2025

As Level

BIOLOGY
Unit 1
Notes
Dr. Rana Essam
 Notes Content

Topic 1: Molecules, transport and health

• Transport around the body ............................ 3
• Cardiovascular diseases ................................. 15
• Biological molecules ....................................... 24

Topic 2: Membranes, proteins, DNA and gene expression

• Gas exchange ................................................ 41
• Cell membrane ............................................. 46
• Enzymes ........................................................ 53
• Genetics ........................................................ 56

Core Practical
• Unit 1 Investigations ................................. 76
• Calculating Standard Deviation .............. 80
• Statistical Analysis .................................... 81
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Topic 1
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Molecules, Transport and Health
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 Chapter 1
Transport around the body
According to circulation, we classify living organisms as follows:
Without With circulation
Circulation
Small unicellular Open Closed

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organisms
Ex. Amoeba The heart is a Single Double
(1 cell) hollow muscular
tube.

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No blood vessels The blood passes The blood passes
through the heart through the heart
once per cycle. twice per cycle.
Ex. Insects Ex. Fish Ex. Mammals
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• How do small unicellular organisms survive without circulation?
- Large surface area to volume ratio.
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- Short diffusion distance.

- Steep concentration gradient.
- Low energy requirements.
So there are no limitations of diffusion.
• When you are asked about larger organisms: you state the opposite as
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circulation helps to overcome limitations of diffusion.

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• Advantages of double circulation:

- To ensure complete separation of oxygenated blood from deoxygenated blood.
- The left side of the heart pumps blood at a relatively high pressure to ensure
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delivery of oxygen and nutrients to all tissues over a long distance.

- The right side of the heart pumps blood at a relatively low pressure to prevent
damage of delicate capillaries around alveoli.
- This helps to overcome limitations of diffusion.

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 The Heart
- Site: center of the thorax.
- Size: fist of one hand.
- Shape: inverted cone with the apex below pointed to the left.
- Supply of blood: Coronary arteries.
- Special features: It is the strongest muscle in the body as it keeps beating since
birth till death and it has its own pace maker (SAN).

Structure

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• Describe the structure of the heart: (4 4 4 SST)

- It has four chambers, two atria above and two ventricles below.
- It has four valves, two AV valves between atria and ventricles (Tricuspid value
on the right side and Bicuspid valve on the left side) and two semi-lunar valves
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(Pulmonary semi-lunar and Aortic semi-lunar).

- It has four vessels, Venacava entering the right atrium, Pulmonary artery
exiting the right ventricle, Pulmonary veins entering the left atrium, and the
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Aorta exiting the left ventricle.

- The two sides of the heart are separated by muscular Septum.
- The heart is Supplied by Coronary arteries.
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- The chamber with the Thickest wall is the Left Ventricle.

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• Describe the circulation through the heart:

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1) Deoxygenated blood from the whole body enters the right atrium carried by
the vena cava.

through Tricuspid valve.

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2) Deoxygenated blood is pumped from the right atrium into the right ventricle

3) Deoxygenated blood is then pumped from the right ventricle to the lungs
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carried by the Pulmonary artery passing through Pulmonary semi-lunar valve.
In the lungs, oxygenation takes place.
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4) Oxygenated blood is returned to the left atrium carried by the pulmonary

veins.
5) Oxygenated blood is pumped from the left atrium into the left ventricle
through Bicuspid valve.
6) The left ventricle pumps oxygenated blood to all the tissues of the body
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carried by the aorta passing through Aortic semi-lunar valve.

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Pulmonary circulation: 3 & 4 only.

Systemic circulation: 1 & 6 only.
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• Describe the function of the heart:

- The heart generates mass flow which pumps blood from higher pressure to
lower pressure over a long distance. This maintains concentration gradient.
- This mass flow helps to overcome limitations of diffusion such as small surface
area to volume ratio, non-steep concentration gradient, long diffusion distance
and high energy requirements.

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 Valves

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Definition: E
Valves are structures that allow blood flow in one direction and prevent back flow
in the opposite direction.
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Mechanism of action:
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A valve opens when the pressure before the valve is higher than pressure after the
valve.
A valve closes when pressure after the valve is higher than pressure before.
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AV valves:
- They open when pressure in the atria is higher than the ventricles.
- They close when pressure in the the ventricles is higher than the atria.
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- The valves are held by tendons to papillary muscles to prevent their inversion
into atria during ventricular contraction.
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Semi-lunar valves:
- They open when pressure in the ventricles is higher than major vessels.
- They close when pressure in major vessels is higher than the ventricles.
- Blood collects in the pockets of the valve closing it.

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 The Cardiac Cycle
Average cardiac cycle duration: 0.8s.

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Points of Diastole Atrial Systole Ventricular Systole
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comparison (0.4s) (0.1s) (0.3s)

Chambers Both Atria and Atria contract & Atria relax &
condition Ventricles relax. Ventricles relax. Ventricles contract.
Pressure Low pressure.
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(Atria slightly Atria higher than Ventricles higher

higher than Ventricles. than Atria.
Ventricles).
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Valves condition AV open AV open AV closed

Semi-lunar closed Semi-lunar closed Semi-lunar open.
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Direction of Cardiac filling From Atria into From Ventricles into

blood flow Ventricles major arteries.
(Ventricular filling)
Volume of blood 0% — 70% 70% —100% 100% — 0%
in ventricles

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Define:
Heart rate: Number of heart beats per minute. (bpm)
Stroke volume: volume of blood pumped in one beat. (cm 3)
Cardiac output: volume of blood pumped per minute. (cm 3)

Pressure Changes Graph

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Describe Explain
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A Bicuspid valve closes. Pressure in left ventricle is higher than

left atrium.
B Semi-lunar valve opens. Pressure in left ventricle is higher than
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Aorta.
C Semi-lunar valve closes. Pressure in the aorta is higher than left
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ventricle.
D Bicuspid valve opens. Pressure in left atrium is higher than left
ventricle.

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How to calculate heart rate from a pressure changes graph?

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- Duration of one beat = Distance from peak to peak
1.1 - 0.3 = 0.8s
- Heart rate = 60 / duration of one beat
60 / 0.8 = 75 bpm E
How to calculate heart rate from a volume changes table?
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Time/s Volume of blood in left ventricle as a percentage of the maximum (%)
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0.0 70
0.1 100
0.2 70
0.3 30
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0.4 0
0.5 35
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0.6 60
0.7 70
0.8 70
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0.9 100
1.0 70

- Duration of one beat = Distance between 2 successive repeated figures.

0.8 - 0.0 Or 0.9 - 0.1 = 0.8s
- Heart rate = 60 / duration of one beat
60 / 0.8 = 75 bpm.
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• Describe the role of valves in the cardiac cycle: **
(location and condition in each phase with explanation)

- AV valves are located between atria and ventricles.

- They are open during atrial systole to allow blood flow from atria to ventricles.
- They are closed during ventricular systole to prevent back flow of blood into
atria.
- They are open during diastole to allow for cardiac filling.

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- Semi-lunar valves are located at the base/origin of major arteries.
- They are open during ventricular systole to allow blood flow from ventricles
into major arteries.
- They are closed during atrial systole and diastole to prevent back flow of blood
into ventricles.

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ventricle: ** E
• Explain the difference in pressure between the left ventricle and the right
(structure and function)
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- The right ventricle pumps blood at a lower pressure for a shorter distance to the
lungs to prevent damage of delicate capillaries around alveoli.
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- The right ventricle has thinner wall with weaker muscles.

- While, the left ventricle pumps blood at a higher pressure for a longer distance
to all body tissues.
- The left ventricle has thicker wall with stronger muscles.
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 Blood vessels

• Arteries:
Function: Arteries carry blood away from the the heart. All arteries carry
oxygenated blood except the pulmonary artery.

Structure:
- Thick wall
- Narrow lumen and no valves in the lumen.

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- Its wall consists of 3 layers:
• Tunica intima: single layer of cells (Endothelium)
• Tunica media: elastic fibers, smooth muscles and connective tissue.
• Tunica adventitia: collagen fibers

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Pressure: Higher than veins and capillaries.

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Adaptations:***
- Thick wall to withstand high pressure.
- Narrow lumen to maintain the high blood pressure.
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- No valves in the lumen as blood is moving under high pressure.

- Tunica intima (endothelium) is smooth to reduce friction with moving blood
and folded to stretch without breaking.
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- Tunica media ** contains elastic fibers that stretch during ventricular systole to
prevent blood pressure from getting too high and recoil during diastole to
prevent blood pressure from getting too low so they keep blood pressure within
a narrow range. It also contains smooth muscles for redistribution of blood
through vasodilation and vasoconstriction.
- Tunica adventitia contains collagen fibers to protect the artery from bursting or
external traumas.
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NB: if you are asked about adaptations of AORTA, you state the same
answer above but:
- Large lumen to accommodate large volume of blood.
- Has semi-lunar valve at the origin to prevent back flow of blood during atrial
systole and diastole.

• Veins:
Function: Veins carry blood towards the heart. All veins carry deoxygenated

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blood except the pulmonary veins.

Structure:
- Thin wall as pressure is low.
- Wide lumen to maintain low blood pressure.

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- Valves in the lumen to prevent back flow of blood.
- Wall: Same as arteries but less developed (less elastic fibers and less smooth
muscles).
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Pressure: Lower than arteries and capillaries.

