mean differences in the components of animals bodies.
Clean- Class -Behavioural adaptations describe differences in behaviour (such as aggression/mating calls)
Or- Order -Physiological adaptations such as differences in the way things are regulated in the body
Frogs- Family (homeostasis)
Get- Genus
Sick- Species
Impacts of agriculture: Biodiversity: The variety of
Humans typically reduce biodiversity within an area by growing different organisms. This
Simpsons index monocultured crops (one species) and using heavy pesticides and means how many
of biodiversity: herbicides. Farmland drainage leaks nitrates and phosphates into organisms in total, as well
the soil, contributing to further reductions in biodiversity. as how many individuals of
N(N-1) Humans can increase biodiversity by: each species in what kind
D= -Planting multiple crops at once instead of monocultures of distribution. A high
Σn(n-1)​​ -Use effective draining mechanisms biodiversity value will mean
-Plant trees and maintain A-shaped hedgerows a large number of different
-Reduced use of pesticides and herbicides organisms.

N = Total number of organisms Fertilisers, runoff and eutrophication:

n = Total number of organisms of each species
Further human impacts:
-Deforestation (loss of habitat)
-Hunting (risks of extinction)
-Emissions (acid rains/fuel emissions)
-Building (loss of habitat)
Variation within populations:
Crossing over during meiosis and the random
assortment of chromosomes causes variation
between individuals to arise.
Mutation (which can be random or induced by
mutagenic agents) causes random changes to
the genetic code, causing further variation.
Natural selection means advantageous alleles
will be more likely to be passed on to the
offspring thereby increasing allelic frequency.
Gene technology:
The sequence of amino acids that make up
proteins translated from specific genes can be
read, and an mRNA sequence can be derived
from it.
Eutrophication describes the long term damaging effect to
aquatic ecosystems in rivers and lakes. Farm and industrial
waste have a high nitrogen content, and so promote algal
growth on the waters surface.
Algal bloom thickens the layer of algae, so much so that light
can no longer penetrate the water beneath. As a result, aquatic
plants and algae die due to lack of available light for
photosynthesis.
This build up of organic waste promotes the growth of
decomposers, or saprobionts. These digest the organic
material, but require oxygen to aerobically do so. As a result,
the oxygen concentration of the water decreases and promotes
the death of aquatic animals such as fish and insects.
Further deoxygenation of the water promotes the activity of
anaerobic bacteria, which produce hydrogen sulphide and
methane, further worsening the water supply.
Comparing genomes and biodiversity:
Sequencing of genomes and then alignment comparison will
allow a measure of how similar two genomes are.
Comparing visible characteristics or behaviour could help
determine how similar organisms are.
Issues with comparing genomes:​
Characteristics coded for by not just one gene (may be more
than one gene)
These similar characteristics (behavioural e.g.) could have
arisen due to environmental effects.

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1.7 DNA & Protein Synthesis
Structure/Function/RNA/Transcription/Translation
DNA Structure vs Function:
Sugar-phosphate backbone negative charge, protects bases
which face inwards.
DNA is very long, can store lots of information as genes which
code for proteins.
Hydrogen bonds between bases are weak, easily broken, but
strong in large numbers. Allows transcription bubble to be
opened/DNA to be easily replicated (by DNA Helicase)
Flexible over long distances, rigid over short distances allows it to
exist as a stable, coiled structure.
Complementary base pairing is always a great phrase to use in
exam answers. Remember that the idea of complementarity is
centred around shape.
DNA Replication:
DNA Helicase unwinds the double stranded DNA by breaking
the hydrogen bonds holding complementary base pairs
together. Formation of the replication fork.
A primer (short oligonucleotide sequence complementary to 3'
end of single stranded DNA)
DNA polymerase attaches to the 3' end of the single stranded
DNA, and polymerises a new strand in the 5'3' direction.
Free-floating nucleotides present in the nucleus. On the other
strand, DNA replication is discontinuous, and therefore is
synthesised in short sections called Okazaki fragments
DNA Ligase seals the sugar phosphate backbone by forming
phosphodiester bonds between nucleotides.
Transcription (making mRNA in the nucleus):
The purpose of transcription is to copy the information held in the
DNA in the nucleus, and to move that information to the ribosome
so it can be read and translated into a protein.
RNA polymerase unwinds DNA and forms a transcription
bubble, which contains regions of single stranded DNA.
Free-floating nucleotides will bind to the exposed bases on
the strand, which acts as a template
RNA polymerase will join these nucleotides together to form a
strand of mRNA, which contains the base Uracil instead of
Thymine.
mRNA is single stranded and is therefore suitable for export
out of the nuclear pore. Here the mRNA will be localised to
the RER or cytoplasmic ribosomes.
Translation (mRNA code read and a protein is made):
The purpose of translation sees the mRNA strand created in the
transcription step being turned into a protein also known as a
polypeptide- a polymer made out of amino acids joined by peptide
bonds).
mRNA is fed into the ribosome, which reads the mRNA three
bases at a time (triplet codons).
This 'reading' is done by tRNA molecules containing a
complementary anticodon to the mRNA triplet codon.
If complementary base pairing occurs, then the amino acid
brought by the tRNA will remain and prepare to bind to the
next amino acid.
Translation is initiated by START codons and terminated by
STOP codons. These are three bases which signal the
DNA, mRNA, tRNA, rRNA:
DNA: Double-helix, deoxyribose sugar, double
stranded. Contains information in the form of
genes
mRNA: Single stranded, moves information from
nucleus to ribosome for translation. Uracil instead
of Thymine.
tRNA: Regions of single and double-stranded
RNA. Clover-leaf shape and contains an
anticodon and a binding site for an amino acid.
rRNA: Component of ribosome. rRNA and
ribosomal proteins make up the translational
machinery.
Evidence for semi-conservative replication:
E-Coli grown in heavy isotopes of nitrogen (15N)
will incorporate the isotope into their nitrogenous
bases in the DNA. After many generations, almost
all bacteria will have only 15N in their genomes.
The bacteria are then transferred to a regular 14N
medium and are allowed to grow. By doing so, the
bacteria incorporated the regular 14N into their
DNA during replication.
-By centrifuging these mixtures out, scientists
were able to see how much 15N and how much
14N were in each sample. What they found was
the amount of 15N present decreases over each
division. This hybrid amount of 15N decreases as
it makes up a smaller fraction of the DNA with
each replication.
15N band
14N becomes fainter
15N over sequential
divisions.
Export + Processing (PTM):
Proteins can be modified following translation.
They can be phosphorylated, methylated, or have
sugar residues added (such as a mannose tag).
These changes are called post translational
modifications.
Phosphorylation
Carbohydrate
added
Methylation (-CH3 added)
Mutation (see mutation 2.5 for more):
Changes made to the sequence of bases in either
DNA or RNA are termed mutation. This can have
consequences on protein folding, as the wrong
amino acid incorporated into a polypeptide chain
could cause the protein to fold completely
different. If it were an enzyme, this could threaten
the specificity of the shape of the active site.
ribosome to stop translating and dissociate from the Other consequences: Truncation (shortening) of
ribosome. protein, elongation, lack of folding altogether.
The newly formed polypeptide chain is often referred to as the
'nascent' polypeptide chain.

