Metabolism

Question 1

How does ATP provide immediate energy?

Answer 1

ATP (adenosine triphosphate) is a high energy molecule that functions as an immediate source of power for cell processes

One molecule of ATP contains three covalently linked phosphate groups – which store potential energy in their bonds
When ATP is hydrolysed (to form ADP + Pi) the energy stored in the phophate bond is released to be used by the cell

Question 2

Products of Glycolysis

Answer 2

Glycolysis breaks down glucose (6-C) into two molecules of pyruvate (3C), and also produces:

Hydrogen carriers (NADH) from an oxidised precursor (NAD+)
A small yield of ATP (net gain of 2 molecules)

Question 3

How does Anaerobic respiration allow for ATP to be produced?

Answer 3

The purpose of anaerobic respiration is to restore stocks of NAD+ – as this molecule is needed for glycolysis

By restoring stocks of NAD+ via anaerobic pathways, the organism can continue to produce ATP via glycolysis

Question 4

How does Anaerobic respiration occur?

Answer 4

Anaerobic respiration proceeds in the absence of oxygen and does not result in the production of any further ATP molecules

In animals, the pyruvate is converted into lactic acid (or lactate)
In plants and yeasts, the pyruvate is converted into ethanol and carbon dioxide

Question 5

Why do we respire anaerobically and what are the consequences of the process?

Answer 5

When exercising at high intensity, the cells’ energy demands will exceed what the available levels of O2 can supply aerobically

Hence the body will begin breaking down glucose anaerobically to maximise ATP production

This will result in an increase in the production of lactic acid, which leads to muscle fatigue

When the individual stops exercising, oxygen levels will increase and lactate will be converted back to pyruvate

Question 6

What are the general processes in aerobic respiration?

Answer 6

Aerobic respiration consists of the link reaction, citric acid cycle (or Krebs cycle) and the electron transport chain

Glycolysis is an anaerobic process that happens before hand

Question 7

How many ATP molecules form in each process between Glycolysis and Chemiosmosis

Answer 7

Glycolysis produce 2 ATP
The Link reaction produces 0 ATP
The Krebs cycle produces 2 ATP
The Electron Transport Chain produces 34 ATP

Question 8

Applications of Anaerobic respiration

Answer 8

In yeasts, fermentation results in the production of ethanol and carbon dioxide

Bread – Carbon dioxide causes dough to rise (leavening), the ethanol evaporates during baking
Alcohol – Ethanol is the intoxicating agent in alcoholic beverages (concentrations above ~14% damage the yeast)

Bacterial cultures can also undergo fermentation to produce a variety of food products

Yogurt / Cheese – Bacteria produce lactic acid anaerobically, which modifies milk proteins to generate yogurts and cheeses

Question 9

What is the range of wave lengths of visible light?

Answer 9

Colours are different wavelengths of white light and range from red (~700 nm) to violet (~400 nm)

Question 10

What wave length is best absorbed and best reflected by chlorophyll?

Answer 10

Chlorophyll absorbs light most strongly in the blue portion of the visible spectrum, followed by the red portion

Chlorophyll reflects light most strongly in the green portion of the visible spectrum (hence the green colour of leaves)

Question 10

What is the structure of Chlorophyl?

Answer 10

Chlorophyll is composed of a Chlorin ring which has a magnesium center and thus ia the light reactiing component

Additionally chlorophyll has a hydrocarbon tail which anchors itself to the tykloid membrane

Question 11

Explain what a metabolic pathway is

Answer 11

Metabolism describes the sum total of all reactions that occur within an organism in order to maintain life

Metabolic pathways are typically organised into chains or cycles of enzyme-catalysed reactions

Metabolic pathways allow for a greater level of regulation, as the chemical change is controlled by numerous intermediates

Question 12

Explain how enzymes catalyse reactions

Answer 12

Enzymes speed up the rate of a biochemical reaction by lowering the activation energy

When an enzyme binds to a substrate it stresses and destabilises the bonds in the substrateThis reduces the overall energy level of the substrate’s transitionary state, meaning less energy is needed to convert it into a product and the reaction proceeds at a faster rate

Question 13

Classify anabolic and catabolic reactions into endergonic and exergonic

Answer 13

Catabolic is exergonic

Anabolic is endergonic

Question 14

Describe competitive inhibition (3)

