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 -The inhibitor does not have a complementary shape to
active site of the enzyme in question. It can therefore the active site, but binds to the enzyme all the same. This
compete with the substrate for the availability of the time it binds at an allosteric site and through interactions
active site. If the inhibitor is bound, the substrate cannot with the enzymes tertiary structure, it causes deformation
bind with the active site as it is occupied. The substrate of the active site. This means that the enzymes active site
cannot therefore be broken down as quickly, so the rate is no longer complementary to the substrate, so less
of reaction decreases. 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 Testing for reducing sugars:
-All monosaccharides as well as some disaccharides are
Proteins/Lipids/Carbohydrates/Nucleic acids reducing sugars, and are therefore able to donate e- (reduce)
specific reagents.
Polymers and bond dynamics: -By using Benedict's reagent, a clear colour change from blue
-Polymers are molecules which are made up out of to brick red can be seen as an insoluble ppt of copper oxide
repeating units. These repeating units are called is formed.
monomers.
-Typically, bonds can form between monomers through 1. Add 2cm3 food sample that is being tested (liquid)
condensation (where water is excluded and a bond is 2. Add 2cm3 Benedict's reagent
formed as a result). 3. Heat mixture in water bath for 5 mins
-Bonds are broken by adding water to them. This type
of bond breaking is known as hydrolysis. *You can also test for non-reducing sugars. The difference to
the experimental procedure here is that 2cm3 of dilute HCl
Monomer example: Nucleotide must be added to the food sample prior to the BR. This HCl
Polymer example: DNA hydrolyses the glycosidic bonds, releasing reducing sugars in
the process. NaHCO3 will then be added to neutralise excess
Polysaccharides and carbohydrates: acid, then the test is run again.
-Polysaccharides are examples of polymerised
carbohydrates. The monomer, or repeating unit to a Test for starch: Iodine stains starch blue-black
polysaccharide is a single sugar, a monosaccharide.
-An example of a common monosaccharide is the
hexose sugar glucose. These join together through Lipids and triglycerides:
condensation reactions, forming a glycosidic bond. -Lipids are made of carbon, hydrogen and oxygen, similar to
-Glucose has two isomers (alpha/beta glucose) which carbohydrates. However, they are structurally different and
differ simply by the orientation of a hydroxyl group. carry differing functions.
Beta-glucose is used in cellulose, whilst alpha glucose
is used in starch (repeating unit)
FATTY ACID
GLYCEROL

Disaccharide:
A-Glucose + A-Glucose = Maltose
A-Glucose + Fructose = Sucrose FATTY ACID
A-Glucose + Galactose = Lactose

Polysaccharides: FATTY ACID

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 Saturated: No double-bonds in fatty acid tail. Carbons
activity for rapid hydrolysis/release of glucose into present are 'saturated' with hydrogen. Found in animal fats.
blood. Insoluble means it does not affect WP of the (solid as room temp)
cell. Unsaturated: Double-bonds present in the fatty acid tail.
Carbons present are not 'saturated' with hydrogen. Found in
Cellulose = Long straight chains of beta-glucose, which plants. (liquid at room temp)
run parallel to one another and form hydrogen bonds to
form microfibrils (strong threads, higher order Properties of triglycerides:
structure). The strong hydrogen bonds make it easy for -Low mass:energy ratio makes them a good storage
plant cell walls to cope with dramatic osmotic pressure molecule. Lots of energy stored in small volume.
changes. -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.
Roles of lipids: -Release water when hydrolysed, so important for animals
-Lipids are used not only as storage and energy living in arid conditions.
molecules, but also as structural components of every
cell.
-The phospholipid bilayer is made up of many Testing for lipids:
phospholipids. It is the hydrophobic nature of the fatty 1. Add 2cm3 of sample to a test tube
acid tails in these phospholipids which allows the 2. Add 5cm3 ethanol to the sample
membrane to arrange itself properly in water. 3. Add 5cm3 water and shake gently
-Glycolipids can be present in this membrane which act 4. Formation of white ppt indicates lipids present
as signalling molecules or binding sites for *Repeat with a control group with no lipids to make sure
hormones/signalling chemicals. solution remain clear!

