Unit 1, Topic 1, Subtopic 1: Chemistry for biology and biological molecules.

1.1
Description of the hydrogen bonds amoung water molecules./ Explanation of water
being a polar molecule:
-The oxygen atom has a greater nuclear charge than the hydrogen atom, so the
attraction between the oxygen atom and the shared electrons is greater (the
electrons are held closer to the oxygen atom), hence oxygen is more
electronegative than hydrogen. Therefore, oxygen has a partial negative charge
while hydrogen has a partial positive charge — water is polar.
-The slightly negatively charged oxygen atom of one water molecule will attract to
the slightly positively charged hydrogen atom of another water molecule in a weak
electrostatic attraction called a hydrogen bond.
Definition of hydrogen bonds:
Weak electrostatic intermolecular bonds formed between polar molecules
containing at least one hydrogen atom.
Dipole:
The separation of charge in a molecule when the electrons in covalent bonds are
not evenly shared.
Draw a molecule of water:

Importance of water due to its properties:

Property Explanation Importance
Polar solvent. Water being a polar molecule Acts as a transport medium so the
allows it to be attracted to and to essential substances for living
form hydrogen bonds with other organisms (eg. Glucose, salts,
ionic compounds and polar vitamins, aa…) can dissolve in it and
solutes. (Universal solvent) be transported to cells in order for
metabolic reactions to take place.

High specific A lot of energy is needed to break Therefore, a lot of energy is required
heat capacity. the hydrogen bonds between to raise the temperature of water,
molecules. meaning there will be little
temperature fluctuation in water
bodies so the aquatic organisms
within have a constant temperature
which is essential for metabolic
reactions to take place inside their
bodies. Also, when temperature
increases, there’s less oxygen
dissolved in water.
 Temperature of water rises less than
temperature of land given the same
energy input.

Adhesion. Due to the polarity of water, Adhesion between water and xylem.
water can be attracted to other
ionic and polar substances.
Cohesion. Due to the polarity of water, Water moves as a column due to
hydrogen bonds are formed cohesive properties in transpiration,
between water molecules making allowing for transport of water in
them stick together. plants. And due to adhesive forces
between water and xylem.
High surface Due to the polarity of water, Animals can move across water.
tension. hydrogen bonds are formed
between water molecules giving
water cohesive property which
results in a net inward force at its
surface.
Explanation of how water is involved in the transport of molecules in living
organisms:
Water is a solvent, is polar, attracts to ions and polar substances, ref to an example.
(Eg. Glucose).

1.2, 1.4
Three main groups of carbohydrates & other definitions:
Monosaccharide: A soluble, single sugar monomer.

Disaccharide: A sugar made up of two monosaccharide units joined together

by a glycosidic bond, formed in a condensation reaction.
Oligosaccharide: Molecules with between 3 and 10 monosaccharide units.

Polysaccharide: An insoluble polymer of more than ten monosaccharide units

joined together by glycosidic bonds.
Monomer: A small molecule that is a single unit of a larger molecule
called a polymer.
Polymer: A long-chain molecule made up of many smaller, repeating
monomer units joined together by chemical bonds.
Isomer: Molecules that have the same chemical formula but different
molecular structures.
Monosaccharides:
General formula:
(CH2O) n
Main categories of monosaccharides:
 Triose sugar: A sugar with three C atoms. -
Pentose sugar: A sugar with five C atoms. Ribose, deoxyribose.
Hexose sugar: A sugar with six C atoms. Glucose, galactose, fructose.
Displayed formula of monosaccharides:

Disaccharides:
Some disaccharides:
Disaccharide: Monomers:
Maltose/ C12H22O11 α-glucose, α-glucose.
Sucrose/ C12H22O11 α-glucose, fructose.
Lactose/ C12H22O11 α-glucose, galactose.
Formation of disaccharides by condensation reaction and splitting of disaccharides
by hydrolysis reaction:
Con. Reaction: A reaction in which a molecule of water is removed from the
reacting molecules as a bond is formed between them.
Hyd. Reaction: A reaction in which a bond is broken by the addition of a
molecule of water.
Formation of maltose (a-g, a-g):

Formation of sucrose (a-g, fructose):

Formation of lactose (a-g, galactose):

Polysaccharides:
Starch (amylose and amylopectin):
Similarities:
Amylose Amylopectin

Both are polymers composed of alpha-glucose.

Both contain 1-4 glycosidic bonds.