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1.8 Genetics
protein. These are exons (expressed).
Genetic switches/Lac operon/Inheritance
Features of the genetic code:
-Degenerate: More than one triplet codon can code
for a given amino acid. This means that, for example, a
substitution mutation could have no effect on the
amino acid sequence.
-Non-overlapping: The code is read in triplets which
are treated as separate entities.
-Universal: The fundamental rules of the genetic code
are conserved across nature.
Evolution by natural selection: Natural selection
describes how the individuals best suited to survive in
a given environment will survive and reproduce,
passing on those advantageous genes (or alleles-
better) to their offspring. As a result of this the allelic
frequency for advantageous traits increases, and
certain characteristics become more common. Over
time, this leads to larger scale changes and evolution.
Lac Operon: Understanding the vocabulary
Promoter: Where RNA pol binds to begin transcribing
a certain gene.
Operator: Where regulatory elements/transcription
factors bind to encourage or discourage transcription.
Transcription factor: A protein which binds to DNA
upstream of the promoter. It helps bind RNA pol to
begin transcription.
Repressor: A protein which binds to an operator
sequence on DNA in order to discourage transcription.
Homeobox gene: A gene that codes for a
transcription factor protein. They have key
developmental roles.
Regulatory gene: A gene which codes for a repressor
protein.
Monohybrid + dihybrid inheritance:
See GCSE inheritance for monohybrid inheritance
Dihybrid inheritance: When two different
characteristics coded for by genes on different
chromosomes are studied , and the relative ratio of the
offspring's genotypes are estimated.
RG Rg rG rg
RRGG
RG RRGg RrGG RrGg
Rg RRGg RRgg RrGg Rrgg
rG RrGG RrGg rrGG rrGg
rg RrGg Rrgg rrGg rrgg
Genes: Genes are sequences of DNA that code for a particular
Definitions:
-Allele: An alternative form of a gene.
-Dominant: One copy of the allele is required in order for
the phenotype to be expressed.
-Recessive: Two copies (homozygous) of the allele are
required for the phenotype to be expressed.
-Homozygous: Has two copies of the same allele.
-Heterozygous: Has two different alleles.
-Genotype: The combination of alleles e.g Gg
-Phenotype: The characteristic/impact of the genotype.
Lac Operon: A mechanism developed by E-Coli to allow
them from using glucose as their primary respiratory
substrate to using lactose as their primary substrate, when in
a lactose (and glucose-free) environment.
Repressor RNA Pol
X
L P O Z Y A
Transcription
L P O Z Y A
Lactose
Lac Operon: The lac operon uses repressors, and the
inhibition of those same repressors in order to switch genes
on/off. When lactose is present, it binds to the repressor and
stops the repressor binding to the operator. Therefore RNA
pol is not discouraged from binding to the promoter, and
transcription occurs. The genes coded for include lactose
hydrolysing enzymes as well as proteins which increase the
permeability of the bacterium to lactose.
Meiosis and variation:
Crossing over: Chromosomes line up and pressure
dynamics in the nucleus cause equivalent portions of each
chromosome to break off and re anneal on the other
chromosome. This means the offspring will have a
combination of alleles.
Independent segregation of chromosomes: In meiosis I,
the homologous chromosomes line up in pairs. Since only
one of the homologous chromosomes will go into the
daughter cell, i.e the division of genetic material is random
Random fertilisation of gametes: Usually only one egg is
fertilised by only one sperm. However, many millions of
sperm compete for one egg, and that egg is genetically
different each month (in the case of humans)
 Phenotype ratio: 9:3:3:1
Parents heterozygous

Sex-Linkage: Since the 23rd pair of chromosomes dictate

CoDominance: This phenomenon describes when two
phenotypes are expressed at the same time. This is
common in feather colouring/fur colour and is when
two different colours are expressed. White flowers and
pink flowers will breed to give a codominant pink flower
(one allele for red, one allele for white.
the sex of an individual, a human can either be XX (female)
or XY (male). The Y chromosome is shortened and serves
no real purpose. This means that if a male inherits a
recessive copy of an allele, it is almost 100% likely that the
phenotype will be displayed despite only one copy of the
allele being present.
XB Y

Epistasis: The interaction between genes which cause

suppression of certain genes. Recessive epistasis B B B
describes how if an individual inherits 2 copies of a XB X X X Y
recessive allele, this genotype will cause the silencing
of another gene at another locus.

Dominant epistasis ratio: 12:3:1

b B b b
X X X X Y
Recessive epistasis ratio: 9:3:4

Learn these ratios for inheritance based questions!

Questions are often asked on mice fur colouring due to
epistatic alleles causing gene silencing of primary fur
colour.
Sex linked diseases date back to the days of Rasputin,
who once claimed he healed Alexei Nikolaevich back to
health after suffering from the sex-linked disease.

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1.9 Nervous Communication
Synapse/Resting potential/Action potential/Nerve cells
Synapse: A gap between two nerve cells. An impulse (better
known as an action potential) travels across a synapse through a
chemical medium in the form of neurotransmitters such as
acetylcholine, dopamine or serotonin. There are an estimated 125
trillion synapses in the cerebral cortex alone.
The human brain structure:
Cerebrum: The largest part of the brain, the cerebrum is divided
into two hemispheres separated by a structure known as the
corpus callosum. The cerebrum is made out of different lobes. The
occipital lobe controls visual processing. The temporal lobe
controls auditory information, whilst the parietal lobe controls
movement and memory.
Cerebellum: Located underneath the cerebrum, the cerebellum is
smaller and carries out the functions of muscle movements and
balance.
Hypothalamus: Involved in thermoregulation and hormone
production from the pituitary gland.
Medulla oblongata: Controls breathing rate and heart rate (and
therefore blood pressure). It is located at the base of the brain.
Different types of neurone:
Sensory: Sensory neurones send impulses from the receptor
(which has detected the stimulus) to the relay neurones (inside
CNS)
Motor: Motor neurones deliver the impulse from relay neurones in
the CNS to effectors (which can be glands or muscles) which
contract or secrete upon stimulation.
Relay: Found in the CNS, relay neurones carry the impulse from
the end of the sensory neurone to the start of the motor neurone.
Resting potential:
Nerve cells have a negative membrane potential at resting state.
This means there are more positive ions outside the cell than
inside. How is this achieved?
The sodium-potassium pump moves 3 sodium ions out and only
2 potassium ions into the neurone.
Due to open potassium channels in the nerve cell, the
potassium ions simply diffuse back out, making the membrane
potential more negative.
The nerve cell therefore has a resting potential value of -70mV,
which is key to remember for exam specific questions.
Action potential and propagation:
When a nerve cell is activated and needs to send an impulse in a
given direction, it must first become depolarised and lose its
negative membrane potential:
The stimulus will first trigger the excitement of the neurone, which
opens its Na+ channels. Since Na+ has been moved initially out
of the cell, it floods in down its concentration gradient.
The influx of positive Na+ ions will make the membrane more
positive. Upon reaching the threshold potential of -55mV, more
Na+ channels open causing more Na+ to flood int, raising the
membrane potential to +30mV.
Nerve cell structure + function
Axon: Extensions of the cell body which conduct
impulses away from the cell body.
Cell body: The larger part of the nerve cell which
contains the nucleus and mitochondria.
Dendrites: Extensions of the cell body which
conduct impulses towards the cell body.
Mitochondria: Make ATP through aerobic
respiration.
Neurotransmitter: Chemicals released by nerve
cells to help transmit an action potential across a
synapse.
Synapse diagram:
Synaptic cleft
Presynaptic
Postsynaptic
neurone neurone
Receptor
The Synapse Dynamics (exam answer):
-AP reaches synapse and causes influx of Ca2+
into presynaptic membrane.
-Influx of Ca2+ stimulates exocytosis of vesicles
containing neurotransmitter.
-Neurotransmitter exocytosed into synapse,
where it diffuses across and binds to specific,
complementary receptors on the postsynaptic
membrane. Upon binding to the receptors (which
are channels), there is an influx of Na+ into the
post synaptic membrane, depolarising it by
decreasing its negative charge.
-A new AP starts in the postsynaptic membrane.
-Excess neurotransmitter in the synapse is
removed using enzymes in the presynaptic
membrane. For example acetylcholinesterase
breaks down acetylcholine and therefore stops
over stimulation of the postsynaptic neurone.
Factors affecting speed of transmission:
Diameter: The larger the diameter of the axon,
the faster the rate at which the impulse travels.
Temperature: The higher the temperature, the
faster the rate of impulse transmission. However,
above a certain temperature proteins such as ion
channels could denature and therefore reduce
impulse speed.
Myelination: Schwann cells deposit an
insulating material called myelin over nerve cells.
Since myelin cannot conduct electricity, the
impulse will jump from node to node in a process
known as saltatory conduction.
Summation: Temporal vs Spatial