Importance of protein:
Proteins make up a huge proportion of structures within any Primary Structure:
organism. They make up all of the enzyme component of Amino acid monomers (lilac) linked together by
cells (as all enzymes are protein), as well as having distinct planar peptide bonds (dark grey)
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.
Protein folding: Protein amino-acid specific interactions:
-The primary structure of a protein describes the sequence -Disulphide bridges form between sulphur atoms present in
of amino acids present. This primary structure will form the cysteine residues (an amino acid with sulphur present in
basis for the folding of the protein. the R-Group)
-The secondary structure describes hydrogen-bond -Ionic/salt bridges form between oppositely charged
interactions that occur when alpha helices and beta- residues such as aspartic acid (negative) and lysine
pleated sheets form from the primary structure. (positive)
-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. Testing for proteins (biruet):
-The quaternary structure describes the association of 1. Place sample in tube and add equal volume of NaOH
more than one individual polypeptide chain. For example, (sodium hydroxide).
haemoglobin (Hb) has four polypeptide chains in its 2. Add a few drops of dilute copper (II) sulphate and mix
quaternary structure. 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 surfaces adaptations:
Exchange/Structures/Functions/Fish/Insects/Practical -Surface area e.g. RHC (root hair cells or
forms of folded membranes)
Exchange surface: The Lungs
The lungs are organs located in the chest cavity. They are -Thin (one cell thick) short diffusion pathway
responsible for removing carbon dioxide and introducing oxygen to so distance travelled is short.
the bloodstream. The carbon dioxide is a respiratory product, and
oxygen is a respiratory requirement (mitochondria). The lungs are -Good blood supply in order to maintain a
surrounded by the ribcage, which protects the organs as well as strong concentration gradient (e.g. alveoli in
assisting in ventilation with the diaphragm and intercostal muscles. the lungs).
The trachea, bronchi and bronchioles aid in getting the air into and
out of the lungs.
Spirometer practical (measuring volume):
Structures and functions:
-Cartilage offers structural support to the trachea and stops collapse -Vital capacity describes the maximum volume
of the airway due to the large pressure changes caused by of air that can be inhaled/exhaled in one
ventilation. breath.
-Ciliated epithelial cells are cells with small hairs that waft mucus, -Tidal volume describes the volume of air we
helping to prevent infections from occurring. breath in and out when we are resting.
-Goblet cells are specialised, mucus secreting cells which make the -Breathing rate is how many times a breath is
mucus which the cilia move. taken per unit time (breaths per minute)
-Smooth muscle fibres allow constriction and relaxation of the airway, -Residual volume is the volume of air always
helping to control the air which reaches the alveoli. present in the lungs.
-Elastic fibres help to deal by stretching and recoiling, offering
structural support. *Know how to answer questions which
-Diaphragm and intercostal muscles are two muscles which contract address how each of these change between
and relax during breathing. resting/exercise etc.

Inspiration: Inspiration:
-External intercostal muscles contract Bony fish rely on a counter current principle in order to exchange gas.
-Internal IC muscles relax. They have four pairs of gills and distinct apparatus set up for this gas
-Ribs are raised upwards and outwards. exchange. The apparatus is held apart by the flow of water, explaining
-Diaphragm contracts and flattens. why fish cannot survive out of water for very long.
-Fish opens mouth and buccal cavity lowers, enabling the flow of water
Expiration: into it.
-Internal IC muscles contract -Fish closes mouth and buccal cavity rises, increasing pressure and
-External IC muscles forcing water over the gills.
-Rib cage lowers -The operculum acts as a valve and pump, letting water out as well as
-Diaphragm relaxes and rises up pumping it in.
-Abdominal muscles contract -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 -You will be expected to outline a practical
spiracles. The pores lead to a system of tracheoles which control measuring the breathing rate of insects.
the exchange of gases through diffusion (constant gradient -This practical involves gently sealing a locust in a
maintained). The end of the tracheoles contain water. syringe then counting how many times its
abdomen moves.
Tracheoles and water: -You then calculate spiracle activity based on how
-The ends of the tracheoles are filled with water. This means when active the abdomen is.
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 Haemoglobin structure/function:
oxygen through the spiracles.
-Quaternary structure of 4 polypeptide chains (2 x
alpha chains and 2 x beta chains. Forms a
OD curves and ppO2 further: globular tertiary + quaternary structure.
-The partial pressure at which oxygen binds to haemoglobin is -Haem group contains a coordinated Fe2+ ion
also dependent on other factors, such as the concentration of using in binding oxygen and carbon dioxide.
carbon dioxide or whether the haemoglobin is fetal haemoglobin. -Hb combines with oxygen to form
oxyhaemoglobin.
The Bohr effect: When cells respire they release carbon dioxide, -Carbon monoxide is poisonous as it binds
which dissolves in solution to form carbonic acid. This causes a irreversibly with the haemoglobin.
low pH to arise, changing the shape of the haemoglobin protein, -The way in which oxygen molecules bind is
decreasing the Hb affinity for CO2. known as positive cooperativity- the idea that by
binding more oxygen molecules, Hb undergoes a
Fetal Hb: Has a higher affinity for oxygen as it must be able to conformational change to make the next binding
cope with surviving at a low ppO2, so O2 moves across placenta. easier.
-This type of behaviour is explained in an oxygen
Decreased affinity: OD curve shifts right. dissociation curve, which shows how the partial
Increased affinity: OD curve shifts left. 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 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)
Red Blood Cells:
-No nucleus so have a large Veins: Move deoxygenated blood from the respiring tissue to the heart, so that the
volume inside cell for storing blood can be pumped back to the lungs and be oxygenated. Veins carry blood at a
oxygen. lower pressure and therefore have valves to stop backflow of blood.
-Biconcave shape for
maximised surface area for Capillaries: The smallest type of blood vessel, capillaries are typically 1 cell thick and
exchange of gas. are therefore suitable sites for exchange to occur. Their lumen is big enough to
-Filled with oxygen transporting accommodate the width of a red blood cell, but only just!
pigment Hb or haemoglobin.

