Chapter 12 Flashcards
1
Q
Why do living organisms need energy
A
To work, examples of work:
- anabolic reactions (building of larger molecules from smaller molecules) (require energy)
- e.g proteins synthesis, synthesis of glycogen, DNA replication, polymerisation
- active transport
- e.g Na+ - K- pump, movement of vesicles in exo/endocytosis
- movement
- e.g muscle contraction, cilia/flagella, movement of chromosomes
- maintenance of a constant body temperature, in warm blooded animals (i.e endothermic)
- bioluminescence / electrical discharge
- e.g in jellyfish, electric eels
2
Q
What is the structure of ATP
A
- adenosine triphosphate
- it is a phosphorylated nucleotide
Has 3 components:
- adenine (organic nitrogenous base)
- ribose sugar (pentose sugar)
- three phosphate groups
- adenine + ribose sugar = adenosine (nucleoside)
3
Q
What are the characteristics of ATP
A
- small
- water soluble
- easily transported around the cell
- readily hydrolysed / lose phosphate to release energy
- small packets of energy released at one time
- ATP can be synthesised and broken down quickly
- high turnover rate
All these characteristics make it ideal as an energy currency in all organisms
4
Q
What are the roles of ATP
A
- the universal link/intermediate energy molecule
- energy currency of the cell
- immediate donor of energy
5
Q
What do we mean by ATP being the universal link/intermediate energy molecule
A
- the universal link/intermediate energy molecule
- between energy-giving reactions and energy-requiring reactions
Example of energy giving reactions: aerobic respiration (complete oxidation of glucose)
- gives a large quantity of energy, 2870 kj per mole of glucose
- C6 H12 O6 + 6O2 —> 6CO2 + 6H2O + 2870kJ
6
Q
Does the hydrolysis of ATP —> Energy have a 100% yield
A
- no
- energy transfers are inefficient
- excess energy is lost at different stages in the multi-step reaction
- as thermal/heat energy
7
Q
What do we mean by ATP being the “energy currency” of the cell
A
- ‘energy currency’ of the cell
- energy giving/yielding reaction are linked to the production of ATP first, which is then used in energy-requiring reactions
8
Q
What do we mean by ATP being an immediate donor of energy
A
- immediate donor of energy
- to reactions requiring energy
9
Q
What is the chemical equation of ATP hydrolysis
A
ATP —> ADP + Pi + 30.5kJ
Where Pi is inorganic phosphate
Or
ATP + H2O —> ADP + H3PO4 + 30.5kJ
- these reactions are all reversible
- because ATP can be synthesised and broken down quickly
- rate of turnover/interconversion of ATP is high
10
Q
How much energy is released during the hydrolysis of ATP
A
- removal of 1st phosphate group from ATP—>ADP
- 30.5 kJ of energy released
- removal of 2nd phosphate group from ADP—>AMP
- 30.5 kJ of energy released
- removal of last phosphate group from AMP—>adenosine
- 14.2 kJ of energy released
11
Q
How is ATP synthesised
A
- ATP is synthesised from energy-yielding reactions
- e.g oxidation of glucose in cellular respiration or LD stage in photosynthesis
- in a series of reaction
12
Q
What is respiration
A
- it is the process where
- organic molecules (like glucose, amino acids, glycerol, fatty acids)
- are broken down in a series of stages
- to release energy
- which is used to synthesise ATP
13
Q
What are the types of respiration
A
- aerobic respiration
- anaerobic respiration
14
Q
What is aerobic respiration
A
- breakdown of organic molecules (like glucose, amino acids, glycerol, fatty acids)
- to release energy
- which is used to synthesise ATP
- in the presence of oxygen
15
Q
What are the 4 stages in the aerobic respiration of glucose and where do they occur
A
- Glycolysis (cytoplasm)
- Link reaction (mitochondrial matrix)
- Krebs cycle (mitochondrial matrix)
- Oxidative phosphorylation (inner mitochondrial membrane / cristae)
16
Q
