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Title: BIOLOGY OCR F214
Description: OCR Board A2 Level Biology F214 SECTION 4: RESPIRATION
Description: OCR Board A2 Level Biology F214 SECTION 4: RESPIRATION
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BIOLOGY
F214: Communication, Homeostasis and Energy
1) Respiration
a) Outline why plants, animals and microorganisms need to respire, with reference to active
transport and metabolic reactions
i) Respiration – process whereby energy stored in complex organic molecules
(carbohydrates, fats and proteins) is used to make ATP
(1) Respiration takes place in all living cells
ii) Metabolic reactions – biochemical reactions that take place within organisms
iii) Anabolic reactions – metabolic reactions that build large molecules
iv) Catabolic reactions – metabolic reactions that break large molecules into smaller ones
v) Reasons why we need energy
(1) Active transport – moving ions and molecules across a membrane against a
concentration gradient
(2) Secretion – large molecules made in some cells are exported by exocytosis
(3) Endocytosis – bulk movement of large molecules into cells
(4) Synthesis – of large molecules from small ones eg
...
flagella in bacteria and undulipodia in eukaryotic
cells
(7) Activation of chemicals – glucose is phosphorylated at the beginning of respiration so
that it is unstable and can be broken down to release energy
b) Describe, with the aid of diagrams, the structure of ATP
i) ATP = phosphorylated nucleotide – a high-‐energy intermediate compound
ii) Each molecule consists of:
(1) Adenosine – adenine and ribose sugar
(2) Three phosphate groups
iii) ATP cycle
(1) ATP is hydrolysed to ADP + Pi – releasing 30
...
Nicotinamide adenine dinucleotide
(d) Made of two linked nucleotides
(e) One nucleotide contains adenine, the other contains a
nicotinamide ring that can accept up to two hydrogen
atoms (is reduced) or loses hydrogen atoms (is
oxidised)
(2) Function
(a) During glycolysis, the link reaction and Krebs cycle
– hydrogen atoms are removed from substrate
molecules (oxidation reactions)
(b) NAD helps dehydrogenase enzymes carry out these
reactions
(c) NAD carries the hydrogen atoms to the inner mitochondrial membranes
(d) Hydrogen atoms can be split into hydrogen ions and electrons
(e) Hydrogen ions then involved in oxidative phosphorylation – producing lots of ATP
(f) Delivery of hydrogens to the cristae reoxidises the coenzymes so they can
combine with more hydrogen atoms from the first three stages of respiration
ii) Coenzyme A (CoA)
(1) Made from pantothenic acid (B group vitamin), adenosine (ribose + adenine), three
phosphate (phosphoryl) groups and a cysteine (amino acid) group
(2) Carries acetate groups made from pyruvate (during Link Reaction) onto Krebs cycle
(3) Can also carry acetate groups that have been made from fatty acids or from some
amino acids onto Krebs cycle
e) State that glycolysis takes place in the cytoplasm
i) Hydrolysis – breaking down of large molecules to smaller molecules by adding water
ii) Glycolysis – metabolic pathway where each glucose molecules is broken down to two
molecules of pyruvate (the oxidation of glucose to pyruvate)
iii) Takes place in the cell cytoplasm in both prokaryotic and eukaryotic cells
iv) First stage of respiration common to both aerobic and anaerobic respiration
v) 2 ATP molecules are consumed in initial phosphorylation (adding phosphate) reactions
vi) 4 ATP molecules are produced by substrate level phosphorylation
vii) Therefore, products…
(1) Net gain of 2 ATP molecules per glucose molecule
(2) 4 hydrogen atoms transported to electron transfer chain (as 2 molecules of reduced