Answer 14

Competitive inhibition involves a molecule, other than the substrate, binding to the enzyme’s active site

The molecule (inhibitor) is structurally and chemically similar to the substrate (hence able to bind to the active site)

The competitive inhibitor blocks the active site and thus prevents substrate binding

Question 15

Describe non-competitive inhibition

Answer 15

Non-competitive inhibition involves a molecule binding to a site other than the active site (an allosteric site)

The binding of the inhibitor to the allosteric site causes a conformational change to the enzyme’s active site

As a result of this change, the active site and substrate no longer share specificity, meaning the substrate cannot bind

Question 16

Describe an example of non-competitive inhibition

Answer 16

Cyanide is a poison which prevents ATP production via aerobic respiration, leading to eventual death

It binds to an allosteric site on cytochrome oxidase – a carrier molecule that forms part of the electron transport chain

By changing the shape of the active site, cytochrome oxidase can no longer pass electrons to the final acceptor (oxygen)

Consequently, the electron transport chain cannot continue to function and ATP is not produced via aerobic respiration

Question 17

Describe an example of competitive inhibition

Answer 17

Relenza is a drug designed to treat individuals infected with the influenza virus

Virions are released from infected cells when the viral enzyme neuraminidase cleaves a docking protein (haemagglutinin)

Relenza competitively binds to the neuraminidase active site and prevents the cleavage of the docking protein

Consequently, virions are not released from infected cells, preventing the spread of the influenza virus

Question 18

Describe endproduct inhibition

Answer 18

In end-product inhibition, the final product in a series of reactions inhibits an enzyme from an earlier step in the sequence

The product binds to an allosteric site and temporarily inactivates the enzyme (via non-competitive inhibition)

As the enzyme can no longer function, the reaction sequence is halted and the rate of product formation is decreased

Question 19

what is the purpose of end product inhibition

Answer 19

If product levels build up, the product inhibits the reaction pathway and hence decreases the rate of further product formation

If product levels drop, the reaction pathway will proceed unhindered and the rate of product formation will increase

Question 20

Describe an example of end product inhibition

Answer 20

In plants and bacteria, isoleucine may be synthesised from threonine

In the first step of this process, threonine is converted into an intermediate compound by an enzyme (threonine deaminase)
Isoleucine can bind to an allosteric site on this enzyme and function as a non-competitive inhibitor

As excess production of isoleucine inhibits further synthesis, it functions as an example of end-product inhibition

This feedback inhibition ensures that isoleucine production does not cannibalise available stocks of threonine

Question 21

State the two hydrogen carriers and their equations

Answer 21

The most common hydrogen carrier is NAD+ which is reduced to form NADH (NAD+ + 2H+ + 2e– → NADH + H+)
A less common hydrogen carrier is FAD which is reduced to form FADH2 (FAD + 2H+ + 2e– → FADH2)

Question 22

Describe the 4 steps of glycolysis

Answer 22

1. Phosphorylation

A hexose sugar (typically glucose) is phosphorylated by two molecules of ATP (to form a hexose bisphosphate)
This phosphorylation makes the molecule less stable and more reactive, and also prevents diffusion out of the cell

2. Lysis

The hexose biphosphate (6C sugar) is split into two triose phosphates (3C sugars)

3. Oxidation

Hydrogen atoms are removed from each of the 3C sugars (via oxidation) to reduce NAD+ to NADH (+ H+)
Two molecules of NADH are produced in total (one from each 3C sugar)

4. ATP formation

Some of the energy released from the sugar intermediates is used to directly synthesise ATP
This direct synthesis of ATP is called substrate level phosphorylation
In total, 4 molecules of ATP are generated during glycolysis by substrate level phosphorylation (2 ATP per 3C sugar)

Question 23

Describe the link reaction

Answer 23

Pyruvate is transported from the cytosol into the mitochondrial matrix by carrier proteins on the mitochondrial membrane
The pyruvate loses a carbon atom (decarboxylation), which forms a carbon dioxide molecule
The 2C compound then forms an acetyl group when it loses hydrogen atoms via oxidation (NAD+ is reduced to NADH + H+)
The acetyl compound then combines with coenzyme A to form acetyl coenzyme A (acetyl CoA)

As glycolysis splits glucose into two pyruvate molecules, the link reaction occurs twice per molecule of glucose

