Enzymes

Enzymes are biocatalysts that speed up cellular metabolic reactions by reducing the activation energy required for reactions to occur. They are made of proteins, are highly specific to their substrates, and can be reused repeatedly because they are not consumed during the reaction.

Enzyme activity is affected by several factors including temperature, pH, substrate concentration, and enzyme concentration.

Catalyst

A catalyst is a substance that increases the rate of a chemical reaction without being changed or used up by the reaction itself. Enzymes are biological catalysts.

Substrate

A substrate is the reactant molecule that binds to an enzyme. When the substrate binds to the enzyme, an enzyme–substrate complex is formed, which lowers the activation energy needed for the reaction to proceed.

Intracellular Enzymes

Intracellular enzymes function inside the cell. An example is enzymes involved in cellular respiration, which occur in the cytoplasm and mitochondria.

Extracellular Enzymes

Extracellular enzymes function outside the cell. Digestive enzymes such as amylase, protease, and lipase are secreted into the digestive tract to break down food molecules.

Nomenclature of Enzymes

Enzymes are usually named after the substrate they act on, with the suffix -ase.

• Lactose → Lactase
• Lipids → Lipase
• Proteins → Protease

Activation Energy

Activation energy is the minimum amount of energy required for a chemical reaction to occur. Enzymes lower this energy barrier, allowing reactions to happen faster and at normal biological temperatures.

Enzyme Action

Enzymes bind to their specific substrate to form an enzyme–substrate complex. This complex lowers activation energy and allows either a catabolic (breaking down) or anabolic (building up) reaction to occur, producing an end product.

Active Site

The active site is a specific region or groove on the enzyme where the substrate binds. It is divided into two functional regions:

• Binding site: The region where the substrate attaches to the enzyme.
• Catalytic site: The region where the chemical reaction takes place.

Lock-and-Key Model

The lock-and-key model explains enzyme specificity by stating that the shape of the enzyme’s active site is exactly complementary to the shape of its substrate. Only the correct substrate can fit into the active site, just as only the correct key fits into a lock. This explains why enzymes are highly specific.

Induced Fit Model

The induced fit model states that enzymes are specific but not rigid. When the substrate binds, the active site slightly changes shape to fit the substrate more tightly. This improves the interaction between enzyme and substrate and further lowers activation energy. However, enzymes cannot permanently change shape.

Factors Affecting the Rate of Enzyme-Controlled Reactions

Temperature

As temperature increases, kinetic energy increases, leading to more frequent collisions between enzyme and substrate and an increased rate of reaction.

• Approximately 40°C is the optimum temperature for many human enzymes.
• Above 40°C, enzymes undergo denaturalisation, causing the active site to lose its shape and the enzyme to stop functioning.

pH Level

Different enzymes have different optimum pH levels. As pH approaches the optimum, the rate of reaction increases.

• Deviations from the optimum pH cause changes in the enzyme’s structure.
• Extreme pH levels result in denaturalisation of the enzyme.The same goes for temperature

Substrate and Enzyme Concentration

Increasing substrate or enzyme concentration increases the rate of reaction because more enzyme–substrate complexes form.

• At a certain point, all active sites are occupied and the reaction rate plateaus.

Enzyme Use in the Food Industry

• Pectinase breaks down substances in apple cell walls, increasing juice extraction.
• Lactase breaks down lactose in milk, producing lactose-free milk.
• Proteases pre-digest proteins in baby food.

Other Uses of Enzymes

• Used in the treatment and prevention of diseases
• Involved in seed germination
• Used to produce low-calorie foods

Lactose Intolerance

Lactose intolerance occurs when an individual produces insufficient amounts of the enzyme lactase. As a result, lactose cannot be broken down into glucose and galactose, leading to digestive discomfort.

Picture taken from: ResearchGate

Structure of a Leaf

• Wax Cuticle: A protective, waterproof layer on the top of the leaf that prevents excessive water loss through evaporation.
• Upper Epidermis: A transparent layer that allows light to pass through to the palisade mesophyll layer underneath.
• Palisade Mesophyll: Tightly packed cells containing a large number of chloroplasts to maximize light absorption for photosynthesis.
• Spongy Mesophyll: Loosely packed cells with large internal air spaces, increasing the surface area for gas exchange.
• Lower Epidermis: Contains guard cells and stomata; this layer does not need direct light.
• Guard Cells: Specialized cells that absorb and lose water to open and close the stomata.
• Stomata: Openings where gas exchange (CO₂ and O₂) and water evaporation (transpiration) take place.
• Vascular Bundle: Contains xylem and phloem tissues.
• Xylem: Transports water and mineral ions from the roots into the leaf.
• Phloem: Transports sucrose and amino acids around the plant.