NAD (NADH2) form
(3) 2 molecules of pyruvate (pyruvic acid) produced for every glucose molecule
f) Outline the process of glycolysis
beginning with the
phosphorylation of glucose to
hexose bisphosphate, splitting
of hexose bisphosphate into two
triose phosphate molecules and
further oxidation to pyruvate,
producing a small yield of ATP
and reduced NAD
i) Glucose (hexose 6-‐Carbon
sugar) needs to be activated
ii) ATP hydrolysed to ADP + Pi
iii) Pi attaches to the carbon-‐6
iv) Glucose 6-‐phosphate produced
v) Another ATP is hydrolysed
vi) Phosphate attached to the
carbon-‐1
vii) Fructose 1,6-‐bisphosphate produced
viii) Molecule is symmetrical so it
has a high activation energy
(activated) and so is more
reactive
ix) Energy from the hydrolysed
ATP molecules activates the
hexose sugar
x) Hexose 1,6 bisphosphate
splits into two x 3-‐carbon
sugars – 2 x triose
phosphates
xi) Dehydrogenase enzymes are used to remove two hydrogen atoms from each triose
phosphate – oxidising it as electrons are lost with the hydrogen (anaerobic process)
xii) The hydrogen atoms are carried away by NAD (hydrogen acceptor)
xiii) NAD becomes reduced NAD (or NADH2) as it combines with hydrogen atoms
xiv) The rearrangement of the molecule makes new bonds
xv) Substrate level phosphorylation – energy released from making the new bonds makes
ATP from ADP + Pi (the Pi is free floating in the cytoplasm)
xvi) Another isomerisation means another ATP molecule is formed from ADP + Pi (this time
the Pi is from the triosphosphate)
xvii) Final products
(1) 2 x 3-‐carbon pyruvates – normally actively transported into the mitochondrial matrix
for the next stage of aerobic respiration (or lactate/ethanol in anaerobic conditions)
(2) 2 molecules of reduced NAD (to carry the hydrogen atoms to the inner mitochondrial
membranes to generate more ATP during oxidative phosphorylation)
(3) … Including 4 hydrogen atoms
(4) 4 ATPs – but a net gain of 2 ATPs
g) State that, during aerobic respiration in animals, pyruvate is actively transported into
mitochondria
i) During aerobic respiration in animals, each pyruvate is actively transported into a
mitochondrion
ii) Glucose itself cannot enter directly as there are no protein channels in the inner and
outer cell surface membranes of the mitochondria for it to enter through
h) Explain, with the aid of diagrams and electron micrographs, how the structure of
mitochondria enables them to
carry out their functions
i) Structure of mitochondria
– organelles found in
eukaryote cells that are
the sites of the Link
Reaction, Krebs cycle and
oxidative phosphorylation
(aerobic stages of
respiration)
(1) Envelope – inner and
outer phospholipid
membranes
(2) Smooth outer phospholipid membrane
(3) Inner phospholipid membrane folded into cristae – giving the inner membrane a
large surface area
(4) Intermembrane space – between the inner and outer membrane
(5) Matrix – semi-‐rigid and gel-‐like section enclosed by inner membrane consisting of a
mixture of proteins and lipids (also contains a looped mitochondrial DNA,
mitochondrial ribosomes and enzymes)
ii) Shape, size and distribution
(1) Changeable rod-‐shaped (can also be thread-‐like)
(2) Range between 0
...
0 micrometres in diameter, and 2-‐5 micrometres long (some
can be 10 micrometres long)
(3) Can be moved around cells by the cytoskeleton (microtubules)
(4) Mitochondria can be permanently positioned near a site of high ATP demand eg
...
Mammalian liver cell may contain up to 2500 mitochondria (20% of cell volume)
iii) Outer membrane
(1) Phospholipid composition (similar to membranes around other organelles)
(2) Can include channels or carries that allow the passage of molecules eg
...
