Test 2 Part 2.1

Question 1

Respiration

Answer 1

• Oxidation of glucose to carbon dioxide.
• The reduction of oxygen to water - redox reaction. The removal of electrons from one material and the addition of electrons to something else.
• Exergonic - energy release. Electrons are moving from glucose to oxygen and oxygen is electronegative and when electrons towards an electronegative atom they lose energy.
• Cells can harness that energy as ATP so they can do work. Some energy is lost as heat.
• Passed to electron carriers - You can’t move electrons directly from food to oxygen as energy released as heat

Question 2

Reduction of NAD+

Answer 2

NAD can cycle as oxidised and reduced. Oxidised is NAD+ and reduced is NADH. adding electrons to NAD+, pick up protons as well (2H+) and then it becomes reduced. It can act as an electron carrier and pass the electrons on to something else.

Question 3

Aerobic respiration

Answer 3

• Respiration when oxygen is present.
• The cytosol in the cell where glycolysis will occur.
• Organelle - mitochondria → inside is the oxidation of pyruvate in the mitochondria and converted to Acetyl CoA and this enters the citric acid cycle.
• Electrons are removed from the metabolites in the cycle and given to electron carriers NADH and FADH2 (which are becoming reduced) and they will pass electrons to the electron transport chain.
• Through a process called chemiosmosis we will produce a lot of ATP (process of oxidative phosphorylation).

Question 4

Mitochondria

Answer 4

Bean shaped organelles. Very dynamic, can grow or shrink. Form a network within cells. Key parts: two membranes - outer and inner membrane - space between the membranes called the intermembrane space - inside the inner membrane is a compartment called the matrix. The inner membrane has in foldings called the cristae.

Question 5

Glycolysis

Answer 5

• Metabolic pathway that occurs within the cytosol - glycolysis. Pathway in metabolism - oxidise the food stuff via a series of 10 reactions.
• 10 reactions:
  
  • 1 glucose converted to 2 pyruvate
  • Yield 2 ATPs per glucose
  • Yield of 2 NADH per glucose
  • Energy investment phase (5 reactions)
  • glucose converted to 2 glyceraldehyde 3-phosphates
  • Energy payoff phase (5 reactions) 2 glyceraldehyde 3-phosphate converted to 2 pyruvates

Question 6

Glycolysis - energy investment phase

Answer 6

• Hexokinase enzyme catalyses the first reaction - will add a phosphate group onto the glucose - converting glucose to glucose 6 phosphate.
• Energy input - initial stage of input. Phosphorylating the glucose which will make it more reactive by raising the free energy.
• You will split the metabolite into 2.
• Add another phosphate - to aid the splitting of the metabolite.
• Energy investment - ATP Enzymes called kinases which are involved in phosphate transfer. Making the metabolites more reactive.

Question 7

Control of respiration - allosteric regulation of an enzyme

Answer 7

• Glycolysis can be allosterically controlled by metabolites - switched on and off
• Allosteric regulation - when something binds to a site that’s not the active site. Changes the active site so that the enzyme is switched off or the enzyme is switched on. Depending on whether the allosteric regulator is an activator or an inhibitor.
• Phosphofructokinase can be activated by AMP (ATP with two phosphates removed). Typically if you have high levels of AMP inside a cell you will have a low level of ATP. indicator that the cell is low in energy. You want to switch glycolysis on so you switch on phosphofructokinase.
• If you have a lot of energy inside the cell, a lot of ATP or citrates (metabolites high when you have a lot of energy inside cells) - these two molecules will switch off phosphofructokinase.

Question 8

Glycolysis - energy payoff phase

Answer 8

• Energy payoff phase: final 5 reactions of glycolysis: ​
• Electron carrier, NAD, is reduced by electrons that are removed from the end product of the first five reactions, giving reduced NAD.
• The reduced NAD will be transferred into the mitochondria and will transfer the electrons onto the electron transport chain - catalysed by a dehydrogenase enzyme.
• (Dehydrogenase - tells you that the enzyme is involved in a redox reaction - removing or adding electrons to something)
• We have two reaction - reaction 7&10 where we start to produce ATP. Taking a phosphate group from a metabolite, adding it to ADP to give ATP.
• In reaction 10 we take the phosphate and add that to the ADP to give ATP. → a process referred to as substrate level phosphorylation.
• The end products: One of the things its split into the glyceraldehyde triphosphate - one end product. And then the other thing its split into (don’t worry about the name) is converted into another molecule of glyceraldehyde triphosphate. Net yield of 2 of these per staring glucose. Hence when we consider the energy pay off phase there will be two of each of the metabolites so we are producing 2 of the reduced NAD, 2 ATPs per single starting molecule of glucose.