Chloroplasts

Chloroplasts are the organelles where photosynthesis takes place. A chloroplast consists of an outer membrane and an inner membrane, enclosing a fluid-filled region called the stroma.

Inside the chloroplast are flattened membrane-bound sacs called thylakoids. The thylakoids are arranged in vertical stacks known as grana (singular: granum), which are interconnected by lamellae.

Thylakoid membranes contain chlorophyll, a green pigment that absorbs light energy and acts as a photoreceptor to initiate photosynthesis.

Unit 2: Diffusion, Osmosis and Active Transport

Diffusion, Osmosis and Active Transport

Diffusion

Diffusion is the movement of a substance from an area of higher concentration to an area of lower concentration. An example of diffusion is oxygen moving from the alveoli into the bloodstream.

Osmosis

Osmosis is the transfer of water from an area of lower solute concentration to an area of higher solute concentration across a partially permeable membrane.

Factors Affecting Osmosis

• Surface area
• Temperature
• Membrane permeability

Exosmosis

Exosmosis occurs when water moves out of a cell.

Endosmosis

Endosmosis occurs when water moves into a cell.

Tonicity

• Hypotonic: Less solute than solvent
• Hypertonic: More solute than solvent
• Isotonic: Equal solute and solvent amounts

Example of Osmosis

When a potato is placed in a cup of normal water, a hole is cut into the potato and filled with sugar water. After some time, normal water moves into the potato.

This happens because sugar water is a hypertonic solution, and hypotonic solutions move towards hypertonic solutions in an attempt to reduce the concentration gradient and increase equilibrium.

Effect of Solutions on Cells

Plant cells become turgid in a hypotonic solution because they need to store more water overall. In an isotonic solution, plant cells become flaccid. In a hypertonic solution, plant cells become plasmolysed, shrink, and may die.

Active Transport

Active transport uses energy to move substances against their concentration gradient. A concentration gradient refers to the difference in concentration of a substance between two regions.

Active transport uses specific carrier proteins called pumps.

• The molecule binds to a carrier protein.
• ATP is used to change the shape of the protein.
• The substance is moved across the concentration gradient.
• The protein returns to its original shape and position.

Cellular Respiration

Cellular respiration is the process by which glucose is converted into energy in the form of ATP.

Types of Respiration

• Aerobic respiration: Requires oxygen
• Anaerobic respiration: Does not require oxygen

Aerobic Respiration

Glycolysis

Glycolysis takes place in the cytoplasm of the cell and produces 2 ATP, 2 NADH, and 2 pyruvate molecules.

Approximately 38 ATP molecules are produced overall during aerobic respiration.

Anaerobic Respiration

Glycolysis

Glycolysis in anaerobic respiration is the same as in aerobic respiration.

Fermentation

• Lactic Acid Fermentation: Produces lactic acid as a by-product.
• Alcoholic Fermentation: Occurs in yeast and produces ethanol.

Anaerobic respiration produces only 2 ATP.

Circulatory System

Double Circulation

In double circulation, blood passes through the heart twice during one complete cycle.

• Occurs completely in animals with four heart chambers
• Occurs incompletely in animals with three heart chambers
• Does not occur in animals with two heart chambers

Single Circulation

Single circulation occurs only in Pisces (fish).

Disadvantages of Single Circulation

• Slow metabolism
• Low blood pressure
• Slower blood circulation

Picture taken from: ShutterStock

Blood Flow Through the Heart

Blood enters the right atrium from the vena cava. The vena cava is the largest vein, and all veins connect to it. This blood is deoxygenated and must be oxygenated to form oxyhaemoglobin.

Blood flows from the right atrium to the right ventricle through the bicuspid (mitral) valve and is transported to the lungs via the pulmonary artery.

In the lungs, blood is oxygenated and returns to the heart through the pulmonary veins into the left atrium.

Blood then moves from the left atrium to the left ventricle through the tricuspid valve. The left ventricle pumps blood through the aorta via the aortic (semilunar) valve.

The aorta distributes oxygenated blood throughout the body. Because it handles high pressure, the aorta has thick muscular walls. Veins, in contrast, have thinner walls and a larger lumen.