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Factors ensuring venous return to the heart:

- Negative intrathoracic pressure during inhalation causes suction of blood in
veins.
- Muscle pump during movement pushes blood in veins.
- Valves prevent back flow of blood.

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• Capillaries:
Function: Delivery of oxygen and nutrients to tissues and removal of carbon
dioxide and waste products from tissues by diffusion.

Adaptations: (Endothelium Only)

- Very thin wall (one cell thick) to shorten diffusion distance.
- Has capillary pores to facilitate exchange of substances.

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Pressure: Higher than veins but lower than arteries (Arteries >capillaries >Veins).
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Causes of blood pressure drop in capillaries:
- Large total surface area of capillaries.
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- Leakage of fluid outside capillaries.

- Long distance from the heart.
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 Blood
• Composition:
- Solid part: blood cells as red blood cells, white blood cells, platelets.
- Liquid part: blood plasma which consists of water (90%) and dissolved
substances as glucose, amino acids, vitamins, and minerals (10%).

• Importance of blood clotting:

- Prevents blood loss.
- Prevents entry of pathogens causing diseases.

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• Mechanism of blood clotting:***

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- The cut blood vessel wall secretes thromboplastin.

- This stimulates platelets to form a platelet plug which secretes more
thromboplastin.
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- Then the coagulation cascade goes as follows:

• Thromboplastin converts prothrombin (inactive enzyme) into thrombin (active
enzyme)
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• Thrombin converts fibrinogen (soluble protein) into fibrin (insoluble protein).

• Fibrin forms a mesh that traps blood cells forming a blood clot.
- This occurs in the presence of Calcium and Vitamin K.
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 Chapter 2
Cardiovascular Diseases

• Energy Budget:
- It is the relationship between energy input & energy output.
Energy input refers mainly to the intake of food and energy output refers to

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exercise.
- If energy input is higher than energy output, this leads to obesity & the
opposite leads to weight reduction. This explains why any weight loss program
should have two arms: The first arm is reducing energy intake through having
smaller quantities of a balanced diet & the second arm is increasing energy loss

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through doing regular exercise.

• Body Mass Index (BMI):

You can calculate whether or not you are obese by using a formula called the BMI
(body mass index).
BMI = Body mass in kg / (Height in m)2.
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• Blood pressure:
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- The force exerted by blood on the walls of the blood vessels.

- Normal blood pressure is 120/80 mmHg measured by sphygmomanometer.
- Hypertension: A chronic disease characterized by blood pressure higher than
140/90 mmHg sustained (3 successive readings) and measured at rest. It is due
to damage of elastic fibers.
- Hypotension: Blood pressure lower than 90/60 sustained and measured at rest.
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 Atherosclerosis

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• Definition: A disease characterized by thickening and hardening of the walls of

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coronary arteries as well as narrowing of the lumen due to presence of
fibrofatty plaques.

• Pathology:***
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- Endothelial damage occurs due to smoking, hypertension, or free radicals.
- This leads to an inflammatory response in which white blood cells move to the
damaged area followed by cholesterol (Atheroma).
-
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Collagen fibers are laid down (Atherosclerosis).
- This causes narrowing of the lumen which stimulates more hypertension,
further endothelial damage (perpetual cycle).
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- NB: The presence of atherosclerosis might stimulate the coagulation cascade

leading to blood clot formation blocking the narrow lumen (Thrombus).
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• Consequences:***
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• Partial obstruction of a coronary

artery [Angina Pectoris]:
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- Severe chest pain occurring during

exercise.
- Relieved by rest and vasodilators.

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• Complete obstruction of a coronary artery [Myocardial Infarction]:

- Severe chest pain occurring at rest and not relieved by vasodilators.

- Explanation:
- Complete obstruction of the lumen occurs.
- So no blood so no oxygen nor glucose
delivered.
- So no aerobic respiration.

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- Anaerobic respiration occurs instead.
- Lactic acid is produced.
- Drop in pH.
- Enzymes are denatured.
- So death of the part supplied by this blocked artery (myocardial infarction).

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NB:
- The extent of damage of the heart depends on the site and size of the blocked
artery.
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- The larger the artery, the greater the damage.
- The higher the obstruction in the coronary artery tree, the greater the damage as
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the area downstream the obstruction is deprived of blood so no oxygen nor
glucose delivered to cells.
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• Complete obstruction of a cerebral artery [Stroke]:

- The symptoms vary according to the area of the brain
supplied by the blocked artery ex. paralysis, deafness, or
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blindness.
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• Widening of the artery at the site of atherosclerosis

[Aneurysm]:
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- It is usually symptomless but may rupture due to high

pressure.

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 Risk Factors of CVD

Risk factors of CVD are divided into non-modifiable (cannot be changed) and
modifiable (can be changed) risk factors.

Non-modifiable Modifiable
Age Smoking
Gender Diet

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Genetic factors Lack of exercise
Obesity
Stress

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• Non-modifiable risk factors:
1. Age: The higher the age, the higher the CVD risk. As aging increases the
chances of elastic fibers damage leading to hypertension.
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2. Gender: Females before menopause are at lower risk than males as estrogen
is protective to the endothelium. After menopause, the risk is equal.
3. Genetic factors: No direct link is found yet between genes and CVD, but
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CVD runs in families.
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• Modifiable risk factors:

• Smoking: It contains carbon monoxide which leads to endothelial damage and
forms carboxyhemoglobin that reduces supply of oxygen to cells. Also,
smoking contains nicotine that leads to hypertension.
• Diet:
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- High total energy input more than energy output lead to obesity which causes
hypertension.
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- High cholesterol intake leads to formation of atheroma.

- High levels of animal fats (saturated fats) leads to the formation of atheroma.
- High LDL:HDL ratio increases fats in blood so higher cholesterol and higher
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risk of atheroma formation.

- High levels of salts in diet leads to more hypertension.
- Caffeine and alcohol consumption increase blood pressure which leads to
hypertension.
- No or low intake of vitamins increases free radicals in blood which leads to
endothelial damage.

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• Lack of exercise: It doubles the risk of CVD, as it decreases energy output so
higher risk of obesity and slows down circulation.
• Obesity: Abdominal obesity is more risky than lower body obesity and is
determined by waist:hip ratio. So the higher the ratio, the higher the risk.
• Stress: It increases adrenaline levels in blood leading to hypertension.

Treatment of CVD

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• Life style modification: [The opposite of risk factors]
- Stop smoking.
- Decrease total energy intake and do regular exercise so lower risk of obesity.
- Decrease cholesterol in diet.

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- Decrease animal fats (saturated fats) and increase plant oils (unsaturated fats).
- Decrease LDL:HDL ratio.
- Decrease salts in diet.
- Stop caffeine and alcohol intake.
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Avoid stress. E
Increase intake of vitamins as vitamins act as antioxidants which decreases free
radicals.
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• Drug Therapy:
1) Antihypertensives:
Antihypertensives are either Vasodilators or Diuretics.
Vasodilators
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- Mechanism of action: They widen blood vessels so reduce blood pressure.

- Side effects: Hypotension, headache, dizziness.
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- Example: B-blockers, ACE inhibitors.

Diuretics
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- Mechanism of action: They increase urine volume so reduce blood volume so

reduces blood pressure.
- Side effects: Renal failure, hypotension, headache, dizziness.
- Example: Loop diuretics.

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2) Statins:
- Mechanism of action: They block certain enzymes in the cholesterol synthesis
pathway so reduces blood cholesterol level.
- Side effects: Constipation, muscle aches, liver damage.
- Example: Atorvastatin.
3) Anticoagulants:
- Mechanism of action: They block certain enzymes in the coagulation cascade
so reduces blood clotting (less risk of thrombus formation).

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- Side effects: Severe bleeding.
- Example: Heparin, baby aspirin.

NB:

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Plant Sterols decrease the absorption of fats from the intestine.
Antioxidants decrease free radicals so reduces endothelial damage.

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 Drug Studies
- Placebo: A control drug with no active ingredient. it eliminates the
psychological effect of being on a medication.
- Double-blind trials: Neither the doctor nor the patient know who is taking the
real drug and who is taking the placebo. This eliminates bias.

- To assess the validity of a study:

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• Sample size: A larger sample size increases validity as it shows variation
within the population.
• Sample selection: Controlled variables in the selected sample increases
validity.

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• Duration: The longer the duration, the more validity of the study.
• Statistical analysis ensures validity.
• Error bars: They show spread of data around the mean. The larger the error
bar, the lower the reliability of data.

For example: The largest

error bar here is Visit 1
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CHD so has the lowest
reliability.
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 Epidemiology (Community medicine)

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- Definition: A branch of medical science that deals with incidence, distribution
and control of diseases in a certain population.

- Morbidity and Mortality:

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• Morbidity: Disease rate in a certain population.
• Mortality: Death rate in a certain population.
They are both calculated as a number /100,000 of the population. Because
population sizes are different so this allows for a valid comparison.

NB:
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If you are asked about difference between two countries in the morbidity/
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mortality rates, it is due to:
- Difference in risk factors with at least 3 examples.
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- Difference in health care quality.

- Difference in the awareness about the disease and how to to avoid.
- Causation and Correlation:
• Causation: A change in one variable directly results in a change of another
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variable. For example: HIV causes AIDS.