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

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

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.
Antigen: Surface -Antibodies are responsible for agglutination (the clumping together
protein/glycoprotein/glycolipid which of multiple pathogenic entities) to allow for rapid en masse
gives cellular recognition for degradation using phagocytes.
bacteria/viruses/cells. Stimulate -Antibodies are also responsible for carrying out opsonisation
antibody production. (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 -The next time someone encounters the
differentiate into different types of cell. antigen from the vaccine, they will be able to
-Cytotoxic T-cells destroy pathogens and infected cells by secreting rapidly generate more antibodies as well as
damaging enzymes into them (perforins + granzymes). other immune cells to help clear the infection
-Helper T-cells release cytokines to stimulate other immune t- faster.
lymphocytes. These are destroyed by HIV. -Modern vaccines e.g the Pfizer vaccine is
-Memory T-cells are formed to retain immunological memory. 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.
HIV: Human Immunodeficiency Virus
AIDS: Acquired Immunodeficiency Syndrome

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

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1.7 DNA & Protein Synthesis DNA, mRNA, tRNA, rRNA:

Structure/Function/RNA/Transcription/Translation DNA: Double-helix, deoxyribose sugar, double

stranded. Contains information in the form of
genes
DNA Structure vs Function:
mRNA: Single stranded, moves information from
Sugar-phosphate backbone negative charge, protects bases nucleus to ribosome for translation. Uracil instead
which face inwards. of Thymine.
DNA is very long, can store lots of information as genes which tRNA: Regions of single and double-stranded
code for proteins. RNA. Clover-leaf shape and contains an
anticodon and a binding site for an amino acid.
Hydrogen bonds between bases are weak, easily broken, but
strong in large numbers. Allows transcription bubble to be rRNA: Component of ribosome. rRNA and
opened/DNA to be easily replicated (by DNA Helicase) ribosomal proteins make up the translational
machinery.
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 Evidence for semi-conservative replication:
centred around shape. E-Coli grown in heavy isotopes of nitrogen (15N)
will incorporate the isotope into their nitrogenous
bases in the DNA. After many generations, almost
DNA Replication: all bacteria will have only 15N in their genomes.
The bacteria are then transferred to a regular 14N
DNA Helicase unwinds the double stranded DNA by breaking medium and are allowed to grow. By doing so, the
the hydrogen bonds holding complementary base pairs bacteria incorporated the regular 14N into their
together. Formation of the replication fork. DNA during replication.
A primer (short oligonucleotide sequence complementary to 3' -By centrifuging these mixtures out, scientists
end of single stranded DNA) were able to see how much 15N and how much
DNA polymerase attaches to the 3' end of the single stranded 14N were in each sample. What they found was
DNA, and polymerises a new strand in the 5'3' direction. the amount of 15N present decreases over each
Free-floating nucleotides present in the nucleus. On the other division. This hybrid amount of 15N decreases as
strand, DNA replication is discontinuous, and therefore is it makes up a smaller fraction of the DNA with
synthesised in short sections called Okazaki fragments each replication.
DNA Ligase seals the sugar phosphate backbone by forming 15N band
phosphodiester bonds between nucleotides. 14N becomes fainter
15N over sequential
divisions.

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 Export + Processing (PTM):
so it can be read and translated into a protein. Proteins can be modified following translation.
They can be phosphorylated, methylated, or have
RNA polymerase unwinds DNA and forms a transcription sugar residues added (such as a mannose tag).
bubble, which contains regions of single stranded DNA. These changes are called post translational
Free-floating nucleotides will bind to the exposed bases on modifications.
the strand, which acts as a template
RNA polymerase will join these nucleotides together to form a Phosphorylation
strand of mRNA, which contains the base Uracil instead of
Thymine.
mRNA is single stranded and is therefore suitable for export Carbohydrate
out of the nuclear pore. Here the mRNA will be localised to added
the RER or cytoplasmic ribosomes.

Translation (mRNA code read and a protein is made): Methylation (-CH3 added)
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). Mutation (see mutation 2.5 for more):
This 'reading' is done by tRNA molecules containing a Changes made to the sequence of bases in either
complementary anticodon to the mRNA triplet codon. DNA or RNA are termed mutation. This can have
If complementary base pairing occurs, then the amino acid consequences on protein folding, as the wrong
brought by the tRNA will remain and prepare to bind to the amino acid incorporated into a polypeptide chain
next amino acid. could cause the protein to fold completely
Translation is initiated by START codons and terminated by different. If it were an enzyme, this could threaten
STOP codons. These are three bases which signal the 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 Genes: Genes are sequences of DNA that code for a particular
protein. These are exons (expressed).
Genetic switches/Lac operon/Inheritance
Features of the genetic code: Definitions:
-Degenerate: More than one triplet codon can code -Allele: An alternative form of a gene.
for a given amino acid. This means that, for example, a
substitution mutation could have no effect on the -Dominant: One copy of the allele is required in order for
amino acid sequence. the phenotype to be expressed.
-Non-overlapping: The code is read in triplets which -Recessive: Two copies (homozygous) of the allele are
are treated as separate entities. required for the phenotype to be expressed.

-Universal: The fundamental rules of the genetic code -Homozygous: Has two copies of the same allele.
are conserved across nature.
-Heterozygous: Has two different alleles.
Evolution by natural selection: Natural selection -Genotype: The combination of alleles e.g Gg
describes how the individuals best suited to survive in
a given environment will survive and reproduce, -Phenotype: The characteristic/impact of the genotype.
passing on those advantageous genes (or alleles-
better) to their offspring. As a result of this the allelic
frequency for advantageous traits increases, and Lac Operon: A mechanism developed by E-Coli to allow
certain characteristics become more common. Over them from using glucose as their primary respiratory
time, this leads to larger scale changes and evolution. substrate to using lactose as their primary substrate, when in
a lactose (and glucose-free) environment.

Lac Operon: Understanding the vocabulary Repressor RNA Pol

Promoter: Where RNA pol binds to begin transcribing X
a certain gene.