The nerve cell repolarises itself by closing the Na+ channels,
opening K+ channels and allowing the Na-K pump to reestablish
the -70mV resting potential.
The action potential will move as a 'wave of depolarisation'
meaning that neighbouring channels will stimulate others to open.
Temporal: Temporal summation is a dynamic
whereby one single neurone stimulates its
neighbour neurone by increasing the
frequency of impulses sent across the
synapse.
In doing so, more neurotransmitter is released
into the synaptic cleft and therefore it makes it
more likely for the threshold potential to be
reached in the next neurone along.

Spatial: Spatial summation is a dynamic

whereby multiple neurones converge onto
one neurone. All of the converging neurones will
fire impulses onto the single neurone in a bid to
again try and raise its membrane potential
above the threshold value required for the
initiation of an action potential.
Myelin sheath diagram:

Saltatory Myelin sheath

conduction Schwann cell

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 2.1 Photosynthesis
LDR/LIDR/ATP/Practical
ATP: Adenosine Triphosphate
ATP ADP + Pi (Hydrolysis, energy release)
ADP + Pi ATP (Condensation)
Properties of ATP:
-Small and soluble (easily transported in cells)
-Easily hydrolysed (instantaneous release)
-Remade easily (condensation, regeneration)
-Makes molecules reactive (phosphorylation)
-Cannot pass out of the cell
ATP used in active process e.g. active transport
Made up of adenine, ribose and 3 x phosphates
6CO2 + 6H2O C6H12O6 + 6O2 (+ATP also made)
Photophosphorylation: Adding a phosphate group to a
molecule using light.
Photolysis: Using light energy to split (lyse) a given entity
e.g. H2O in the LDR.
Photoionisation: Light energy causes electrons to be raised
to high energy level + released e.g. photoexcitation of
chlorophyll in LDR.
Decarboxylation: Removal of CO2 (carboxyl group) from a
given entity
Dehydrogenation: Removal of hydrogen from a given entity.

ATP is made by:

-Respiration in animals and plants
-Photosynthesis in plants Light dependent reaction:
ATP

Light energy H+

e
as
Structure of the chloroplast

th
ADP + Pi

n
Sy
P
AT
PSII PSI
Chloroplasts are double-membrane bound
organelles found in plant cells. They are responsible E- ETC
for carrying out photosynthesis.
Chlorophyll P680 P700
Thylakoid membranes: Contain important membrane
proteins to carry out photosynthesis. H2O

H+ H+
2H+ + 0.5O2
Thylakoid membranes: Form a stack called a
granum, the plural of which is grana.

Integranal lamellae: Connect grana and provide a

larger surface area for increased capture of light. Light dependent reaction explained:

Chlorophyll: Small photosynthetic pigment which
reflects green parts of the spectrum. Respond to
light energy by releasing electrons.
Stroma: Aqueous medium which contains sugars,
enzymes and some (organic) acids.
Photosystems: Protein machinery which couple light
energy to the generation of an electrochemical
gradient.
Cyclic photophosphorylation uses PSI only.
No NADPH or O2 is produced, only small
amounts of ATP (ATP synthase)
-Light energy absorbed by PSII, causing a pair of electrons to
become excited and move to a higher energy level, being
released.
-Electrons move to the ETC (electron transport chain) where
the movement of electrons drives H+ pumping into the
thylakoid lumen.
-Electrons move to PSI, where they are passed to NADP to
form reduced NADP (NADPH).
-H+ building up in lumen generates an electrochemical
gradient (H+ gradient/proton gradient)
-H+ move down electrochemical gradient through ATP
synthase, which couples proton movement to ATP synthesis
(ADP + Pi = ATP)
-The photolysis of water replaces the electrons lost from the
photoexcitation step.

Light independent reaction explained: The Calvin cycle:

Carbon dioxide
1. Carbon fixation- CO2 diffuses in through the stomata and joins RuBP
(5 carbon compound). Catalysed by RuBisCo (enzyme). RuBisCo

2. 6C product is unstable and breaks down to form two 3C products

known as G3P (Glycerate-3-phosphate)
RuBP
3. G3P reduced to Triose Phosphate (TP) using 1xATP and 1xNADPH 2 x G3P
(from LDR). Note: This is per G3P molecule.
2 x ATP
4. Most TP is recycled to form RuBP, with some TP molecules going on
to form organic compounds for the plant.
5. Regenerating RuBP requires ATP (LDR) 2 x ADP + Pi

ADP + Pi 2 x NADPH

ATP
TP

*The calcin cycle needs six turns to make one hexose sugar. This is
because 6x(2xTP, where each TP has 3C). Total carbon = 36C
6xRuBP regenerated (30C demand) leaving 6C for hexose.
Limiting factors for photosynthesis:
-Light: Plants absorb specific wavelengths of light. They reflect green
light and so appear green (absorb red and blue)
-Temperature: Temperature affects kinetic energy of particles, stomata
opening as well as enzyme action. If temperature is too high, enzyme
active sites denature and lose complementarity to substrate (less ES-
complexes formed). If temperature is too high, stomata close (water
retention, less CO2 enters)
-Carbon dioxide: CO2 makes up a very small percentage of gas in the
air. Increasing this concentration will increase the rate of
photosynthesis, up to a point where stomata close (4%).
Investigating dehydrogenase activity in chloroplasts
-Cut and grind up leaves using pestle and mortar. Make sure this is
done under ice (reduce enzyme activity).
-The isolation buffer should also contain sucrose, KCl and pH7
phosphate buffer.
-Transfer to centrifuge tubes and spin at high speed for 10 minutes.
Chloroplasts form pellet, discard supernatant.
-Resuspend pellets in chilled isolation buffer and store on ice.
-Set up colorimeter using red filter and zero using cuvette with distilled
water.
-Set up test tube rack and switch on light.
-Add volume of chloroplast extract and volume of DCPIP and mix.
-Immediately transfer small amount into cuvette and record reading of
absorbance on the colorimeter.
*If dehydrogenase activity present, absorbance will decrease because
DCPIP is reduced and the blue colour of the solution is lost. Plot
absorbance against time for different variables (light intensity,
temperature, distance from the lamp etc). The greater the decrease of
absorption, the higher the dehydrogenase activity.
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ATP
2 x NADP
Thin Liquid Chromatography (TLC)
-Grind up leaves from plant and add anhydrous
sodium sulphate, then a few drops of
pronanone.
-Transfer to test tube, add ether (petroleum)
then extract top layer (pigments). Transfer to
second test tube and add a few more drops of
ether.
-Draw line in pencil at bottom of TLC plate,
create spots by adding small concentrated
drops (point of origin) to the plate and ensuring
they dry.
-Place plate into glass with a prepared solvent,
place lip on top and allow time to develop.
-When solvent has nearly reached the top,
remove the plate from the glass and mark the
distance travelled by the solvent.
-Observe spots and calculate Rf values for
each spot using the equation distance travelled
by spot/distance travelled by solvent.
Practical knowledge:
Colorimeter: Measures how much light is
absorbed by a solution when light is passed
through it.
TLC: Allows determination of what pigments
are present in the leaves
*Thin liquid chromatography involves a
mobile phase (molecules can move- liquid
solvent) and a stationary phase (molecules
cannot move)
2.2 Respiration C6H12O6 + 6O2 6CO2 + 6H2O (+ATP also made)