Differences:
Amylose Amylopectin
Has 1-4 glycosidic bond only. Has both 1-4 glycosidic bonds and 1-6
glycosidic bonds.
Has a helical, chain-like shape. It is Branched.
unbranched.
Glycogen:
It is very similar to the amylopectin molecule, but glycogen has more 1,6 glycosidic
bonds than starch, giving it more side branches, this means that glycogen can be
broken down by enzymes at many side branches at once very rapidly, making it
ideal source of glucose for animals may require rapid release of energy.
Explain how the structure of glycogen relates to its role as an energy storage
molecule:
-The polysaccharide is a polymer of alpha-glucose, so it has a high energy content.
-The polysaccharide is large and insoluble, so no osmotic effect on the cell.
-Glycogen is highly branched so it can be broken down by enzymes at several points
at once which makes hydrolysis faster.
-It is compact as it is branched, so high energy density, lots of energy stored in a
small space.

1.5
Displayed formula of the formation of a triglyceride molecule by the condensation
reaction between a glycerol and three fatty acids forming ester bonds and the
reverse hydrolysis reaction:

Glycerol stays the same so variation in the structure and properties of fats (solids)
and oils (liquids) comes from the fatty acids:
All fatty acids have a carbonyl group at one end and a hydrocarbon chain attached.
Differences in lipids:
Saturated: A fatty acid in which one carbon atom is joined to another by
single covalent bonds, there is no double bonds between the
carbon atoms of the hydrocarbon chain.
 Monounsaturated: A fatty acid with one double covalent bond between carbon
atoms in its hydrocarbon chain.
Polyunsaturated: A fatty acid with two or more double covalent bonds in its
hydrocarbon chain.

-Saturated lipids are likely to be fats which are solid at room temperature because
they are straight/ linear molecules due to a lack of double bonds. So they can pack
together tightly and rigidly to form the regular arrangement of molecules of solids.
-Unsaturated lipids are likely to be lipids which are liquid at room temperature as
they contain C double bonds, this means the molecules are kinked/ bent, so they
don’t have a regular arrangement.
Give two differences between the structures of saturated and unsaturated lipids:
-Saturated lipids have linear chains but unsaturated lipids have bent/ kinked chains
due to the presence of C double bonds.
-Saturated lipids don’t have any double bonds between their carbon atoms but
unsaturated lipids have at least one carbon double bond between their carbon
atoms.
Explain why glucose is more soluble in water than NaCl:
-Water is a polar solvent.
-Glucose has much more hydroxyl groups than NaCl thus can form more hydrogen
bonds with water molecules.
-Also, glucose is a larger molecule so can be surrounded by more water molecules.
Explain why fatty acids are less soluble in blood than glucose and sodium chloride:
-Water is a polar solvent.
-Fatty acids have non-polar tails.
-Thus don’t form hydrogen bonds with water.
Unit 1, Topic 1, Subtopic 2: Mammalian transport systems.
1.6
As the size of an organism increases:
It’s surface area to volume ratio decreases.
larger organisms need mass transport systems because:
Since large animals have a smaller SA to V ratio, there is a larger diffusion distance
of nutrients into the cells, which is inefficient to meet the animals’ very high
metabolic demands. Thus, mass transport system is needed to overcome this
limitation as it increases the SA of the exchange surfaces, and its fast supply is
achieved through active transport and the heart pump.
1.7
Explain how the structure of an artery is related to its function:
1)Narrow lumen to maintain high blood pressure.
2)Artery walls are thick with collagen to withstand high pressure.
3)Contains elastic fibers which stretch and recoil to maintain pressure.
4)Contains smooth muscle that contract and relax to maintain high pressure.
5)Smooth endothelium to reduce resistance/ friction to blood flow.
6)Folded endothelium allowing for expansion.
(…to maintain pressure by changing the diameter of the lumen.)
Explain how the structure of a vein is related to its function:
1)Wide lumen reduces friction between the blood and the vein endothelium, so
less resistance to blood flow.
2)Contains valves to prevent blood back flow, ensuring the one-way flow of blood
towards the heart.
3)Aided by body muscles that contract, squeezing the blood back towards the
heart.
Explain how the structure of a capillary is related to its function:
1)Very narrow lumen so RBCs flow in single files, blood travels more slowly, more
opportunities/ time for diffusion to occur.
2)One cell thick wall so very short diffusion distance facilitates diffusion rate and
thus nutrient exchange.
3)Pores allowing WBCs to squeeze through, entering infected tissues to combat
pathogen for immunity.
4)Capillaries branch between cells meaning no cell is far from a capillary so
substances can diffuse quickly due to the short diffusion distance.
 1.9
Components of the blood:
Component. Function. Structure related to function.