Operator: Where regulatory elements/transcription

factors bind to encourage or discourage transcription. L P O Z Y A

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 Transcription

sequence on DNA in order to discourage transcription.

Homeobox gene: A gene that codes for a L P O Z Y A

transcription factor protein. They have key
developmental roles.
Lactose
Regulatory gene: A gene which codes for a repressor
protein. 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
Monohybrid + dihybrid inheritance: stops the repressor binding to the operator. Therefore RNA
See GCSE inheritance for monohybrid inheritance pol is not discouraged from binding to the promoter, and
transcription occurs. The genes coded for include lactose
Dihybrid inheritance: When two different hydrolysing enzymes as well as proteins which increase the
characteristics coded for by genes on different permeability of the bacterium to lactose.
chromosomes are studied , and the relative ratio of the
offspring's genotypes are estimated. Meiosis and variation:

Crossing over: Chromosomes line up and pressure

dynamics in the nucleus cause equivalent portions of each
RG Rg rG rg chromosome to break off and re anneal on the other
chromosome. This means the offspring will have a
combination of alleles.
RRGG
RG RRGg RrGG RrGg
Independent segregation of chromosomes: In meiosis I,
the homologous chromosomes line up in pairs. Since only
Rg RRGg RRgg RrGg Rrgg one of the homologous chromosomes will go into the
daughter cell, i.e the division of genetic material is random

rG RrGG RrGg rrGG rrGg 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
rg RrGg Rrgg rrGg rrgg 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

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
CoDominance: This phenomenon describes when two allele being present.
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. 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 Nerve cell structure + function

Synapse/Resting potential/Action potential/Nerve cells Axon: Extensions of the cell body which conduct
impulses away from the cell body.
Synapse: A gap between two nerve cells. An impulse (better
known as an action potential) travels across a synapse through a Cell body: The larger part of the nerve cell which
chemical medium in the form of neurotransmitters such as contains the nucleus and mitochondria.
acetylcholine, dopamine or serotonin. There are an estimated 125
trillion synapses in the cerebral cortex alone. Dendrites: Extensions of the cell body which
conduct impulses towards the cell body.

The human brain structure: Mitochondria: Make ATP through aerobic

respiration.
Cerebrum: The largest part of the brain, the cerebrum is divided
into two hemispheres separated by a structure known as the Neurotransmitter: Chemicals released by nerve
corpus callosum. The cerebrum is made out of different lobes. The cells to help transmit an action potential across a
occipital lobe controls visual processing. The temporal lobe synapse.
controls auditory information, whilst the parietal lobe controls
movement and memory.

Cerebellum: Located underneath the cerebrum, the cerebellum is Synapse diagram:

smaller and carries out the functions of muscle movements and Synaptic cleft
balance.

Hypothalamus: Involved in thermoregulation and hormone

production from the pituitary gland.

Medulla oblongata: Controls breathing rate and heart rate (and Presynaptic
therefore blood pressure). It is located at the base of the brain. Postsynaptic
neurone neurone
Receptor
Different types of neurone:

Sensory: Sensory neurones send impulses from the receptor The Synapse Dynamics (exam answer):
(which has detected the stimulus) to the relay neurones (inside -AP reaches synapse and causes influx of Ca2+
CNS) into presynaptic membrane.
-Influx of Ca2+ stimulates exocytosis of vesicles
Motor: Motor neurones deliver the impulse from relay neurones in containing neurotransmitter.
the CNS to effectors (which can be glands or muscles) which -Neurotransmitter exocytosed into synapse,
contract or secrete upon stimulation. where it diffuses across and binds to specific,
complementary receptors on the postsynaptic
Relay: Found in the CNS, relay neurones carry the impulse from membrane. Upon binding to the receptors (which
the end of the sensory neurone to the start of the motor neurone. are channels), there is an influx of Na+ into the
post synaptic membrane, depolarising it by
decreasing its negative charge.
Resting potential: -A new AP starts in the postsynaptic membrane.
Nerve cells have a negative membrane potential at resting state. -Excess neurotransmitter in the synapse is
This means there are more positive ions outside the cell than removed using enzymes in the presynaptic
inside. How is this achieved? membrane. For example acetylcholinesterase
breaks down acetylcholine and therefore stops
The sodium-potassium pump moves 3 sodium ions out and only over stimulation of the postsynaptic neurone.
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 Factors affecting speed of transmission:
potential more negative.
Diameter: The larger the diameter of the axon,
The nerve cell therefore has a resting potential value of -70mV, the faster the rate at which the impulse travels.
which is key to remember for exam specific questions.
Temperature: The higher the temperature, the
faster the rate of impulse transmission. However,
above a certain temperature proteins such as ion
Action potential and propagation: channels could denature and therefore reduce
When a nerve cell is activated and needs to send an impulse in a impulse speed.
given direction, it must first become depolarised and lose its
negative membrane potential: Myelination: Schwann cells deposit an
insulating material called myelin over nerve cells.
The stimulus will first trigger the excitement of the neurone, which Since myelin cannot conduct electricity, the
opens its Na+ channels. Since Na+ has been moved initially out impulse will jump from node to node in a process
of the cell, it floods in down its concentration gradient. known as saltatory conduction.
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 Summation: Temporal vs Spatial
membrane potential to +30mV.
 Temporal: Temporal summation is a dynamic
The nerve cell repolarises itself by closing the Na+ channels, whereby one single neurone stimulates its
opening K+ channels and allowing the Na-K pump to reestablish neighbour neurone by increasing the
the -70mV resting potential. frequency of impulses sent across the
synapse.
The action potential will move as a 'wave of depolarisation'
meaning that neighbouring channels will stimulate others to open. 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 6CO2 + 6H2O C6H12O6 + 6O2 (+ATP also made)
LDR/LIDR/ATP/Practical
Photophosphorylation: Adding a phosphate group to a
ATP: Adenosine Triphosphate molecule using light.
ATP ADP + Pi (Hydrolysis, energy release)
ADP + Pi ATP (Condensation) Photolysis: Using light energy to split (lyse) a given entity
e.g. H2O in the LDR.
Properties of ATP:
-Small and soluble (easily transported in cells) Photoionisation: Light energy causes electrons to be raised
-Easily hydrolysed (instantaneous release) to high energy level + released e.g. photoexcitation of
-Remade easily (condensation, regeneration) chlorophyll in LDR.
-Makes molecules reactive (phosphorylation)
-Cannot pass out of the cell Decarboxylation: Removal of CO2 (carboxyl group) from a
given entity
ATP used in active process e.g. active transport
Made up of adenine, ribose and 3 x phosphates 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 -Light energy absorbed by PSII, causing a pair of electrons to
reflects green parts of the spectrum. Respond to become excited and move to a higher energy level, being
light energy by releasing electrons. released.
-Electrons move to the ETC (electron transport chain) where
Stroma: Aqueous medium which contains sugars, the movement of electrons drives H+ pumping into the
enzymes and some (organic) acids. thylakoid lumen.
-Electrons move to PSI, where they are passed to NADP to
Photosystems: Protein machinery which couple light form reduced NADP (NADPH).
energy to the generation of an electrochemical -H+ building up in lumen generates an electrochemical
gradient. gradient (H+ gradient/proton gradient)
-H+ move down electrochemical gradient through ATP
synthase, which couples proton movement to ATP synthesis
(ADP + Pi = ATP)
Cyclic photophosphorylation uses PSI only. -The photolysis of water replaces the electrons lost from the
No NADPH or O2 is produced, only small photoexcitation step.
amounts of ATP (ATP synthase)