Why is the oxidation of glucose a multi-step reaction involving multiple small steps
A
- allows precise control
- cells could not fully harness total energy releases if all were released at one instant
17
Q
Why doesn’t the reaction (oxidation of glucose) happen easily
A
- because glucose is quite a stable substance
- it requires a high activation energy for reaction to take place
How do organisms overcome this:
A) usage of enzymes to lower activation energy
B) raising energy level of glucose by phosphorylation
18
Q
What are the steps/stages of glycolysis
A
- Glucose (6C) is phosphorylated
- by 2 ATP
- forms hexose / fructose biphosphate (6C)
- this raises chemical potential energy of glucose
- provides activation energy for split
- Fructose biphosphate breaks down to
- 2 triose phosphate (3C)
- 6C —> 2x3C
- 2 hydrogen atoms are removed
- 2 reduced NAD (NADH) is formed
- this is a dehydrogenation/oxidation reaction
- 4 ATP produced
- 4 ATP - 2 ATP = glycolysis has net gain of 2 ATP
- chemical potential energy is released from intermediate steps
- 2 pyruvate (3C) produced
19
Q
What are the initial reactants and final products in glycolysis
A
Initial reactants:
- 1 glucose (6C)
- 2 ATP
- 4 ADP, 2 NAD
Final products per molecule of glucose
- 2 pyruvate (3C)
- 2 NADH
- 4 ATP —> but 4-2 = net gain of 2 ATP only
20
Q
What are the types of hydrogen carrier molecules
A
Also called hydrogen acceptor molecules
- NAD - nicotinamide adenine dinucleotide
- used in respiration
- NADP - nicotinamide adenine dinucelotide phosphate
- used in photosynthesis
- FAD - flavin adenine dinucleotide
- used in respiration
21
Q
What are all hydrogen carrier molecules
A
they are all coenzymes = a non-protein complex organic substance that is required for an enzymes activity
22
Q
What is NAD
A
- nicotinamide adenine dinucleotide
- coenzyme
- H carrier molecules in respiration
23
Q
What is the structure of NAD
A
- two linked nucleotides
- both have ribose sugar and a phosphate group each
- 1 has adenine base, the other has a nicotinamide ring
- nicotinamide ring accepts H
- NAD + H —> reduced NAD (reversible arrow)
24
Q
What is the function of NAD
A
- H carrier molecule in respiration
- carry hydrogens from all stages of respiration (stage 1,2,3)
- to take part in oxidative phosphorylation (stage 4) where most ATP is synthesised
25
What is NADP
- nicotinamide adenine dinucleotide phosphate
- coenzyme
- H carrier molecule used in photosynthesis
- different form of NAD
26
What is the structure of NADP
- similar to NAD
- but has a phosphate group instead of H on carbon 2 on ribose ring with adenine
27
What is FAD
- flavin adenine dinucleotide
- coenzyme
- H carrier molecules in respiration
- used to carry H produced in Krebs cycle (stage 3) only
- then used in oxidative phosphorylation (stage 4)
28
What is the structure of FAD
- two linked nucleotides
- one nucleotide with phosphate, ribose and adenine
- another nucleotide with phosphate, ribitol and flavin
29
What are the equation of FAD
FAD + 2H —> reduced FAD
FAD+ + 2H+ + 2e —> FADH2
30
What are the steps/stages of the link reaction
- pyruvate is transported from cytoplasm into the mitochondrial matrix via active transport
- when oxygen is available, pyruvate (3C) is:
1. Decarboxylated
- to form carbon dioxide
2. Dehydrogenated
- NADH produced
3. Combined with coenzyme A (CoA)
- to from acetyl coenzyme A (2C)
31
What is coenzyme A and what is its structure
- complex molecule
- made of a nucleoside (adenine + ribose) and a vitamin (pantothenic acid)
32
What is the function of coenzyme A
- carry acetyl groups (2C) to Krebs cycle (stage 3)
33
What are the initial reactants and final products of the link reaction
Initial reactants:
- 1 pyruvate (3C)
- 1 NAD
- 1 CoA
Final products per molecule of pyruvate:
- 1 acetyl CoA (2C)
- 1 NADH
- 1 CO2 -> waste gas, released
