IB Biology - Theme C

C1.1.1—What are enzymes?

They are proteins (some are RNA) that function as biological catalysts. This means they increase the rates of reaction in cells.

"C1.1.1—What are the two main benefits of enzymes in cells.

Many chemical reactions do not occur spontaneously, or they may happen very slowly.

A) Catalysts allow reactions to happen without - high temperatures, high pressures, extremes of pH, by maintaining high concentrations of the reacting molecules.

B) By controlling enzymes we can control which chemical reactions actually happen, we can control metabolism.

"

C1.1.2—Role of enzymes in metabolism

Because of enzyme specificity, many different enzymes are required by living organisms, and control over metabolism can be exerted through these enzymes.

C1.1.2—What do we call the is the complex network of interdependent and interacting chemical reactions occurring in living organisms.

Metabolism

C1.1.2—What is the meaning of specificity in enzymes.

Different enzymes are needed for different substrates, therefore many different enzymes are required by living organisms

C1.1.3—Give three examples of anabolism

Protein synthesis, glycogen formation and photosynthesis.

C1.1.3—Give three examples of catabolism

Hydrolysis of monomers in digestion, and oxidation of substrates in respiration.

"C1.1.3—Name the two types of chemical reactions.

Anabolic reactions (formation of macromolecules from monomers by condensation reactions)

Catabolic reactions (breakdown of larger molecules into simple moleculesby by hydrolysis reactions)

"

C1.1.4— Is the active site small or large?

The active site is composed of a few amino acids only, but interactions between amino acids within the overall three-dimensional structure of the enzyme ensure that the active site has the necessary properties for catalysis.

"C1.1.4— What do we call the part of an enzyme molecule where the substrate molecule binds and

catalysis occurs.

Active site.

"

C1.1.4—Describe the structure of enzymes.

Globular proteins with an active site for catalysis

C1.1.5— What is the induced fit model?

The model of enzyme action where binding of the substrate to the enzyme causes a change in the shape of the enzyme AND the substrate, resulting in the proper alignment of the catalytic groups on its surface, which enables catalysis to take place.

C1.1.6—Give reasons why an enzyme controlled reaction between substrate and enyzme might not happen.

They don't collide with the active site, or they collide at the wrong angle (orientation), or the wrong speed.

C1.1.6—What is immobilisation and how can it assist enzyme catalysis?

Sometimes large substrate molecules are immobilized while sometimes enzymes can be immobilized by being embedded in membranes. This makes the enzyme more stable, creates a better environment and orientation.

C1.1.7—Is the primary structure of proteins changed during denaturation?

No, peptide bonds are strong and are not hydrolysed.

C1.1.7—What happens during denaturation?

the weaker intramolecular bonds break, changing the 3D shape of of the active site, so enzyme and substrate can no longer bind (are no longer specific).

C1.1.8—Can models in the form of sketch graphs be used with enzyme experiments.

Yes.

C1.1.8—Effects of pH on the rate of enzyme activity (relate to graphs)

As pH increases above or below optimum - the environment is flooded with H+ ions (acid) or OH- ions (alkali), which interfere with intramolecular bonding, changing the 3D shape of the enzyme, whic become denatured so the amount of active enzyme decreases and reactions go slower.

"C1.1.8—Effects of substrate concentration on the rate of enzyme activity (relate to graph)

At a low concentration of substrate - Reaction rate is slow due to the small number of substrate molecules, however all molecules can find an active site without delay, there is an excess of enzyme present.

As substrate concentration increases - there are more collisions between substrate and the enzyme, with a higher likelihood of the substrate binding with the active site of the enzyme and enzyme-substrate

complexes forming, causing more reactions to take place.

As substrate concentrations increases beyond enzyme concentration - there is more substrate than

enzyme and substrate molecules must 'wait' for access to an active site and there is

now no increase in the rate of reaction.

"

"C1.1.8—Effects of temperature on the rate of enzyme activity (relate to graphs)

As temperatures increase - substrate and enzymes have more kinetic energy, and more collisions (at higher speed), and so reactions go faster.

As temperatures increase above optimum - enzymes become denatured so the amount of active enzyme decreases and reactions go slower.

"

"C1.1.8—Improve this explanation: 'because

there are more collisions with the enzyme'.

A better answer is: because there are more FREQUENT collisions between the substrate and the active site.