Glycolysis/Link/Krebs/anaerobic/practical
Mitochondria
ATP: Adenosine Triphosphate Structure and function:
ATP ADP + Pi (Hydrolysis, energy release) Mitochondria are double-membrane bound organelles
ADP + Pi ATP (Condensation) responsible for carrying out respiration. They share similarities
to bacteria in shape and structure, and also have their own
Properties of ATP: DNA.
-Small and soluble (easily transported in cells)
-Easily hydrolysed (instantaneous release) Matrix: The aqueous medium inside a mitochondrion. This is
-Remade easily (condensation, regeneration) where the electrochemical gradient is established to drive ATP
-Makes molecules reactive (phosphorylation) synthesis.
-Cannot pass out of the cell
Cristae: Folds in the inner membrane of the mitochondrion.
ATP used in active process e.g. active transport This helps the inner membrane to have a large surface area, for
Made up of adenine, ribose and 3 x phosphates an increased amount of reactions to occur on (chemiosmosis)
ATP is made by:
-Respiration in animals and plants
-Photosynthesis in plants Glucose 6C
Glycolysis: ATP
Glycolysis overview: ADP + Pi
Glycolysis splits glucose into smaller molecules of Glucose phosphate 6C
pyruvate and occurs in the cytoplasm of cells. It is ATP
split into two stages:
ADP + Pi
Phosphorylation: Hexose bisphosphate 6C
-Glucose is phosphorylated using a phosphate taken
from an ATP molecule.
-Another phosphate is added making hexose
bisphosphate. 2NAD 2 x Triose phosphate 3C
-Hexose phosphate is then split to form two
molecules of triose phosphate. 4 x ATP
4 x ADP + Pi
Oxidation: 2NADH 3C
2 x Pyruvate
-Triose phosphate(s) oxidised to pyruvate(s),
regenerating 4 x ATP per glucose, as well as 2
molecules of reduced NAD.
Anaerobic respiration:
*Net gain of 2 x ATP, 2 x NADH and 2 x pyruvate -Pyruvate in glycolysis converted to lactate (animals) or
ethanol (plants) using reduced NAD.
-Regeneration of NAD allows glycolysis to continue and
Link reaction explained: therefore making ATP
-Pyruvate decarboxylated then oxidised by -Lactate turns to lactic acid which causes muscle fatigue.
NAD. It is overcome by repaying oxygen debt.
-This forms acetate, which then combines with
coenzyme A to form acetyl-CoA.
-No ATP produced Krebs cycle explained:
The purpose of the Krebs cycle is to use the acetyl CoA
Link: Pyruvate 3C (formed from the link reaction), a 4C compound and a
NAD
NB: Each glucose
molecule produces
series of redox reactions to release ATP and reduced
2 molecules of CO2 coenzymes (NADH, FADH2 for oxidative
pyruvate.
phosphorylation). This occurs in the matrix.
NADH Acetate 2C Combination + dissociation:
-Acetyl CoA combines with oxaloacetate (4C) to form a
6C citrate compound. CoA leaves here and is returned to
Coenzyme A the link reaction.
Acetyl-CoA 2C Decarboxylation + Dehydrogenation:
-A primary decarboxylation event shortens the 6C to a 5C
compound. Here another NAD is reduced to NADH.
-This reduction is driven by dehydrogenation.
-A secondary decarboxylation event shortens the 5C to
Anaerobic respiration: the 4C oxaloacetate initially used (regeneration).
Decarboxylation: Where a carboxyl (CO2) group -Here another 2 NAD are reduced to NADH, and a FAD
is removed from a compound. is reduced to FADH2. ATP is also made via condensation
Dehydrogenation: Removal of hydrogen of ADP + Pi
Oxidation: Where a species loses electrons
Reduction: Where a species gains electrons
Substrate-level phosphorylation: Where a
phosphate group is transferred from an
intermediate compound to a species.
-The reduction of NAD and FAD involves another
dehydrogenation step.
-ATP production is driven by a phosphate transfer from
one of the intermediates. This is known as substrate level
phosphorylation.

Oxidative phosphorylation: Krebs cycle diagram:

The purpose of oxidative phosphorylation is to ​
use the energy carried by the electrons in CoA
NADH and FADH2 to generate ATP through a
condensation reaction. It occurs across the Acetyl-CoA NAD
Citrate (6C)
inner mitochondrial membrane (double-
membrane bound). NADH
NADH
-Various protein complexes span the IMM. CO2
-Reduced NAD and FAD are oxidised at one of NAD
these protein complexes. This oxidation Oxaloacetate (4C)
releases electrons and hydrogen ions 5C Compound
(H+/protons).
-The electrons move down an ETC (electron FADH2 NAD
transport chain) across the protein complexes. NADH
-The movement of electrons is coupled to the FAD
pumping of H+ ions into the inter-membrane
space, building an electrochemical gradient (H+
ATP ADP + Pi CO2
gradient)
-H+ ions move back down their electrochemical
gradient through ATP synthase, which combines
Pi to ADP through rotary motion, forming ATP. H+
-Oxygen acts as the terminal electron acceptor H+ H+
H+ H+
in the ETC. It combines with H+ ions and
electrons to form water (H2O).
-This process is known as chemiosmosis. 1 2 3 ADP + Pi
NAD
H2O ATP
NADH ATP Synthase