But since 1 molecule of glucose is oxidised into 2 pyruvate
Final products per molecule of glucose:
- 2 acetyl CoA (2C)
- 2 NADH
- 2 CO2 -> waste gas, released
34
What are the steps/stages of the Krebs cycle
1. Acetyl CoA (2C)
- combines with oxaloacetate (4C)
- to form citrate (6C)
- CoA is removed and can be used agin in link reaction
2. Citrate (6C) goes through a series of dehydrogenation and decarboxylation
- 7 steps by products of each step are:
1. Nothing
2. Reduced NAD and CO2
3. Reduced NAD and CO2
4. ATP
5. Reduced FAD
6. Nothing
7. Reduced NAD
3. Oxaloacetate (4C) regenerated
- can combine with another acetyl CoA
- Kreb cycle continues
35
What are the initial reactants and final products of the Krebs cycle
Initial reactants:
- 1 acetyl CoA (2C)
- 1 oxaloacetate (4C)
- 1 ADP, 3 NAD, 1 FAD
Final products per molecule of acetyl CoA (1 turn of the Krebs cycle):
- 3 NADH
- 1 FADH2 (reduced FAD)
- 2 CO2 -> waste gas, released
- 1 ATP
- oxaloacetate (4C) —> regenerated
But since 1 molecule of glucose is oxidised into 2 pyruvate, which is converted to 2 acetyl CoA in the link reaction…
Final products per molecule of glucose (2 turns of the Krebs cycle):
- 6 NADH
- 2 FADH2 (reduced FAD)
- 4 CO2 -> waste gas, released
- 2 ATP
- oxaloacetate (4C) —> regenerated twice
36
Where does oxidative phosphorylation occur
- occurs in the cristae of mitochondria
- there is a high release of electrical potential energy here
- for the production of ATP (ADP + Pi —> ATP)
- involves a chain of electron carrier molecules in the inner membranes
- these molecules make up the electron transport chain (ETC)
- ATP synthesis is catalysed by ATP synthase
37
What are the steps/stages of oxidative phosphorylation
1. Hydrogens removed from reduced NAD and reduced FAD
- reduced NAD and reduced FAD are from glycolysis, link reaction, Krebs cycle
- this occurs at the inner mitochondrial membrane
- through dehydrogenation/oxidtaion reaction
- catalysed by dehydrogenase enzymes
- NAD and FAD regenerated (can be reduced again in glycolysis, link reaction, Krebs cycle)
2. Hydrogen atoms split into electrons and protons (H+ ions)
- H —> H+ + e
3. Electrons are passed along ETC
- passed along a series of electron carriers in inner membrane
- electron carriers are associated with 4 types of membrane proteins (forms a functional unit called a respiratory complex (ETC))
- energetic electrons release energy as they pass through the ETC
4. Energy released is used to pump protons
- across inner mitochondrial membrane
- from mitochondrial matrix to intermembrane space
- since innermembrane is impermeable to protons
- and there is high concentration of H+ in intermebrane space
- this forms a proton gradient / electrochemical gradient
5. Protons move down electrochemical gradient
- by facilitated diffusion through ATP synthase
- back into mitochondrial matrix
- this provides energy for ATP synthesis
- this process is called chemiosmosis
6. ATP synthase enzyme rotates
- ADP + Pi —> ATP
- ATP is synthesised
- the movement of 3 H+ ions back into matrix = 1 ATP molecule
7. Oxygen is the final hydrogen acceptor and final electron acceptor
- O2 + 4H+ + 4ē —> 2H2O
- forms water
- so previous electron carrier in ETC can be reduced again
- ensures electrons can keep flowing across ETC
- oxygen is why it’s called oxidative phosphorylation and aerobic respiration
38
What are the initial reactants and final products of oxidative phosphorylation
Per molecule of glucose
Initial reactants:
- 10 NADH
- 2 FADH2
- O2 and ADP+Pi
Final products:
- 28 ATP
- water
39
What are the two ways ATP can be synthesised in respiration
1. Substrate level phosphorylation
2. Oxidative phosphorylation
40
What is substrate linked phosphorylation
- occurs during glycolysis at cytoplasm —> 2 ATP produced
- occurs during Krebs cycle at mitochondrial matrix —> 2 ATP produced