Question 9

Substrate level phosphorylation

Answer 9

Phosphorylating ADP at the level of the substrate. Which means that we have the enzyme, the substrate and we will take a phosphate from that substrate and add it to ADP to give us ATP. See different types of phosphorylation in the mitochondria - oxidative phosphorylation. When we do photosynthesis we see other types of phosphorylation.

Question 10

Oxidation of Pyruvate

Answer 10

• The pyruvate is moved into the mitochondria.
• Pyruvate moves from the outer membrane into the inner membrane by transport proteins into the mitochondrial matrix.
• When the pyruvate is in the matrix it is then oxidised into acetyl CoA - redox reaction.
• Producing some reduced NAD (in the mitochondrial matrix) that will act as an electron carrier and transfer electrons to the electron transport chain.
• There are three different reactions occurring.
  
  • A removal of carbon dioxide,
  • an addition of co enzyme A,
  • in addition to the removal of electrons.
• Each of these reactions requires a different enzyme to catalyse them. →
• So to ensure this reaction to go more quickly the three different enzymes are held together in a multi-enzyme complex which in this reaction is called the pyruvate dehydrogenase complex:
• Ensures that the three reactions occur very quickly. Way of ensuring efficiency.

Question 11

Citric acid cycle

and what happens after….

Answer 11

• After the oxidation of pyruvate, the acetyl CoA then enters the citric acid cycle.
• Comprises 8 reactions.
  
  • Start with acetyl CoA. Produce 3 NADH (reduced NAD) for each acetyl CoA and therefore 6 reduced NAD per original glucose.
  • Produce 1 reduced FAD - the other electron carrier important inside cells and therefore 2 per original glucose.
  • Produce 1 GTP and therefore 2 per original glucose. Substrate level phosphorylation
  • The GTP is very quickly converted to ATP. Will also produce some CO2 - 2 per Acetyl CoA and therefore 4 per original glucose.
• ​Transferring electrons from the metabolites to these electron carriers

​Next step: We’ve oxidised glucose to carbon dioxide. Electrons have been passed on to NADH and FADH2. They are then passed on to oxygen via the electron transport chain. 90% of the oxygen that you are breathing in is so that the oxygen can accept these electrons that you have removed from glucose and the various metabolites along these metabolic pathways.

Question 12

Oxygen is reduced to water. Reduction part of Respiration

Answer 12

Transferred to oxygen by the electron transport chain. When oxygen grabs the electrons at the end of the chain the oxygen is reduced to water. Now we have the reduction part of the equation for respiration.

Question 13

Electron transport chain and oxidative phosphorylation

Answer 13

Four large protein complexes in the inner mitochondrial membrane - complex 1,2,3,4. Also got two mobile electron carriers Q and cytochrome C - Q (present in the inner mitochondrial membrane, so its lipid/fat soluble so can exist in the hydrophobic environment - fatty acid tails - where Q situates). Water soluble enzyme cytochrome C. the ATP synthase - rotary enzyme that enables the production of ATP.

Question 14

Mobile electron carrier Q

Answer 14

Q - referred to as ubiquinol, ubiquinone, coenzyme Q. Shuttles electrons between complex 1 and 3, and between complex 2 and 3. Which route Q will use depends on where the enzymes are derived from - if from reduced NAD they go from complex 1 to complex 3 and if from reduced FAD they go between complex 2 and complex 3. The same compound found in face creams. To prevent ageing it’s good a picking up free radicals so able to prevent oxidative damage so it will make the skin appear younger.

Question 15

Cytochrome C

Answer 15

• Carries an electron in the electron transport chain.
• Small protein - fairly well conserved through evolution. 100-104 amino acids long
• Used in evolutionary studies
• Biologist have used this to study how organisms are related. Analyse the cytochrome C.

Question 16

What happens to electrons as they move along the electron transport chain?

Answer 16

Moving electrons from the electron carriers - reduced NAD, reduced FAD, transporting the electrons through the protein complexes (e.g., Fe-S, various cytochromes)(1,2,3,4). Transporting those electrons to oxygen. Potential energy is transformed into kinetic energy - shape changes in the proteins The figure shows the relative free energy of the electrons as they are at different parts of the electron transport chain. So we are looking at free energy levels of electrons as they are moving from reduced NAD and FAD, to molecular oxygen. As they move down through the complexes they are losing energy. Moving towards the more electronegative oxygen so they are losing energy. The energy is not lost, its transferred from the electrons to the large protein complexes and enables them to change their shape. Essentially got potential energy (electrons and where they are) benign transformed into kinetic energy (shape changes in the proteins). The shape changes enable the large protein complexes to act as proton pumps. Move protons across in the inner mitochondrial membrane.

Question 17

Complex 3 -electron transport chain

Answer 17

The purple bit swivels - as the electrons move through the complex they enable the purple bit to swivel. The protein then can move protons from the mitochondrial membranes into the inter-membrane space. Acting as a proton pump.

