IB Biology Topic 4: Molecular Biology (II) – Enzymes, Cell Respiration & Photosynthesis

A comprehensive set of question–answer flashcards covering enzymes and metabolism, cellular respiration, and photosynthesis for IB Biology Topic 4 (first assessment 2025).

What is the primary role of enzymes in cells?

They act as biological catalysts that speed up chemical reactions without being consumed.

Why can’t most cellular reactions be sped up by high temperature or extreme pH?

Cells are sensitive to such extremes; they would denature proteins and damage cellular structures.

Define metabolism.

The sum of all chemical reactions that occur within a cell or organism.

What is a metabolic pathway?

A series of inter-linked enzyme-catalysed reactions.

Differentiate between anabolic and catabolic reactions.

Anabolic reactions build complex molecules and are endergonic; catabolic reactions break molecules down and are exergonic.

Why are enzymes described as globular proteins?

They fold into compact, spherical shapes with hydrophilic exteriors, making them soluble in water.

What is the active site of an enzyme?

A region whose shape and chemical properties bind the substrate and catalyse its conversion to product.

Explain enzyme–substrate specificity.

Only substrates with complementary shape and chemistry can bind a particular enzyme’s active site.

What model best explains enzyme–substrate interaction today?

The induced-fit model, in which both enzyme and substrate undergo slight conformational changes to achieve ideal binding.

How does molecular motion influence enzyme catalysis?

Greater kinetic energy increases collision frequency and proper orientation between substrate and active site.

State two advantages of immobilised enzymes.

Products aren’t contaminated with enzyme, and the enzyme can be reused, making processes cost-effective.

What happens to an enzyme during denaturation?

Its tertiary structure alters, permanently changing the active site so the substrate can no longer bind.

Sketch-graph trend: effect of temperature on enzyme activity.

Rate rises with temperature to an optimum, then drops sharply as enzymes denature.

Sketch-graph trend: effect of pH on enzyme activity.

Rate is highest at an enzyme-specific optimum pH and falls on either side due to changes in charge and bonding.

Sketch-graph trend: effect of substrate concentration on enzyme activity.

Rate rises rapidly then plateaus when all active sites are saturated.

How is initial rate of an enzyme reaction calculated from a graph?

Draw a tangent at t = 0 and determine its gradient (Δy/Δx).

How do enzymes lower activation energy?

They destabilise substrate bonds and provide an alternative reaction pathway requiring less energy input.

Give one example of an intracellular enzyme pathway.

Glycolysis inside the cytoplasm.

Give one example of an extracellular enzyme.

Digestive enzymes such as amylase secreted into the gut.

Define competitive inhibition.

A reversible inhibitor resembles the substrate and competes for binding at the active site.

Explain non-competitive (allosteric) inhibition.

An inhibitor binds to an allosteric site, changing enzyme conformation and reducing active-site activity.

Why are statins considered competitive inhibitors?

They mimic the substrate of cholesterol-synthesising enzymes, occupying active sites and lowering LDL production.

Describe feedback (end-product) inhibition using isoleucine synthesis.

Excess isoleucine binds allosterically to threonine deaminase, slowing its own production until levels fall.

What is mechanism-based (irreversible) inhibition? Example?

An inhibitor forms covalent bonds with the active site; penicillin irreversibly blocks DD-transpeptidase in bacteria.

Contrast linear and cyclical metabolic pathways.

Linear pathways have distinct start and end (e.g., glycolysis); cyclical pathways regenerate the starting molecule (e.g., Krebs cycle).

What is ATP often called and why?

The universal energy currency because it is used in all cells for various energy-requiring processes.

List the components of an ATP molecule.

Adenine base, ribose sugar, and three phosphate groups.

How much energy (approx.) is released when one phosphate is removed from ATP?

≈ 30.5 kJ mol⁻¹.

Define cell respiration.

The controlled release of energy from organic compounds to produce ATP.

Where does glycolysis occur and what are its net products?

In the cytoplasm; 2 pyruvate, 2 ATP (net), and 2 NADH.

What is the purpose of the link reaction?

It converts pyruvate to acetyl-CoA, producing NADH and releasing CO₂, linking glycolysis to the Krebs cycle.

How many ATP are produced directly in one turn of the Krebs cycle per acetyl-CoA?