stalked particles
(a) Large and protrude from the inner membrane into the matrix
(b) Allows protons to pass through them via the channel part of the enzyme
(6) FAD (flavine adenine dinucleotide) dehydrogenase enzyme
(a) FAD is bound to a dehydrogenase enzyme embedded in the inner membrane
(b) Hydrogen atoms accepted by FAD do not get pumped into the intermembrane
space – they stay back in the mitochondrial matrix
v) Matrix – site of the Link Reaction and Krebs cycle containing…
(1) Enzymes that catalyse stages in the Link Reaction and Krebs cycle
(2) Molecules of coenzyme NAD
(3) Oxaloacetic – 4 carbon compound that accepts acetate from the Link Reaction
(4) Mitochondrial DNA – some codes for mitochondrial enzymes and other proteins
(5) Mitochondrial ribosomes – where proteins are assembled
i) State that the link reaction takes place in the mitochondrial matrix
j) Outline the link reaction, with reference to decarboxylation of pyruvate to acetate and the
reduction of NAD
k) Explain that acetate is combined with coenzyme A to be carried to the next stage
i) Link Reaction – converts pyruvate to acetate, NAD is reduced
(NB: no ATP is produced)
ii) Link Reaction occurs in the mitochondrial matrix
iii) Pyruvate is actively transported into the matrix of
the mitochondria, across the inner and outer
mitochondrial membranes
iv) Decarboxylation of pyruvate occurs with the aid of
pyruvate decarboxylase enzymes (removing a
carboxyl group which eventually becomes CO2)
v) Dehydrogenation occurs with the aid of pyruvate
dehydrogenase enzymes
vi) NAD is reduced to form reduced NAD – accepting
the hydrogen atoms, taking them to the inner mitochondrial membrane to make ATP
during oxidative phosphorylation
vii) Coenzyme A (CoA) accepts acetate…
viii) Product – acetyl coenzyme A (2-‐carbon) to be carried to the next stage (Krebs Cycle)
ix) 2 Pyruvate + 2NAD+ + 2CoA à 2CO2 + 2 reduced NAD + 2 acetyl CoA
l) State that the Krebs cycle takes place in the mitochondrial matrix
m) Outline the Krebs cycle, with reference to the formation of citrate from acetate and
oxaloacetate and the reconversion of citrate to oxaloacetate (names of intermediate
compounds are not required)
n) Explain that during the Krebs cycle, decarboxylation and dehydrogenation occur, NAD and
FAD are reduced and substrate level phosphorylation occurs
i) Krebs Cycle – series of small steps catalysed by enzymes, oxidising acetate to CO2, NAD
and FAD are reduced and ATP is made by substrate level phosphorylation
ii) The Krebs Cycle takes place in the mitochondrial matrix
iii) Acetate is offloaded from coenzyme A (then free to collect more acetate)
iv) Citrate (6-‐C) is the first intermediate formed from the 4-‐carbon oxaloacetate (acceptor
molecule) and the 2-‐carbon acetate
v) Decarboxylation – 2 molecules of carbon dioxide are released per turn of the cycle,
catalysed by decarboxylase enzymes
vi) Dehydrogenation – 4 pairs of hydrogen atoms are released per turn of the cycle,
catalysed by dehydrogenase enzymes
vii) This leaves a 4 carbon compound which is changed into another 4 carbon compound
during which ATP is formed by substrate level phosphorylation
viii) The second 4 carbon compound is changed into another 4 carbon compound – a pair of
hydrogen atoms is removed and accepted by FAD (to produce reduced FAD)
ix) The third 4 carbon compound is further dehydrogenated and regenerates oxaloacetate –
another molecule of NAD is reduced
x) 4 pairs of hydrogen atoms are picked up by NAD and FAD (hydrogen acceptors) –
resulting in 6 NAD and 2 FAD both becoming reduced per glucose molecule (two turns)
xi) Amino acids and fatty acids can also be fed into the cycle
Product per molecule of glucose Link Reaction Krebs Cycle (2 turns of the cycle)
Reduced NAD
2
6
Reduced FAD
0
2
Carbon Dioxide
2
4
ATP
0
2
o) Outline the process of oxidative phosphorylation, with reference to the roles of electron
carriers, oxygen and the mitochondrial cristae
p) Outline the process of chemiosmosis, with reference to the electron transport chain, proton
gradients and ATPsynthase (HSW7a)
q) State that oxygen is the final electron acceptor in aerobic respiration
i) Oxidative Phosphorylation takes place on the cristae – on and within the inner
membrane of the mitochondrion
ii) Key Definitions
(1) Oxidative phosphorylation – formation of ATP by adding a phosphate group to ADP
in the presence of oxygen (the final electron acceptor)
(2) Chemiosmosis – the diffusion of ions through a partially permeable membrane –
specifically the flow of protons through channels of ATP synthase enzymes and
across the inner mitochondrial membrane, down the proton gradient from the
intermembrane space to the mitochondrial matrix
(3) Proton Motive Force – force generated by the flow of protons which changes the
configuration of parts of ATP synthase and causes ADP and Pi to join to make ATP
(4) Oxido-‐reductase enzyme – enzyme that catalyses a reduction reaction that is
coupled with an oxidation reaction
iii) Hydrogens are brought to the Electron Transport Chain (ETC) on the cristae of the
mitochondrion by the coenzymes NAD and FAD (reduced in the mitochondrial matrix)
iv) Hydrogens split forming H+ ions (protons) and electrons using dehydrogenase enzymes
v) The electrons pass along a series of electron carriers/cytochromes (protein complexes),
at three places in the chain the electrons drop to a lower energy level
vi) The first electron carrier is complex I (aka
...
