Topic 8: Metabolism, cell respiration and photosynthesis

Question 1

Energy changes in chemical reactions

Answer 1

• During chemical reactions, reactants/substrates are converted into products.
• Before a molecule of the reactant can take part in the reaction, it has to gain some energy - activation energy.
• During the reaction, energy is given off as new bonds are made - most biological reactions are exothermic - the energy released is greater than the activation energy.
• Enzymes reduce the activation energy of the reactions that they catalyse - make it easier for them to occur.
• The chemical environment provided by the active site for the substrate causes changes within the substrate molecule which weakens its bonds.
• Substrate is changed into a transition stage.

Question 2

Calculating rates of reaction

Answer 2

The rate of a reaction catalysed by an enzyme can be assessed by measuring the quantity of substrate used per unit time or the quantity of a product formed per unit time.
Measured as a mass or volume.

Question 3

Competitive and non-competitive inhibitors

Answer 3

Enzyme inhibitors - chemical substances that reduce the activity of enzymes or even prevent it completely. There are two main types- competitive and non-competitive.

• Competitive - substrate and inhibitor are chemically similar, the inhibitor binds to the active site of the enzyme, inhibitor occupies the active site and prevents the substrate from binding.
  Activity of an enzyme is reduced if a fixed low concentration of inhibitor is added, but as the substrate concentration rises. the effect of the inhibitor becomes less and less.
  At very high substrate concentration + low inhibitor -substrate wins and binds to the active site (nearly identical rate as when no inhibitor).
• Non-competitive - substrate and inhibitor are chemically different, the inhibitor binds to the enzyme at a different site, the inhibitor changes the conformation of the active site (even if the substrate does bind, no reaction is catalysed).
  Activity of the enzyme is reduced at all substrate concentrations if a fixed low concentration of non-competitive inhibitor is added.
  The substrate cannot prevent the binding of the inhibitor, even at very high substrate concentrations. Even at very high substrate concentrations, the enzyme activity is lower than when no inhibitor.

Question 4

Metabolic pathways

Answer 4

Metabolic pathways have these features:

1. An enzyme catalyses each reaction in the pathway.
2. All the reactions occur inside cells.
3. Some pathways build up organic compounds (anabolic pathways), others break them down (catabolic pathways).
4. Some contain chains of reactions - Glycolysis.
5. Others consist of cycles of reactions - Krebs cycle.

Question 5

End-product inhibition

Answer 5

End-product inhibition - the product of the last reaction in the pathway inhibits the enzyme that catalyses the first reaction.
The enzyme that is inhibited by the end products is an example of an allosteric enzyme.
Allosteric enzymes have two non-overlapping binding sites - one of them is the active site, the other one is the allosteric site.

• The end product binds to the allosteric site - this changes the structure of the enzyme - substrate less likely to bind to the active site - the end product acts as an inhibitor.
• Binding of the inhibitor is reversible and if it detaches, the enzyme returns to its original conformation.
• Advantage: if excess of the end product, the whole pathway is stopped and intermediates don’t build up. Also, if the level of the product falls, more and more of the enzymes that catalyse the first reaction will start to work and the pathway becomes activated again.
• End-product inhibition is an example of negative feedback
  Example: Inhibition of threonine dehydratase by isoleucine.

Question 6

Finding new anti-malarial drugs

Answer 6

• The malarial parasite, Plasmodium, has evolved resistance to most anti-malarial drugs so there is an urgent need for new drugs.
• The search is made easier by the huge bioinformatics databases that are held on computers.
• Recent study - 5,655 chemicals that might act as an enzyme inhibitor in Plasmodium were identified from a database - tested with nine Plasmodium enzymes (also identified using the database)
• Inhibitors were found for six of the nine enzymes and these are now being researched as potential anti-malarial drugs.

Question 7

Cell respiration and glycolysis

Answer 7

• Cell respiration involves the production of ATP using energy released by the oxidation of glucose, fat or other substances.
• If glucose is the substrate, the first stage of cell respiration is a metabolic pathway called glycolysis.
• Glycolysis is catalysed by enzymes in the cytoplasm.
• Glucose is partially oxidised in glycolysis, and a small amount of ATP is produced.
• This partial oxidation is achieved without the use of oxygen so glycolysis can form part of both aerobic and anaerobic cell respiration.

Question 8

Oxidation and reduction

Answer 8

Cell respiration involves many oxidation and reduction reactions - reverse of each other and can occur in different ways..

Oxidation reactions - addition of oxygen atoms, removal of hydrogen, loss of electrons.
Reduction reactions - removal of oxygen, addition of hydrogen, addition of electrons.