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
 ATP
*The calcin cycle needs six turns to make one hexose sugar. This is 2 x NADP
because 6x(2xTP, where each TP has 3C). Total carbon = 36C
6xRuBP regenerated (30C demand) leaving 6C for hexose.

Limiting factors for photosynthesis: Thin Liquid Chromatography (TLC)

-Light: Plants absorb specific wavelengths of light. They reflect green -Grind up leaves from plant and add anhydrous
light and so appear green (absorb red and blue) sodium sulphate, then a few drops of
pronanone.
-Temperature: Temperature affects kinetic energy of particles, stomata -Transfer to test tube, add ether (petroleum)
opening as well as enzyme action. If temperature is too high, enzyme then extract top layer (pigments). Transfer to
active sites denature and lose complementarity to substrate (less ES- second test tube and add a few more drops of
complexes formed). If temperature is too high, stomata close (water ether.
retention, less CO2 enters) -Draw line in pencil at bottom of TLC plate,
create spots by adding small concentrated
-Carbon dioxide: CO2 makes up a very small percentage of gas in the drops (point of origin) to the plate and ensuring
air. Increasing this concentration will increase the rate of they dry.
photosynthesis, up to a point where stomata close (4%). -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.
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. Practical knowledge:
-Set up colorimeter using red filter and zero using cuvette with distilled
water. Colorimeter: Measures how much light is
-Set up test tube rack and switch on light. absorbed by a solution when light is passed
-Add volume of chloroplast extract and volume of DCPIP and mix. through it.
-Immediately transfer small amount into cuvette and record reading of
absorbance on the colorimeter. TLC: Allows determination of what pigments
are present in the leaves
*If dehydrogenase activity present, absorbance will decrease because
DCPIP is reduced and the blue colour of the solution is lost. Plot *Thin liquid chromatography involves a
absorbance against time for different variables (light intensity, mobile phase (molecules can move- liquid
temperature, distance from the lamp etc). The greater the decrease of solvent) and a stationary phase (molecules
absorption, the higher the dehydrogenase activity. cannot move)

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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 -The reduction of NAD and FAD involves another
Reduction: Where a species gains electrons dehydrogenation step.
Substrate-level phosphorylation: Where a -ATP production is driven by a phosphate transfer from
phosphate group is transferred from an one of the intermediates. This is known as substrate level
intermediate compound to a species. 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 Structure of the leaf:
-The waxy cuticle covers the upper epidermis and protects the
Transpiration/Translocation/RHC 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
Guard cells control stomatal opening:
Each stoma (singular of stomata) is made up of two palisade cells, which have a high SA:vol ratio and a large number
of chloroplasts for efficient photosynthesis. It is on the upper side
kidney bean shaped cells called guard cells, which
of the leaf, and is the main site of photosynthesis.
respond to differences in water. Guard cells must
-The spongy mesophyll contains air spaces to encourage gas
control gas exchange through these stomata
exchange through diffusion.
(oxygen, carbon dioxide, water vapour).
Plant has high water concentration:
Water moves into the guard cells by osmosis. This Waxy cuticle
causes them to swell and become turgid. This UE
turgid conformation opens up the stoma. And Palisade cell
encourages gas exchange.
Plant has low water concentration:
Water moves out of guard cells by osmosis and Spongy
cells become flaccid. This closes the stoma, Mesophyll
reducing gas exchange.
Stomata are found almost exclusively on the lower
epidermis, apart from in hydrophytes, which have Stoma
LE
stomata on the upper epidermis.