Coronary Heart Disease (CHD)

Coronary Heart Disease (CHD) occurs when the coronary artery, which supplies blood and oxygen to the heart muscle (along with the vena cava), becomes narrowed or blocked.

When plaque builds up in the coronary artery, the supply of oxygenated blood to the heart is reduced. This can lead to chest pain (angina), shortness of breath, and if the plaque buildup becomes severe, a heart attack.

Causes of Coronary Heart Disease

• High LDL cholesterol and low HDL cholesterol: High levels of “bad” cholesterol (LDL) and low levels of “good” cholesterol (HDL) are often caused by diets high in fast foods, fried foods, and trans fats.
• Lack of movement: Physical inactivity gives the heart less work to do, reducing blood circulation and contributing to the progression of CHD.
• Atherosclerosis: Fatty acids build up inside the artery walls, narrowing the lumen and restricting blood flow.
• Genetic and lifestyle factors: Family history, obesity, and long-term inactivity increase the risk of CHD.

Blood

Red Blood Cells (Erythrocytes)

• Concave disc shape
• Smaller than white blood cells
• Main function is to transport oxyhaemoglobin
• Use passive transport to carry oxygen
• Do not contain mitochondria
• Produced in red bone marrow
• Formed in the same location as white blood cells and platelets

White Blood Cells (Leucocytes)

Phagocytes / Monocytes

• Non-specific immune attackers
• Carry out phagocytosis to engulf bacteria
• Collect at infection sites to ingest harmful microorganisms
• Kidney-shaped nucleus

Lymphocytes

• Produce specific antibodies
• Include B-cells and T-cells
• Large circular nucleus

Neutrophils

• First cells to arrive at infection sites
• Destroy microorganisms
• Cause inflammation
• Poly / star-shaped nucleus

Basophils

• Involved in allergic responses
• Release histamine and other chemicals
• Cause inflammation and allergic reactions
• Mononucleus split at the top

Eosinophils

• Fight bacteria and parasitic infections
• Bilobed nucleus

Lysosomes

Lysosomes contain proteins and enzymes that help destroy bacteria and other pathogens within immune cells.

Ventilation

Picture taken from: Theory Pages – Labster

Adaptations for Efficient Ventilation

Alveoli

• Thin walls for rapid diffusion
• Moist surface to allow gases to dissolve
• Large surface area
• Rich blood supply from capillaries

Nose

• Nasal hairs filter dust particles
• Mucus traps bacteria and pathogens
• Turbinates increase surface area for air–mucus contact
• Rich blood supply warms and humidifies air

Intercostal Muscles

• Located between the ribs
• Assist inhalation and exhalation
• Expand and contract the chest cavity

Diaphragm

• Contracts during inhalation, increasing thoracic cavity volume
• Relaxes during exhalation
• Works antagonistically with intercostal muscles

Gaseous Exchange

Gaseous exchange is a passive process. Oxygen is inhaled and diffuses into the blood, while carbon dioxide diffuses from the blood into the lungs and is exhaled.

In humans, gaseous exchange occurs in the alveoli and surrounding capillaries. In plants, oxygen diffuses out of the stomata while carbon dioxide diffuses into the plant.

Digestive System

Colon

• Part of the large intestine
• Absorbs water and salts from undigested food
• Forms and stores feces
• Contains bacteria that assist digestion
• Moves waste by peristalsis
• Connects the small intestine to the rectum

Small Intestine

• Longest part of the digestive system
• Consists of the duodenum, jejunum, and ileum
• Main site of digestion and nutrient absorption
• Receives bile from the liver and pancreatic juice from the pancreas
• Contains villi to increase surface area
• Absorbs nutrients into the bloodstream

Stomach

• Muscular, J-shaped organ
• Stores and churns food to form chyme
• Secretes gastric juice containing acid and enzymes
• Hydrochloric acid kills germs and aids digestion
• Pepsin begins protein digestion
• Thick mucus lining protects stomach walls

Digestive Enzymes

Amylase

• Produced in the mouth and pancreas
• Breaks down carbohydrates and starch

Lipase

• Produced in the pancreas
• Breaks down fats

Protease

• Produced in the pancreas
• Breaks down proteins

Enzyme reaction example:
2H₂O₂ → 2H₂O + O₂

Duodenum

• First part of the small intestine
• Receives chyme from the stomach
• Receives bile and pancreatic juice
• Bile emulsifies fats
• Pancreatic enzymes digest proteins, fats, and carbohydrates