"

C1.1.8—What do we call the temperature, or pH at which an enzyme works best.

Optimum

C1.1.9—How do you calculate the relative rate of reaction from the time taken in an enzyme controlled reaction.

Relative rates of reaction can be calculated using the reciprocal of time (1/t). The units are x/s.

"C1.1.9—Name two ways of measuring an enzyme-catalysed experiment.

The production of product e.g. The production of oxygen gas from hydrogen perioxide by catalase.

The loss of substrate e.g. The hydrolysis of starch by amyalse.

"

"C1.1.10—What energy changes take place when products are formed in an enzyme-controlled reaction.

There is an energy yield when bonds are made to form the products.

The products have a lower energy than the substrate.

"

C1.1.10—What is the activation energy required to do?

Break or weaken bonds in the substrate to produce a transition state.

C1.1.10—What is the effect of enzymes on activation energy

Lowers it (does not remove it).

C1.1.10—What is the energy required by a substrate molecule before it can undergo a chemical change.

Activation energy

"C1.1.11—What do we call an enzyme

secreted by a cell that functions outside the cell.

Extracellular enzyme e.g. chemical digestion in the gut

"

"C1.1.11—What do we call an enzyme that

functions within the cell in which it was produced.

Intracellular enzyme e.g. glycolysis and the Krebs cycle

"

C1.1.12—Describe the nature of an exergonic reaction

A kind of reaction where the products have less stored energy than the reactants.

C1.1.12—In what kind of reaction does energy have to be put in, because the products have more stored energy than the reactants.

Endergonic reaction

C1.1.12—Name three types of animals that depend on this heat production for maintenance of constant body temperature.

Mammals, birds and some other animals

C1.1.12—What kind of energy is always generated by the reactions of metabolism

Heat energy - because metabolic reactions are not 100% efficient in energy transfer.

"C1.1.13—Name two types of pathways in metabolism with examples.

Cyclical e.g. Krebs cycle and the Calvin cycle

Linear e.g. glycolysis

"

C1.1.14—Can any substance bind to an allosteric site?

No only specific substances.

C1.1.14—How does non-competitive inhibition work?

A inhibitor binds to an allosteric site (a site other than the active site) which causes interactions within an enzyme that lead to conformational changes, which alter the active site enough to prevent catalysis. Binding is reversible.

C1.1.14—What is an enzyme inhibitor? Name two types.

A substance that slows or blocks enzyme action. Competitive or non-competitive.

"C1.1.15—Compare competitive and non-competitive inhibition.

Non-competitive: Binds irreversibly, to allosteric site, excess substrate does not overcome inhibition so Vmax is reduced.

Competitive: Binds reversibly, to active site, excess substrate overcomes inhibition so Vmax is not reduced.

"

C1.1.15—Explain how statins function.

They are competitive inhibitors of an enzyme which is needed to make cholesterol. Statins compete with HMG‑CoA for the active site of HMG-CoA reductase

C1.1.15—How does competitive inhibition work?

A inhibitor that binds reversibly to the active site of an enzyme, slowing or blocking enzyme action.

C1.1.16—End-product inhibition is a method of regulating metabolic pathways. Explain how it works.

The product of the last reaction in a metabolic pathway reversibly inhibits the enzyme that catalyses the first reaction of the pathway.

"C1.1.16—Give a real life example of end-product inhibition as a method of regulating metabolic pathways.

Bacteria can synthesize isoleucine from threonine.

Threonine -> Intermediate A -> Intermediate B -> Intermediate C -> Intermediate D -> Isoleucine

Isoleucine acts as a non-competitive inhibitor by binding to the allosteric site of the enzyme

threonine deaminase (enzyme in the first stage of the metabolic pathway).

So when isoleucine concentration is still low, the metabolic pathway can proceed as non-competitive inhibition is low. As isoleucine concentration increases, non-competitive inhibition takes place and the metabolic pathway is regulated.

"

"C1.1.17— A process that occurs when

unreactive molecules are transformed into

an active form through catalytic reactions to inhibit the enzyme, typically through

covalent modification of the active site. It is

an irreversible form of enzyme inhibition.

Mechanism-based inhibition.

"

C1.1.17—Explain how bacteria might become resistant to penicillin.

A mutation to the gene that produces the enzyme DD-transpeptidase changes the active site so it loses its affility to penicillin. The bacteria with the mutation become resistant.