H+ 0.5O2

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2.3 Transport in Plants
Transpiration/Translocation/RHC
Guard cells control stomatal opening:
Each stoma (singular of stomata) is made up of two
kidney bean shaped cells called guard cells, which
respond to differences in water. Guard cells must
control gas exchange through these stomata
(oxygen, carbon dioxide, water vapour).
Plant has high water concentration:
Water moves into the guard cells by osmosis. This
causes them to swell and become turgid. This
turgid conformation opens up the stoma. And
encourages gas exchange.
Plant has low water concentration:
Water moves out of guard cells by osmosis and
cells become flaccid. This closes the stoma,
reducing gas exchange.
Stomata are found almost exclusively on the lower
epidermis, apart from in hydrophytes, which have
stomata on the upper epidermis.
Driving Transpiration:
Low pressure at stomata: Evaporation of water
molecules from the stomata lowers the pressure.
This causes water to be drawn up the xylem due to
a pressure gradient.
High pressure at roots: Active loading of roots with
inorganic ions and nutrients lowers the RHC water
potential. Water moves into the roots via osmosis,
increasing the pressure exerted by water at the
roots.
Cohesion-tension theory: Numerous hydrogen
bonds form between water molecules (cohesion) as
well as between the water molecules and xylem
wall (adhesion). The water moving through the
xylem of a plant is usually described as an
'unbroken column held under tension'
Driving Translocation:
Low WP at source: Loading of sugars into the
phloem at the source side will lower the water
potential of the phloem due to the presence of
sugars. This causes water to move from the xylem
to the phloem by osmosis.
High WP at roots: After the sugars move out into
the respiring tissue (such as RHC), the water
potential in the phloem increases, so water moves
back into xylem by osmosis.
Xylem cell structure:
[
-Xylem cells are dead, hollow cells joined
[ end-to-end.
-They are hollow (have no cytoplasm)
-They are lignified (a protein which
supports the plant structurally as well as
[
acting as a waterproofing layer.
[ Formation:
-Top and bottom cell wall and membrane
break down
Structure of the leaf:
-The waxy cuticle covers the upper epidermis and protects the
uppder epidermis. It is water resistant and contains a polymer
called cutin, as well as suberin.
-The palisade mesophyll in the upper epidermis is composed of
palisade cells, which have a high SA:vol ratio and a large number
of chloroplasts for efficient photosynthesis. It is on the upper side
of the leaf, and is the main site of photosynthesis.
-The spongy mesophyll contains air spaces to encourage gas
exchange through diffusion.
Waxy cuticle
UE
Palisade cell
Spongy
Mesophyll
Stoma
LE
Phloem loading:
Phloem loading describes how sugars produced through
photosynthesis are moved from the photosynthesising cell into
the phloem. This involves co transport mechanisms and the use
of pH gradients, as well as the presence of a companion cell.
-Sucrose produced by the source cell during photosynthesis
(sucrose = glucose + fructose).
-H+ ions actively transported out of companion cell, increasing its
pH and establishing a proton gradient.
-H+ ions then move down concentration gradient into companion
cell from source cell. This movement includes the co transport of
sucrose from the source to the companion cell.
-From here the sucrose can move by facilitated diffusion through
plasmodesmata into the phloem.
H+
H+
X P Source Cell
H+ H+
Suc Suc
Companion
Cell
Water moving in the root:
Apoplast pathway:
Water moves through cells in the root through the
spaces in the cell walls filled with cellulose. Since
water is not passing through the plasma
membrane, the water can carry dissolved metal
ions/mineral ions/salts.
Symplast pathway:
Water moves through the cytoplasm of cells joined
to one another through plasmodesmata. This
 -Nucleus, organelles and cytoplasm leak
out
-Cell is lignified in rings of lignin
Evidence for mass flow: Ringing experiments
This experiment describes a section of bark being taken
from a tree, all the way round. This bark contains the
xylem and the phloem, so by removing it the scientists
are removing that which they believe is responsible for
mass transport. Cells above the cut will swell as sucrose
accumulates in them (and water) whilst cells below the
cut will die owing to the fact that they will not be able to
receive the sugars for respiration.
method of water movement cannot carry any
additional ions
Evidence for mass flow: Radiolabelled 14C
This experiment describes a plant being grown in a
radioactive isotope of 12C, 14C. This can be in the form of
radiolabelled CO2, which the plant will take up and
assimilate in photosynthesis. Exposure of a cross section of
the plant will show radioactivity in a dark form. This
technique is known as autoradiography and is widely used
in tracing experiments.

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 2.4 Ecosystems + Ecology
Definitions/Competition/Sampling/Conservation/Succession
Definitions:
Habitat: Place where an organism lives e.g. field
Population: All of the organisms of one species in a habitat living
together at the same time.
Community: Populations of different species in a habitat living at the
same time.
Ecosystem: A community plus all the non-living factors (abiotic) in the
area in which it resides.
Abiotic: Non-living factors e.g. temperature/pH/light intensity/wind
speed.
Biotic: Living factors e.g. predation/competition/food availability.
Niche: The role of an organism within its habitat (where it goes/what it
eats).
Species: Individuals with similar characteristics which can breed
successfully to produce fertile offspring.
NPP: Net Primary Production (NPP) which is the energy available
from producers after respiratory losses have been taken into account.
Random sampling:
-Grid out an area of habitat e.g. field/woodland and map out the grid
into a series of coordinates.
-Use a random number generator to generate sets of coordinates.
-Place quadrat at coordinate corner and measure number of
individuals or percentage cover of quadrat.
-Use a large sample size (number of samples) to make results more
representative, as well as calculate a mean.
-Repeat the process multiple times, reducing the likelihood of the
results arising due to chance.
-Number of individuals for the whole area/habitat calculated by
multiplying quadrat mean with size of the area.
Biotic factors: Competition
Intraspecfic competition:
This describes the competition between
individuals of the same species for resources
(light/food etc)
Those individuals better adapted to compete
for the resources will survive and reproduce
and out compete others.
Interspecific competition:
This describes the competition between
individuals of different species for certain
resources. This usually means there are less
resources to share between the two species,
so one may out compete the other. This would
cause the number of individuals of each
species to change.
Predator-prey population relationship:
As the population size of the prey increases,
there is more food available for the predator
population. This means the predator
population is more able to survive and
reproduce, and therefore predator population
numbers rise.
The increased population of predators means
that more prey is eaten. It also means there is
typically more intraspecific and interspecific
competition between predators. This makes it
less likely for the predators to survive and
reproduce and therefore predator population
decreases. Predator and prey populations are
therefore in a dynamic state of flux.
Distribution along a line:
-Taking samples using quadrats along a tape
measure is known as a belt transect. Leaving
intervals between samples is a method of
systematic sampling.
-The disadvantage of this is that some areas
are not sampled (missed).

Mark-release-recapture technique: MRR Assumptions:

-Capture number of organisms using an
appropriate technique.
-Mark the individuals with a tag that won't be
lost and is non-toxic to the organism.
-Release them back into their habitat and
allow a sufficient time for them to mix to give
rise to a uniform distribution.
-Capture second sample of organisms and
count how many of the second capture are
marked individuals from the first capture.
-Estimate total population size using:
Number caught 1st x Number caught 2nd
Number marked in the 2nd sample
-Marking has no effect on organism (physiologically or socially)
-Enough time has been given for organisms to mix.
-No births/deaths/migration events (no change in pop. size)
Succession explained:
-Pioneer species (e.g. moss) colonise new surface where abiotic
factors may be harsh. Pioneer species adapted to harsh abiotic
factors.
-Pioneer species change abiotic factors and make them less hostile
(decomposition/soil formation)
-New species with different adaptations can grow on surface. These
also die and are broken down, making the abiotic factors less hostile
again. Water retention begins to increase.
-Some species change the habitat and its abiotic factors to make it
less suitable for other species to survive (competition).

Quadrat or MRR?: The importance of conservation:

-Quadrats and transects are used for non-motile organisms such as -Without conservation there is an impact on
plants or slow moving insects, for example. food chains.
-Mark-release-recapture is used for motile organisms e.g. deer. This is -Animals have a 'right to exist'
because they move around too much to try and estimate population -Aesthetic reasonings (pretty
size through using quadrats. flowers/landscapes)
-Also due to size! Quadrats used for smaller organisms. -Economic reasonings (attraction of tourism
etc)
Understanding biodiversity: Advantage of conserving seeds:
-Range of alleles (in a given area at a given time) -Small (easy to store).
-Variety of alleles (in a given area at a given time) -Collected with minimal damage to seed and
-Variety of ecosystems and habitats (at the same time) environment.
-Last a long time (viability).
*More species = More diversity -Can store an increased diversity of seeds (as
*More habitats = More diversity there are more seeds).