In respiration, the oxidation is carried out by removing pairs of hydrogen atoms (and at the same time electrons as each hydrogen atom has one electron). Hydrogen is accepted by a hydrogen carrier which is therefore reduced.
NAD + 2H - reduced NAD
/ NAD+ + 2H - NADH + H+

Question 9

Phosphorylation

Answer 9

• In some metabolic reactions, a phosphate group is added to an organic molecule - phosphorylation.
• The effect is to make the organic molecule less stable - more likely to react in the next stage.
• Phosphorylation can turn an endothermic reaction (which occurs slowly) to an exothermic one (rapid).
• The phosphate group is usually transferred from ATP.

Question 10

Stages in glycolysis

Answer 10

4 Main stages of glycolysis:

1. Two phosphate groups are added to a molecule of glucose to form hexose biphosphate (phosphorylation). Two molecules of ATP provide the phosphate groups - raises the energy level of the hexose and makes it less stable.
2. The hexose biphosphate is split to form two molecules of triose phosphate (lysis).
3. Two atoms of hydrogen are removed from each triose phosphate (oxidation). 2 NAD are converted to 2 NADH (reduction). Energy released by oxidation is used to convert two ADP molecules to ATP.
4. The end product of glycolysis is Pyruvate.

Question 11

Anaerobic and aerobic respiration

Answer 11

• Glycolysis can occur without oxygen - so forms the basis of anaerobic cell respiration.
• Pyruvate produced in glycolysis can only be oxidised further with the release of more energy from it if oxygen is available.
• This occurs in the mitochondrion.
• Enzymes in the matrix of the mitochondrion (after the link reaction) catalyse a cycle of reactions called the Krebs cycle.

Question 12

The link reaction

Answer 12

• Pyruvate from glycolysis is absorbed by the mitochondrion. Enzymes in the matrix of the mitochondrion remove carbon dioxide and hydrogen from the pyruvate - oxidative decarboxylation.
• Product is an acetyl group - attached to coenzyme A to form acetyl coenzyme A.

Question 13

The Krebs cycle

Answer 13

1. Acetyl group is transferred from acetyl CoA to a four-carbon compound to form a six-carbon compound called citrate.
2. Citrate is converted back into oxaloacetate in the other reactions of the cycle.
3. Carbon dioxide is removed in two of the reactions - decarboxylations.
4. Hydrogen is removed in four of the reactions - oxidations.
5. ATP is produced directly in one of the reactions - substrate level phosphorylation.

Question 14

The electron transport chain

Answer 14

• Electron transport chain - a series of electron carriers located in the inner membrane of the mitochondrion including the cristae.

1. Reduced NAD (NADH) supplies two electrons to the first carrier in the chain - two electrons come from oxidation reactions in earlier stages of cell respiration and bring energy released by these oxidations.
2. As the electrons pass along the chain from one carrier to the next they give up energy.
3. Some of the electrons act as proton pumps and use this energy to pump protons against the concentration gradient from the matrix of the mitochondrion to the intermembrane space.
4. Reduced FAD (FADH) also feeds electrons into the chain but at a slightly later stage than NADH. Cause pumping at only two stages compared to three for NADH.

Question 15

The role of oxygen

Answer 15

• At the end of the electron transport chain the electrons are given to oxygen - happens in the matrix.
• At the same time, oxygen accepts free protons to form water - the use of protons in this reaction contributes to the proton gradient across the inner mitochondrial membrane.
• The use of oxygen as the terminal electron acceptor at the end of the electron transport chain is the only stage where oxygen is used in cell respiration.
• If oxygen is not available, electron flow along the electron transport chain stops and reduced NAD cannot be converted back to NAD. Supplies of NAD in the mitochondrion run out and the link reaction and Krebs cycle cannot continue.

Question 16

Chemiosmosis in the mitochondrion

Answer 16

• Energy is released as electrons pass along the electron transport chain is used to pump protons across the inner mitochondrial membrane into the intermembrane space including the space inside the cristae.
• This creates a concentration gradient which is a store of potential energy.
• ATP synthase in the inner mitochondrial membrane also allows the protons to diffuse back across to the matrix
• ATP synthase uses the energy that the protons release during this diffusion to produce ATP.
• The generation of ATP using energy released by the movement of hydrogen ions across a membrane - chemiosmosis.
• Proposed by Peter Mitchell in 1960s, not widely accepted until much later - represented a paradigm shift in the field of bioenergetics and took time to be accepted regardless of strong evidence.

Question 17

Structure and function of the mitochondrion

Answer 17

• Outer mitochondrial membrane - separates the contents of the mitochondrion from the rest of the cell, creating a compartment with ideal conditions for aerobic respiration.
• Inner mitochondrial membrane - contains electron transport chains and ATP synthase, which carry out oxidative phosphorylation.
• Cristae - tubular or shelf-like projections in the inner -membrane which increase the surface area available for oxidative phosphorylation.
• Intermembrane space - protons are pumped into this space by the electron transport chain, because the space is very small a high proton concentration can easily be formed in chemiosmosis.
• 70S ribosomes + naked loop of DNA.
• Matrix - fluid containing enzymes for the Krebs cycle and link reaction.