C1.1.17—Explain mechanism-based inhibition using penicillin as an example.

Penicillin binds to the enzyme DD-transpeptidase (an enzyme that forms peptide crosslinks between polysccharide chains in cellulose), the structure of penicillin is modified by the enzyme, forming an inactive enenzymes-penicillin complex so no further linkages can be formed.

C1.2.1—Name the molecule that distributes energy within cells

ATP (adenosine triphosphate)

"C1.2.1—Name the properties of ATP that make it suitable for use as the energy currency within cells.

1. Moves easily within cells and organisms - by facilitated diffusion

2. Very reactive molecule - can take part in many steps of cellular respiration and reactions of metabolism

3. Immediate source of energy

4. Delivers energy in relatively small amounts, sufficient to drive individual reactions and physical processes.

"

C1.2.1—What kind of molecule is ATP?

Nucleotide.

C1.2.2—Name four life processes within cells that ATP supplies with energy

Active transport across membranes, synthesis of macromolecules (anabolism), movement of the whole cell, or cell components such as chromosomes.

C1.2.3—Describe the energy transfers during interconversions from ADP to ATP

Energy is required to synthesize ATP from ADP and phosphate.

C1.2.3—Describe the energy transfers during interconversions from ATP to ADP

Energy is released by hydrolysis of ATP (adenosine triphosphate) to ADP (adenosine diphosphate) and phosphate. Students are not required to know the quantity of energy in kilojoules

C1.2.4—Name processes which is commonly confused with cell respiration, but which is distinctly different.

Gas exchange

"C1.2.4—Name the principal substrates for cell respiration.

Glucose (directly enter glycolysis) and fatty acids (need to enter gluconeogenesis first),

...but that a wide range of carbon/organic compounds can be used (e.g. hydrolyzed into amino acids, then deaminated (NH group removed) before they can enter the respiratory pathway. This requires ATP, so the net production of ATP is less

"

C1.2.4—Name the system for producing ATP within the cell using energy released from carbon compounds

Cell respiration.

"C1.2.5—Differences between anaerobic and aerobic cell respiration in humans

Respiratory substrates used - Same

Whether oxygen is required - Only aerobic

Yields of ATP - Aerobic makes around 38, anaerobic around 2.

Types of waste product - Aerobic makes carbon dioxide and water, Anaerobic makes lactic acid in animals, or ethanol and carbon dioxide in plants.

Where the reactions occur in a cell - Aerobic is cytoplasm and mitochondria, anaerobic is cytoplasm only.

"

C1.2.5—Word equation for aerobic respiration, using glucose as a substrate.

glucose + oxygen --> carbon dioxide + water

"C1.2.5—Word equation for anerobic respiration, using glucose as a substrate.

glucose --> carbon dioxide + ethanol (plants, fungi)

glucose --> lactic acid (animals)

"

C1.2.6—Describe the equipment used to measure the rate of cell respiration.

Respirometer (measured uptake of oxygen per unit time). The manometer in this apparatus detects change in the pressure or volume of a gas. Carbon dioxide is absorbed by the soda lime

"C1.2.6—Name six variables affecting the rate of cell respiration

a) Metabolic rate of the cell e.g. muscle cells will require more energy and therefore have higher

b) The size of the organism e.g. smaller organisms have a larger surface area compared to their size and have a correspondingly higher respiratory rate to allow for heat loss.

c) Supply of oxygen: cells need a constant supply of oxygen to release the maximum amount of ATP; inadequately supplied cells will respire anaerobically

d) Supply of substrates for respiration, e.g. glucose. Other substrates can also be used in the

respiratory pathway; the rate of respiration and the quantity of products produced (carbon dioxide and water) will depend on the respiratory substrate.

e) Temperature: because respiration is controlled by enzymes, temperature affects the rate of

respiration by increasing it up to an optimum temperature.

f) pH: the release of carbon dioxide during the process of respiration decreases the pH (i.e.

increases acidity) of cell content and body tissues, which affects the functioning of enzymes

involved in respiration.

"

"C1.2.7—Name two roles of the coenzyme NAD during cell respiration

1). Carrier of hydrogen

2). Carries out oxidation by removal of hydrogen

"

"C1.2.7—Respiration involves a series of redox reactions. Explain what this means.

reduction-oxidation reactions (redox) involve both these processes.