Question 18

Complex 1,2,3,4 acting as proton pumps: explanation

Answer 18

Move protons from the matrix into the intermembrane space. For each pair of electrons that move through the large protein complexes, you have different amounts of protons that can move through. Complex 1 and 3 moves 4 protons and complex 4 moves 2 protons.Complex 2 isn’t able to act as a proton pump. For each reduced NAD there will be a total of 10 protons moved. For each reduced FAD there will be a total of 6 protons moved. → important for the yield of ATP.

Question 19

Cyanide is a poison as it attaches to Complex 4

Answer 19

Importance of the large protein complexes to life - if you inhibit them you can die. Cyanide will bind to complex 4 of the electron transport chain.

Question 20

Proton gradient is….

Answer 20

a form of potential energy. Creating an unequal distribution of a molecule. More protons one side of the mitochondrial inner membrane than on the other side. So we hqv high free energy, potential energy stored in the proton gradient. The only way that the protons can move back into the mitochondrial matrix to go to this lower energy situation - spontaneous drive for this to occur because of the laws of thermodynamics → This can only occur through the ATP synthase.

Question 21

ATP synthase forms a pathway for protons to move down their electrochemical gradient

Answer 21

• The action of atp synthase - large protein composed of many different polypeptide subunits which come together to form this large complex.
• Works as a rotor where you get protons moving through binding to some of the amino acid residues and they cause the residues to move - so you get rotation of the top ‘wheel’ and that will cause the gamma subunit to rotate which interacts with these catalytic knobs and change the shape. When they change the shape they will add a phosphate group onto ADP to give us ATP

Question 22

Uncouplers.

Answer 22

• Another way for protons to move back into the mitochondrial membrane.
• Routes via proteins that act as uncouplers.
• You find uncoupling proteins in bears - anything that hibernates will have uncoupling proteins.
• They work by grabbing the protons and move them through the mitochondrial membrane into the matrix. So they bypass ATP synthase.
• If the energy in the proton gradient isn’t used to produce ATP - that energy has to go somewhere and the energy as the protons move back into the mitochondrial matrix is dissipated as heat.
• Organisms can’t use heat energy to do work.
• But if you’re a bear and you’re hibernating in the winter you need to keep warm. So the heat energy is used to keep their body temperatures relatively warm through the winter. Uncoupling proteins are important for hibernating animals to help them keep warm through the winter.
• You also find uncoupling proteins in certain plants that want to attract insects for reproduction. Flies attracted to skunk cabbage: They do this by creating a stink and the smell attracts the insects. The smell is enhanced because the plants have uncoupling proteins. They generate heat and make the flowers hotter. The volatiles which make the stink of the skunk cabbage are released further so the insects come in.

Question 23

ATP yield per glucose - producing reduced NADH

Answer 23

• Producing reduced NADH.
• For each reduced NAD when the electrons are passing through complex 1,3 and 4 - they will move 4,4, and 2 protons so a total of 10 protons from the mitochondrial matrix into the inter membrane space.
• NADH (reduced NAD) → 10 protons pumped into intermembrane space.
• For each ATP that the protons will produce as they move through ATP synthase, we have approximately 4 protons moving through ATP synthase per ATP produced.
• Therefore per reduced NAD you will produce 10/4 = 2.5 ATP.
• How many reduced NAD do we produce in respiration?
  
  • In the mitochondria we have 2 with the oxidation of pyruvate (per single starting glucose molecule),
  • 6 in the citric acid cycle, and in glycolysis in the first reaction of the energy payoff phase - reaction 6 catalysed by a dehydrogenase so we produce 2 reduced NAD in that reaction = 6 + 2 + 2 = 10 Total of 10 reduced NAD 10 x 2.5 = 25 ATPs

Question 24

ATP yield per glucose - producing reduced FAD

Answer 24

• Other electron carriers - reduced FAD.
• Producing 2 reduced FAD in the citric acid cycle.
• The route that the electrons take when they move from reduced FAD to molecular oxygen is different to the route that electrons take moving from reduced NAD - with FAD they move through complex 2, 3, and 4.
  
  • Complex 2 pumps 0 protons,
  • complex 3 pumps 4 protons and
  • complex 4 pumps 2 protons.
• For reduced FAD we have 6 protons pumped into the intermembrane space. 4 of these protons are needed to move through ATP synthase to produce an ATP. So per reduced NAD we have 6/4 = 1.5 ATPs 2 reduced NAD = 2 x 1.5 = 3 ATPs 25 ATPs + 3 ATPs = 28 ATPs

Question 25

ATP yield per glucose - producing 26 ATPs

Answer 25

* We can also produce 26 ATPs: The 2 reduced NADs that are produced in glycolysis, when they’re transported into the mitochondria - in some cases are converted into reduced FADs. * They move there by a transfer of electrons which can be either passed on to NADH or FADH. * If they are passed onto FADH the yield is reduced because the electrons from FADH are going through complex 2, 3, and 4 so you're moving fewer protons.