Malnutrition

Kwashiorkor

• Protein deficiency disease
• Common in children in developing countries
• Swollen belly due to fluid buildup
• Thin muscles with fat-looking appearance
• Dry, scaly skin and reddish hair
• Weakness and irritability

Prevention

• Consume protein-rich foods (milk, eggs, pulses, fish, meat)
• Maintain a balanced diet

Marasmus

• Deficiency of both protein and calories
• Common in young children
• Extreme thinness and visible bones
• Sunken eyes and wrinkled skin
• Stunted growth

Prevention

• Provide balanced diet with proteins, carbohydrates, and fats
• Ensure proper infant nutrition

Respiratory Diseases

Asthma

Asthma is a chronic respiratory disease involving inflammation and narrowing of the airways.

• Triggered by dust, pollen, smoke, cold air, or exercise
• Causes wheezing, chest tightness, and coughing

Management

• Avoid triggers
• Use prescribed inhalers
• Maintain clean surroundings

Emphysema

Emphysema is a chronic lung disease that damages alveoli, reducing gas exchange efficiency.

• Mainly caused by smoking
• Causes shortness of breath and fatigue

Management

• Quit smoking
• Avoid pollution
• Use inhalers or oxygen therapy

Transpiration

Transpiration is the process of water leaving a body.

In Humans

Water vapour is released through breathing and sweating, helping regulate body temperature and remove salts.

In Plants

Water is absorbed from the soil by active transport, moves up the xylem, evaporates in mesophyll air spaces, and diffuses out through the stomata.

Factors Affecting Transpiration

• Humidity: Higher humidity reduces transpiration rate
• Light intensity: Increased light opens stomata
• Wind speed: Higher wind increases transpiration
• Leaf surface area: Larger area means more stomata

Measuring Transpiration

A potometer measures water uptake as a proxy for transpiration. As transpiration occurs, water is absorbed, moving an air bubble along a scale to calculate the rate.

Excretory System

Photo taken from: Deposit Photos

• Renal Vein: Carries filtered deoxygenated blood along with some reabsorbed nutrients away from the kidneys to the heart.
• Renal Artery: Carries a large amount of oxygenated blood from the heart to the kidneys.
• Ureter: Transports urine from the kidneys to the bladder.
• Urethra: Urine escapes from here.
• Bladder: Urine is stored here; when pressure gets too high it escapes automatically by the urethra.
• Adrenal Gland: Covered in the endocrine system.
• Nephrons: Tiny filtering units of the kidney.
• Medullary Pyramid: Composed of loops of Henle and collecting ducts, creating a concentration gradient allowing the kidney to reabsorb water and concentrate urine.
• Kidney: Filters blood to remove waste and excess water, creating urine.

Nephrons

Each nephron has a strong blood supply from arterioles. The afferent arteriole brings blood to the glomerulus, while the efferent arteriole is narrower and carries blood away, creating high pressure for filtration.

Steps in Urine Formation

1. Glomerular Filtration:
   Blood passes through the narrow efferent arteriole at high pressure, causing ultrafiltration. Small molecules such as urea, glucose, amino acids, and water are filtered from the blood into Bowman’s capsule.
2. Selective Reabsorption:
   The glomerular filtrate (primary urine) passes through the proximal convoluted tubule. Useful substances such as glucose, amino acids, and water are reabsorbed back into the blood.
3. Tubular Secretion:
   Occurs mainly in the distal convoluted tubule. Toxic waste products and excess ions are actively secreted into the tubule.
4. Collection:
   Urine is transported via the ureter to the bladder, which can hold up to approximately 300 mL of urine before excretion through the urethra.

• In a normal human, glucose is fully reabsorbed. Presence of glucose in urine indicates diabetes.
• ADH (Antidiuretic Hormone): Maintains water balance in the body. A deficiency causes continuous dilute urine.
• Presence of proteins in urine indicates kidney damage.
• Low body water levels trigger increased ADH release, increasing water reabsorption.

Dialysis

Dialysis is used when kidneys fail to function properly. A dialysis machine removes toxic waste products such as urea from the blood.

Types of Dialysis

Hemodialysis

Blood is drawn from a vein and passed through tubing inside a dialysis machine. The tubing is surrounded by a special fluid and has semi-permeable synthetic fibers. Waste products diffuse out of the blood before it is return