Red - Reduction e.g. Oxygen is reduced to water

Ox - Oxidation e.g. Glucose is oxidised to carbon dioxide, hydrogen atoms are removed (dehydrogenation)

along with the electrons.

"

C1.2.7—What is meant by biological oxidation.

Addition of oxygen, loss of hydrogen, loss of electrons, release of energy.

C1.2.7—What is meant by biological reduction.

Removal of oxygen, addition of hydrogen, gain of electrons, uptake of energy.

C1.2.7—What is OIL RIG

Oxidation Is Loss of electrons, Reduction Is Gain of electrons (best definition).

C1.2.7—When the coenzyme NAD accepts hydrogen is it being oxidised or reduced.

Reduced (RIG) e.g. NAD+ + 2H+ + 2e− → NADH + H+ (NADH can also be represented as NADH )

"C1.2.8—Describe the steps in glycolysis

Conversion of glucose to pyruvate by stepwise reactions, each catalysed by a different reaction, with a net yield of ATP and reduced NAD.

1) Phosphorylation (by 2ATP to make the glucose more unstable and likely to react).

2) Lysis (to form two 3 carbon molecules)

3) Oxidation (by the removal of hydrogen by dehydrogenase enzymes, to be carried by NAD)

4) ATP formation (4ATP are released when each of the 3 carbon molecules are converted to pyruvate).

Students are not required to know the names of the intermediates, but students should know that each step in the pathway is catalysed by a different enzyme.

"

"C1.2.8—Name the four steps in respiration.

1) Glycolysis

2) Link reaction

3) Kreb cycle

4) Oxidative phosphorylation

"

"C1.2.9—In anaerobic respiration, in animals, what is a problem in allowing glycolysis to continue?

A lack of oxidised (empty) hydrogen-acceptor molecules i.e. NAD

Converting pyruvate to lactate transfers the hydrogen to the lactate, thus reoxidising the NAD moelcule and allowing glycolysis to continue.

"

C1.2.9—What is the yield of ATP in glycolysis.

Net gain of 2ATP per molecule of glucose.

"C1.2.10—Explain how anaerobic cell respiration in yeast is used by humans to create useful products.

Brewing (ethanol makes the drinks alcoholic)

Baking (carbon dioxide makes dough rise)

"

"C1.2.10—The pathways of anaerobic respiration are the same in humans and yeasts except for one difference. Explain what this is and how it affects the products.

The regeneration of NAD

Instead of using pyruvate as a hydrogen acceptor, yeasts convert pyruvate to ethanal (with the release of 2CO2) which is used as a hydrogen acceptor.

The final products are therefore, ethanol and carbon dioxide.

"

C1.2.10—What happens to pyruvate at the end of glycolysis?

It diffuses into the matrix of the mitochondrion by ?facilitated diffusion?

"C1.2.11—Describe the link reaction in aerobic cell respiration

Decarboxylation - The 3-carbon pyruvate is decarboxylated by removal of carbon dioxide

Oxidation - by removal of hydrogen to form reduced NAD is formed.

An acetyl group (2-carbon fragment) if formed which combines with coenzyme A, forming acetyl coenzyme A (acetyl-CoA).

"

"C1.2.12—Describe the Krebs cycle and the products.

The acetyl coenzyme A enters the Krebs cycle

... reacts with the 4C oxaloacetate, OAA

... to form the 6C citrate (and coenzyme A which is released and reused in the link reaction).

...which is converted back to oxaloacetate, ready to restart the cycle with the release of:

2x carbon dioxide (separate decarboxylation reactions)

1x ATP is formed

3x reduced NAD

1x reduced other hydrogen acceptor flavin adenine dinucleotide (FAD)

There are two ""turns"" of the Kreb cycle per molecule of glucose.

"

C1.2.12—How many oxidations and decarboxylations are involved in the regeneration of oxaloacetate?

Four oxidations (dehydrogenation reactions)) and two decarboxylations.

C1.2.13—How is energy transferred by reduced NAD to the electron transport chain in the mitochondrion.

Energy is transferred when a pair of electrons is passed to the first carrier in the chain, converting reduced NAD back to NAD.

"C1.2.13—What happens to reduced coenzymes in the first part of oxidative phosphorylation.

