Topic 8 - Metabolism, Cell Respiration, and Photosynthesis

Question 1

anabolism

Answer 1

• type of metabolic reaction
• synthesizes complex molecules from its constituents
• endergonic (requires absorption of energy)
  e. g. photosynthesis

Question 2

catabolism

Answer 2

• type of metabolic reaction
• breaks down complex molecules into its constituents
• exergonic (releases energy)
  e. g. cell respiration

Question 3

induced fit enzyme model

Answer 3

• similar to lock and key model
• except it proposes that the substrate causes a conformational change in the enzyme
• this is due to changes in R-groups of amino acids at the enzyme’s active site

Question 4

mechanism of enzyme action

Answer 4

1. Surface of substrate contacts enzyme’s active site
2. Enzyme changes shape to accommodate substrate
3. Temporary complex (enzyme-substrate complex) forms
4. Activation energy is lowered and the substrate is altered by the rearrangement of atoms
5. The product is released from the active site
6. The (unchanged) enzyme is free to combine with other substrates

Question 5

competitive inhibition

Answer 5

• the inhibitor only binds to the active site
• so it has to “compete” with the substrate to bind
• it should have a similar structure to the substrate
• can be reversible or irreversible
• if reversible, it can be minimized by increasing substrate conc

Question 6

non-competitive inhibition

Answer 6

AKA allosteric inhibition

• the inhibitor binds away from the active site
• the site it binds to is the “allosteric site”
• the binding will cause a change to the active site that prevents substrates from binding to it
• can be reversible or irreversible

Question 7

end-product inhibition

Answer 7

• metabolic reactions occur in an assembly-line process
• each step is catalyzed by a different, specific enzyme
• when the end product reaches a sufficient concentration, the assembly line is shut down via end-product inhibition

Question 8

how end-product inhibition works

Answer 8

• at sufficient concentrations, the end product acts as a non-competitive inhibitor to the enzyme at the first step of the assembly line
• when the concentration is low, less inhibition occurs and thus there is more enzyme activity
• thus the inhibition of the first pathway prevents the build-up of intermediates in the cell

Question 9

oxidation

Answer 9

• lose electrons
• gain oxygen
• lose hydrogen
• results in many C-O bonds
• results in product with lower potential energy

Question 10

reduction

Answer 10

• gain electrons
• lose oxygen
• gain hydrogen
• results in many C-H bonds
• results in product with higher potential energy

Question 11

glycolysis

Answer 11

• first step of all forms of cell respiration
• occurs in cytosol of a cell
• does not use oxygen!
• uses a hexose (usually glucose)

Question 12

most commonly used hydrogen carrier (oxidant)

Answer 12

NAD (nicotinamide adenine dinucleotide)
- as an oxidant, it undergoes reduction

NAD + 2H → reduced NAD
reduced NAD usually takes the form of NADH + H+

Question 13

phosphorylation

Answer 13

• reaction in which a phosphate group (PO 4 3-) is added to an organic molecule
• usually transferred from ATP
• creates a less stable molecule which is therefore more likely to react
• can turn a slow endothermic rxn into a fast exothermic rxn

Question 14

process of glycolysis

Answer 14

1. • 2 ATP molecules used to begin glycolysis
     - phosphorylation occurs to form fructose-1,6-biphosphate
2. • phosphorylated hexose splits into two 3-carbon sugars triose phosphate (G3P) in a process called “lysis” (literally ‘splitting of molecules)
3. • once the two G3P molecules are formed, they are oxidized with NAD to remove 2 H from each G3P
     - reduced NAD+ (NADH) forms
     - released energy used to add another phosphate to the remaining 3-carbon compound
     - results in a compound with 2 phosphate groups
     - enzymes remove phosphate groups so that they can be added to ADP to produce ATP

Question 15

results of glycolysis

Answer 15

• 4 ATP (as 2 ATP were used up, there’s a net gain of 2 ATP)
• 2 NADP
• 2 pyruvate (ionized form of pyruvic acid)

Question 16

what happens to pyruvate in anaerobic conditions

Answer 16

• no oxygen
• so oxidation of pyruvate cannot occur
• products: ethanol + lactate (in humans) or CO2 (in yeast)

Question 17

what happens to pyruvate in aerobic conditions

Answer 17

• more energy can be obtained from oxidation of pyruvate
• obviously this only happens in aerobic respiration
• link reaction and Krebs cycle proceed
• products: CO2 and H2O