Per glucose molecule, the link reaction produces acetyl CoA (×2), NADH + H+ (×2) and CO2 (×2)

Question 24

Describe the krebs cycle

Answer 24

In the Krebs cycle, acetyl CoA transfers its acetyl group to a 4C compound (oxaloacetate) to make a 6C compound (citrate)

Coenzyme A is released and can return to the link reaction to form another molecule of acetyl CoA

Over a series of reactions, the 6C compound is broken down to reform the original 4C compound (hence, a cycle)

Two carbon atoms are released via decarboxylation to form two molecules of carbon dioxide (CO2)
Multiple oxidation reactions result in the reduction of hydrogen carriers (3 × NADH + H+ ; 1 × FADH2)
One molecule of ATP is produced directly via substrate level phosphorylation

As the link reaction produces two molecules of acetyl CoA (one per each pyruvate), the Krebs cycle occurs twice

Per glucose molecule, the Krebs cycle produces: 4 × CO2 ; 2 × ATP ; 6 × NADH + H+ ; 2 × FADH2

Question 25

Describe the electron transport chain

Answer 25

Step 1: Generating a Proton Motive Force

-The hydrogen carriers (NADH and FADH2) are oxidised and release high energy electrons and protons
-The electrons are transferred to the electron transport chain, which consists of several transmembrane carrier proteins
-As electrons pass through the chain, they lose energy – which is used by the chain to pump protons (H+ ions) from the matrix
-The accumulation of H+ ions within the intermembrane space creates an electrochemical gradient (or a proton motive force)

Step Two: ATP Synthesis via Chemiosmosis

-The proton motive force will cause H+ ions to move down their electrochemical gradient and diffuse back into matrix
-This diffusion of protons is called chemiosmosis and is facilitated by the transmembrane enzyme ATP synthase
-As the H+ ions move through ATP synthase they trigger the molecular rotation of the enzyme, synthesising ATP
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Step Three: Reduction of Oxygen

-In order for the electron transport chain to continue functioning, the de-energised electrons must be removed
-Oxygen acts as the final electron acceptor, removing the de-energised electrons to prevent the chain from becoming blocked
-Oxygen also binds with free protons in the matrix to form water – removing matrix protons maintains the hydrogen gradient
-In the absence of oxygen, hydrogen carriers cannot transfer energised electrons to the chain and ATP production is halted

Question 26

What are 3 features of mitochondria that suggest endosymbiosis

Answer 26

-They have a double membrane structure (due to vesicular coating as part of the endocytotic process)
-They have their own DNA (circular and naked) and ribosomes (70S)
-Their metabolic processes are susceptible to certain antibiotics

Question 27

Explain how the mitochondria structure is adapted to its function

Answer 27

Outer membrane – the outer membrane contains transport proteins that enable the shuttling of pyruvate from the cytosol

Inner membrane – contains the electron transport chain and ATP synthase (used for oxidative phosphorylation)

Cristae – the inner membrane is arranged into folds (cristae) that increase the SA:Vol ratio (more available surface)

Intermembrane space – small space between membranes maximises hydrogen gradient upon proton accumulation

Matrix – central cavity that contains appropriate enzymes and a suitable pH for the Krebs cycle to occur

Question 28

Outline the differences between anaerobic and aerobic respiration

Answer 28

Anaerobic | Aerobic
Glucose | Glucose and oxygen [reactants]
Incomplete combustion | Complete combustion
2 ATP | 36 ATP [yield]
Cytoplasm | Cytoplasm and Mitochondria [location]

Question 29

Describe the light dependent reaction of photosynthesis

Answer 29

Step 1: Excitation of Photosystems by Light Energy

-Photosystems are groups of photosynthetic pigments (including chlorophyll) embedded within the thylakoid membrane
-Photosystems are classed according to their maximal absorption wavelengths (PS I = 700 nm ; PS II = 680 nm)
-When a photosystem absorbs light energy, delocalised electrons within the pigments become energised or ‘excited’
-These excited electrons are transferred to carrier molecules within the thylakoid membrane