Reduced coenzymes (NADH) pass to the electron transport chain. The reduced NAD is oxidised:

A) a pair of electrons is passed to the first carrier in the chain,

B) H+ (protons) are created

As electrons pass from carrier to carrier energy is released in a controlled way and H+ ions are pumped into the inter-membrane space creating a significant concentation gradient (proton gradient). This represents a store of potential energy.

which are transported along a series of carriers to be combined finally with oxygen to form water.

"

"C1.2.13—What is the electron transport chain?

A series of proteins on the inner mitochondrial membrane that transfer electrons received from reduced coenzymes, generating a gradient of protons that drives the synthesis of adenosine triphosphate (ATP).

These proteins function as a: dehydrogenase enzyme, hydrogen pumps, and oxidase enzymes.

"

C1.2.13—What is transferred from the Kreb Cycle to oxidative phosphorylation?

reduced NAD

C1.2.13—Where does reduced NAD (or FAD) come from in aerobic respiration?

Glycolysis (2 NAD), the link reaction (2 NAD) and the Krebs cycle (6 NAD, 2 FAD).

C1.2.14—How is a proton gradient generated?

Electrons from reduced coenzymes flow along the electron transport chain providing energy to pump hydrogen ions from the matrix of the mitochondria to the space between the inner and outer mitochondrial membranes.

"C1.2.15—How is ATP synthesised in the final part of aerobic respiration in the mitochondrion

The protons concentrated in the space between the inner and outer mitochondrial membranes flow

back into the matrix, via channels in the ATP synthase enzyme (ATPase), the energy is transferred as ATP synthesis occurs. The ATPase has a rotational mechanism - energy generated by the rotation of the enzyme leads to the production of ATP.

"

"C1.2.15—What is chemiosmosis?

The process by which the synthesis of ATP is coupled to electron transport via the

movement of protons.

"

C1.2.16—Summarise the locations where NAD (or FAD) is reduced.

Glycolysis (2 NAD), the link reaction (2 NAD) and the Krebs cycle (6 NAD, 2 FAD).

C1.2.16—What is the terminal electron acceptor in aerobic cell respiration

Oxygen - it accepts electrons from the electron transport chain and protons from the matrix of the mitochondrion, producing metabolic water and allowing continued flow of electrons along the chain.

C1.2.16—What is the total yield of ATP in aerobic respiration?

32 (30 from NAD or FAD, 4 at substrate level)

"C.1.2.17—Summarise the differences between lipids and carbohydrates as respiratory substrates

Yield of energy per gram - higher in lipids due to less oxygen and more oxidizable hydrogen and carbon.

Glycolysis and anaerobic respiration - occurring only if carbohydrate is the substrate, with 2C acetyl groups from the breakdown of fatty acids entering the pathway via acetyl-CoA (acetyl coenzyme A).

"

"C1.3.1—What is the transformation of energy in photosynthesis?

Light energy to chemical energy (in carbon compounds).

This energy transformation supplies most of the chemical energy needed for life processes in ecosystems.

"

C1.3.2—How is the hydrogen needed to convert carbon dioxide to glucose in photosynthesis obtained?

by splitting water

C1.3.2—Write a simple word equation for photosynthesis.

carbon dioxide + water (+ light) --> glucose + oxygen

C1.3.3—Name the by-product of photosynthesis in plants, algae and cyanobacteria

Oxygen

"C1.3.4—Name the process used for separation and identification of photosynthetic pigments by chromatography

Thin layer or paper chromatography

Calculating Rf values (distance moved by substance / distance moved by solvent) then the identification of pigments by colour and value.

"

C1.3.5—Describe the absorption spectrum of chlorophyll.

Shows maximum absorbance in red and violet wavelengths, minimal absorbance in green wavelenths.

C1.3.5—Name five photosynthetic pigments

Carotene, phaeophytin, xanthophylls, chlorophyll a, chlorophyll b.

C1.3.5—What colours of light are 450nm, 550nm and 750nm?

Blue, green, red

C1.3.5—What determines the absorption of blue and red light by chlorophyll?

The chemical structure of the chlorophyll molecule

C1.3.5—What happens when photosynthetic pigments absorb light?

Excitation of electrons within the molecule, accessory pigments transfer excited electrons to chlorophyll a

C1.3.5—What is an absorption spectrum?

Graph showing the relative absorbance of different wavelengths of light by a pigment.

C1.3.5—Why are there different photosynthetic pigments

Different pigments absorb different and specific wavelengths of light.