• Correlation: A change in one variable is reflected by (accompanied by) a
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change in another variable. For example: Smoking increases the risk of CVD.

To suggest a correlation for the

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graph, look at the pattern of change:

- Similar pattern = positive
correlation.
- Opposite pattern= negative
correlation.
- Constant or fluctuating pattern= no
correlation.
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- Actual risk and Perceived risk:
• Actual risk (Relative risk): A mathematically calculated probability of
occurrence of a certain event compared to other groups. For example, lack of
exercise doubles the risk of CVD.
• Perceived risk: Perception of the community to a certain risk factor. For
example, the community believe that motorbikes accidents are more frequent
and serious than car accidents, however, that is not true.

Awareness campaigns aim at lowering the gap between the actual risk and

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the perceived risk.

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 Chapter 3
Biological Molecules

• Types of reaction:
- Condensation: Removing water to join 2 small
molecules forming a larger one.

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- Hydrolysis: Adding water to break down a
large molecule into smaller ones.

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• Definitions:
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- Molecular formula: Number of atoms in a certain molecule. Ex: Glucose
(C6H12O6).
- Structural formula: Arrangement of atoms in a certain
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molecule. Ex: Ring form.
- Isomers: Molecules with the same molecular formula but
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different structural formula. Ex: α-glucose and β-glucose

(both C6H12O6).
- Macromolecule: A large molecule with many subunits called monomers.
- Polymer: A macromolecule with identical subunits.
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NB: All polymers are macromolecules, but not all macromolecules are polymers.
For example, polypeptides and polysaccharides are polymers, while lipids are
macromolecules but not polymers as their subunits are not identical (fatty acids &
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glycerol).
- Polar: Uneven distribution of charges = charged = soluble in water =
hydrophilic.
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- Non-polar: Not charged = insoluble in water = hydrophobic.

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 Water (H2O)

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- Water is a dipolar molecule due to uneven distribution of charges on both
ends.

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- This allows water to form hydrogen bonds with any polar particles. Positive
particles bond with the negative end of water and negative particles bond with
the positive end of water so they dissolve in it. This makes water an excellent

-
solvent.
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Water molecules also form hydrogen bonds with each other (Cohesion), and
with nearby surfaces (Adhesion). This allows water to move as one unbroken
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column.

NB: Excellent solvent + One unbroken column = Perfect Transport Medium

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• Features of water: (E A T Low High)

- Excellent solvent + One unbroken column = Perfect Transport Medium.
- Amphoteric: Keeps constant pH as it acts as a proton donor or a proton
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acceptor.
- Transparent: So sunlight can pass through it for marine life to exist.
- Low density of ice: So it floats on the surface insulating lower water allowing
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for existence of marine life.

- High Specific Heat Capacity: So temperature is within narrow limits for
proper enzyme activity of marine organisms.
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 Carbohydrates

• Consists of Carbon, Hydrogen, and Oxygen Only.

• Ratio of H:O is 2:1.
• Classification:
- Monosaccharide (1 subunit): [CnH2nOn]
Ex: Pentose (C5H10O5) as Ribose or Hexoses (C6H12O6) as Glucose, Galactose,

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and Fructose.

- Disaccharides (2 subunits): [Cn H2n-2 On-1]

Maltose = α-Glucose + α-Glucose
Lactose = α-Glucose + Galactose

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Sucrose = α-Glucose + Fructose

NB: Monosaccharides and disaccharides are Small/low molecular weight,

Soluble, and Sweet.
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- Polysaccharides (Many glucose subunits): [Cx (H2O)y]
Ex: Starch, Glycogen, and Cellulose.
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Polysaccharides are large/high molecular weight, Insoluble, and Non-sweet.
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• How to draw an α-glucose molecule:***

- Draw an empty ring.
- Add Carbon 6.
- Add the OHs (All OHs down except Carbon 3 up).
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- Complete by Hs.
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NB: β-glucose is similar to α-glucose except for the OHs.

β-glucose: All OHs down except Carbon 1 and 3 up.
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• Maltose Formation:
2 α- glucose molecules joined by Condensation Reaction

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α-glucose + α-glucose ——> Maltose + Water
Type of reaction= Condensation reaction.
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DO NOT FORGET THE WATER MOLECULE PRODUCED IN YOUR

REACTION!!

• Galactose Structure:
- Draw an empty ring.
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- Add Carbon 6.
- Add the OHs (All OHs up except Carbon 2 down).
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- Complete by Hs.
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• Lactose Formation:
α-glucose and Galactose joined by Condensation Reaction.

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α-glucose + Galactose ——> Lactose + Water

Type of reaction= Condensation reaction.
DO NOT FORGET THE WATER MOLECULE PRODUCED IN YOUR
REACTION!!
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 Polysaccharides

• Starch Structure:
- It is a polymer of α-glucose monomers joined together by α1,4 glycosidic
bond formed through condensation reactions.

- There are 2 types of starch molecules:

Amylose Amylopectin

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Helical and unbranched. Straight and branched.
Has α1,4 glycosidic bonds ONLY. Has α1,4 glycosidic bonds and α1,6
glycosidic bonds at the branching
points.

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• Glycogen Structure:

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- It is a polymer of α-glucose monomers joined together by α1,4 glycosidic
bond formed through condensation reactions.

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- It is straight, branched, and has α1,4 glycosidic bonds and α1,6 glycosidic
bonds at the branching points.
- Its structure is similar to amylopectin but with more frequent branching.

•
-
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Adaptations of Polysaccharides/Starch/Glycogen to their storage function:
Large number of glucose monomers to store a lot of energy.
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- Compact to store a large number of molecules occupying less space.
- Rapidly hydrolyzed by enzymes as α1,6 glycosidic bonds are easily broken
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down.
- Insoluble as not to affect the osmotic pressure.
- Non-reactive as not to interfere with metabolic reactions.
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 Fats/Lipids
• Consists of Carbon, Hydrogen, and Oxygen Only.
• Ratio of H:O is higher than 2:1.
• Building units: Fatty acids and glycerol.
• The most common form of lipids is Triglycerides.

• Triglyceride Formation:
Glycerol and 3 fatty acids joined by Condensation Reaction.

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Glycerol + 3 fatty acids —-> Triglyceride + 3 water molecules.

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Type of reaction= Condensation reaction.

DO NOT FORGET THE 3 WATER MOLECULES PRODUCED IN YOUR
REACTION!!
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NB:
- All fatty acids have a carboxyl group.
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- All fatty acids have a hydrocarbon chain.

- However, they differ in the number of Carbons
and Hydrogen atoms in the chain.
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• Types of fatty acids:

Unsaturated Fatty acids Saturated Fatty acids

Have the maximum number of Have less than the maximum possible
hydrogen atoms in the hydrocarbon number of hydrogen atoms in the
chain. hydrocarbon chain.
No Carbon = Carbon double bonds. Have Carbon = Carbon double bonds.
Straight molecules. Kinky molecules.

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Have high melting points. Have low melting points.
They increase the risk of CVD. (Less They do not increase the risk of CVD.
mobility) (More mobility).

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Example: Animal Fats. Example: Plant Oils.

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NB:
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- Being straight makes saturated fatty acid molecules tightly packed so they have
strong intermolecular forces and thus a high level of heat energy is needed to
break them. This explains why they have a high melting point.
- The general formula of Saturated fatty acids is Cn H2n O2.

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• How to draw a fatty acid:
- Unknown fatty acid:

- Known saturated fatty acid: Ex.

C18H36O2

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- Known unsaturated fatty acids: Ex.
C18H34O2 (C=C between C13 and
C14)

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• Phospholipid Formation:

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Hydrophilic phosphate group + glycerol + 2

hydrophobic fatty acids —-> Phospholipid + 3
water molecules
D

Type of reaction= Condensation reaction.

DO NOT FORGET THE 3 WATER
MOLECULES PRODUCED IN YOUR
REACTION!!

33
NB:
- All fats are hydrophobic.
- Only phospholipids have a hydrophilic phosphate head and 2 hydrophobic fatty
acid tails.
- Since fats are hydrophobic, they can’t dissolve in the water of plasma. So to be
transported in blood, they must be coated by hydrophilic proteins forming
lipoproteins.
- They are 2 types of lipoproteins: LDL (Low Density
Lipoproteins) which transports fats from liver to blood

am
and HDL (High Density Lipoproteins) which
transports fats from blood to liver.

ss
E
a
an
R
r.
D

34
 Proteins
• Consists of Carbon, Hydrogen, Oxygen, and Nitrogen.
• Building units: Amino acids.
• There are 20 different amino acids that can form up to 70,000 proteins.
• Amino acid Structure:

am
ss
- An amino acid consists of a central carbon with a carboxyl group on one side
and an amino group on the other side.
- E
Each amino acid has a variable part called the R group.

• Peptide bond Formation:

a
A peptide bond is formed by removing OH from a carboxyl group and H from the
adjacent amino group.
an
R
r.
D

Type of reaction= Condensation reaction.

DO NOT FORGET THE WATER
MOLECULE PRODUCED IN YOUR
REACTION!!

35
• Levels of Protein Structure:
- Primary Protein Structure: (Specific)
The number, type and sequence of amino acids in the
polypeptide chain.
Held by Peptide bonds.