Driving Transpiration:

Low pressure at stomata: Evaporation of water

molecules from the stomata lowers the pressure. Phloem loading:
This causes water to be drawn up the xylem due to Phloem loading describes how sugars produced through
a pressure gradient. photosynthesis are moved from the photosynthesising cell into
the phloem. This involves co transport mechanisms and the use
High pressure at roots: Active loading of roots with of pH gradients, as well as the presence of a companion cell.
inorganic ions and nutrients lowers the RHC water
potential. Water moves into the roots via osmosis, -Sucrose produced by the source cell during photosynthesis
increasing the pressure exerted by water at the (sucrose = glucose + fructose).
roots. -H+ ions actively transported out of companion cell, increasing its
pH and establishing a proton gradient.
Cohesion-tension theory: Numerous hydrogen -H+ ions then move down concentration gradient into companion
bonds form between water molecules (cohesion) as cell from source cell. This movement includes the co transport of
well as between the water molecules and xylem sucrose from the source to the companion cell.
wall (adhesion). The water moving through the -From here the sucrose can move by facilitated diffusion through
xylem of a plant is usually described as an plasmodesmata into the phloem.
'unbroken column held under tension'
H+
H+
Driving Translocation: X P Source Cell

Low WP at source: Loading of sugars into the

phloem at the source side will lower the water H+ H+
potential of the phloem due to the presence of
sugars. This causes water to move from the xylem Suc Suc
to the phloem by osmosis.
Companion
High WP at roots: After the sugars move out into Cell
the respiring tissue (such as RHC), the water
potential in the phloem increases, so water moves
back into xylem by osmosis.

Xylem cell structure: Water moving in the root:

[
-Xylem cells are dead, hollow cells joined
[ end-to-end.
-They are hollow (have no cytoplasm)
-They are lignified (a protein which
Apoplast pathway:
Water moves through cells in the root through the
spaces in the cell walls filled with cellulose. Since
supports the plant structurally as well as water is not passing through the plasma

[
acting as a waterproofing layer. membrane, the water can carry dissolved metal
[ Formation:
-Top and bottom cell wall and membrane
ions/mineral ions/salts.

Symplast pathway:
break down Water moves through the cytoplasm of cells joined
to one another through plasmodesmata. This
 -Nucleus, organelles and cytoplasm leak method of water movement cannot carry any
out additional ions
-Cell is lignified in rings of lignin
Evidence for mass flow: Ringing experiments Evidence for mass flow: Radiolabelled 14C
This experiment describes a section of bark being taken This experiment describes a plant being grown in a
from a tree, all the way round. This bark contains the radioactive isotope of 12C, 14C. This can be in the form of
xylem and the phloem, so by removing it the scientists radiolabelled CO2, which the plant will take up and
are removing that which they believe is responsible for assimilate in photosynthesis. Exposure of a cross section of
mass transport. Cells above the cut will swell as sucrose the plant will show radioactivity in a dark form. This
accumulates in them (and water) whilst cells below the technique is known as autoradiography and is widely used
cut will die owing to the fact that they will not be able to in tracing experiments.
receive the sugars for respiration.

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

Mark-release-recapture technique: MRR Assumptions:

-Capture number of organisms using an -Marking has no effect on organism (physiologically or socially)
appropriate technique. -Enough time has been given for organisms to mix.
-Mark the individuals with a tag that won't be -No births/deaths/migration events (no change in pop. size)
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 Succession explained:
rise to a uniform distribution. -Pioneer species (e.g. moss) colonise new surface where abiotic
-Capture second sample of organisms and factors may be harsh. Pioneer species adapted to harsh abiotic
count how many of the second capture are factors.
marked individuals from the first capture. -Pioneer species change abiotic factors and make them less hostile
-Estimate total population size using: (decomposition/soil formation)
-New species with different adaptations can grow on surface. These
Number caught 1st x Number caught 2nd also die and are broken down, making the abiotic factors less hostile
again. Water retention begins to increase.
Number marked in the 2nd sample -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 Substitution Mutation: A base in the code is simply swapped for a
different base. For example A-G would be a substitution mutation.
Mutagens/Mutations/Impact of 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:
AAAT C G C G ATA C T G
Code: A A A T G G C G A T A C T G
Mutations:

AAAT C G G ATA C T G
Deletion Mutation: A base in the code is removed altogether. This
can be highly influential on the resulting polypeptide. Deletion
AAAT C C G C G ATA C T G 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
AAAT G G C G ATA C T G altogether.

Code: A A A T C G G A T A 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. 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
Impact of mutation (protein folding/cancer): 1) and therefore any triplet codon following the addition mutation
can be altered. This can cause improper protein folding, early STOP
Mutation can cause many different codons (truncation) or a completely different protein altogether to be
consequences, or often none at all. coded for.