Plasma. Carry dissolved urea, glucose, A liquid made up of 90% water

hormones, amino acids and heat capable of having proteins and gases
(maintaining body temperature) dissolved in it.
around the body.
Erythrocytes. Contains hemoglobin which binds No nucleus to free up space to bind
to oxygen and some carbon to more oxygen.
dioxide, transport of … Biconcave shape to increase its SA to
volume ratio.
Small to pass through capillaries.
Leukocytes. Phagocytes engulf pathogens Irregular shape of phagocytes
while lymphocytes produce and allowing them to change shape and
release antibodies — defend squeeze out of blood vessels and get
against infection. to the site of infection.
Many ribosomes to make
antibodies.
How is oxygen transported in RBCs:
Each Hb molecule contains four peptide chains, each with an iron containing heme
prosthetic group. Each heme group can bind to one oxygen; hence four oxygen
molecules bind to one Hb molecule to form oxyhemoglobin.

The first bonded oxygen molecule changes the arrangement of the molecule
(conformational change) making it progressively easier for the following oxygen
molecules to bind. (As the affinity of Hb increases.) In reverse, it gets progressively
harder to remove oxygen.
The removal of O2 from the RBCs’ cytoplasm is important because a steep
concentration gradient for more diffusion of O2 is maintained.
How is carbon dioxide transported in RBCs:
1)Very low percentage is dissolved and transported directly in the plasma.
2)30% Binds with Hb forming carbaminoharmogobin.
3)Reacts with water in the cytoplasm to form carbonic acid (catalysed by the
enzyme carbonic anhydrase) then dissociates into HCO3- and H+ ions. The
hydrogencarbonate ions pass out of the RBCs by diffusion into the plasma and
chloride ions move in; the hydrogen ions bind to Hb.

Hb is considered to be a buffer because Hydrogen ions can combine with

haemoglobin, forming haemoglinic acid and preventing the H+ ions from lowering
the pH of the red blood cell.
The chloride shift is important as it prevents an electrical imbalance, as negative
hydrogencarbonate ions have been transported out.

The oxygen association/ dissociation curve:

Shows the rate at which oxygen associates/ dissociates with Hb at different partial
pressures of oxygen.
Partial pressure of oxygen refers to the pressure exerted by oxygen within a mixture
of gases.
The sigmoidal shape of the curve results from the fact that Hb’s affinity for oxygen
changes at different partial pressures of oxygen.

Association:
1)It is difficult for the first O2 molecule to bind to Hb, so Hb
has a low affinity for oxygen at low pO2. Hence, the binding
of the first O2 is slow, explaining the relatively shallow
curve.
2)After the first O2 molecule binds to the Hb, the Hb
protein has a conformational change in shape, making it
progressively easier for the next O2 molecule to bind, so Hb
has a higher affinity for oxygen at medium/ high pO2.
Hence, the binding of the remaining O2 molecules is sped
up, explains the gradient of the graph becomes increasingly
steeper in the middle.
3)As the Hb molecule approaches saturation, increasing the
pO2 by a large amount only has a small effect on the
percentage saturation of Hb, this is because most. Binding
sites on Hb are already occupied.
Dissociation:

Bohr-effect:
When the partial pressure of CO2 in blood is high, Hb’s affinity for oxygen is
reduced so to release oxygen more readily for aerobic respiration of respiring
tissues (which are also producing CO2) at the same pO2.
Fetal Hb:
Curve shifted to the left. The fetal Hb has a higher affinity for oxygen than adult Hb
to maintain a steep concentration gradient for the diffusion of oxygen from the
maternal blood to the fetal blood across the placenta for sufficient O2 to be
transferred across the placenta in support of the fetus’ aerobic respiration.
Myoglobin:
Found in the muscles. Myoglobin has a higher affinity for O2 at any pO2 thus it only
releases O2 at very low pO2. It acts as a storage of O2, keeping aerobic respiration
for longer when the pO2 is low.