- Secondary Protein Structure: (Non-specific and

am
Insoluble)
Slight bending of the polypeptide chain producing an α-
helix or β-pleated sheets.
Held by Hydrogen bonds between slightly charged
atoms in the backbone of amino acids.

ss
Examples: Keratin, Collagen, Fibrin.

- Tertiary Protein Structure: (Specific and Soluble)

E
The bending and folding of the polypeptide chain into
precise globular shape.
a
Held by bonds between R groups such as Hydrogen
bonds, Ionic bonds, Disulphide bonds, and hydrophobic
interactions.
an

Examples: Enzymes, Hormones, Antibodies.

NB: The 3ry structure also ensures that hydrophilic R groups

R

are pointing outwards and hydrophobic R groups pointing

inwards ensuring protein solubility.
r.

- Quaternary Protein Structure: (Specific and

Soluble)
D

The protein consists of more than one polypeptide

chain.
Held by bonds between R groups such as Hydrogen
bonds, Ionic bonds, Disulphide bonds, and
hydrophobic interactions.
Example: Hemoglobin.

36
• Conjugated Proteins
They are proteins attached to non-protein parts.
Examples: Lipoproteins, Glycoproteins, Hemoglobin.

• Compare between 2ry and 3ry Protein Structures:

Points of comparison Secondary Protein Tertiary Protein

(Fibrous Protein) (Globular Protein)

am
Structure Slight bending of the Bending and folding of
polypeptide chain, held the polypeptide chain,
by hydrogen bonds held by bonds between R
between slightly charges groups such as Hydrogen

ss
atoms in the backbone of bonds, Ionic bonds,
amino acids. Disulphide bonds, and
Hydrophobic interactions.
Fibrous (Long Parallel Globular (Ball shaped)
Shape
E
fibres)
a
an
R
r.

Specificity Non-specific Specific

D

Solubility Insoluble Soluble

Examples Collagen, Keratin, Fibrin Enzymes, Hormones,
Antibodies.

37
 Important Questions
• How the primary structure determines the tertiary structure and
properties of an enzyme:***

- The primary structure is the number, type and sequence of amino acids in the
polypeptide chain held by peptide bonds.
- This determines the arrangement of R groups and consequently determines the
bonds to be formed between those R groups such as Hydrogen bonds, Ionic

am
bonds, Disulphide bonds, and Hydrophobic interactions.
- The formed bonds lead to bending and folding of the polypeptide chain into a
specific precise globular shape.
- This specific globular shape guarantees that the active site is complementary to

ss
the shape of the substrate. (Enzyme Specificity)
- This 3ry structure also ensures that hydrophilic R groups are pointing outwards
and hydrophobic R groups pointing inwards ensuring (Enzyme Solubility).

•
-
E
Describe the structure of a Fibrous protein:***
Chains of amino acids held by peptide bonds forming the primary structure.
a
- The polypeptide chains are held by Hydrogen bonds.
- The polypeptide chains run parallel to each other with minimal folding.
an

• Describe the structure of Collagen:***

- It is a fibrous protein.
- It is composed of triple helix (three strands held by hydrogen bonds).
- Every third amino acid is glycine/Repeated sequence of hydroxyproline and
R

glycine.
r.

• Explain how the primary structure of collagen determines its properties:

- The primary structure is the number, type and sequence of amino acids in the
polypeptide chain held by peptide bonds.
-
D

This determines the formation of hydrogen bonds between the slightly charged
atoms in the backbones of amino acids leading to the formation of helical
structure.
- It is insoluble as hydrophobic R groups are exposed.

38
• Denaturing of Proteins:
Loss of the complex precise 3D shape leading to
loss of the function.

Causes:
1. Very high temperature: breaks Hydrogen
bonds only.
2. Major changes in pH: breaks Hydrogen bonds
and Ionic bonds.

am
3. Reducing agents: break Disulfide bonds.

ss
E
a
an
R
r.
D

39
 am
ss
Topic 2
Membranes, Proteins, DNA and Gene
E
Expression
a
an
R
r.
D

40
 Chapter 1
Gas exchange

am
ss
• Gas exchange in lungs: Addition of Oxygen to blood and removal of Carbon
dioxide from blood by Diffusion. Occurs in the the capillaries around alveoli.
• Gas exchange in tissues: Addition of Carbon dioxide to blood and removal of
Oxygen from blood by Diffusion. Occurs in the capillaries around the tissues.
E
Fick’s law of diffusion
Fick’s law shows the relationship between the variables that affect diffusion.
a
an

The larger the numerator (top number) and the smaller the denominator
R

(bottom number) the faster the rate of diffusion.

r.

• Features of any Gas exchange surface:

- Large surface area.
- Steep concentration gradient.
D

- Low thickness of gas exchange surface (small diffusion distance).

41
 Important Questions
• Adaptations of Alveoli:
- Large surface area (80-90 m2) to increase the rate of diffusion.
- Supplied by a rich network of capillaries to maintain concentration gradient.
- Very thin and permeable walls (1 cell thick) to shorten diffusion distance.
- Lined by a moist surface to dissolve gases and protect the cells from drying
out.

am
• Describe the role of the Respiratory system for Gas exchange:
- Ventilation maintains concentration gradient as it removes carbon dioxide
outside the alveoli through exhalation and brings oxygen inside the alveoli

ss
through inhalation.

- Adaptations of Alveoli:
4. Large surface area (80-90 m2) to increase the rate of diffusion.
5.
6.
7.
E
Supplied by a rich network of capillaries to maintain concentration gradient.
Very thin and permeable walls (1 cell thick) to shorten diffusion distance.
Lined by a moist surface to dissolve gases and protect the cells from drying
a
out.

- The above helps to overcome limitations of diffusion such as small surface area
an

to volume ratio, non-steep concentration gradient, long diffusion distance and

high energy requirements.

• Adaptations of Capillaries for Gas exchange:

R

- Large total surface area to increase the rate of diffusion.

- Very thin walls to shorten diffusion distance.
-
r.

Capillary pores to facilitate exchange of substances.

• Adaptations of the Heart:

- The heart generates mass flow which pumps blood from higher pressure to
D

lower pressure over a long distance. This maintains concentration gradient.

42
• Describe the role of the Circulatory system for Gas exchange:
- The heart generates mass flow which pumps blood from higher pressure to
lower pressure over a long distance. This maintains concentration gradient.

- Adaptations of Capillaries:
• Large total surface area to increase the rate of diffusion.
• Very thin walls to shorten diffusion distance.
• Capillary pores to facilitate exchange of substances.

am
- The above helps to overcome limitations of diffusion such as small surface area
to volume ratio, non-steep concentration gradient, long diffusion distance and
high energy requirements.

ss
Oxygen Dissociation Curve

E
a
an
R

- It is sigmoid-shaped curve showing partial pressure of oxygen on the X-axis

r.

and percentage oxygen saturation of Hemoglobin on the Y-axis.

- The higher the pressure of oxygen in blood, the higher the percentage
D

saturation of hemoglobin. This means that hemoglobin binds to oxygen at sites

with high oxygen pressure (The lungs) and releases this oxygen at sites with
lower oxygen pressure (The tissues). This explains why hemoglobin is
considered as the oxygen transporter from the lungs to tissues.

- Hemoglobin has higher affinity for oxygen in tissues with high pressure of
oxygen.
43
• The Bohr Effect:

am
ss
- It is the effect of carbon dioxide on the oxygen dissociation curve.
- A higher carbon dioxide concentration leads to more release of oxygen from
hemoglobin which decreases the percentage saturation and shifts the curve
downwards (To the right).
- E
A lower carbon dioxide concentration leads to more binding of oxygen to
hemoglobin which increases the percentage saturation and shift the curve
upwards (To the left).
a
• Fetal Hemoglobin Vs. Adult Hemoglobin:
an
R
r.
D

- The fetal hemoglobin has a slightly different molecular composition to adult

hemoglobin. Consequently, it has higher affinity to oxygen so the
disassociation curve is shifted to the left.
- Following birth, fetal hemoglobin is replaced by adult hemoglobin. (6 months
after birth).
44
• How the structure of hemoglobin causes the oxygen dissociation curve to
be this sigmoidal (S) shape:***

am
-

ss
Hemoglobin is composed of four polypeptide chains.
- Binding of the first oxygen molecule is difficult.
- The binding of the other molecules becomes easier.
- Due to conformational changes.
- E
Then as hemoglobin becomes saturated with oxygen, no more oxygen can bind
so the curve flattens.
a
an
R
r.
D

45
 Chapter 2
Cell Membrane

am
ss
• Thickness: About 7nm.
• Consists of fats (mainly), carbohydrates and proteins.
• Components:
Lipids:
E
Phospholipids forming the bilayer.
a
Cholesterol in between phospholipid tails.
Proteins:
an

Intrinsic proteins which are spanning the full thickness of the cell membrane.
Extrinsic proteins which are found in one layer only.
Carbohydrates:
Glycoproteins and Glycolipids.
R

• The Fluid Mosaic Model:

Fluid: Phospholipids are in continuous motion within their monolayer,
r.

exchanging places and pumping into each other.

Mosaic: This term refers to the random distribution of proteins among the
phospholipid bilayer.
D

NB: The old model was the Davson-

Danielli model: 2 hydrophilic protein
layers with a phospholipid bilayer in
between.