Structure and function are closely related in living organisms - adaptation as a result of evolution by natural selection.

Question 18

Electron tomography of mitochondria

Answer 18

• Developed recently.
• Used to obtain three-dimensional images of active mitochondria.
• Electron tomography revealed that cristae are connected with the intermembrane space between the inner and outer membranes via narrow openings.
• The shape and volume of the cristae change when a mitochondrion is active.

Question 19

Light absorption

Answer 19

Pigments such as chlorophyll absorb certain wavelengths of light - cause an election in the pigment molecule to be raised to a higher energy level.
Light energy transferred to chemical energy held by the excited election.
Main photosynthetic pigment - chlorophyll.
Chlorophyll is part of larger groups of pigment molecules called photosystems.
Pigments in photosystems absorb light energy by an electron becoming excited.
Electron pass along the chain of electron carriers until reach a special chlorophyll molecule at the reaction centre which passes them away to electron acceptors.

Question 20

Photosystem II and ATP production

Answer 20

A pair of excited electrons from PSII is passed to a chain of electron carriers.
The electrons give up energy as they pass along the chain.
This energy is used to pump protons into the thylakoid space - proton gradient is created.
ATP synthase, also located in the thylakoid membranes, allows protons to diffuse back across to the stroma - uses this energy to produce ATP.
Chemiosmosis - generation of ATP using energy released by the movement of H ions across a membrane.
Production of ATP in chloroplasts is called photophosphorylation (energy comes from absorbing light).

Question 21

Photosystem I and reduction of NADP

Answer 21

A pair of excited electrons is emitted from the reaction centre of PSI and passes along a short chain of electron acceptors.
At the end of this chain, the electrons are passed to NADP in the stroma.
NADP is reduced to NADPH.
The electrons given away by PSI are replaced by electrons that were initially emitted by PSII and passed along the chain of electron carriers.

Question 22

Photolysis

Answer 22

PSII must replace excited electrons:
Photolysis - water is split and electrons are passed along the chain.
Oxygen and H ions are by-products.
Oxygen is a waste product and is excreted.
H ions contribute to the proton gradient.

Question 23

Structure and function of the chloroplast

Answer 23

• Granum - a stack of thylakoids for absorption of light.
• Thylakoid membranes - a large SA for light-absorbing photosystems, and a site for electron flow, generation of a proton gradient and chemiosmosis.
• Starch grain - storage of carbohydrates produced by photosynthesis until exported.
• Chloroplast envelope - creates a compartment where enzymes and other components of photosynthesis can be concentrated.
• Lipid droplets.
• Stroma - contains enzymes for Calvin cycle (rubisco), naked DNA, 70S ribosomes.
• Thylakoid space - small volume so a steep proton gradient can build up fast.

Question 24

The Calvin Cycle

Answer 24

The light independent reactions take place in the stroma of the chloroplast.
The 1st ration involves a 5C sugar RuBP which is regenerated by light independent reactions.
Calvin cycle discovered by biochemists led by Melvin Calvin.
1. RuBP is carboxylated by Rubisco to form Glycerate 3-Phosphate.
2. Glycerate 3-Phosphate is reduced and ATP - ADP+P to form Triose Phosphate.
3. 1/6 of Triose Phosphate is used to produce Glucose Phosphate, 5/6 is used to regenerate RuBP (where ATP - ADP+P).

Question 25

Improvements in apparatus

Answer 25

1. Radioactive labelling - radioisotopes of elements have the same chemical properties as other isotopes of an element but can be distinguished by being radioactive. Used to label organic compounds - such as 14C.
2. Double-way paper chromatography - separating and identifying compounds - a spot of the mixture placed in one corner of a large sheet of chromatography paper. A solvent run up through the paper to separate the mixture in one direction. Paper is dried and a second solvent then run up at 90 degrees to the first - separating products of carbon fixation.
3. Autoradiography - a sheet of chromatography paper is placed next to a sheet of film of same size, kept together for two weeks in darkness, and the X-ray film is then developed. Black spots appear and show the location of radioisotopes.

Question 26

Calvin’s experiment + results

Answer 26

1. Chlorella placed in a thin glass vessel + illuminated.
2. Chlorella was supplied with radioactive 14C.
3. Took samples of algae at very short intervals and immediately killed it with hot methanol.
4. Extracted the carbon compounds and separated by double-way paper chromatography and then used autoradiography.
5. Measured the amount of radioactivity in the different compounds. Autoradiograms showed that first product was Glycerate 3-Phosphate, followed by Triose Phosphate.