-It must first be noted that mutation can affect

how a protein folds and is translated- remember Code: A A A T C C G C G A T A C T G
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 Inversion Mutation: A region of the base code is inverted. For
(enzymes, receptors) to be coded 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
-It must also be recognised that mutation can a discrepancy of 1 with regard to the correct sequence of amino
have no effect on the synthesis of the protein acids. This, much like the substitution mutation, can be silent or non-
(the idea that the same/a similar AA is coded for silent.
by the mutation) and therefore mutation can
often have no effect at all.
-Mutations in genes which control cell division Code: A A A G C T C G A T A C T G
and growth can lead to cancer- the idea that
mutations to genes controlling cell division will
cause uncontrollable cell division to occur-
cancer.
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
Coronavirus Mutations: E484K mutation) found in cigarette smoke. These chemicals intercalate in
The Kent variant shows a mutation at amino between DNA bases and distort the DNA, mutating it as it does so.
acid number 484. At the position, an EK -Damage to cells can even cause mutation. Cancer cells typically
substitution mutation has occurred, meaning respond in a similar way to wounded cells, secreting signals which
that glutamic acid has been mutated to lysine. stimulate the growth of blood vessels into the tumour
E (glutamic acid) = negative charge (angiogenesis). This supplies the cancer with its own private supply
K (lysine) = positive charge of oxygen and glucose for the high metabolic demand cancer cells
This change in charge in the spike domain of have.
the virus may be responsible for increased -Cancers arise due to mutations in genes controlling cell division and
transmissibility. growth.
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2.6 Genomes & Biotechnology Reverse Transcriptase:
Reverse transcriptase is an enzyme that
Genetic engineering/Sequencing/Cloning/Biotechnology synthesises a complementary strand of DNA
from a single strand of RNA. It is therefore the
reverse of transcription because we make
Definitions: DNA from RNA, not RNA from DNA. Viruses
have RT so that they can synthesise a DNA
Restriction endonuclease: An enzyme which recognises a strand once they have deposited their RNA
palindromic sequence of DNA. It cuts DNA leaving sticky-ends or genome into the host cell. By making DNA and
blunt-ends. then integrating it into the host genome using
an integrase enzyme, the virus goes
Recombinant DNA: DNA from two or more different organisms undetected and starts to use the host cell as a
protein factory.
Oligonucleotide: Short sequence of nucleotides complementary to a
specific sequence of DNA.

Sequencing: Mapping out the entire genome, or the section of a Gene markers/probes:
genome of a particular organism. This can be achieved in many These are short oligonucleotide sequences
different ways such as Sanger sequencing/Illumina sequencing and which bind by complementary base pairing to
modern day mini-Ion sequencing. single stranded DNA. Picture a specific known
mutated sequence ACCG.
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 A C C G
can also be viewed as an overhang.

T G G C
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 Probe
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 Probe:
ends to the plasmid. This single stranded sequence is
The gene is then ligated into the plasmid using DNA ligase, which combined with fluorescent labelling for
seals the nucleotides together with phosphodiester bonds. visualisation of the mutated gene being
Ca2+ shock and electrical shock stimulate the bacteria to take up present.
the plasmid and divide by binary fission, increasing the amount of The probe is made by taking a double
the gene as well as synthesising the protein product. stranded DNA sample of the mutated
sequence and then melting it (breaking
Identifying successful candidates: hydrogen bonds between base pairs
By inserting the desired gene into a pre-existing gene that the bacteria across double-helix.
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 Genetic fingerprinting: The non-coding
resistance gene). Pressure plating can be used to transfer colonies regions (introns) of DNA can often be
and grow the sample. 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
PCR: VNTRs (variable number tandem repeats),
-DNA is heated to 95 degrees Celsius, double strand melts to form two where discrete sequences of DNA are
single strands. repeated. Since each individual has their own
-Mixture cooled to 60 degrees Celsius to allow primers to anneal. unique VNTR profile, by screening people for
-Mixture heated to 72 degrees Celsius to allow Taq polymerase to these genetic markers of individuality genetic
synthesise two new strands. fingerprinting has applications in crime and
-Cycle repeats paternity testing.
This occurs in a thermocycler- a machine specifically designed to
cycle these temperatures. It contains the primer mixture, free floating
nucleotides and Taq pol. Gel Electrophoresis separates DNA
fragments based on size using electricity.
First, the sample is digested using many
RT-PCR: different restriction endonucleases. This
Reverse Transcriptase Polymerase Chain Reaction allows a leaves DNA in small fragments. When run on
complementary strand of DNA to be made from RNA. This single a GE plate, each person will have unique
stranded DNA template of the RNA can then be made into a double- bands correlating to their DNA makeup. Small
helix using DNA polymerase. In this way it allows for the synthesis of fragments move quicker towards the positive
working double-stranded genes. terminal, whilst large fragments migrate
slowly.
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 2.7 Homeostasis Glucose regulation:
-If the glucose concentration in the blood is too high, it will lower the
Glucose/Water/Temperature/Nephron water potential of the blood and cause water to move into the blood
from surrounding cells by osmosis, causing the cells to crenate and
Homeostasis is the constant maintenance of an die.
internal environment through regulatory -If the blood glucose level is too low, there will not be enough
processes. 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 -High temperatures and high/low pH can cause important enzymes
an amplification of that same change. to denature and lose enzyme-substrate complementarity. This
means no ES complexes can form and metabolic reactions lose
Negative feedback: efficiency.
Where a change made to the equilibrium causes -Low temperatures mean there is often not enough kinetic energy
a restoration to the same equilibrium, working for successful frequent collisions between particles, and therefore
against the effect of the change. reducing metabolic activity again.