- 4 ATP produced by substrate linked phosphorylation in total
- chemical potential energy releases from reorganisation of chemical bonds used to directly combine Pi to ADP
41
What is oxidative phosphorylation
- occurs at cristae
- requires proton/electrochemical gradient, ATP synthase, ETC
- electric potential energy released by chemiosmosis is used by ATP synthase to catalyse formation of ATP
- 28 ATP produced by oxidative phosphorylation in total
- also happens in the chloroplast during photosynthesis
42
What is the mitochondria the site for
- link reaction (matrix)
- Krebs cycle (matrix)
- oxidative phosphorylation (cristae)
43
What is the function of the matrix in the mitochondria
- has small circular mitochondrial DNA
- has 70S ribosomes
- which can synthesis mitochondrial proteins
- have many enzymes in matrix for link reaction and Krebs cycle
44
What is the function of cristae/inner membrane in mitochondria
- inner membrane is the site of ETC and oxidative phosphorylation
- inner membrane holds many special proteins and electron carriers
- i.e. ATP synthase, channels for H+ ions
- linear arrangement of ETC on inner membrane
- greater efficiency
- inner membrane/cristae is folded
- increases total surface area for ATP synthase and membrane proteins
- active cells have more foldings / dense cristae
- inner membrane impermeable to H+ ions
- maintains proton gradient
- H+ only go through channels i.e. ATP synthase
45
What is the function of the outer membrane in mitochondria
- different in composition from inner membrane
- smooth, not folded
- more permeable to small molecules than inner membrane
- contains transport proteins to transport pyruvate into the mitochondria for link reaction and Krebs cycle
46
What is the function of the intermembrane space in mitochondria
- allows accumulation of H+ ions
- lower pH than mitochondrial matrix
- more acidic
- due to pumping of H+ ions from matrix by the activity of ETC
47
What is anaerobic respiration
- synthesis of ATP in the absence of oxygen
48
What happens when free oxygen is not available
- no final electron and H acceptor
- H from reduced NAD and FAD cannot be removed
- ETC stops working
- no ATP from oxidative phosphorylation
- NAD and FAD not regenerated
- no Krebs cycle and link reaction
- no ATP from Krebs cycle
49
What can still occur without the presence of oxygen
- glycolysis still occurs at the cytoplasm
- only net 2 ATP formed per glucose molecule by substrate level phosphorylation
- so glucose not completely broken down without oxygen
- pyruvate still contains energy
- 2 NADH are formed too
- special pathways are used to regenerate NAD
- but this is not sustainable / cannot go on indefinitely
- due to toxic byproducts
50
Where does anaerobic respiration occur / what pathways are used to regenerate NAD
1. In yeast cells / plant tissues
- ethanol pathway / alcoholic fermentation
2. In animals / mammalian muscles / some bacteria
- especially when muscle activity is high and cells do not have enough oxygen to perform aerobic respiration
- lactate pathway / lactic fermentation
- these pathways are used to regenerate NAD
- but this is not sustainable / cannot go on indefinitely
- due to toxic byproducts
51
What are the steps of ethanol pathway / alcoholic fermentation (anaerobic respiration in yeast)
- it is a 2 step reaction: pyruvate —> ethanal —> ethanol
- it is irreversible
1. Glycolysis: glucose —> pyruvate (3C)
- net gain of 2 ATP
- 2 NADH produced
2. Pyruvate (3C) undergoes decarboxylation
- forms ethanal (2C)
- CO2 produced
3. Ethanal (2C) / acetaldehyde acts as a H acceptor
- reduced by receiving hydrogen from reduced NAD
- ethanal —> ethanol (2C)
- catalysed by alcohol dehydrogenase
- this also prevents H+ from lowering pH in yeast cell
4. NAD is regenerated
- allows glycolysis to continue
- to produce ATP
52