1.8
Structure of the heart and the main blood vessels:
Double circulatory system:
The blood passes through the heart twice in one complete circuit around the body.
Two separate circuits separating oxygenated and deoxygenated blood.
Explain the advantages of the double circulatory system:
Oxygenated blood and deoxygenated blood are kept separate, maintaining steep
concentration gradient for the diffusion of O2.
Pressure is lower in lungs to prevent damage. Pressure is higher to body so blood
can be delivered to all parts of body which is a longer distance.
Events of the cardiac cycle:
1)During the atrial systole, the muscles (walls) of atria contact, the pressure in the
atria rises above the ventricles increases, forcing the AV valves open, blood is
forced into the ventricles.
2)During the ventricular systole, the muscles of ventricles contract, the pressure in
the ventricles rises above that in the atria forcing the AV valves to close, preventing
back flow. On the other hand, the pressure in the ventricles rises above that in the
aorta and pulmonary artery forces the SL valves to open, blood is forced into the
arteries and out of the heart.
3)During diastole, the ventricles and atria are both relaxed and the pressure in the
ventricles drop below that in the arteries, forcing the SL valves to close. However,
the atria continue to fill with blood, pressure in the atria rises above the ventricles
forcing the AV valves to open — blood flows passively into the ventricles.
Explain the delay between the atrial systole and the ventricular systole:
For the AV valves to close in order to prevent back flow of blood into the atria.
When calculating heart beats in bpm:
Always round up to an integer.
1.11
Events of the blood clotting process (thrombosis):
1)Platelets are released.
2)Thromboplastin (a soluble protein) is released and it acts as an enzyme.
3)Thromboplastin triggers catalyses the convention of prothrombin to thrombin
together with the presence of calcium ions in the blood.
4)Thrombin catalyses the conversion of the soluble protein fibrinogen to the
insoluble protein fibrin.
5)Fibrin forms a mesh, trapping platelets and RBCs.
6)A blood clot is formed.

1.10
Events that lead to atherosclerosis:
1)Damage to the endothelium of arteries.
2)Triggers an inflammatory response.
3)Accumulation of cholesterol in the endothelium forms atheroma.
4)Calcium salts added to the atheroma.
5)Formation of a plaque.
6)Loss of elasticity of artery and narrowed lumen reduce the blood flow to the
heart.
7)Also blood pressure is raised.
Unit 1, Topic 1, Subtopic 3: CVD.
1.12
BMI calculation:
Weight (kg)* height squared (m)
Issues with BMI as a predictor of CVD:
-Doesn’t account for different ages and races.
-Doesn’t account for body fat % nor its distribution.
-Makes no allowance for people’s body compositions, eg. muscle.
Indication of obesity:
-A waist to hip ration larger than 1.
-A BMI larger than 30.
Smoking increases the risk of CVD:
-Smoking increases the blood pressure.
-Which increases the risk of damage in the endothelium of arteries.
-Which increases the risk of the formation and buildup of atheroma and plaques.
-The arterial lumen is narrowed, reduced blood flow to the heart.
High levels of LDL (high LDL/ HDL ratio) increase the risk of CVD:
-LDL is made from saturated fat, protein and cholesterol.
-LDL bind to cell membranes and if the cell membranes are saturated, LDL remains
in the blood.
-LDL increases blood cholesterol as it remains in the blood.
-Cholesterol is deposited to form atheroma and plaques in the arterial
endothelium.
-The lumen of the artery is narrowed, reduced blood flow to the heart.
High levels of HDL (low LDL/ HDL) decrease the risk of CVD.
-HDL is made from unsaturated fat, cholesterol and more protein.
-HDL removes blood cholesterol by carrying it to the liver to be broken down.
-The risk of plaque formation/ atherosclerosis is reduced.
Regular exercise (opposite to inactivity) decreases the risk of CVD.
-lower blood pressure.
-Prevention of obesity and diabetes (type 2 can cause endothelial damage).
-Lower blood cholesterol levels (lower risk of atherosclerosis).
-Balance of lipoproteins (LDL/ HDL ratio).
-Reduced stress (lower blood pressure).
The following diet reduces the risk of CVD:
-Low levels of cholesterol and saturated fat intake.
-Low salt (as sodium can increase the blood pressure).
-Low in LDL.
-Antioxidants (eg. VC) intake.
1.13
Dietary antioxidants reduce the risk of CVD by:
-Reducing and neutralizing the free radicals (ROS) in the blood.
-Free radicals cause cell damage.
-Thus, preventing them from oxidizing the LDL.
-Less oxi-LDL means less activation of monocytes in the inflammatory response.
-Less formation of macrophages.
-Reduced chances of foam cell formation thus plaque formation (Foam cells are
cholesterol-laden cells which forms a plaque after the macrophages have
phagocytoses lipids).