46
• Membrane Fusion trials: To prove the fluid mosaic feature of the cell
membrane.
- Proteins of a certain membrane were labelled with green colour.
- Proteins of another membrane were labelled with red colour.
- When we fused the membranes, the following occurred:
1) A single membrane was produced with the same total number of proteins
(Fluid).
2) Red and green proteins are scattered randomly in the fused membrane
(Mosaic).

am
Lipids
• Phospholipids:
- Orientation (How the properties of

ss
Phospholipids contributes to the structure of the
cell membrane?)***: They form a bilayer with
hydrophilic phosphate heads facing outwards and
E
inwards to form hydrogen bonds with the two
aqueous media (Extracellular fluid outside the cell
and Cytoplasm inside), while the hydrophobic tails
a
are facing each other in the center of the bilayer
held together by hydrophobic interactions.
an

- Functions:
1) They form the structural framework of the cell membrane.
2) They are responsible for fluidity. Fluidity increases with increasing
temperature, increasing unsaturated:saturated fatty acid ratio, and decreasing
R

percentage of cholesterol.
3) They are responsible for selective permeability. Phospholipids allow ONLY
r.

the diffusion of non-polar molecules as gases, small polar molecules such

as water, and lipid soluble molecules such as ethanol and ethanol.
D

• Cholesterol:
- It fits between the hydrophobic fatty acid tails.
- Held by hydrophobic interactions.
- Functions: Regulates fluidity and maintains
structural stability.

47
• Membrane Proteins:

am
- They are globular proteins with hydrophilic R-groups facing outwards and
inwards while hydrophobic R-groups are in the center towards fatty acid tails
and held in place by hydrophobic interactions.

ss
- They could be either embedded in one layer (Extrinsic proteins) or occupying
the full thickness of cell membranes (Intrinsic proteins).

- Functions:
• Carrier proteins for Active Transport.
E
• Channel proteins for Facilitated Diffusion.

• Enzymatic proteins to catalyze important metabolic reactions.

a
an

• Carbohydrates: [Glycoproteins or
Glycolipids]
- They act as receptors for important
chemicals such as hormones.
-
R

They also act as recognition receptors as

antigens.
r.
D

48
 Movement of Substances across the Cell Membrane

Movement of substances across the cell membrane is either:

Passive (No Energy Needed) Active (Needs Energy)
Simple Diffusion Facilitated Active Transport Cystosis
Diffusion
Through the Through Channel Through Carrier Bulk Transport.

am
Phospholipid Proteins. Proteins.
bilayer.

• Simple Diffusion:
- Definition: Passive movement of substances/molecules down concentration

ss
gradient through the phospholipid bilayer.

- Examples:
1. Non-polar molecules as Gases.
E
2. Small polar molecules such as water. [Despite being dipolar, it is small
enough to pass in between the hydrophobic tails of the phospholipid
bilayer].
a
3. Non-polar lipid soluble molecules such as ethanol and ethanol.
an

NB: Increasing fluidity increases the movement of substances by simple diffusion

leading to higher membrane permeability.

• Facilitated Diffusion:
R

- Definition: Passive movement of substances/molecules down concentration

gradient through channel proteins.
- Channel proteins form hydrophilic tunnels through the hydrophobic center of
r.

the bilayer allowing the passage of large polar molecules.

- Examples: Large polar molecules such as glucose, amino acids and ions.
D

NB: Water molecules can pass through one of two pathways:

1) In between phospholipids by simple diffusion.
2) Through channel proteins by facilitated diffusion.
In both cases, movement must be down water potential gradient and is sometimes
called Osmosis.

49
• Active Transport:
- Definition: Active movement of substances against concentration gradient
through carrier proteins.

- Mechanism:
• The molecule/ion binds to a receptor on
the surface of a carrier protein.
• Inside the cell, ATP (Adenosine
Triphosphate) is broken down into ADP

am
(Adenosine Diphosphate) and Pi
(Inorganic Phosphate).
• Pi binds to the carrier protein.
• Now the carrier protein changes
position by rotation and the molecule enters the cell.

ss
• Pi detaches from the carrier protein, so the carrier protein restores its original
shape.

- Evidence for Active Transport:

• Occurs only in living cells.
• More in cells with more mitochondria.
E
a
• Respiratory poisons as cyanides stop active transport.

- Factors affecting Active Transport:

an

• Oxygen concentration, since aerobic respiration provides ATP.

• Number of carriers.
• Number of mitochondria in the cell to provide ATP.
• Presence of respiratory poisons as cyanide.
R

• Cytosis (Bulk Transport):

r.

- Definition: Transporting substances enclosed in

vesicles or vacuoles. It is an active process.
D

- Types:
• Endocytosis: A vesicle enters the cell. Ex:
Phagocytosis.
• Exocytosis: A vesicle exits the cell. Ex:
Secretion of hormones.

50
 Graphs showing Diffusion and Active Transport

am
First region: Steepest increase in the concentration of substance X inside the cell.
Explanation: Highest concentration gradient so highest rate of diffusion.

ss
Second region: Less steep increase in the concentration of substance X inside the
cell.
E
Explanation: Lower concentration gradient so lower rate of diffusion.

Last region: No change in concentration of substance X inside the cell (Levels

a
off).
Explanation: Equilibrium is achieved so diffusion stops.
an
R
r.
D

Active transport graph shows a linear change as it’s NOT affected by

concentration gradient.

51
 Graph showing effect of Temperature on Diffusion through
the Cell membrane

am
ss
First region: Increasing temperature increases concentration inside the cell.
Explanation: Higher kinetic energy so higher rate of diffusion.

Second region: Marked increase in concentration of substance X inside the cell.

E
Explanation: Very high temperature leads to melting of the phospholipid bilayer
and coagulation of membrane proteins. This damage to the cell membrane ends by
loss of selectivity and marked increase in permeability.
a
Last region: No change in concentration of substance X inside the cell.
Explanation: Equilibrium is achieved so diffusion stops.
an

NB: High concentrations of ethanol dissolve the phospholipid bilayer leading to

cell membrane damage. This damage ends by loss of selectivity and marked
increase in permeability.
R
r.

Comparison between a synthetic membrane and the natural membrane:

• Both membranes allow movement of gases through the phospholipid bilayer.
• Synthetic membranes allow lower movement of water than the natural
membrane as there is only one pathway of water movement which is through
D

the phospholipid bilayer only, while in natural membranes water can pass
through two pathways (Through the phospholipid bilayer and through channel
proteins).
• No movement of any polar structures through the synthetic membranes as there
are no channel proteins.
• No active transport in synthetic membranes as no carrier proteins present.
52
 Chapter 3
Enzymes

am
• Definition: They are Biological Catalysts. Biological as they are proteins
formed inside the cell and Catalysts as they speed up the rate of reactions

ss
without being used up or changed.

• Mechanism of Action:
- Each enzyme is formed of an active site

-
and body. The active site fits with the
shape of the substrate.
They work by lowering the Activation
E
a
Energy which is the energy needed for
the reaction to take place.
an

- As collisions between the enzyme and

the substrate weaken the bonds in the
substrate.
- Enzymes provide an alternative reaction pathway inside the active site which
requires less energy to start.
R

• Specificity:
r.

Enzymes bind their substrate at the active site using one

of two mechanisms:
- Key and Lock Mechanism: The shape of the active
D

site is Exactly complementary to the shape of the

substrate.
- Induced Fit Mechanism: The shape of the active site
is NOT Exactly complementary to the shape of the
substrate. However, on entry of the substrate, it
induces minor changes in the active site to fit in it.

53
 Factors affecting Enzyme Activity
• Temperature:

A: Increasing temperature leads to higher

kinetic energy, so higher frequency of
successful collisions, so higher Enzyme-
Substrate complexes, so higher rate of

am
reaction.

NB: At temperature 0°C, enzymes and

substrates are frozen and there is no kinetic
energy for movement, so no reaction until

ss
temper increases. This is known as
reversible deactivation.

B: Increasing temperature above the optimum temperature breaks Hydrogen

E
bonds between amino acids of the enzyme leading to permanent loss of the shape
of the active site that can no more fit its substrate. The enzymes is said to be
denatured.
a
NB: Only the upper extreme of temperature denatures enzymes.
an

• pH:
- Optimum pH is the pH at which the highest
R

rate of reaction takes place.

- Minor changes from the optimum pH
reduces the rate of reaction.
r.

- Major changes from the optimum pH

denature enzymes. This is explained by the
ability of pH changes to break ionic bonds
D

between amino acids forming the active site

leading to to permanent loss of the shape of
the active site that can no more fit its
substrate. The enzymes is said to be
denatured.

NB: Both extremes of pH denature enzymes.

54
• Enzyme Concentration:
A: Increasing enzyme concentration,
increases the rate of reaction. [Steepest
Increase]
Explanation: More enzyme concentration
means more active sites available and there is
plenty of substrate molecules available at the
start of the reaction so they have the highest
chances of successful collisions.

am
B: Increasing enzyme concentration,
increases the rate of reaction. [Less Steep Increase]
Explanation: Less substrate molecules available, so less chances of successful

ss
collisions.

C: Increasing enzyme concentration has no effect on the rate of reaction. [Graph

levels off]
E
Explanation: No more substrates available, so no chances of successful
collisions. (Substrate concentration is a limiting factor.)
a
an

NB: Why do we prefer measuring the initial rate of reaction?