Alpha cells: Glucagon:

Alpha cells secrete glucagon, which inhibits the In low blood sugar concentrations, alpha cells are activated and
action of B-cells in the pancreas. secrete a hormone called glucagon. This stimulates glycogen
stored in cells to be broken down to release glucose into the blood
Beta-Cells: (for respiration). This process is known as glycogenolysis.
Secrete insulin, which inhibits the action of
alpha cells in the pancreas. B-cells are found in Insulin:
small clusters known as islets of Langerhans. 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.

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)
Alpha (blue) and Beta (Black) cell clustering -This depolarisation opens voltage-gated Ca2+ channels. When an
in the pancreas. 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: Reabsorption of water in the nephron:
-High pressure generated by pumping of heart and -PCT (proximal convoluted tubule) permeable to
difference in size between afferent and efferent arteriole. AA/vitamins, H2O, sugars, so all of these reabsorbed here.
Efferent is narrower. -Ascending limb impermeable to water, but actively
-Pressure squeezes small molecules through transports Na+/Cl- ions out of nephron into medulla,
fenestrations in glomerulus (network of capillaries). lowering WP of surrounding tissue.
-Podocytes and basement membrane act as filtration -Descending limb permeable to water. Lowered WP of
and rescue mechanisms for incorrect substances medullary tissue generates gradient, water reabsorbed by
passing out of the blood. osmosis.
-What is left in the efferent arteriole is red blood cells, -The loop of Henle is incredibly concentrated, and the ion
white blood cells and plasma proteins) gradient present means Na+ and Cl- diffuse passively out of
-Glucose, water, ions, sugars, amino acids and vitamins loop.
are passed through into the nephron. -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
Afferent Efferent permeable to water.
Glomerulus

Bowman's
capsule

H2O/Ions/Glucose/AA

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.

Thermoregulation: Responses to heat:

Thermoregulation is important because maintaining heat
energy allows sufficient energy for frequent successful Sweating: Water has a high specific heat capacity,
collisions between particles. therefore sweating removes a lot of heat energy and
therefore acts as a cooling mechanism.
Temperature too high: Active sites of enzymes denature.
Complementarity to substrate lost. Decrease in ROR of Hairs life flat: No warm layer of air trapped, so more heat
important enzymatic reactions. radiated from blood through skin.
Temperature too low: Not enough KE for frequent Vasodilation: Widening of blood vessels/capillaries closer
successful collisions, so ROR decreases due to lack of to skin surface, increases radiation of heat from blood
energy. through skin.
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(such
as in endoderms) around a narrow range. Responses to cold:
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Shivering: Increases mean KE of particles, brings up
Coordination and regulation: average energy through movement.
These processes are brought about by the
thermoregulatory centre in the brain. It has Hairs stand on end: Warm layer of air trapped, so less
thermoreceptors to detect changes in temperature of the heat radiated from blood through skin.
blood, and elicits an appropriate response. Sensory
receptors in the skin also send signals to the Vasoconstriction: Constriction of blood vessels/capillaries
thermoregulatory centre. close to skin surface, decreases radiation of heat from
Humans maintain a body temperature of 37.5 degrees blood through skin and blood flow.
Celsius in this way.
2.8 Genetics Mutations and causes: Mutations (see A2 Mutations) are
characterised by a change to the genetic code. Mutations can
Inheritance/Epistasis/Patterns arise randomly due to transcription/replication errors, or can be
induced through mutagenic agents, or mutagens such as
Definitions: benzopyrene (cigarette smoke) and UV light (the sun).
Mutations can be silent or non-silent, depending on where the
Epistasis: Where the expression of one allele mutation happens and what type of mutation it is (addition,
blocks the expression of another allele. deletion,inversion,translocation).
Remember that mutations can occur in introns (non-coding
Stem cell: A cell which is capable of differentiation regions) and therefore have no large effect on the phenotype.
and self-renewal. Mutations can also give rise to the same amino acid that the
triplet codon would have originally coded for- owing to the
DNA profiling: Technique used to identify degenerate nature of the code.
individuals based on what their DNA looks like.

Probe: A short sequence of nucleotides Stem cells: Stem cells are special cells which can
complementary to a specific sequence. differentiate (turn into) almost any other type of cell. Stem cells
can be adult stem cells (found in the bone marrow) or
Human genome project: A project which has embryonic (taken from an embryo) stem cells. Embryonic
successfully mapped out the entire human genome, stem cells can differentiate into a wider array of cells
allowing us to track evolution and screen for (totipotent) compared to adult stem cells (pluripotent).
diseases. However, taking stem cells from embryos has ethical
implications (playing god/destroying life/potential for life).
Proteome: All the proteins that a genome can code Stem cells are self-renewing (they make more copies of
for (exons) 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 Cellular communication and recognition:
-Glycoproteins from the plasma membrane act as unique
Brain/Adrenaline/Nervous&Endocrine/Heart rate identifiers for cells. These glycoproteins can be called
antigens.
-Cells communicate by binding to the glycoproteins using
Homeostasis:
specific shaped receptors.
Simply put, homeostasis is the constant maintenance of -Cells can also secrete cytokines (chemical signals) which
an internal environment. This includes water, pH,
again bind to specific shaped receptor molecules to elicit
temperature etc, and is often controlled by negative
certain cellular behaviour.
feedback loops.

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.

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

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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