Step 2: Production of ATP via an Electron Transport Chain

-Excited electrons from Photosystem II (P680) are transferred to an electron transport chain within the thylakoid membrane
-As the electrons are passed through the chain they lose energy, which is used to translocate H+ ions into the thylakoid
-This build up of protons within the thylakoid creates an electrochemical gradient, or proton motive force
-The H+ ions return to the stroma (along the proton gradient) via the transmembrane enzyme ATP synthase (chemiosmosis)
-ATP synthase uses the passage of H+ ions to catalyse the synthesis of ATP (from ADP + Pi)
-This process is called photophosphorylation – as light provided the initial energy source for ATP production
-The newly de-energised electrons from Photosystem II are taken up by Photosystem I

Step 3: Reduction of NADP+ and the Photolysis of Water

-Excited electrons from Photosystem I may be transferred to a carrier molecule and used to reduce NADP+
-This forms NADPH – which is needed (in conjunction with ATP) for the light independent reactions
-The electrons lost from Photosystem I are replaced by de-energised electrons from Photosystem II
-The electrons lost from Photosystem II are replaced by electrons released from water via photolysis
-Water is split by light energy into H+ ions (used in chemiosmosis) and oxygen (released as a by-product)

Question 30

Describe cyclic phosphorylation

Answer 30

Cyclic photophosphorylation involves the use of only one photosystem (PS I) and does not involve the reduction of NADP+
When light is absorbed by Photosystem I, the excited electron may enter into an electron transport chain to produce ATP
Following this, the de-energised electron returns to the photosystem, restoring its electron supply (hence: cyclic)
As the electron returns to the photosystem, NADP+ is not reduced and water is not needed to replenish the electron supply

Question 31

Describe non-cyclic phosphorylation

Answer 31

Non-cyclic photophosphorylation involves two photosystems (PS I and PS II) and does involve the reduction of NADP+
When light is absorbed by Photosystem II, the excited electrons enter into an electron transport chain to produce ATP
Concurrently, photoactivation of Photosystem I results in the release of electrons which reduce NADP+ (forms NADPH)
The photolysis of water releases electrons which replace those lost by Photosystem II (PS I electrons replaced by PS II)

Question 32

Compare and contrast between cyclin and non cyclic phosphorylation

Answer 32

Cyclic | Non -cyclic
Only PS I | PS I and II
Water is NOT required | Water is required
Oxygen is not produced | Oxygen is produced
NADPH not synth. | NADPH synth.

Question 33

Describe the light independent step of photosynthesis

Answer 33

Step 1: Carbon Fixation

The Calvin cycle begins with a 5C compound called ribulose bisphosphate (or RuBP)
An enzyme, RuBP carboxylase (or Rubisco), catalyses the attachment of a CO2 molecule to RuBP
The resulting 6C compound is unstable, and breaks down into two 3C compounds – called glycerate-3-phosphate (GP)
A single cycle involves three molecules of RuBP combining with three molecules of CO2 to make six molecules of GP

Step 2: Reduction of Glycerate-3-Phosphate

Glycerate-3-phosphate (GP) is converted into triose phosphate (TP) using NADPH and ATP
Reduction by NADPH transfers hydrogen atoms to the compound, while the hydrolysis of ATP provides energy
Each GP requires one NADPH and one ATP to form a triose phosphate – so a single cycle requires six of each molecule

Step 3: Regeneration of RuBP

Of the six molecules of TP produced per cycle, one TP molecule may be used to form half a sugar molecule
Hence two cycles are required to produce a single glucose monomer, and more to produce polysaccharides like starch
The remaining five TP molecules are recombined to regenerate stocks of RuBP (5 × 3C = 3 × 5C)
The regeneration of RuBP requires energy derived from the hydrolysis of ATP

Question 34

Explain how the chloroplast’s structure is adapted to its function

Answer 34

Thylakoids – flattened discs have a small internal volume to maximise hydrogen gradient upon proton accumulation
Grana – thylakoids are arranged into stacks to increase SA:Vol ratio of the thylakoid membrane
Photosystems – pigments organised into photosystems in thylakoid membrane to maximise light absorption
Stroma – central cavity that contains appropriate enzymes and a suitable pH for the Calvin cycle to occur
Lamellae – connects and separates thylakoid stacks (grana), maximising photosynthetic efficiency

Question 35

Evidence for endosymbiosis with chloroplasts

Answer 35

They have a double membrane structure (due to vesicular coating as part of the endocytotic process)
They have their own DNA (circular and naked) and ribosomes (70S)
Their metabolic processes are susceptible to certain antibiotics