1.15, 1.16, 1.17

Correlation and causation:
Correlation is a measure of the linear relationship between two variables, it is
different from causation, further research is always needed to prove that one
variable causes the other.
To prove causation, the following may be done:
-Induction studies (The risk factor X is increased to see any increase in the risk of
disease Y).
-Intervention studies (The risk factor X is removed to see any decrease in the risk of
Y).
-Reasonable scientific explanation.
-Stats test.
Risk:
The probability that an event can happen. A risk factor increases the probability
(the mathematical chance of an event occurring) that you will develop a particular
NCD.
Actual risk:
Number of selected outcomes over number of possible outcomes.
Perceived risk:
The subjective judgement people make about the severity of a risk, it is the reason
why people underestimate/ overestimate the risks due to diet and other lifestyle
factors in the development of CVD. This can often be explained by a lack of
awareness/ education.
Key components of designing a study:
-Validity:
Properly designed for the aim, by ensuring only the one independent variable is the
factor that affected the results (Improved by setting up control variables).
-Reliability:
The investigation is repeatable by other scientists and can get similar results
(Improved by repeats with averages, or a larger sample size).
-Precision:
Measurements with little difference between them (similar readings) which
improved accuracy.
1.20
Benefits and risks of CVD treatments.
-Antihypertensives. (By lowering the blood pressure.)
Diuretics. Increase the volume of urine produced. Nausea.
This eliminates excess fluids and salts in Coughing.
the kidney, so that the blood volume Constipation.
decreases, thus a smaller volume of Fainting.
blood is pumped which decreases the Tiredness.
heart rate and blood pressure. Muscle cramps.
Beta blockers. Block the response of the heart to
adrenaline. Thus lower the heart rate
and weaken the ventricular systole.
Blood pressure falls as a result.
Sympathetic Prevent muscles in the arterial walls
nerve blockers. contract by blocking the impulse from
the sympathetic nervous system (which
normally increase arterial constriction).

-Statins. (By lowering the level of cholesterol in blood.)

By inhibiting the enzyme in the Nausea.
liver responsible for making Constipation.
cholesterol/ LDL. Muscle and joint aches.

-Anticoagulants/ warfarin. (By reducing thrombosis.)

By interfering/ inhibiting the Reduced blood clotting
manufacture of prothrombin might lead to excessive
in the body. bleeding.

-Platelet inhibitory drugs/ eg. Aspirin. (By reducing the blood clotting ability.)
By making the platelets Aspirin irritates stomach
less sticky so they don’t linings.
aggregate as much. Higher chance of
bleeding in the stomach.
Unit 1, Topic 2, Subtopic 1: Membranes and transport.
2.20
Structures of membranes:
-Structure of a phospholipid.

The head (glycerol and phosphate) is polar because the presence of negatively
charged ion, making the head part hydrophilic and dissolve in water.
The tails (2 fatty acids) are non-polar because the lack of ions and charged groups,
making the tail part hydrophobic and insoluble in water.
The fluid bilayer and the fluid mosaic model.

As there are aqueous solution on either side of the membrane (cytoplasm and
tissue fluid), the hydrophilic head faces towards the water as it dissolves/ interacts/
associates with water, the hydrophobic tail orientates itself away from water.
Other components in the bilayer
Explain the importance of the fluidity of membranes:
-Membranes can change shape.
-Allowing for fusion of membranes, eg. During fertilisation.
-Allowing for phagocytosis, exocytosis, endocytosis.
-And substances can move across the membrane.
Explain why an increase in temperature increases the fluidity of the membrane.
-An increase in temperature increases the kinetic energy of the phospholipids.
-Bonds like hydrophobic interactions between fatty acids are broken.
-So, the phospholipids move more in the bilayer.
Explain why a decrease in cholesterol increases the fluidity of membranes.
-Cholesterol interacts and form bonds with the fatty acids of phospholipids.
-Thus, cholesterol restricts the movement of the phospholipids in their bilayer.
-A decrease in cholesterol increases the movement of phospholipids.
Explain why fatty acids with shorter side chains increase the fluidity of a
membrane.
-They require less energy to move.
2.10
Diffusion definition:
The movement of molecules (liquid/ gas) from an area of their higher concentration
to an area of their lower concentration down their concentration gradient until
uniform equilibrium due to the random motion of molecules.
Types of diffusion:

Simple diffusion Facilitated diffusion

Types of Small, non-polar, lipid soluble. Large, polar, charged, water soluble.
molecules The molecules pass through The molecules pass through are specific
are not specific. to their protein carriers.
Examples CO2, O2. H2O, amino acids, ions, glucose.
Mechanisms Through phospholipids. Through protein channels (hydrophilic)
and carrier proteins of specific shape to
the molecules. They don’t require
energy and the process is all passive.
Describe how carrier proteins enable facilitated diffusion:
The molecule whose shape is specific to a particular carrier protein/ channel binds
to the carrier protein passively, this causes a conformational change in the carrier
protein (opens and closes), so the molecule is carried across and released to the
other side of the membrane down its concentration gradient.
Factors affecting diffusion:
Temperature. More kinetic energy so faster movement of molecules.
Concentration gradient. The steeper the concentration gradient, the faster the
rate of diffusion. This is done as the body immediately
metabolising a substance, chemical changes or take it
away from its location immediately.
Size of particles. The smaller the particles, the faster the rate.
Thickness of exchange The thinner the exchange membrane, the shorter the
membrane. (If present.) diffusion distance, thus the faster the rate.
Surface area to volume The larger the surface area to volume ratio, the more
ratio. particles can be exchanged at one time, the faster the
rate.
The number or density The larger the number, more exchange of particles at.
of protein channels or One time, the higher the rate of facilitated diffusion.
carrier proteins.
Fick’s law of diffusion (for a given temperature):