As there is plenty of substrate molecules available, so the maximum chances of
successful collisions occur, and the highest possible rate of reaction is achieved.
R

(Substrate concentration is not yet a limiting factor)

r.
D

55
 Chapter 4
Genetics
• DNA Structure:
Building units of DNA are nucleotides.

Nucleotide Structure:

am
- Pentose sugar (Deoxyribose).
- Phosphate group attached to C5.
- Nitrogenous base attached to C1
(Which may be Adenine or Thymine or
Cytosine or Guanine).

ss
NB: The DNA nucleotide has a constant part known as sugar phosphate
backbone. The only variable part between nucleotides is the nitrogenous base.

NB: Types of Nitrogenous Bases:

• Purines: [Consist of 2 rings]: Adenine,
E
Guanine.
a
• Pyrimidines:[Consist of 1 ring]: Thymine,
Cytosine, Uracil.
an

Polynucleotide Chain:
R

- Consists of many DNA nucleotides joined

together by phosphodiester bonds between
phosphate attached to C5 of one nucleotide &
r.

C3 of the next nucleotide formed through

condensation reactions forming the Sugar-
Phosphate Backbone.
D

- The polynucleotide chain has 2 ends: 5’end and

3’end.

56
DNA Molecule:
- It consists of 2 polynucleotide
chains running anti-parallel
(5’end of one chain is facing the
3’end of the other chain), so
nitrogenous bases of both strands
face each other.
- The 2 polynucleotide chains are
held together by Hydrogen bonds

am
between nitrogenous bases
according to complementary
base pairing rules [A with T and
C with G].
- The 2 DNA strands are coiled

ss
around each other forming a double helix.

NB: Explain the base pairing rules:

E
• A and T form 2 Hydrogen bonds, while C and G form 3 Hydrogen bonds.
• The space between the 2 chains is just enough for 3 rings (Purines have 2 rings
and Pyrimidines have 1 ring).
a
• DNA Replication: [Semi-conservative Replication]***
an

3) The 2 polynucleotide chains unwind and

unzip catalyzed by DNA Helicase enzyme.
4) The 2 free strands attract free active DNA
nucleotides according the complementary
R

base pairing rules (A with T and C with G).

5) The sugar phosphate backbones of the 2
newly formed strands are joined by
r.

phosphodiester bonds.
6) This process is catalyzed by DNA
polymerase and DNA ligase enzymes.
D

7) Each of the 2 newly formed molecules

winds into a double helix.

NB: DNA Replication is described as Semi-conservative Replication. As each of

the newly formed DNA molecules is half old (Parent Strand) and half new
(Formed from free DNA Nucleotides).

57
• RNA Structure:
Building units of RNA are nucleotides.

Nucleotide Structure:
- Pentose sugar (Ribose).
- Phosphate group attached to C5.
- Nitrogenous base attached to C1
(Which may be Adenine or Uracil or

am
Cytosine or Guanine).

RNA Molecule: Consists of One polynucleotide chain (1 Strand).

Types of RNA:

ss
E
a
1) Messenger RNA (mRNA): Found in the nucleus or cytoplasm.
2) Transfer RNA (tRNA): Found in the nucleus or cytoplasm.
an

3) Ribosomal RNA (rRNA): Found only in the cytoplasm.

NB:
- RNA is much less stable than DNA.
- DNA is only found in the nucleus and never in the cytoplasm.
R

DNA RNA
r.

Structure Deoxyribose Sugar Ribose Sugar

Has Thymine Has Uracil
Double Stranded Single Stranded
D

Types 1 Type 3 types: mRNA, tRNA,

and rRNA
Site Only in the nucleus May be in the nucleus or
the cytoplasm
Stability More Stable Less Stable

58
 Protein Synthesis

am
- A chromosome consists of one DNA molecule (2 strands).
- A gene is a short length of 1 strand of a DNA molecule.
- Each gene is responsible for the synthesis of a certain protein.
-

ss
A gene consists of many genetic codes. Each genetic code is responsible for the
position of a certain amino acid.

• Genetic Codes:
- Definition: A genetic code consists
of 3 successive nitrogenous bases on
a DNA strand. Each genetic code
E
a
codes for a certain amino acid.

- Properties:***
an

1) Universal: They are shared by almost all living organisms.

2) Triplet: Each code consists of 3 successive nitrogenous bases. So we have 64

different genetic codes for the 20 different amino acids. (43 = 64) [In which 4
R

represents the no. of different bases A,T,C,G and 3 represents the triplet code].
r.

NB: If genetic codes were doublet (only 2 nitrogenous bases), they would not be
enough for the 20 amino acids (42 = 16).
D

3) Degenerate: Each amino acid can have more than one genetic code.

4) Non-overlapping: A nitrogenous base cannot be shared between 2

successive codes.

59
 Protein Synthesis is divided into Transcription and then Translation.

Transcription: The formation of mRNA from a gene on the anti-sense (Active)

strand of DNA inside the nucleus.

Process:***
- A specific length of The DNA molecule (Gene)
unwinds and unzips by breaking Hydrogen bonds
catalyzed by DNA Helicase Enzyme.

am
- One of the 2 free strands formed is the anti-sense
(Active) strand acts as a template and the other
strand remains inactive.
- The free anti-sense strand attracts free active
RNA nucleotides according to complementary

ss
base pairing rules A with U and C with G.
- RNA polymerase enzyme forms the Hydrogen bonds between nitrogenous
bases and joins the sugar phosphate backbone (Phosphodiester bonds).
- RNA polymerase and the formed mRNA both detach and leave.
E
- The mRNA exits the nucleus through nuclear pores heading to the ribosome.
- The 2 DNA strands rejoin each other forming a double helix again.
a
NB:
• Every 3 successive nitrogenous bases on mRNA are known as codons.
an

• tRNA is a clover shaped molecule with anticodons on one side and amino acid
binding site on the other side.
• The ribosome has 2 subunits: Large Subunit and Small Subunit.
• The ribosome is chemically composed of rRNA and proteins.
R
r.
D

60
Translation: The process by which the ribosome reads the mRNA sequence and
translates it into the amino acid sequence on the polypeptide chain.

Process:***

am
ss
- tRNA molecules bind to their specific amino acids ready for translation.
- The ribosome reads the first (Start) codon on mRNA bringing the first tRNA
-
with the first amino acid. E
This tRNA has complementary anticodon to the codon of mRNA so that
Hydrogen bonding takes place ensuring proper positioning of the amino acid.
a
- The ribosome then reads the second codon on mRNA bringing the second
tRNA with the second amino acid.
an

- A peptide bond is formed between the first 2 amino acids catalyzed by

Peptidyl Transferase Enzyme.
- Now the first tRNA detaches and leaves.
- The process continues until a stop codon is reached.
- This ends amino acid sequencing and releases the polypeptide chain in the
R

cytoplasm.
r.

NB:
• Start Codon: It starts amino acid sequencing and places the first amino acid.
• Stop Codon: It ends amino acid sequencing and releases the polypeptide chain.
D

(It does not place any amino acids).

Example: If a mRNA molecule is composed of 101 codons, this means we have a

total of 100 amino acids because of the stop codon.

61
 Comparison between mRNA and tRNA

mRNA tRNA
Both consist of RNA nucleotides.
Both are single stranded.
Straight Folded
Has codons Has anti-codons

am
Length is variable Length is constant
No amino acid bing site Has amino acid binding site
No hydrogen bonds Has hydrogen bonds

ss
• Describe the roles of RNA in the synthesis of proteins:***
- mRNA is formed in the nucleus during transcription.
- mRNA is a copy of DNA genetic codes that is read by the ribosome to
-
-
E
synthesize the primary structure in the cytoplasm by translation.
tRNA attaches to a specific amino acid.
It has anticodons complementary to mRNA codons.
a
- When it forms Hydrogen bonds, amino acids are positioned properly.
an

• State what is meant by the term Semi-conservative Replication:***

- Replication means producing two identical DNA molecules from one parent
molecule.
-
R

Semi-conservative means that each of the daughter molecules has a strand from
the parent molecule while the other strand is newly formed (Half old and Half
new).
r.
D

62
 Evidence of Semi-conservative Replication
Meselson and Stahl Experiment
A parent DNA molecule was labelled by heavy nitrogen (N15). This DNA
molecule was allowed to replicate for 3 successive generations in the presence of
free active nucleotides with light nitrogen (N14). The products are shown below:

am
ss
E
a
an
R
r.
D

63
 Inheritance

• Definitions:
Gene: Short length of the antisense strand of DNA coding for a certain
characteristic through protein synthesis.

Alleles: Alternative forms of the same gene. Which may be dominant or

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recessive.

Dominant Allele: An allele that can show itself on the phenotype in the presence
or absence of the recessive one (B). Expressed if the genotype is homozygous
dominant (BB) or heterozygous (Bb).

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Recessive Allele: An allele that can only show itself on the phenotype in the
absence of the dominant allele (b). Only expressed if the genotype is homozygous
recessive (bb).
E
Homozygous: A person with two similar alleles for the same gene, both dominant
(BB) or both recessive (bb).
a
Heterozygous: A person having two different alleles for one gene, one is
an

dominant and the other is recessive (Bb).