Why can the ethanol pathway not go on indefinitely
- ethanol is toxic
- reaction is irreversible
- remaining chemical potential energy in ethanol is wasted
53
What are the steps/stages of the lactate pathway / lactic fermentation (anaerobic respiration in mammals)
- 1 step reaction: pyruvate —> lactate
- reversible
1. Glycolysis: glucose —> pyruvate (3C)
- net gain of 2 ATP
- 2 NADH produced
2. Pyruvate acts as the H acceptor
- receives H from NADH
- pyruvate reduced to lactate / lactic acid
- catalysed by lactate dehydrogenase
3. NAD is regenerated
- allows glycolysis to continue
- to make ATP
54
Why can’t the lactate pathway go on indefinitely
- lactate is toxic
- causes drop in pH / acidic
- but the reaction is reversible!
55
What happens to lactate after you stop exercising
- lactate is transported by blood plasma
- for muscles to be broken down in liver
In liver:
- lactate converted back to pyruvate
- by lactate dehydrogenase
When oxygen is present again:
- pyruvate is further broken down / oxidised in aerobic respiration
- i.e. link reaction —> Krebs cycle —> oxidative phosphorylation
- produce carbon dioxide + water
- if there’s excess lactate it is converted to glycogen
56
What happen in terms of oxygen uptake at rest
- rate of oxygen uptake at resting levels is low
57
What happen in terms of oxygen uptake during exercise
- oxygen demand and uptake by cells increases
- but heart and lungs are unable to meet demands immediately
- results in oxygen deficit = the volume difference between ideal and real oxygen uptake
- so anaerobic respiration occurs
58
What happen in terms of oxygen uptake during recovery
- breathing rate / oxygen uptake is still higher than resting levels
- to ‘pay back’ oxygen debt
- oxygen debt = volume of oxygen required to metabolise lactate accumulated during anaerobic respiration to CO2 and water after exercise
59
What is oxygen debt
oxygen debt = volume of oxygen required to metabolise lactate accumulated during anaerobic respiration to CO2 and water after exercise
60
How do you calculate oxygen debt
- oxygen consumed = oxygen inhaled - oxygen exhaled
- measure oxygen consumption at rest (x) and after exercise stops (y)
- extra oxygen consumed = oxygen debt = y-x
- divide by mass of organism
61
What are the similarities between the ethanol and lactate pathway
1. Both occur when oxygen is absent/low in conc
2. Both occur in cytoplasm
3. Both involve glycolysis
4. Both produce only 2 ATP net per glucose molecule
5. Both involve usage and regeneration of NAD
62
What are the respiratory substrates
1. Glucose
- essential respiratory substrate for neurones in brain, RBC, lymphocytes
- oxidised in glycolysis, link reaction, Krebs cycle
2. Lipids
- converted to acetyl CoA (2C)
- oxidised in Krebs cycle
3. Proteins
- amino acid converted to pyruvate (3C) or acetyl CoA (2C)
- oxidised in link reaction and/or Krebs cycle
- NADH and FADH2 are produced in all these reactions
- passed on to the ETC in oxidative phosphorylation
- to produce ATP
63
How to determine which molecule contains the most enrgy
- H needed for ATP production/chemiosmosis
- the higher the number of C-H bonds / H atoms in a respiratory substrate
- the more hydrogens can be carried by NAD and FAD
- more reduced NAD produced
- more oxidative phosphorylation / ETC
- more hydrogen ions pumped across inner mitochondrial membrane / steeper proton gradient
- the more ATP made per gram of respiratory substrate
- the greater the energy value
64
What is the energy value of lipids
- has the most C-H bonds / number of H atoms per unit mass
- compared to carbs and protein
- so releases most energy per unit mass
- has a high energy density
- many more H available to reduce oxygen to water
- more water produced from metabolism of lipid
- oxidation of lipids can only happen in the presence of oxygen
65
What is the energy value of proteins