Understand how the structure of the mammalian lung is adapted for rapid gas
exchange:
-Alveolus has only a thin, single layer of epithelial cell. (One cell thick).
-Capillary consists of a single layer of endothelial cell.
This shortens the diffusion distance for O2 and CO2.
-Lots of alveoli forming a network.
This increases the surface area to volume ratio of the gas exchange membrane.
-A thin layer of firm of water in alveoli.
O2 first dissolve in water as a solution before simple diffusion, this makes diffusion
easier.
-Constant and rapid flow of blood.
Removes O2 and brings CO2 at a high rate to maintain a steep concentration
gradient of O2 and CO2.
2.40
Osmosis definition:
The net movement of free water molecules through a partially permeable
membrane from an area of higher water potential to an area of lower water
potential down a water potential gradient.
(From a dilute solution to a concentrated solution.)
Osmosis in plant cells:

The solution is hypotonic to the cell’s cytoplasm,

meaning the concentration of solutes outside the cell is
lower than inside, which means the water potential
outside is higher than inside.
Water moves into the cell, making the vacuole swell and
pressing the cytoplasm against the cell wall, exerting
turgor pressure, the cell is turgid. The cellulose plant cell
wall prevents the cell from bursting.

The solution is isotonic to the cell’s cytoplasm, meaning

both the concentration of solutes and the water
potential inside and outside the cell are the same.
No net movement of water/ equal volume of water
moves in and out of the cell, the vacuole shrinks and
doesn’t push against the cell wall, the cell loses turgor,
incipient plasmolysis.

The solution is hypertonic to the cell’s cytoplasm,

meaning the concentration of solutes outside the cell is
higher than inside, which means the water potential
outside is lower than inside.
Water moves out of the cell, the vacuole and the
cytoplasm shrink, the cell membrane is pulled away
from the cell wall.
Osmosis in animal cells:

The solution is hypotonic to the cell’s cytoplasm, so water

moves in by osmosis down a water potential gradient, the
cell bursts and is lyses as too much water moves in.

The solution is isotonic to the cell’s cytoplasm, so there’s no

net movement of water, the cell maintains its normal
biconcave shape.

The solution is hypertonic to the cell’s cytoplasm, so water

moves out by osmosis, the cell shrivels and becomes
cremated.

2.50
Active transport definition:
The movement of molecules (large ions and polar) from an area of their lower
concentration to an area of their higher concentration against a concentration
gradient across a membrane using the energy in ATP that has been broken down by
ATPase.

Active transport mechanism:

-Molecule of a specific shape binds to its specific protein carrier.
-ATPase catalyses the hydrolysis of ATP.
-ATP is hydrolysed to ADP and phosphate. The energy released is used to cause a
conformational change/ change in shape of the carrier protein which carries the
molecule across the membrane/ released to the other side.
-Finally, carrier protein returns to its original shape passively to allow more
molecules to enter.
Endocytosis:
Phagocytosis mechanism:
-Membrane protein receptors interact with bacteria.
-Macrophage membrane surrounds the bacteria.
-The field movements of phospholipids allow the membrane that surrounds the
bacteria to fuse.
-Formation of a vesicle that contains the bacteria.
U1, T2, Subtopic 2: Structures of proteins and enzyme activity.
2.60
Structure of an amino acid:

-The elements proteins/ amino acids are made of are C, H, O, N, S (in cysteine).
-There are 20 naturally occurring amino acids, the only difference between them is
the nature of the R groups.
-The amino/ amine group is basic, and the carbonyl group is acidic.

The formation of peptide bonds between amino acids:

-A hydroxyl is lost from the carbonyl group of one amino acid while a hydrogen is
lost from the amine group of the other amino acid, resulting in the formation of a
dipeptide, the R groups are not involved.

The four levels of protein structures:

The primary structure of protein:

-The sequence of amino acids that that makes up the polypeptide chain.
-The primary structure determines the folding of a protein as the types and
positions of amino acids determines the type of bonds between R groups. This
ultimately determines the shape and properties of a protein.
-The amino acids are bonded together by peptide bonds.