1 ATP (substrate-level phosphorylation).

State the role of NAD⁺ in respiration.

It acts as an electron (hydrogen) carrier, becoming reduced to NADH.

What is oxidative phosphorylation?

ATP synthesis powered by the transfer of electrons along the mitochondrial electron transport chain and chemiosmosis.

Why is oxygen essential for aerobic respiration?

It serves as the terminal electron acceptor, forming water and allowing the ETC to continue.

Compare ATP yield per glucose in aerobic vs anaerobic respiration.

≈36–38 ATP aerobically; 2 ATP anaerobically.

What are the end-products of anaerobic respiration in yeast?

Ethanol and carbon dioxide.

What causes muscle fatigue during vigorous exercise?

Accumulation of lactate produced during anaerobic respiration to regenerate NAD⁺.

Name two factors that can change the rate of cellular respiration measured with a respirometer.

Temperature and substrate (glucose) availability.

Formula to calculate oxygen volume in a respirometer using capillary measurements.

Volume (mm³) = π r² h (r = capillary radius, h = distance moved).

What is the chemical summary equation of photosynthesis?

6 CO₂ + 6 H₂O → C₆H₁₂O₆ + 6 O₂ (in the presence of light and pigments).

From which reactant is the oxygen released during photosynthesis derived?

Water, via photolysis in photosystem II.

What is the main photosynthetic pigment?

Chlorophyll a.

Why do plants appear green?

Chlorophyll reflects green wavelengths while absorbing red and blue light.

Define Rf value in chromatography.

Distance moved by pigment ÷ distance moved by solvent front.

Which pigment generally has the highest Rf value in TLC of leaf pigments?

Carotenoids.

Distinguish absorption spectrum from action spectrum.

Absorption spectrum shows wavelengths absorbed by pigments; action spectrum shows rate of photosynthesis at each wavelength.

At which two visible regions is photosynthetic rate highest?

Blue-violet (~450 nm) and red (~680 nm) regions.

What experimental variable does moving a lamp closer to elodea primarily change?

Light intensity.

How does increasing CO₂ concentration affect photosynthetic rate before saturation?

It increases the rate because CO₂ is a substrate for carbon fixation.

Name the two major stages of photosynthesis.

Light-dependent reactions and light-independent reactions (Calvin cycle).

Where are photosystems located?

In the thylakoid membranes of chloroplasts.

Give the reaction centre wavelength names for PSI and PSII.

PSI: P700; PSII: P680.

Explain photolysis.

Light-driven splitting of water into electrons, protons, and oxygen in PSII.

What is chemiosmosis in chloroplasts?

ATP synthesis driven by proton diffusion through ATP synthase across the thylakoid membrane.

Differentiate cyclic from non-cyclic photophosphorylation.

Cyclic uses PSI only, returns electrons to PSI, makes ATP only; non-cyclic uses both photosystems, electrons flow to NADP+, makes ATP and NADPH.

What enzyme catalyses carbon fixation in the Calvin cycle?

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco).

Identify the three phases of the Calvin cycle.

Carbon fixation, reduction of GP to TP, regeneration of RuBP.

Which Calvin-cycle intermediate exits to form sugars and other compounds?

Triose phosphate (TP).

How many TP molecules are needed to net-synthesize one glucose?

Two TP molecules (each 3C) form one hexose after multiple turns.

Why are the light-dependent and light-independent reactions interdependent?

ATP and NADPH from light reactions power the Calvin cycle, which in turn regenerates ADP, Pi and NADP+ for light reactions.

What is the Great Oxidation Event?

The rise of atmospheric O₂ to ~2% about 2.2 billion years ago due to photosynthetic organisms.

How do FACE experiments help predict plant responses to climate change?

They elevate CO₂ around plants in natural ecosystems to study long-term effects on photosynthesis and growth.

Why do lipids yield more ATP per gram than carbohydrates?

Lipids contain more reduced carbon and hydrogen, providing more electrons for oxidative phosphorylation.

Which respiratory substrate can enter glycolysis directly without prior modification?

Glucose.

What is feedback inhibition's main advantage in metabolism?

Prevents accumulation of intermediates and conserves resources by down-regulating pathways when end products are abundant.

Explain the term ‘activation energy’.

The minimum energy required to bring reactant molecules to a transition state for reaction.