NADH dehydrogenase)
vii) The last electron carrier is called cytochrome oxidase
viii) Each protein complex is associated with a co-‐factor – the iron ion which accepts
electrons to form Fe2+ but is oxidised to Fe3+ (alternately reduced and oxidised)
ix) As the electrons are transferred from one complex to the next along the series of
electron carriers, a small yet sufficient amount of energy is released
x) The coenzymes associated with complexes I, III and IV pump H+ ions through to the
intermembrane space
xi) The inner and outer membranes are impermeable to small ions so the proton gradient
(also a pH and electrochemical gradient) builds up as hydrogens ions accumulate in the
intermembrane space, creating a potential source of energy
xii) Chemiosmosis – protons pass back through the ion channels of the ATP synthase
enzymes, flowing down the proton gradient from
the intermembrane space to the matrix
xiii) A proton motive force is created
xiv) This drives the rotation of the headpiece on the ATP
synthase enzyme
xv) The force allows the phosphorylation of ADP to ATP
xvi) The electrons are passed from the last electron
carrier in the chain to molecular oxygen
xvii) Oxygen is the final electron and proton acceptor
(essential for aerobic respiration only as it is
required for oxidative phosphorylation)
xviii) Oxygen accepts an electron and a hydrogen joins
the electron – oxygen is reduced to water
xix) 4H+ + 4e-‐ + O2 à 2H2O
xx) The next electron can then move along the ETC
r) Evaluate the experimental evidence for the theory of chemiosmosis (HSW1)
i) More detailed structure of the mitochondria was only discovered in the 1960s
ii) 1978 – Peter Mitchell received the Nobel Prize for chemistry and chemiosmosis theory
iii) Modern researchers have treated isolated mitochondria by placing them in solutions of
very low water potential so that the outer membrane is ruptured – forming mitoblasts
iv) With strong detergent, they could also rupture the inner membrane and release the
contents of the mitochondrial matrix
v) Allowed them to work out that the Link Reaction and Krebs Cycle take place in the
mitochondrial matrix and the ETC are embedded in the inner membrane
vi) Lower pH in the intermembrane space than in the mitochondrial matrix
(1) High acidity is caused by an accumulation of H+ ions
(2) Intermembrane space has a low pH due to an accumulation of hydrogen ions here
(3) This fits with the idea that hydrogen ions are pumped out of the mitochondrial
matrix by active transport into the intermembrane space
vii) The more negative potential on the matrix side of the inner mitochondrial membrane
(1) A negative potential on the matrix side of the inner mitochondrial membrane proves
the existence of a proton gradient
(2) Proton gradient must have a high concentration of protons in the intermembrane
space and a lower concentration in the mitochondrial matrix
viii) No ATP made in mitoblasts (mitochondria stripped of their outer membrane)
(1) Stripping mitochondria of their outer membrane releases the contents of the
intermembrane space
(2) No ATP is produced as the intermembrane space is involved in the production of ATP
(3) The hydrogen ions cannot accumulate in the intermembrane space, producing a
proton gradient
ix) No ATP made if headpieces are removed from the stalked particles
(1) Shows that the headpieces of the ATP synthases have a role in the production of ATP
(2) During chemiosmosis, the headpieces act as rotors which spin due to the proton
motive force produced
(3) This force is produced when hydrogen ions pass back from the intermembrane space
into the mitochondrial matrix, allowing the phosphorylation of ADP to ATP
x) No ATP made in the presence of oligomycin
(1) Oligomycin is an antibiotic that blocks the flow of protons through the ion channel
part of the ATP synthase enzymes
(2) If the ion channel is blocked by oligomycin, no ATP is produced
(3) Shows that the ion channel has a role in the production of ATP during chemiosmosis
(4) The ion channel is required in chemiosmosis to allow the hydrogen ions to pass down
the proton gradient
(5) The movement of hydrogen ions across the cristae of the mitochondria, moving back