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2.5 Mutation
Mutagens/Mutations/Impact of mutation
Code:
AAAT C G C G ATA C T G
Mutations:
AAAT C G G ATA C T G
AAAT C C G C G ATA C T G
AAAT G G C G ATA C T G
AAA G C T C G ATA C T G
Mutants: Each of the above four codes
represent a mutation to the original code.
Try and identify which is which.
Impact of mutation (protein folding/cancer):
Mutation can cause many different
consequences, or often none at all.
-It must first be noted that mutation can affect
how a protein folds and is translated- remember
that the primary sequence (the sequence of AA)
determines the secondary and tertiary structure
of a protein. Even single changes made to this
sequence can cause mis functional proteins
(enzymes, receptors) to be coded for.
-It must also be recognised that mutation can
have no effect on the synthesis of the protein
(the idea that the same/a similar AA is coded for
by the mutation) and therefore mutation can
often have no effect at all.
-Mutations in genes which control cell division
and growth can lead to cancer- the idea that
mutations to genes controlling cell division will
cause uncontrollable cell division to occur-
cancer.
Coronavirus Mutations: E484K
The Kent variant shows a mutation at amino
acid number 484. At the position, an EK
substitution mutation has occurred, meaning
that glutamic acid has been mutated to lysine.
E (glutamic acid) = negative charge
K (lysine) = positive charge
This change in charge in the spike domain of
the virus may be responsible for increased
transmissibility.
Substitution Mutation: A base in the code is simply swapped for a
different base. For example A-G would be a substitution mutation.
This can be silent or non-silent, as the resulting mutation can cause
a different AA to be coded for by the triplet codon, or the same AA.
This is because of the degenerate nature of the genetic code.
Code: A A A T G G C G A T A C T G
Deletion Mutation: A base in the code is removed altogether. This
can be highly influential on the resulting polypeptide. Deletion
causes frameshift to occur (the whole code's reading frame is
displaced by 1) and therefore any triplet codon following the deletion
mutation can be altered. This can cause improper protein folding,
early STOP codons (truncation) or a completely different protein
altogether.
Code: A A A T C G G A T A C T G
Addition Mutation: A base in the code is added. This can be highly
influential on the resulting polypeptide. Addition also causes
frameshift to occur (the whole code's reading frame is displaced by
1) and therefore any triplet codon following the addition mutation
can be altered. This can cause improper protein folding, early STOP
codons (truncation) or a completely different protein altogether to be
coded for.
Code: A A A T C C G C G A T A C T G
Inversion Mutation: A region of the base code is inverted. For
example, a triplet codon reading AUG (START) could be mutated to
GUA. This can cause a single amino acid to be changed, leading to
a discrepancy of 1 with regard to the correct sequence of amino
acids. This, much like the substitution mutation, can be silent or non-
silent.
Code: A A A G C T C G A T A C T G
Causes of mutation & mutagenic agents:
-Exposure to UV radiation can cause mutations to arise, sometimes
through the fusion of bases or damage to bases.
-Benzopyrenes are mutagenic agents (chemicals which induce
mutation) found in cigarette smoke. These chemicals intercalate in
between DNA bases and distort the DNA, mutating it as it does so.
-Damage to cells can even cause mutation. Cancer cells typically
respond in a similar way to wounded cells, secreting signals which
stimulate the growth of blood vessels into the tumour
(angiogenesis). This supplies the cancer with its own private supply
of oxygen and glucose for the high metabolic demand cancer cells
have.
-Cancers arise due to mutations in genes controlling cell division and
growth.
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2.6 Genomes & Biotechnology
Genetic engineering/Sequencing/Cloning/Biotechnology
Definitions:
Restriction endonuclease: An enzyme which recognises a
palindromic sequence of DNA. It cuts DNA leaving sticky-ends or
blunt-ends.
Recombinant DNA: DNA from two or more different organisms
Oligonucleotide: Short sequence of nucleotides complementary to a
specific sequence of DNA.
Sequencing: Mapping out the entire genome, or the section of a
genome of a particular organism. This can be achieved in many
different ways such as Sanger sequencing/Illumina sequencing and
modern day mini-Ion sequencing.
Binary fission: The way in which bacteria asexually reproduce to
make 2 new bacteria.
Sticky end: A region of ssDNA on the end of a region of dsDNA. This
can also be viewed as an overhang.
In-vivo gene cloning + recombinant DNA Technology:
Cloning a gene in vivo can be difficult to understand. First grasp that
cloning in vitro is PCR (see below). This is using a dividing organism in
order to amplify a gene/protein product.
Plasmids from bacteria are cut using a restriction endonuclease,
which cuts the plasmid leaving sticky end overhangs.
The same RE are used to excise the desired gene. Since the
same RE is used, it cuts out the gene with complementary sticky
ends to the plasmid.
The gene is then ligated into the plasmid using DNA ligase, which
seals the nucleotides together with phosphodiester bonds.
Ca2+ shock and electrical shock stimulate the bacteria to take up
the plasmid and divide by binary fission, increasing the amount of
the gene as well as synthesising the protein product.
Identifying successful candidates:
By inserting the desired gene into a pre-existing gene that the bacteria
has for antibiotic resistance, you can see which bacteria have taken up
the gene as they will die (if the desired gene inserted into antibiotic
resistance gene). Pressure plating can be used to transfer colonies
and grow the sample.
PCR:
-DNA is heated to 95 degrees Celsius, double strand melts to form two
single strands.
-Mixture cooled to 60 degrees Celsius to allow primers to anneal.
-Mixture heated to 72 degrees Celsius to allow Taq polymerase to
synthesise two new strands.
-Cycle repeats
This occurs in a thermocycler- a machine specifically designed to
cycle these temperatures. It contains the primer mixture, free floating
nucleotides and Taq pol.
RT-PCR:
Reverse Transcriptase Polymerase Chain Reaction allows a
complementary strand of DNA to be made from RNA. This single
stranded DNA template of the RNA can then be made into a double-
helix using DNA polymerase. In this way it allows for the synthesis of
working double-stranded genes.
Reverse Transcriptase:
Reverse transcriptase is an enzyme that
synthesises a complementary strand of DNA
from a single strand of RNA. It is therefore the
reverse of transcription because we make
DNA from RNA, not RNA from DNA. Viruses
have RT so that they can synthesise a DNA
strand once they have deposited their RNA
genome into the host cell. By making DNA and
then integrating it into the host genome using
an integrase enzyme, the virus goes
undetected and starts to use the host cell as a
protein factory.
Gene markers/probes:
These are short oligonucleotide sequences
which bind by complementary base pairing to
single stranded DNA. Picture a specific known
mutated sequence ACCG.
A C C G
T G G C
Probe
Probe:
This single stranded sequence is
combined with fluorescent labelling for
visualisation of the mutated gene being
present.
The probe is made by taking a double
stranded DNA sample of the mutated
sequence and then melting it (breaking
hydrogen bonds between base pairs
across double-helix.
Genetic fingerprinting: The non-coding
regions (introns) of DNA can often be
misunderstood. Whilst on the surface it may
appear that non-coding regions of DNA are
'junk', when looked at closely, it has been
noted that satellite regions of DNA express
VNTRs (variable number tandem repeats),
where discrete sequences of DNA are
repeated. Since each individual has their own
unique VNTR profile, by screening people for
these genetic markers of individuality genetic
fingerprinting has applications in crime and
paternity testing.
Gel Electrophoresis separates DNA
fragments based on size using electricity.
First, the sample is digested using many
different restriction endonucleases. This
leaves DNA in small fragments. When run on
a GE plate, each person will have unique
bands correlating to their DNA makeup. Small
fragments move quicker towards the positive
terminal, whilst large fragments migrate
slowly.
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 2.7 Homeostasis
Glucose/Water/Temperature/Nephron
Homeostasis is the constant maintenance of an
internal environment through regulatory
processes.
Glucose regulation:
-If the glucose concentration in the blood is too high, it will lower the
water potential of the blood and cause water to move into the blood
from surrounding cells by osmosis, causing the cells to crenate and
die.
-If the blood glucose level is too low, there will not be enough
glucose available as a respiratory substrate, so little/no ATP will be
able to be formed through respiration.