How many NADH are produced in glycolysis per glucose?

Two NADH.

What is substrate-level phosphorylation?

Direct transfer of a phosphate group from an intermediate substrate to ADP, forming ATP.

Where does chemiosmosis occur inside mitochondria?

Across the inner mitochondrial membrane (cristae).

Name the protein complex that uses the proton gradient to make ATP in both mitochondria and chloroplasts.

ATP synthase.

During anaerobic respiration in human muscle, how is NAD+ regenerated?

Pyruvate accepts electrons from NADH, forming lactate.

Why is hydrogen peroxide dangerous to cells and which enzyme decomposes it?

It is a reactive oxygen species; catalase decomposes it into water and oxygen.

Give one reason immobilised enzymes often tolerate higher temperatures.

Attachment to a solid matrix restricts conformational changes, stabilising the protein.

How does penicillin kill bacteria?

It irreversibly inhibits transpeptidase, preventing peptidoglycan cross-linking and causing cell-wall lysis.

What is the function of ferredoxin in photosynthesis?

Accepts electrons from PSI and helps reduce NADP+ to NADPH.

Which step of photosynthesis directly produces ATP?

Photophosphorylation (cyclic and non-cyclic) in the thylakoids.

Why does increasing temperature above optimum decrease photosynthetic rate?

RuBisCO and other enzymes denature, lowering Calvin-cycle efficiency.

What is the main experimental evidence that oxygen in photosynthesis comes from water?

Isotope-tracer experiments using H₂¹⁸O show released O₂ contains ¹⁸O.

State one controlled variable in a pondweed light-intensity experiment.

CO₂ concentration (via fixed NaHCO₃ amount) or temperature (using a water bath).

How is ATP regenerated in cells after hydrolysis to ADP + Pi?

By phosphorylation during respiration or photophosphorylation, requiring energy input.

What is the principal difference between NADH and FADH₂ in the ETC?

NADH donates electrons to the first complex, generating ~3 ATP, whereas FADH₂ donates later, generating ~2 ATP.

During which respiration stage is most CO₂ produced?

Krebs cycle (and link reaction).

Explain the term ‘chemiosmotic theory’.

Proposes that a proton gradient across a membrane drives ATP synthesis via ATP synthase.

Why is Rubisco considered inefficient?

It has a slow turnover rate and can catalyse oxygenation of RuBP, leading to photorespiration.

What pigment group extends the range of light absorption beyond chlorophyll?

Accessory pigments such as carotenoids and xanthophylls.

Name two products of the light-dependent reactions that enter the Calvin cycle.

ATP and reduced NADP (NADPH).

Which metabolic pathway supplies acetyl-CoA in lipid breakdown?

β-oxidation of fatty acids.

Give one example of a model in biology mentioned in the notes.

Generalised sketch graphs showing enzyme activity vs temperature, pH or substrate concentration.

Why do smaller organisms often have higher mass-specific respiration rates?

They have a larger surface-area-to-volume ratio, losing heat faster and needing more energy to maintain metabolism.

Which variable does a respirometer’s NaOH or KOH solution control?

It absorbs CO₂ to ensure only O₂ uptake is measured.

What term describes energy-absorbing reactions such as photosynthesis or anabolic pathways?

Endergonic reactions.

During alcoholic fermentation, what enzyme converts pyruvate to ethanol?

Alcohol dehydrogenase (after pyruvate decarboxylase forms ethanal).

What is the overall proton motive force used for in both respiration and photosynthesis?

To drive the synthesis of ATP via ATP synthase.

Explain ‘substrate analogue’.

A molecule structurally similar to an enzyme’s substrate that can bind and be modified to an irreversible inhibitor.

Why is ATP not stored in large quantities in cells?

It is highly reactive and unstable, so cells continuously regenerate it from ADP.

Which wavelengths of light are least effective for photosynthesis and why?

Green-yellow (~500–600 nm) because chlorophyll reflects rather than absorbs them.

Name the intermediate that links glycolysis to the Krebs cycle.

Acetyl-Coenzyme A.

How many CO₂ are released per glucose in aerobic respiration?

Six CO₂ (2 in link reactions, 4 in Krebs cycles).

Which light-dependent reaction product supplies reducing power to convert GP to TP?

NADPH.