Genotype: The combination of alleles of a certain gene of an individual.

Phenotype: External appearance of a certain individual as a result of interaction

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between the genotype and environment.

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64
 Genetic Diagram
To calculate the probability of the offspring having a certain characteristic.

- Sample Question: Two parents with Black hair produced a child with Brown
hair. Draw a genetic diagram. (B for black hair, b for brown hair).

Parents’s Phenotype: Black x Black

Parents’s Genotype: Bb x Bb

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Gametes:

Offspring’s Genotype: BB, Bb, Bb, bb

Offspring’s Phenotype: Black, Black, Black, Brown

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Ratio: 3:1
• Calculate the probability of the second child having brown hair: 0.25
• Calculate the probability of having two children, both with brown hair:
0.252 = 0.0625
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NB: For a characteristic to appear in the offspring while it did not exists in the
parents, the parents must be heterozygous and the offspring is homozygous
a
recessive.
an

Family Pedigree
R
r.
D

NB: If 2 normal parents gave rise to a diseased child, these are the following
conclusions:
- The disease is recessive inherited.
- The parents are heterozygous (carriers).
- The diseases child is homozygous recessive as this child must have inherited
the 2 recessive alleles one from each parent.
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 Autosomal Genetic Diseases

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• Definition: A disease caused by a faulty allele on an autosome.
We have 46 chromosomes, 44 are autosomes and 2 are sex chromosome.

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• Types:
Recessive inherited Dominant inherited
Definition The faulty allele is a The faulty allele is a
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recessive allele (e.g.
Cystic fibrosis)
dominant allele (e.g.
Achondroplasia)
a
Alleles F: normal A: Below average height
f: diseased a: Average height
an

Genotype options FF: normal AA: diseased

Ff: normal (carrier) Aa: diseased
ff: diseased aa: normal
R
r.
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 Mutations
• Definition: Random change in the DNA
nitrogenous base sequence which might alter
protein structure. It mostly occurs during DNA
replication. It may be through insertion,
deletion or substitution of a nitrogenous base.

• Types and Effects:

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Substitution:
- Substitution only affects one genetic code as
only 1 nitrogenous base is placed by another.
- This may be change one amino acid only, so different amino acid exists in the

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primary structure, but it doesn’t significantly affect the folding of the protein.
Also, the altered code may still code for the same amino acid as genetic codes
are degenerate. This is known as silent mutation.
- However, a substitution mutation may result in a stop code. This ends amino
E
acid sequencing earlier than it should producing shorter non-functioning
protein.
a
Deletion:
- Deletion mutation means the removal of 1 nitrogenous base which leads to a
an

frame shift mutation. This means that all the bases after the mutation are shifted
backwards.
- So different mRNA is produced from the mutated gene.
- So different sequence of amino acids is produced.
- So different primary structure and thus different bending and folding of the
R

protein leading to a non-functioning protein.

- The closer the the mutation to the start of the gene, the greater the effect.
r.

Insertion:
- Insertion mutation means the addition of 1 nitrogenous base which leads to a
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frame shift mutation. This means that all the bases after the mutation are shifted
forwards.
- So different mRNA is produced from the mutated gene.
- So different sequence of amino acids is produced.
- So different primary structure and thus different bending and folding of the
protein leading to a non-functioning protein.
- The closer the the mutation to the start of the gene, the greater the effect.
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 Cystic Fibrosis
• Definition:
A recessive inherited genetic disorder caused by a faulty allele on an autosome
(Chromosome 7). A mutation in the CFTR gene leading to abnormal CFTR
protein which ends by sticky mucus.

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E
a
• Pathology:***
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Normal Diseased
- CFTR protein allows the exit of - CFTR is abnormal or absent, so
Chloride ions (Cl −) outside Chloride ions (Cl −) remains inside
epithelial cells. the epithelial cells.
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- Sodium ions (Na +) moves from the - Sodium ions (Na +) moves from the
intercellular space to join Chloride intercellular space to join Chloride
ions (Cl −) outside the cells forming ions (Cl −) inside the cells forming
r.

NaCl in the mucus. NaCl in the mucus.

- Mucus become hypertonic - Cytoplasm becomes hypertonic
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(Concentrated). (Concentrated).
- Water moves from cytoplasm to - Water moves from mucus to
mucus so mucus becomes watery. cytoplasm so mucus becomes sticky.

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• Effects:
Lungs:
- Mucus produced is too sticky and
blocks small airways leading to alveoli.
So less air entry into alveoli leads to a
non-steep concentration gradient
between alveoli and blood, so less gas
exchange by diffusion. This leads to
less oxygen in blood, so less aerobic

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respiration, leading to less energy
which reduces growth and leads to
easy fatigue.
- Sticky mucus cannot be removed by
cilia so it accumulates leading to

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recurrent chest infections.

Digestive system:
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- Sticky mucus blocks the bile duct and the pancreatic duct, so digestive
enzymes cannot reach the small intestine, leading to maldigestion.
- Auto-digestion of the pancreas (when its enzymes return back to it) leads to
a
failure of secreting insulin causing diabetes.
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Reproductive system:
Sticky mucus blocks Vas deferens (Sperm ducts) in males and Fallopian tubes
(Oviducts) in females so fertilization cannot occur (Infertility).
R

• Treatment:
No definite treatment, ONLY a symptomatic treatment:
r.

- Physiotherapy: Rythmic tapping of the chest and Positive Expiratory Pressure

[PEP] to break down mucus and widen airways.
- Antibiotics: To treat chest infections.
D

- Nutrition through IV fluids.

- Insulin to treat Diabetes.
- IVF to treat infertility.

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 am
NB: How a mutation in the CFTR gene leading an abnormal protein:***
- Random change in the DNA nitrogenous base sequence in the CFTR gene.
- So different mRNA is formed.
- So different primary protein structure.

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- So different number, type and sequence od amino acids in the polypeptide
chain.
- So different arrangement of R groups and consequently different bonds to be
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formed between those R groups such as hydrogen bonds, ionic bonds,
disulphide bonds and hydrophobic interactions.
- So different bending and folding of the polypeptide chain leading to different
CFTR protein.
a
an
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r.
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 Genetic Screening

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- It is undergoing DNA analysis on a large sample of the population to identify
carriers.
- In this process, samples are removed containing diploid somatic cells. (For
example: from the lining of the cheek)
-
-
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Gametes can’t be used in screening as they are haploid with half the DNA only.
This carries very high chances of having a false negative test result.
Cystic fibrosis might arise from a wide range of different mutations in the
a
CFTR gene, so we should screen for all these possible mutations to avoid
having a false negative test result.
an

- When we identify carriers, we screen the rest of the family members in order to
know if they’re also carriers or not. This provides them with a real opportunity
of making informed choices.

- If none of the parents is a carrier, the risk of having a diseased child is low but
R

not zero, Why?

1. The test may be false negative.
r.

2. A mutation might occur in the gametes before fusion or in the formed zygote.

- If a couple realized that they are carriers, they have one of these options:
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• To continue hoping for being lucky.

• Never to have children.
• To continue and undergo genetic testing of the offspring.

71
 Genetic Testing

Genetic Testing could be either:

Pre-implantation Genetic Testing/ Prenatal Testing
Diagnosis (PIGT/PIGD)
During IVF, healthy embryos are It is the testing during pregnancy.
selected for implantation.

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However, during IVF, the female is Chorionic Villus Sampling
given high doses of hormones which Or
may be carcinogenic. Amniotic Fluid Sampling
(Amniocentesis)

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• Chorionic Villus Sampling:
- A needle is inserted through the cervix to remove a
sample of the chorionic villi.
-
-
-
E
The chorionic villi (Placenta) contains fetal cells.
Fetal DNA is analyzed looking for the defective gene.
This is done at week 8 and requires no culture.
a
• Amniotic Fluid Sampling (Amniocentesis):
an

- A needle is inserted through the abdomen to

remove a sample of the amniotic fluid.
- The amniotic fluid contains fetal cells.
- Fetal DNA is analyzed looking for the
R

defective gene.
- This is done at week 16 and requires culture
for 3 weeks.
r.

Advantage Disadvantage
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Chorionic Villus Earlier so the termination Higher risk of

Sampling decision is less traumatic. miscarriage.
Amniocentesis Lower risk of Late so the termination
miscarriage. decision is more
traumatic.

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Ethical & Social Implications of Genetic Testing

• Religious/Moral/Ethical Implication:
- An embryo is a potential life. Termination of a potential life is a murder/
unethical.

• Social Implications:
- It might give rise to marital conflicts about who owns the decision of
termination or continuation.

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- Disclosure of genetic information affects the chances of future employment and
medical insurance.
- The test result may be false negative leading to improper decision of
continuation or false positive leading to improper decision of termination.

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Sex-linked Disorders
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• Definition: A disease caused by a faulty allele on a sex chromosome (X-
chromosome). They can be passed to the offspring.
a
• Types of sex-linked disorders:
an

Recessive Inherited Dominant Inherited

Disorders Disorders
Examples Red Green Colour Night Blindness
R

Blindness and
Haemophilia
r.