Positive feedback: Temperature and pH regulation:

Where a change made to the equilibrium causes
an amplification of that same change.
Negative feedback:
Where a change made to the equilibrium causes
a restoration to the same equilibrium, working
against the effect of the change.
-High temperatures and high/low pH can cause important enzymes
to denature and lose enzyme-substrate complementarity. This
means no ES complexes can form and metabolic reactions lose
efficiency.
-Low temperatures mean there is often not enough kinetic energy
for successful frequent collisions between particles, and therefore
reducing metabolic activity again.

Alpha cells: Glucagon:

Alpha cells secrete glucagon, which inhibits the
action of B-cells in the pancreas.
Beta-Cells:
Secrete insulin, which inhibits the action of
alpha cells in the pancreas. B-cells are found in
small clusters known as islets of Langerhans.
In low blood sugar concentrations, alpha cells are activated and
secrete a hormone called glucagon. This stimulates glycogen
stored in cells to be broken down to release glucose into the blood
(for respiration). This process is known as glycogenolysis.
Insulin:
In high blood sugar concentrations, beta cells are activated and
secrete a protein called insulin. This causes glucose transporters to
fuse with cell surface membranes (in the liver/gut/fat) and therefore
causes glucose to be taken into cells from the blood. Once taken
in, the glucose monomers are polymerised to form glycogen. This is
known as glycogenesis.

Gluconeogenesis describes the synthesis of glucose from

derivatives such as amino acids or lipids.

Alpha (blue) and Beta (Black) cell clustering
in the pancreas.
B-Cell activation:
-High [glucose] in blood means B-cells respire more (producing
more ATP by oxidative phosphorylation)
-ATP produced binds to ATP-gated K+ channels in membrane,
which close upon binding, building membrane potential.
-Membrane resting potential initially -70mV as net K+ out. When
depolarisation occur, membrane becomes more positive (K+ efflux
reduced, Ca2+ influx)
-This depolarisation opens voltage-gated Ca2+ channels. When an
influx of calcium occurs, vesicles containing insulin are exocytosed
to the cell membrane and move insulin into the blood.

Insulin mechanism of action:

-Insulin is carried in the blood and binds to receptors on cells. Upon binding, it activates adenylate cyclase, which
catalyses the formation of cyclic AMP (cAMP) from ATP.
-cAMP can act as a secondary messenger (activating protein kinase A), but the main output from cAMP action is
exocytosis of vesicles containing GLUT transporters to the membrane.
-Increased presence of GLUT transporters at membrane = more glucose absorbed by cells (more glycogenesis)
Ultrafiltration in the Bowman's capsule:
-High pressure generated by pumping of heart and
difference in size between afferent and efferent arteriole.
Efferent is narrower.
-Pressure squeezes small molecules through
fenestrations in glomerulus (network of capillaries).
-Podocytes and basement membrane act as filtration
and rescue mechanisms for incorrect substances
passing out of the blood.
-What is left in the efferent arteriole is red blood cells,
white blood cells and plasma proteins)
-Glucose, water, ions, sugars, amino acids and vitamins
are passed through into the nephron.
Afferent Efferent
Glomerulus
Bowman's
capsule
H2O/Ions/Glucose/AA
Thermoregulation:
Thermoregulation is important because maintaining heat
energy allows sufficient energy for frequent successful
collisions between particles.
Temperature too high: Active sites of enzymes denature.
Complementarity to substrate lost. Decrease in ROR of
important enzymatic reactions.
Temperature too low: Not enough KE for frequent
successful collisions, so ROR decreases due to lack of
energy.
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(such
as in endoderms) around a narrow range.
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Coordination and regulation:
These processes are brought about by the
thermoregulatory centre in the brain. It has
thermoreceptors to detect changes in temperature of the
blood, and elicits an appropriate response. Sensory
receptors in the skin also send signals to the
thermoregulatory centre.
Humans maintain a body temperature of 37.5 degrees
Celsius in this way.
Reabsorption of water in the nephron:
-PCT (proximal convoluted tubule) permeable to
AA/vitamins, H2O, sugars, so all of these reabsorbed here.
-Ascending limb impermeable to water, but actively
transports Na+/Cl- ions out of nephron into medulla,
lowering WP of surrounding tissue.
-Descending limb permeable to water. Lowered WP of
medullary tissue generates gradient, water reabsorbed by
osmosis.
-The loop of Henle is incredibly concentrated, and the ion
gradient present means Na+ and Cl- diffuse passively out of
loop.
-DCT (distal convoluted tubule) where fine tuning of water
potential occurs again through the gradient setup by ion
pumping.
-ADH influences water reabsorption in the collecting duct,
where water is absorbed through channels in cell
membranes known as aquaporins, which are highly
permeable to water.
ADH Mechanism of action:
ADH (anti-diuretic hormone) binds to cells on the collecting
duct, causing their intracellular cAMP to increase. This
cAMP stimulates the exocytosis of vesicles containing
aquaporins to migrate to the collecting duct membrane,
increasing its permeability to water. Coffee is an example of
a diuretic.
Responses to heat:
Sweating: Water has a high specific heat capacity,
therefore sweating removes a lot of heat energy and
therefore acts as a cooling mechanism.
Hairs life flat: No warm layer of air trapped, so more heat
radiated from blood through skin.
Vasodilation: Widening of blood vessels/capillaries closer
to skin surface, increases radiation of heat from blood
through skin.
Responses to cold:
Shivering: Increases mean KE of particles, brings up
average energy through movement.
Hairs stand on end: Warm layer of air trapped, so less
heat radiated from blood through skin.
Vasoconstriction: Constriction of blood vessels/capillaries
close to skin surface, decreases radiation of heat from
blood through skin and blood flow.
2.8 Genetics
Inheritance/Epistasis/Patterns
Definitions:
Epistasis: Where the expression of one allele
blocks the expression of another allele.
Stem cell: A cell which is capable of differentiation
and self-renewal.
DNA profiling: Technique used to identify
individuals based on what their DNA looks like.
Mutations and causes: Mutations (see A2 Mutations) are
characterised by a change to the genetic code. Mutations can
arise randomly due to transcription/replication errors, or can be
induced through mutagenic agents, or mutagens such as
benzopyrene (cigarette smoke) and UV light (the sun).
Mutations can be silent or non-silent, depending on where the
mutation happens and what type of mutation it is (addition,
deletion,inversion,translocation).
Remember that mutations can occur in introns (non-coding
regions) and therefore have no large effect on the phenotype.
Mutations can also give rise to the same amino acid that the
triplet codon would have originally coded for- owing to the
degenerate nature of the code.