The secondary structure of protein:

-The arrangement of the polypeptide chain into a regular, repeating 3D structure,
either an alpha-helix or a beta-pleated sheet.
-Hydrogen bonds form between the negatively charged N or O atoms with the
positively charged H atoms.
-Peptide bonds also present.

The tertiary structure of a protein:

-A more compact structure of the bent/ twisted polypeptide chain.
(Conformational)
-Hydrogen bonds between a +H and an electronegative atom, both on R groups.
-Disulphide bonds between two cysteine amino acids.
-Ionic bonds between charged R groups.
-Hydrophobic interactions between non-polar R groups.

The quaternary structure of a protein:

-A 3D structure consists of the combination of two or more tertiary polypeptide
chains.
-All the bonds in a tertiary protein plus non-protein prosthetic groups may be
associated in conjugated proteins.

How does the primary structure of a protein determine its structure and function:
-The primary structure determines the types and sequence of amino acids.
-The types and positions of amino acids determine the types and positions of
disulphite, ionic, hydrogen and hydrophobic bonds.
-This determines the folding and the 3D structure of the protein.

Differences between fibrous and globular proteins:

-Fibrous proteins have secondary structures but globular proteins have tertiary or
quaternary structures.
-Fibrous proteins are insoluble but globular proteins are soluble due to the inward
orientation of hydrophobic R groups while the hydrophilic/ polar R groups orientate
themselves towards the aqueous surroundings.
-Fibrous proteins have long, parallel polypeptide chains held together by H-bond
cross-links; globular proteins have spherical shapes with tightly folded polypeptide
chain(s).
-Fibrous proteins have structural functions and globular proteins have physiological
functions.
-Examples of fibrous proteins are collagen, elastin, keratin and fibrin. Examples of
globular proteins are enzymes, HB, fibrinogen, hormones.

Collagen:
-An extremely long fibrous protein that provides tensile strength support to
tendons, ligaments, bones and skins, also forming connective tissues.
-The primary structure is repeating unites of glycine and two other amino acids.
-The secondary structure is an alpha-chain.
-The quaternary structure contains 3 alpha chains arranged in a triple helix, held
together by a lot of H-bonds.
-The H-bonds and covalent bonds hold the triple helix together as fibrils which are
held together forming collagen fibres.

Haemoglobin:
-Contains four polypeptide chains bonded together by disulphide bonds, each
polypeptide chain surrounds an iron-containing haem prosthetic group that each
bind or releases one oxygen molecule.

Enzymes:
-Biological (found and produced in living organisms) catalysts that speed up the
rate of a reaction without being used up or undergoing a permanent change.
-Enzymes lower the activation energy of a reaction with alternative energy
pathways by bringing reactants together, holding them in the correct orientation
and destabilising the bonds in reactants.
The induced fit model of an enzyme:
-Substrate(s) which has complementary shape to the active site of an enzyme binds
to the active site.
-The ES complex is formed as both the active site and the substrate undergo a
conformational change for an induced fit that allows for an ideal tight bonding.
-Substates have been converted into their products after the reaction.
-Products released and the enzyme carries on binding to another substrate without
being used up.

The effect of temperature on an enzyme catalysed reaction.

-As temperature increases, the enzyme and its substrate gain more kinetic energy.
-The rate of successful collisions increases.
-More ES complexes are formed.
-The rate of enzyme reaction increases till the optimum temperature.
-At higher temperatures, too much increase in kinetic energy causes hydrogen and
ionic bonds to be broken.
-The enzyme is denaturing as its tertiary 3D structures and active site change shape.
-Substrates can no longer bind to the active site, less ES complexes formed.
-Rate decreases sharply.

The effect of pH on an enzyme catalysed reaction.

-At extremes of pH, charged H+ ions and OH- ions disrupt/ break the ionic and H
bonding in the enzyme.
-This alters the 3D tertiary structure of the enzyme.
-This alters the shape and charge of the active site.
-Substrates can no longer bind to it.
-ES complexes are less likely to form.

The effect of substrate concentration on an enzyme catalysed reaction.

-As the concentration of substrate increases, the number of substate molecules

increases.
-A greater chance of successful collisions between enzymes and substrates.
-More ES complexes forming.
-The rate eventually levels off when all enzymes are saturated.

