Chapter 12 Flashcards
Why do living organisms need energy
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
What is the structure of ATP
- 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)
What are the characteristics of ATP
- 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
What are the roles of ATP
- the universal link/intermediate energy molecule
- energy currency of the cell
- immediate donor of energy
What do we mean by ATP being the universal link/intermediate energy molecule
- 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
Does the hydrolysis of ATP —> Energy have a 100% yield
- no
- energy transfers are inefficient
- excess energy is lost at different stages in the multi-step reaction
- as thermal/heat energy
What do we mean by ATP being the “energy currency” of the cell
- ‘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
What do we mean by ATP being an immediate donor of energy
- immediate donor of energy
- to reactions requiring energy
What is the chemical equation of ATP hydrolysis
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
How much energy is released during the hydrolysis of ATP
- 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
How is ATP synthesised
- 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
What is respiration
- 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
What are the types of respiration
- aerobic respiration
- anaerobic respiration
What is aerobic respiration
- 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
What are the 4 stages in the aerobic respiration of glucose and where do they occur
- Glycolysis (cytoplasm)
- Link reaction (mitochondrial matrix)
- Krebs cycle (mitochondrial matrix)
- Oxidative phosphorylation (inner mitochondrial membrane / cristae)
Why is the oxidation of glucose a multi-step reaction involving multiple small steps
- allows precise control
- cells could not fully harness total energy releases if all were released at one instant
Why doesn’t the reaction (oxidation of glucose) happen easily
- 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
What are the steps/stages of glycolysis
- 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
What are the initial reactants and final products in glycolysis
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
What are the types of hydrogen carrier molecules
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
What are all hydrogen carrier molecules
they are all coenzymes = a non-protein complex organic substance that is required for an enzymes activity
What is NAD
- nicotinamide adenine dinucleotide
- coenzyme
- H carrier molecules in respiration
What is the structure of NAD
- 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)
What is the function of NAD
- 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
What is NADP
- nicotinamide adenine dinucleotide phosphate
- coenzyme
- H carrier molecule used in photosynthesis
- different form of NAD
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
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)
What is the structure of FAD
- two linked nucleotides
- one nucleotide with phosphate, ribose and adenine
- another nucleotide with phosphate, ribitol and flavin
What are the equation of FAD
FAD + 2H —> reduced FAD
FAD+ + 2H+ + 2e —> FADH2
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:
- Decarboxylated
- to form carbon dioxide
- Dehydrogenated
- NADH produced
- Combined with coenzyme A (CoA)
- to from acetyl coenzyme A (2C)
What is coenzyme A and what is its structure
- complex molecule
- made of a nucleoside (adenine + ribose) and a vitamin (pantothenic acid)
What is the function of coenzyme A
- carry acetyl groups (2C) to Krebs cycle (stage 3)
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
What are the steps/stages of the Krebs cycle
- Acetyl CoA (2C)
- combines with oxaloacetate (4C)
- to form citrate (6C)
- CoA is removed and can be used agin in link reaction
- 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
- 7 steps by products of each step are:
- Oxaloacetate (4C) regenerated
- can combine with another acetyl CoA
- Kreb cycle continues
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
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
What are the steps/stages of oxidative phosphorylation
- 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)
- Hydrogen atoms split into electrons and protons (H+ ions)
- H —> H+ + e
- 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
- 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
- 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
- ATP synthase enzyme rotates
- ADP + Pi —> ATP
- ATP is synthesised
- the movement of 3 H+ ions back into matrix = 1 ATP molecule
- 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
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
What are the two ways ATP can be synthesised in respiration
- Substrate level phosphorylation
- Oxidative phosphorylation
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
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
What is the mitochondria the site for
- link reaction (matrix)
- Krebs cycle (matrix)
- oxidative phosphorylation (cristae)
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
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
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
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
What is anaerobic respiration
- synthesis of ATP in the absence of oxygen
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
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
Where does anaerobic respiration occur / what pathways are used to regenerate NAD
- In yeast cells / plant tissues
- ethanol pathway / alcoholic fermentation
- 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
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
- Glycolysis: glucose —> pyruvate (3C)
- net gain of 2 ATP
- 2 NADH produced
- Pyruvate (3C) undergoes decarboxylation
- forms ethanal (2C)
- CO2 produced
- 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
- NAD is regenerated
- allows glycolysis to continue
- to produce ATP
Why can the ethanol pathway not go on indefinitely
- ethanol is toxic
- reaction is irreversible
- remaining chemical potential energy in ethanol is wasted
What are the steps/stages of the lactate pathway / lactic fermentation (anaerobic respiration in mammals)
- 1 step reaction: pyruvate —> lactate
- reversible
- Glycolysis: glucose —> pyruvate (3C)
- net gain of 2 ATP
- 2 NADH produced
- Pyruvate acts as the H acceptor
- receives H from NADH
- pyruvate reduced to lactate / lactic acid
- catalysed by lactate dehydrogenase
- NAD is regenerated
- allows glycolysis to continue
- to make ATP
Why can’t the lactate pathway go on indefinitely
- lactate is toxic
- causes drop in pH / acidic
- but the reaction is reversible!
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
What happen in terms of oxygen uptake at rest
- rate of oxygen uptake at resting levels is low
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
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
What is oxygen debt
oxygen debt = volume of oxygen required to metabolise lactate accumulated during anaerobic respiration to CO2 and water after exercise
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
What are the similarities between the ethanol and lactate pathway
- Both occur when oxygen is absent/low in conc
- Both occur in cytoplasm
- Both involve glycolysis
- Both produce only 2 ATP net per glucose molecule
- Both involve usage and regeneration of NAD
What are the respiratory substrates
- Glucose
- essential respiratory substrate for neurones in brain, RBC, lymphocytes
- oxidised in glycolysis, link reaction, Krebs cycle
- Lipids
- converted to acetyl CoA (2C)
- oxidised in Krebs cycle
- 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
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
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
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
What are the energy values of each respiratory substrate
- carbohydrate = 15.8
- lipid = 39.4
- protein = 17.0
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
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
What is the function of RQ
- Shows the type of substrate being used in respiration
- Shows if anaerobic respiration is occurring
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
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
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
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
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
What are the adaptions of rice with submerged roots in water
- Rice tolerant to higher levels of alcohol
- Presence of aerenchyma
- Grow taller in response to flooding
- Leavers underwater have hydrophobic, corrugated surface
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
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
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
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
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
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