into the mitochondrial matrix, produces a proton motive force
(6) There is sufficient energy to form ATP from ADP and Pi (phosphorylation of ADP)
xi) Coenzymes within complexes I, III and IV can use energy released from the transfer of
electrons to pump hydrogen ions across the inner mitochondrial membrane to the
intermembrane spaces
(1) Coenzymes in the electron transfer chain can pump protons actively using energy
released from the inner mitochondrial membrane to the intermembrane space
(2) Hydrogen ions are able to accumulate in the intermembrane space creating a proton
gradient
(3) This proton gradient is essential for the protons to move back into the mitochondrial
matrix as this produces the proton motive force that allows the phosphorylation of
ADP to ATP
s) Explain why the theoretical maximum yield of ATP per molecule of glucose is rarely, if ever,
achieved in aerobic respiration
i) Per glucose molecule…
(1) Glycolysis – (net) 2 molecules of ATP
(2) Krebs Cycle – 2 molecules of ATP
(3) Reduced NAD = 10 molecules can theoretically yield 26 molecules of ATP during
oxidative phosphorylation
(a) Glycolysis – 2
(b) Link – 2
(c) Krebs Cycle – 6
(4) Reduced FAD = 2
(a) Glycolysis – 0
(b) Link – 0
(c) Krebs Cycle – 2
(5) Therefore the total yield per glucose molecule should = 30 molecules of ATP
ii) Roles of NAD and FAD
(1) Both provide electrons to the electron transport chain for oxidative phosphorylation
(2) Reduced NAD also provides hydrogen ions that contribute to the build up of a
protein gradient for chemiosmosis
(3) The hydrogen ions from reduced FAD stay in the matrix but can combine with oxygen
to form water
iii) Why the maximum yield per molecule of glucose is theoretical and rarely achieved
(1) Some protons leak across the mitochondrial membrane, reducing the number of
protons to generate the proton motive force
(2) Some ATP is used to actively transport the pyruvate into the mitochondria
(3) Some ATP is used to bring hydrogen from reduced NAD made during glycolysis, in the
cytoplasm, into the mitochondria
t) Explain why anaerobic respiration produces a much lower yield of ATP than aerobic
respiration
i) Anaerobic respiration – release of energy in the form of ATP from substrates, eg
...
when running where
the demand for oxygen is high (muscle contraction) and oxygen deficit is the result
(2) Reduced NAD must be reoxidised to NAD+
(3) Pyruvate is the hydrogen acceptor – accepting hydrogen atoms from reduced NAD
(4) NAD is now reoxidised and is available to accept more hydrogen atoms from glucose
during glycolysis
(5) This is catalysed by lactate dehydrogenase – reducing pyruvate to lactate too
(6) Glycolysis can continue, generating enough ATP to sustain muscle contraction
(7) Lactate produced is carried away in the blood, from the muscles, to the liver
(a) When more oxygen is available, the lactate can be converted back to pyruvate
(b) The pyruvate may then enter the Krebs Cycle via the Link Reaction or be recycled
to glucose and glycogen
(c) The reduction in pH due to the build of lactate will cause muscle fatigue as
enzyme activity in the muscles is reduced – not due to the excess lactate itself
(8) Cyanide – a respiratory poison
(a) Has no effect on the production of lactate from glucose
(b) Binds to cytochrome oxidase (the final carrier on the electron transport chain)
(c) Electrons cannot pass along the electron transport chain and NAD isn’t reoxidised
(d) Aerobic respiration will therefore stop
(e) Lactate fermentation pathway will be used instead
ii) Ethanol Fermentation
(1) Facultative anaerobe eg
...
In a 1 minute period, or
the time taken for the liquid to travel a given distance eg
...
8kJg-‐1
(1) Highest respiratory quotient = 1
...
0kJg-‐1 (only aerobic) (protein composition varies so
energy values can vary depending on different amino acid proportions)
(1) Respiratory quotient = 0
...
4kJg-‐1 (almost double the energy yield) (only aerobic)
(1) Respiratory quotient = 0
Title: BIOLOGY OCR F214
Description: OCR Board A2 Level Biology F214 SECTION 4: RESPIRATION
Description: OCR Board A2 Level Biology F214 SECTION 4: RESPIRATION