Allele Options X R: Normal X N: Diseased

X r: Diseased X n: Normal
Genotype Options X R X R: Normal Female X N X N: Diseased Female
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X R X r: Normal Female X N X n: Diseased Female

(carrier) X n X n: Normal Female
X r X r: Diseased Female X NY: Diseased Male
X RY: Normal Male X nY: Normal Male
X rY: Diseased Male

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• Example Question:
Red green colour blindness is a sex-linked genetic disorder. Draw a genetic
diagram showing the offspring of a normal male and a carrier female.

Parents’ Phenotype: Normal Male x Carrier Female

Parents’s Genotype: X RY x XRXr

Gametes:

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Offspring’s Genotype: X R X R, X R X r, X RY, X rY
Offspring’s Phenotype: Normal Female, Carrier Female, Normal Male, Diseased Male

NB: Explain why sex-linked recessive disorders are more common in males.

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- The male is XY so he has only 1 allele. If this allele is recessive, he will have
the disease.
- This is unlike a female who is XX, so to be diseased she must inherit 2
recessive alleles, one from each parent.
E
a
an
R
r.
D

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 D
r.
R
an

75
a
E
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• Investigating Vitamin C content of different juices
Steps:
- Add 2 cm 3 of 0.1% DCPIP to a test tube.
- Prepare juices from the fruits to be compared using the same extraction
method.
- Use a pipette to add equal sized drops of one juice to A test tube containing
DCPIP solution.
- Shake well after adding each drop.

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- Record the number of drops needed to change DCPIP from blue to colorless.
- Repeat the whole process with the other juice.
- Compare the results.
- The higher the number of drops needed to decolorize DCPIP, the lower the
Vitamin C content.

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- To determine the exact vitamin C concentration in the the solution, you can
compare with a standard Vitamin C solution or use a calibration curve.
- To improve accuracy, record the volume of juice needed to decolorize DCPIP
rather than just counting drops.
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- To ensure validity, control all other variables such as volume and concentration
of DCPIP, storage age and storage temperature of used fruits, same juice
a
extraction method, and same extent of shaking.
- To ensure reliability, repeat 3 times for each juice and calculate the average
volume of juice needed to decolorize DCPIP.
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Volume of Standard juice x Concentration of Standard juice = Volume of

Tested juice x Concentration of Tested juice
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r.
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• Semi-quantitative Food Tests
Testing for reducing sugars:
- Add the food sample to water and shake well.
- Add a known volume of Benedict’s reagent to the
test tube.
- Heat in a water bath at 95°C for a few minutes.
- Observe any colour change if occurs.

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- Any colour change shows presence of glucose
(Positive Test Result). However, the produced colour gives an indication about
the amount of glucose present. That is why it is said to be semi quantitative
test.

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Testing for proteins:
- Add the food sample to water and shake well.
- Add a known volume of Biuret’s reagent.
- If colour changes from blue into purple, proteins are
present (Positive test result). E
- How semi quantitative: The intensity of purple
a
colour is proportional to the amount of proteins present. The deeper the colour,
the higher the protein concentration. Use a colorimeter to measure absorbance
of colour or transmission of light. Then compare the the produced value from
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the colorimeter to a standard curve produced from solutions of known protein

concentrations. This gives an estimate of protein concentration.

Testing for starch:

R

- Add iodine to the food sample.

- If colour changes from yellow-brown into blue-black then
starch is present.
r.

- How semi quantitative: The intensity of blue colour is

proportional to the amount of starch present. The deeper the
colour, the higher the starch concentration. Use a colorimeter
D

to measure absorbance of colour or transmission of light.

Then compare the the produced value from the colorimeter to a standard curve
produced from solutions of known starch concentrations. This gives an
estimate of starch concentration.

77
• Investigating Membrane Permeability
NB Beetroot cells have Betalain pigment stored in their
vacuoles. The cell membrane is normally impermeable
to Betalain.

Steps:
- Cut equal sized beetroot cubes using a cork borer.
- Rinse all discs under running water for 5 minutes to remove any pigment
- produced from cutting.

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- Add six cubes of beetroots to a test tube.
- Add known volume of distilled water to the test tube.
- Place the test tube in water bath set at 10°C.
- Leave for 1 hour.
- After the hour, shake the test tube and record any colour change.

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- Repeat the exact same process for with temperatures 20, 30, 40, 50 and 60°C.
- Compare the results.
- To improve accuracy, use a clean cuvette and insert it into a colorimeter which
- could either measure absorbance of color or transmission of light.
E
- To ensure validity, control all variables such as size of beetroot cubes, volume
of water in the test tubes, species of beetroot, number of the cubes in the test
a
tubes, storage age and storage temperature of the beetroots, time left in water.
- To ensure reliability, repeat the process 3times for each temperature and
calculate the average.
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Expected outcome:
As the temperature increases, the intensity of red color
increases. High temperatures causes melting of the
R

phospholipid bilayer and coagulation of membrane

proteins leading to loss of selectivity, marked increase
in permeability and escape of the Betalain pigment
r.

from the vacuole into cytoplasm then outside the cells

into water.
D

NB: Ethanol also causes loss of membrane permeability as it dissolves the

phospholipid bilayer. To investigate the effect of ethanol on the cell membrane,
Repeat the same investigation but with constant temperature and a range of
ethanol concentrations.

78
• Investigating the effect of enzyme concentration on the rate of reaction:
2H2O2 —-> 2H2O + O2

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Steps:
- Add 10 cm 3 of purees potato to a conical flask.
- Connect this conical flask using a delivery tube, to a half full water bowl with
an inverted measuring cylinder.
E
- Use a syringe to add a known volume of hydrogen peroxide to the conical flask
containing the pureed potato (Potato is the source of catalase enzyme
[Hydrogen peroxidase]).
a
- After 30 seconds, measure the volume of oxygen collected in the measuring
cylinder.
an

- Divide the volume by 30 to get the initial rate of reaction in cm 3 /s.

- Repeat the whole process with 20, 30, 40 cm 3 of pureed potato.
- To ensure validity, control all variables such as temperature using a
thermostatic water bath and pH using a buffer solution and volume of hydrogen
R

peroxide.
- To ensure reliability, repeat several times for each volume of pureed potato
and calculate the average rate of reaction.
r.

NB: Why use catalase?

- Abundant in nature as it is found in most living organisms
D

- It is an enzyme with very high specific activity.

- The product is oxygen which is easy to measure.
NB: To investigate the effect of substrate concentration on the rate of reaction,
repeat the same investigation but with varying the hydrogen peroxide
concentrations and constant volume of pureed potatoes is used.

79
 Calculating Standard Deviation

∑
= Sum of
n = Sample size

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X − = mean
• Example:
The table below shows the number of snails found in 10 quadrats. Calculate the
standard deviation for this sample.

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Quadrat Number Number of snails X2 (X − X −)2
found in each
quadrat [X]
1 14 196 (14 − 14)2 = 0
2
3
15
14
E 225
196
(15 − 14)2 = 1
(14 − 14)2 = 0
a
4 16 256 (16 − 14)2 = 4
5 12 144 (12 − 14)2 = 4
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6 14 196 (14 − 14)2 = 0

7 14 196 (14 − 14)2 = 0
8 12 144 (12 − 14)2 = 4
R

9 16 256 (16 − 14)2 = 4

10 13 169 (13 − 12)2 = 1
r.

Total 140 1978 18

Mean 14
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SD = 1.41
80
 Statistical Analysis
• Some Aspects:
- Mean: The average value = Sum / Number.
- Mode: Most repeated value.
- Median: The middle value with equal number
of values on both sides.

NB: In a normal distribution curve, the mean, the

median and the mode are the same value.

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• Hypothesis (H1): An educated conclusion based on an observation.
Ex: Caffeine affect heart rate.
• Null Hypothesis (H0): The rejection of the hypothesis. It states that the

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hypothesis arises accidentally by chance or error.
Ex: There is no significant difference in the heart rate with or without caffeine.

Degree of freedom: (n-1) or (n1-1)+(n2-1) if 2 groups of data

Ex: A+B+C=10 E
So if I have the freedom to choose A and B, I do not have the freedom to choose C
a
Critical Value: at the 0.05 significance level.
an

Statistical Test Value: A value produced from several mathematical calculations.

Compare the statistical value to the critical value at the 0.05 significance
level. If the statistical test value is ≥ the critical value so we reject the null
hypothesis.
R

Example: A t-test was applied to the data to test the null hypothesis. The
calculated value if t was 2.24. The table shows the critical values of t with 16
r.

degrees of freedom at different significance levels.

Significance 0.20 0.10 0.05 0.01 0.001

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level
Critical value 1.34 1.75 2.12 2.92 4.02
of t

What conclusion can be drawn from this data?

- The critical value at the 0.05 significance level is 2.12.
- The t-test value is higher than the critical value so we reject the null hypothesis.
81
 Statistical Tests

Frequencies Measurments
Difference Correlation
Chi-Squared Test If normally If not normally Spearman Rank
distributed data distributed data Correlation Test
Student t-test Mann-Whitney U
Test

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X 2 value t value u value Rs value

Compare the statistical value to the critical value at the 0.05 significance
level. If the statistical test value is ≥ the critical value so we reject the null

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hypothesis.

NB: This applies to all statistical tests EXCEPT the Mann-Whitney U test (The
opposite. If the u value is higher than or equal to the critical value at the 0.05
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significance level, we accept the null hypothesis.
a
an
R
r.
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