Question 18

link reaction

Answer 18

• follows glycolysis

- occurs before krebs cycle

Question 19

decarboxylation

Answer 19

removal of CO2

Question 20

oxidative decarboxylation

Answer 20

simultaneous oxidation and decarboxylation

- in link reaction it’s removal of H and CO2 simultaneously

Question 21

link reaction: process

Answer 21

• pyruvate enters matrix of mitochondria via active transport
• enzymes in matrix catalyse oxidative decarboxylation with NAD+ and coenzyme A (CoA)

byproducts: reduced NAD (NADH), CO2
main product: Acetyl CoA
- if ATP levels are high already, acetyl CoA can be synthesized into a lipid for storage

Question 22

krebs cycle

Answer 22

AKA tricarboxylic acid cycle

• series of reactions
• begins and ends with the same substance (thus ‘cycle’)
• doesn’t directly require oxygen but does require products from electron transport chain
• occurs in matrix of mitochondria
• requires Acetyl CoA (2C)
• starting compound is oxaloacetate (4C)
• each glucose molecule = 2 pyruvates = 2 Acetyl CoAs
• so for each glucose molecule = 2 krebs cycles
• actually hexose is not a requirement, other lipids/carbohydrates can be substituted
• acetyl CoA can be produced from most carbohydrates and fats

Question 23

krebs cycle: process of 1 cycle

Answer 23

1. Acetyl CoA (2C) + oxaloacetate (4C) → citrate (6C)
   byproduct: CoA
2. citrate (6C) undergoes oxidative decarboxylation with NAD to form 5C compound
   byproducts: NADH, CO2
3. 5C compound undergoes oxidative decarboxylation with NAD to form 4C compound
   byproducts: reduced NAD, CO2
4. 4C compound undergoes various changes to form oxaloacetate
   - coenzyme FAD reduced to form FADH2
   - NAD+ reduced to form NADH
   - ADP reduced (1 phosphate group added) to form ATP
   byproducts: NADH, FADH2, ATP

CYCLE REPEATS!

Question 24

products of each krebs cycle

Answer 24

• 1 ATP
• 3 NADH
• 2 FADH2
• 4 CO2 (waste)

Question 25

usefulness of NADH and FADH2

Answer 25

• used as e- sources in electron transport chain
• FADH2 enters the electron transport chain at a lower free energy level than NADH
• so FADH2 produces 2 ATPs while NADH produces 3 ATPs
• at the very end of the chain, the de-energized e-s combine with available oxygen

Question 26

electron transport chain

Answer 26

• series of e- carriers in the inner membrane of the mitochondrion (including cristae)
• most of the ATPs from aerobic respiration are produced here
• only stage of cellular respiration where oxygen is needed
• releases small amounts of energy whenever an e- is transported
• e-s step down in potential energy as they are passed from one carrier to another
• coenzymes NADH and FADH2 (byproducts in krebs cycle) are used as e- sources

Question 27

nature of e- carriers in electron transport chain

Answer 27

• mostly proteins
• packed close together to reduce amount of energy lost in exchanges
• easily reduced/oxidized
• pass the e-s from one to another using an energy gradient
• some carriers act as proton pumps and pump H+ from the matrix to the intermembrane space
• each carrier has a slightly different electronegativity
• 1 of the carriers is not a protein but CoQ (coenzyme Q)
• oxygen is the final acceptor as it’s highly electronegative

Question 28

why is the energy released from each exchange in the electron transport chain low?

Answer 28

• low energy is easily harnessed
• this ensures that the energy is maximised for use (phosphorylation of ADP)
• if it was too high, the cell could be damaged

Question 29

role of oxygen in electron transport chain

Answer 29

• oxygen is the last e- acceptor (terminal electron acceptor)
• it’s the last bc it’s highly electronegative
• this occurs in the matrix (on the surface of the inner membrane)
• at the same time, oxygen accepts H+ ions to form water
• the use of protons contributes to the proton gradient across the inner mitochondrial membrane
• only stage where oxygen is used in cell respiration

Question 30

what if oxygen isn’t available?

Answer 30

• e- flow stops and reduced NAD can’t be converted back
• NAD supplies in mitochondrion run out so the link reaction and Krebs cycle stops
• the only part of cell respiration that can continue is glycolysis

Question 31

chemiosmosis

Answer 31

• generation of ATP using energy released by movement of protons across a membrane
• the electron transport chain proteins act as proton pumps that pump H+ out of the matrix and into the intermembraneous space of the mitochondrion
• they diffuse back via ATP synthase and the energy released upon diffusion is harnessed to produce ATP

Question 32

ATP synthase

Answer 32

• enzyme located in the inner mitochondrial membrane
• allows protons to diffuse back across the membrane to the matrix
• energy released by the protons upon diffusion is harnessed by ATP synthase to produce ATP