Question 26

Fermentation - Anaerobic respiration

Answer 26

* In the absence of oxygen anaerobic respiration occurs (yeast = fermentation). * Rather than the pyruvate moving into the mitochondria and being converted into acetyl CoA it can be converted into some other molecules - ethanol if you're a yeast → glycolysis, pyruvate (end product of glycolysis), pyruvate converted into acetaldehyde which converted into ethanol. * In our cells the pyruvate is converted into lactate → lactic acid. * The purpose of fermentation and anaerobic respiration is to ensure that glycolysis can keep continuing even though there is no oxygen present. * The reason it can keep occurring is because of the reactions - acetaldehyde to ethanol and pyruvate to lactate, those reactions involve the removal of electrons from reduced NAD. * So producing some reduced NAD in glycolysis in reaction 6, if you need glycolysis to keep occurring then you need to have oxidised NAD present. * These reactions work as a recycling mechanism for NAD, more NAD present which can accept electrons and glycolysis can keep occurring. Recycling mechanism for the electron carriers - anaerobic respiration.

Question 27

Other catabolic pathways

Answer 27

* Other metabolites can feed into the central pathways of glycolysis: * You can oxidise fats and if your body is seriously struggling for energy your body will start breaking down proteins (broken down into amino acids and they can be converted into pyruvate, acetyl CoA). * You can produce energy through the breakdown of fats, proteins and carbohydrates.

Question 28

Getting energy from fats

Answer 28

* Fats = energy storage. Stored in adipose cells. Most of your energy is stored as fats. * Highly reduced molecules. Because they are hydrophobic you can store them very compactly. * If you're storing carbohydrates you have to have a lot of water around - lots of hydroxyl groups and hydrophilic. * Water + the carbohydrates is a lot of volume. Fats can press close together - don't need water - you can fit a lot more fat into a volume than you can carbohydrates. * Hibernating animals: the hedgehogs - so greedy because when they hibernate through the winter they need some energy stores on which it can survive - it generates large fat stores. Will lose about 40% of its weight. Migratory birds have big fat stores.

Question 29

How do we get energy through fats

Answer 29

* Fat structure: triacelglyceride - glycerol head group and three fatty acid tails - highly reduced and equal distribution of electrons between the carbons and hydrogens because no electronegative atoms there. Hydrophobic. * How do we get energy through fats - occurs through a process called beta oxidation. * If you need to break your fats down, your fat reserves are released. * In the mitochondrial matrix you will start to metabolise the fats - the process of beta oxidation you break off two carbons from the fatty acid tails at a time - referred to as Acyl units which can be converted to acetyl CoA. * Acetyl CoA can link fat breakdown and carbohydrate breakdown. Each of these Acetyl CoA feed into the citric acid cycle and will produce 3 reduced NAD, 1 reduced FAD and 1 ATP and will all feed into the electron transport chain - oxidative phosphorylation- producing the 25 (or however many) ATP molecules. * Glucose 32 ATPs → 110,000 mmol ATP Triacylglycerol 300 ATPs → 4 million mmol ATP It takes longer to get energy from fat compared to carbohydrates. * Glucose: 16.7 mmol s^-1 Fats: slowly 6.7 mmol ATP sec^-1 When you do athletic events you are initially going to be using carbohydrate reserves. Long distance = fat reserves.

Question 30

Prokaryotes: how does respiration occur?

Answer 30

* Eukaryotes - membrane bound organelles. * Prokaryotes - don't have organelles. * How does respiration occur in these cells? * Electron transport proteins and ATP synthase occurs in the plasma membrane - as electrons are transferred from the electron carriers through the electron transport chain proteins then the protons are moved across the plasma membrane and (the proton gradient is created exactly the same as in the mitochondria) the proteins move back across the plasma membrane through ATP synthase producing ATP. * ATP yield per glucose for prokaryotes - able to get higher yields of ATP - more efficient. * Reason is because when we produce ATP (in the mitochondrial matrix), the ATP had to be move out of the mitochondrial matrix into the cytosol of the cell, protein moved ATP out of the mitochondria and ADP in, there is an energetic cost of the movement of ATP out and ADP into the mitochondria. * Prokaryotes don't have that problem because they are producing ATP in the cytosol where the ATP can do work. We have to move ATP to the areas where it can do work so there is an energetic cost. We aren't as efficient.

Question 31

Which produces more ATP substrate level phosphorylation or oxidative phosphorylation?

Answer 31

* 26 or 28 is made in oxidative phosphorylation compared to 4 in substrate level phosphorylation. * Producing a lot of ATPs because of these electron carriers, electron transport chain and oxidative phosphorylation.