Probe: A short sequence of nucleotides
complementary to a specific sequence.
Human genome project: A project which has
successfully mapped out the entire human genome,
allowing us to track evolution and screen for
diseases.
Proteome: All the proteins that a genome can code
for (exons)
Stem cells: Stem cells are special cells which can
differentiate (turn into) almost any other type of cell. Stem cells
can be adult stem cells (found in the bone marrow) or
embryonic (taken from an embryo) stem cells. Embryonic
stem cells can differentiate into a wider array of cells
(totipotent) compared to adult stem cells (pluripotent).
However, taking stem cells from embryos has ethical
implications (playing god/destroying life/potential for life).
Stem cells are self-renewing (they make more copies of
themselves).

iPS: Induced pluripotent stem cells, which are made

out of unipotent stem cells.
Transcriptional and Translational regulation: Epigenetic
changes
Transcriptional and Translational regulation:
DNA methylation: The process whereby -CH3 (methyl) groups
Oestrogen and siRNA
are added to DNA, which typically inhibits transcription. Only
-Oestrogen is lipid soluble and therefore can
cytosine bases can be methylated. The methyl group makes it
diffuse into cells through the plasma membrane.
difficult for RNA pol to access the gene and begin transcription.
-Once inside a cell, oestrogen binds to a receptor
site on a transcription factor.
Histone acetylation: DNA associates with proteins called
-Binding to the transcription factor changes the
histones so that it can super coil and form very dense structures
shape of the TF so that it is now complementary to
containing lots of information. Histone proteins have a positive
DNA.
charge, which is how they bind negatively charged DNA tightly.
-TF binds, transcription initiated by RNA pol
However, acetylation of histones decreases this positive charge,
causing them to hold DNA in a looser configuration and therefore
-siRNA stands for small interfering RNA. siRNA is
facilitate RNA pol action for transcription.
single stranded and is complementary to a region of
mRNA.
-When it localises to the mRNA, it forms
complementary base pairs with the exposed bases
on mRNA and therefore generates a short section
of dsRNA. It is important to note that these epigenetic changes (turning
-The double-stranded region is recognised as a genes on/off etc) are highly regulated and in a constant state of
termination for transcription, so the gene is chopped flux to help keep cell division happening but not at an
up by enzymes. uncontrollable rate.

Genes and cancer: Control of expression & Cancer survival Normal cell abnormally
methylated at tumour
Oncogenes/Proto-oncogenes: suppressor genes
Proto-oncogenes are genes which produce proteins which are used to
stimulate cell division. Mutations in these useful genes turns them to
oncogenes, which stimulate uncontrollable cell division. They do so by
activating receptors on the cell surface or by producing large amounts of
growth factors.

Tumour supressor genes:

These genes, as advertised, stop tumours from forming. They do so by
causing cells to stop dividing (either by exiting the cell cycle or by Cell begins to divide
programmed death-apoptosis) If these genes become uncontrollably
mutated/abnormally methylated, cancer can arise.

Benign vs Malignant
Tumours can fall under one of two categories depending on their severity.
Benign tumours do not proliferate in an invasive manner, do not
metastasise, whereas malignant tumours grow quickly and spread.
Malignant tumours are more serious and require chemotherapy or
surgical removal of the tumour.
Cancer survival:
Cancer cells have clever mechanisms of staying alive. They give off
chemical signals that wounded cells do (VEGF) which stimulates our
bodies to grow new blood vessels into the tumour. This is known as
angiogenesis, and supplies the tumour tissue with the sugar and oxygen
that the cancer demands for continued cell growth, division and
proliferation. Angiogenesis
Cancer cells can also metastasise, where a piece of the tumour breaks
off and enters the bloodstream or lymph. By doing so it encourages that
small lump of cells to become wedged somewhere else and continue
their proliferation. This is a quality of malignant tumours.

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2.9 Communication
Brain/Adrenaline/Nervous&Endocrine/Heart rate
Homeostasis:
Simply put, homeostasis is the constant maintenance of
an internal environment. This includes water, pH,
temperature etc, and is often controlled by negative
feedback loops.
Cellular communication and recognition:
-Glycoproteins from the plasma membrane act as unique
identifiers for cells. These glycoproteins can be called
antigens.
-Cells communicate by binding to the glycoproteins using
specific shaped receptors.
-Cells can also secrete cytokines (chemical signals) which
again bind to specific shaped receptor molecules to elicit
certain cellular behaviour.

How homeostasis is achieved: Cell A

Sensory receptors: Specific shaped proteins/glycoproteins/glycolipids which detect
changes in the internal conditions. Examples include osmoreceptors (water),
baroreceptors (pressure) and chemoreceptors (pH).
Effectors: Glands or muscles which when active can help carry out the negative Cell B
feedback loop and bring equilibrium about and provide a response. Examples can
be the pituitary gland or hair erector muscles.

Neuronal/hormonal system: The system to which the sensory receptor passes the
message to, in order to carry it to the effector in question.

= Antigen (glycoprotein)
Nervous vs Hormonal:
Nervous: Faster action due to electrical impulses, shorter acting.
Hormonal: Slower action due to chemical messenger in blood, longer acting. = Receptor

Temperature is regulated by Thermoregulation in endoderm's using the hypothalamus:

negative feedback As mentioned, homeostasis, this case in the regulation of temperature, requires
receptors in the form of thermoreceptors, and a neuronal system (the
hypothalamus) to coordinate the signal to the effector(s). The neuronal signals are
transmitted to the effectors which include hair erector muscles, sweat glands,
arterioles and skeletal muscles.

Temperature too high: Hair erector muscles relax so hairs lie flat, sweat glands
produce sweat which absorbs heat from blood by radiation, arterioles dilate.

Negative feedback is
opposing the change made to
equilibrium and bringing
about the original state
Temperature too low: Hair erector muscles contract raising hairs. This traps a
layer of still warm air that reduces heat loss by radiation, shivering by contraction of
skeletal muscles raises the mean kinetic energy of cells and generates heat,
vasoconstriction reduces diameter of arterioles. Sweat glands inactive.

Control of heart rate through the medulla oblongata:

Heart rate must be increased and decreased for many different reasons. High CO2 Receptors involved:
concentration (from exercise) or low pH from the CO2 dissolving in the blood as -pH of blood detected by
carbonic acid, or low blood pressure are three examples of why heart rate might be chemoreceptors.
increased. Adrenaline can also cause this. -Pressure of blood measured
by baroreceptors.
Increase in heart rate: Impulses are sent from the sinoatrial node to the medulla -Movement of muscles
oblongata via a neurone. Once the signal is processed by the MO, impulses are detected by stretch receptors.
sent along the accelerator nerve (sympathetic nervous system) back to the -Adrenaline detected by
sinoatrial node to increase rate of contraction. adrenergic receptors
Decrease in heart rate: Impulses are sent from the SA node to the MO, and then
down the vagus nerve to the SA node to decrease heart rate.

The fight-or-flight response: Adrenaline mechanism of action

When a potentially dangerous stimulus is detected, a hormone called adrenaline is released in the endocrine system
(carried in the blood). Outcomes of adrenaline secretion involve widening of the pupils, the inhibition of the digestive
system and increased blood flow/stroke rate volume.
It binds to and interacts with adrenergic receptors present on the walls of cells. Binding of adrenaline activates the
membrane-bound enzyme adenylate cyclase, which converts ATP to cAMP. cAMP acts as a secondary messenger and
triggers a cascade of intracellular events, such as the activation of kinase enzymes (PKA) which phosphorylate specific
targets. Since cAMP is the secondary messenger, adrenaline is the primary messenger.
The Brain: Structure and Function:

Cerebrum: Main area of the brain, made out of two hemispheres (left and
right, separated by the corpus callosum). Within these hemispheres, there are
different lobes which control different things. The occipital lobe controls visual
signals, the temporal lobe processes auditory signals. The parietal lobe
processes orientation movement and some forms of memory.

Cerebellum: Small area of the brain which controls muscle movement and
balance.

Hypothalamus: Controls temperature regulation and is also used in making

hormones for the pituitary gland.

Medulla oblongata: Found at the base of the brain, the MO controls speeding
up or slowing down of the heart rate.

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