- slightly more C-H bonds per unit mass than carbohydrates
- but less than lipids
- used during starvation / lack of fats or carbs
- oxidation of amino acids can only happen in the presence of oxygen
66
What are the energy values of each respiratory substrate
- carbohydrate = 15.8
- lipid = 39.4
- protein = 17.0
67
How are energy values determined
- using a calorimeter
- burning a known mass of substance
- with oxygen
- measure rise in temperature
- of a known mass of water
68
What is respiratory quotient (RQ)
- RQ = ratio of the volume of carbon dioxide produced to oxygen used per unit time
- RQ = volume of CO2 given out in unit time / volume of O2 taken in in unit time
- different respiratory substrate has a different RQ
69
What is the function of RQ
1. Shows the type of substrate being used in respiration
2. Shows if anaerobic respiration is occurring
70
What is the respiratory quotient of each respiratory substrate
- carbohydrate = 1.0
- lipid = 0.7
- protein = 0.9
- anaerobic in yeast = infinity or greater than 1
- anaerobic in muscles = 0
71
What are the challenges of rice with submerged roots in water
Oryza sativa
- low oxygen in water, roots do not get enough oxygen
- gas diffuses much more slowly through water than in air
- anaerobic respiration occurs
- toxic alcohol produced
72
What are the challenges of rice with submerged roots in water
Oryza sativa
- low oxygen in water, roots do not get enough oxygen
- gas diffuses much more slowly through water than in air
- anaerobic respiration occurs
- toxic alcohol produced
73
What are the challenges of rice with submerged roots in water
Oryza sativa
- low oxygen in water, roots do not get enough oxygen
- gas diffuses much more slowly through water than in air
- anaerobic respiration occurs
- toxic alcohol produced
74
What are the challenges of rice with submerged roots in water
Oryza sativa
- low oxygen in water, roots do not get enough oxygen
- gas diffuses much more slowly through water than in air
- anaerobic respiration occurs
- toxic alcohol produced
75
What are the adaptions of rice with submerged roots in water
1. Rice tolerant to higher levels of alcohol
2. Presence of aerenchyma
3. Grow taller in response to flooding
4. Leavers underwater have hydrophobic, corrugated surface
76
How does rice being tolerant to higher levels of alcohol help
- rice produces high levels of alcohol dehydrogenase to break down alcohol
- can respire anaerobically for longer periods
77
How does the resend of aerenchyma in rice help
- air spaces between cells in mesophyll / cortex of stems
- oxygen able to diffuse through aerenchyma from aerial tissues to roots
- this provides oxygen for aerobic respiration
- also allows for
- escape of ethane
- buoyancy
- enable active transport in roots because aerobic respiration produces energy
78
How does the presence of aerenchyma in rice help
- air spaces between cells in mesophyll / cortex of stems
- oxygen able to diffuse through aerenchyma from aerial tissues to roots
- this provides oxygen for aerobic respiration
- also allows for
- escape of ethane
- buoyancy
- enable active transport in roots because aerobic respiration produces energy
79
How does rice growing taller in response to flooding help
- grow taller in response to flooding
- leave flowers and spikes are above water
- O2 and CO2 can diffuse in/out through stomata on leaves
80
How do leaves underwater having hydrophobic, corrugated surfaces help
- leaves under water have hydrophobic, corrugated surface
- results in air trapped between ridges
- so holds thin layer of air in contact with leaf surface
81
How do leaves underwater having hydrophobic, corrugated surfaces help
- leaves under water have hydrophobic, corrugated surface
- results in air trapped between ridges
- so holds thin layer of air in contact with leaf surface