Question 33

features of a mitochondrion

Answer 33

• outer mitochondrial membrane
• matrix
• cristae
• inner mitochondrial membrane
• intermembraneous space

Question 34

mitochondrial intermembraneous space

Answer 34

H+ (proton) reservoir

Question 35

cristae

Answer 35

• tubular regions surrounded by membranes

- increases SA for oxidative phosphorylation

Question 36

matrix

Answer 36

• internal cytosol-like area

- contains enzymes for Krebs cycle and link reaction

Question 37

plastid

Answer 37

• group of closely related organelles that occur in photosynthetic eukaryotic cells
• all plastids developed from a common proplastid

Question 38

types of plastids and their functions

Answer 38

• chloroplasts, which are green and involved in photosynthesis
• leucoplasts, which are white or ‘clear’ and function as energy storehouses
• chromoplasts, which are brightly coloured and synthesize and store large amounts of orange, red, or yellow pigments

Question 39

photosystems

Answer 39

• large groups of pigment molecules

- they work together to harvest light energy

Question 40

components of photosystems

Answer 40

• accessory pigments

its reaction centre contains:

• a pair of chlorophyll a molecules
• a protein matrix
• a primary electron acceptor.

Question 41

differences between types of photosystems

Answer 41

• Photosystem I absorbs light more efficiently at 700 nm (so it’s called P700)
• Photosystem II absorbs light more efficiently at 680 nm (so it’s called P680)

Question 42

nature of pigments

Answer 42

• absorb certain wavelengths of light

- as certain wavelengths cause excitement of an e- in the pigment molecule

Question 43

how pigments in photosystems work together

Answer 43

• when an e- of a pigment is excited, it’s passed from pigment to pigment
• until it reaches a special chlorophyll molecule at the reaction centre of the photosystem
• the chlorophyll passes pairs of excited e-s away to e- acceptors in the thylakoid membrane

Question 44

where does the light-dependent reaction occur?

Answer 44

in the thylakoids/grana of the chloroplast

Question 45

photophosphorylation

Answer 45

production of ATP in chloroplasts

Question 46

chemiosmosis

Answer 46

• generation of ATP using energy released by movement of protons across a membrane
• facilitated by some e- carriers acting as proton pumps in the electron transport chain

Question 47

process of light-dependent reaction

Answer 47

1. photon of light absorbed by pigment in photosystem II is transferred until it reaches the reaction centre
2. chlorophyll e-s in p680 (photosystem II) get excited and are passed to a chain of carriers
3. • water is photolysed by an enzyme
     - produces e-s, H+ ions, and an oxygen atom
     - e-s are supplied one by one to chlorophyll a molecules in P680
4. (process similar to electron transport chain)
   - at one stage enough energy is released to pump protons from stroma across the thylakoid membrane
   - this contributes to a proton gradient
   - ATP synthase allows protons to diffuse back to the stroma
   - uses energy released to bring about phosphorylation of ADP to produce ATP (chemiosmosis)
5. • P700 undergoes a similar process in first 2 steps
6. • de-energized e-s from P680 fills the void left by the newly energized electron
     - the energized e- is then passed down a second electron transport chain, now involving the carrier ferredoxin
7. NADP reductase catalyses transfer of the e- from ferredoxin to NADP+
   - 2 e-s used to reduce NADP+ to NADPH

Question 48

final products of light-dependent reaction in photosynthesis

Answer 48

• NADPH

- ATP

Question 49

light-independent reaction in photosynthesis

Answer 49

• occurs in the stroma
• the ATP and NADPH made with the light-dependent reaction are needed for the light-independent reaction
• involves the Calvin cycle

Question 50

Calvin cycle process

Answer 50

1. Ribulose bisphosphate (RuBP, a 5C compound) binds to incoming CO2 (carbon fixation, catalysed by rubisco)
   - product: 6 unstable 6C compounds
2. Being unstable, the 6C compound breaks down
   - product: 12 (3C) glycerate 3-phosphate (GP) molecules
3. 12 ATP and 12 NADPH reduce GP
   - products: 12 (3C) triose phosphates (TP)
   - byproducts: 12 ADP, 12 reduced NADP, 12 H+
4. TP then undergoes one of 2 pathways:
   - continue in the cycle to reproduce the originating compound of the cycle, RuBP
   - leave the cycle to become sugar phosphates that may become more complex carbohydrates (this is also where the ‘glucose’ comes from in the summarized photosynthetic reaction)
5. Normally 10 of the 12 TPs are left and ATP is used to regain RuBP from those TP molecules
   - product: 6 RuBP
   - byproducts: 6 ADP, 6 H+