Why do we measure the initial rate of a reaction:

-To ensure that substrate concentration is not a limiting factor.
-As the reaction proceeds the substate concentration decreases as the substates are
being used up.
U1, T2, Subtopic 2: Structures of proteins and enzyme activity.
The nature of genetic codes:
Non-overlapping:
Each triplet code is discrete, so each codon is read once only.
Degenerate:
The same amino acid is coded by more than 1 triplet code. (This reduces the effect
of mutation as there will be no effect on the resulting protein since the same amino
acid is produced.) Hence, there are more codes than the number of amino acids.
Universal:
The same sequence of genetic codes shared by many organisms.
DNA replication process:
-DNA helicase unwinds the double helix by breaking H bonds between
complementary base pairs.
-Both strands act as templates.
-DNA polymerase lines up free nucleotides along the template strands and
catalyses the phosphodiester bonds between the nucleotides.
-The new nucleotides bind with the original nucleotides complementarily, A-T, C-G.
-DNA ligase reforms the H bonds and catalyses the phosphodiester bonds,
annealing the fragments.
-Semi-conservative model.
Transcription process:
-Transcription happens in the nucleus.
-DNA unwinds as RNA polymerase catalyses the breaking of H bonds.
-Mononucleotides line up with complementary bases on the template/ non-
coding/ anti-sense strand of the DNA.
-RNA polymerase then catalyses the formation of phosphodiester bonds between
the nucleotides, a condensation reaction.
-The mRNA detaches from the DNA.
-The mRNA strand leaves the nucleus into the cytoplasm via the nuclear pores.
Translation process:
-Translation happens in the cytoplasm.
-The ribosome first binds to the starting codon (AUG) of an mRNA strand.
-A tRNA with complementary anticodons bind to the codons on the mRNA while
bringing a specific amino acid.
-H bonds between tRNA and mRNA.
-The ribosome moves along the mRNA, bringing together 2 tRNAs.
-The two amino acids are joined together by peptide bonds using an enzyme and
ATP.
-The first tRNA gets released and is free to collect another amino acid.
-When the stop codon is reached, the mRNA strand and the last tRNA detach and
the polypeptide chain is complete.

The role of mRNA in protein synthesis:

-mRNA is a copy of a section of DNA.
-It moves out of nucleus into the cytoplasm to the ribosomes.
-It acts as a template for translation as it carries the genetic information for the
protein being synthesized to the ribosome.
The role of tRNA in protein synthesis:
-Involved in translation as it has anticodons complementary to the codons on the
mRNA.
-Brings its specific amino acid to the ribosome.
-Holds the amino acids in place for the formation of a polypeptide chain.
Differences between tRNA and mRNA:
-tRNA is folded and has a clover leaf shape while mRNA is straight.
-tRNA contains one polynucleotide (NOT polypeptide!) strand with hydrogen bonds
but mRNA, although also contains only one polynucleotide strand, there’s no
hydrogen bonds.
-tRNA has anticodons but mRNA has codons.
-tRNA has an amino acid binding site.
-tRNA has a fixed length but mRNA has variable length.
Genotype:
The combination of alleles.
Describe how a mutation results in cystic fibrosis:
-Mutation causes random changes in the CFTR gene.
-This results in a faulty CFTR protein.
-Chloride ions can’t move out of the cells by facilitated diffusion and since ENAC is
not inhibited, the sodium ions accumulate in the cells as well.
-The water potential inside the cells is reduced, causing water to enter or stay in the
cells by osmosis.
-As a result, the mucus in the airway becomes very sticky due to a lack of water.
The benefits of a prenatal test for diseases caused by recessive alleles:
-Couples who are both heterozygous informed and identified.
-So, they can make an informed decision on whether to have baby or not.
The cons of prenatal testing/ implications of genetic screening:
-Might result in false results.
-It can be considered unethical as the parents might abort their baby though the
baby has a right to live.
-Other genetic conditions might be discovered.
Health problems linked to sticky mucus due to cystic fibrosis.
-The airway of the trachea and bronchi blocked so insufficient air reaches the
alveoli in the lungs.
-The thick mucus also blocks the pancreatic duct so pancreatic enzyme are unable
to reach the duodenum.
-Hence, large insoluble nutrient molecules are not broken down and are therefore
unable to be absorbed…n
-The sticky mucus can also block the cervix, so sperm cells are unable to reach the
egg cell for fertilisation. (Causing infertility.)
Why the number of babies with a recessive disease went down following an
introduction on a prenatal genetic screening:
-Couples who are both heterozygous identified.
-So, they can make an informed decision on other to have babies or not.
-Resulting in fewer babies with the recessive disease born.
Possible reasons why a conclusion with given data is not valid:
-Other factors not controlled/ taken into account.
-Small sample size.
-False results.
-No statistics presented.
Assessing studies:
Reliability/ repeatability:
-Sample size.
-Presence of statistical data.
-Presence of statistical tests.
Validity:
-Control variables. Don’t forget explanations given to each examples provided.
-Provide multiple examples for control variables.
-Whether numbers of sample are identical in each category.
-Placebos used as controls.