Biology: Energy & Equilibrium: Respiration

Respiration Photosynthesis EYA Corrections
Biology: Energy & Equilibrium

Respiration

Cellular Respiration
- Process by which chemical energy in organic molecules (e.g. glucose) is released
by oxidation; involves metabolic processes that allow organisms to obtain energy
from organic molecules
- Aerobic respiration occurs only in the p resence of oxygen
- Anaerobic respiration occurs in the a bsence of o xygen
- Main Function: Production of ATP, the primary energy currency of the cell
- Locations: Aerobic → Cytosol + Mitochondria; Anaerobic: Cytosol

By Jermaine Wong (2020)

Aerobic Respiration
In a eukaryotic cell, aerobic respiration involves 4 main stages that req. different
enzymes
1. Glycolysis in c ytosol
2. Link reaction in mitochondrial matrix
3. Krebs cycle in mitochondrial matrix
4. Oxidative phosphorylation involving electron transport chain (ETC) on cristae

- NADH: R educed nicotinamide adenine dinucleotide

- FADH2: R
educed flavin adenine dinucleotide

Suitability of ATP as an Energy Source
- Universally used: All cells and organisms use ATP as an energy source
- ATP is soluble + highly mobile → Can be transported readily to point of need
- Easy interconversion: ADP + Pi to ATP → ATP to ADP + Pi to release energy

Glycolysis (cytosol)
● glucose + 2 ADP + 2 Pi + 2 NAD+ → 2 pyruvate + 2 ATP + 2 NADH
- Oxidation of glucose (6C) to form two pyruvate (3C)
- Does not require O2 and does not release CO2
1. P
hosphorylation of Glucose
- Initial investment of 2 ATP molecules, where 1 phosphate group from each ATP is
used to phosphorylate glucose, to produce f ructose 1,6-bisp hosphate
- Phosphorylation activates glucose, making it more reactive and committing it to
glycolytic pathway + confers negative charge to glucose, making it impermeable
so it cannot diffuse across CSM (through transport proteins)
- Phosphofructokinase (PFK) catalyzes the addition of 2nd phosphate group
- Inhibited by excess ATP and/or citrate in cell → End-product inhibition (not
repression); stimulated by AMP and A DP → Allosteric activators
2. L ysis
- Phosphorylated 6C sugar, fructose 1,6-bisphosphate, is split into two 3C sugar
phosphates, triose phosphate* (TP) and dihydroxyacetone phosphate
- The two sugar phosphates are isomers and can be converted from one
form to another by isomerase; reaction favors TP
*also known as glyceraldehyde-3-phosphate (G3P) or phosphoglyceraldehyde (PGAL)
3. O
xidation by Dehydrogenation
- TP is oxidized by dehydrogenation; at the same time, coenzyme nicotinamide
adenine dinucleotide (NAD+) is r educed to N
ADH

- Energy released by highly exergonic redox reaction is used to add a 2nd
phosphate group to TP to form 1,3-bisphosphoglycerate
4. S
ubstrate-Level Phosphorylation
- 1,3-bisphosphoglycerate is dephosphorylated to form pyruvate, with 2
phosphate groups being transferred by enzymes to 2 ADP molecules to form 2
ATP
- Process where enzyme transfers phosphate group directly from substrate
molecule to ADP → Substrate-level phosphorylation
- Each TP yields 2 ATP + 1 NADH; Two TP yield 4 ATP + 2 NADH → Net gain of 2
ATP (4-2=2) + 2 NADH per glucose
Glucose + 2 ADP + 2 Pi + 2 NAD+ → 2 pyruvate + 2 ATP + 2 NADH

Link Reaction (mitochondrial matrix, x2)
● 2 pyruvate + 2 NAD+ + 2CoA → 2 acetyl CoA + 2 NADH + 2CO2
- Transport protein embedded in mitochondrial membrane translocates pyruvate
from cytosol into mitochondrion via active transport
- Within mitochondrial matrix, each pyruvate (3C) is decarboxylated, where a C is
removed from pyruvate through the r elease of CO2
- Oxidation by dehydrogenation occurs, yielding NADH and a 2C compound, which
combines with coenzyme A to form a cetyl coenzyme A (acetyl CoA)
- Acetyl CoA moves on into Krebs cycle, which also occurs in mitochondrial matrix



Krebs Cycle (mitochondrial matrix, x2)
● 2 acetyl CoA + 2 ADP + 6 NAD+ + 2 FAD → 4 CO2 + 2 ATP + 6 NADH + 2 FADH2
1. Krebs cycle takes place in matrix of mitochondria in presence of oxygen
2. Acetyl CoA (2C) combines with o xaloacetate (4C) to form citrate (6C)
3. Citrate (6C) is decarboxylated and dehydrogenated to form ɑ-ketoglutarate (5C)
and N ADH → O xidative decarboxylation (1 CO2 + 1 NADH)
a. Each decarboxylation step results in loss of C in the form of a CO2
4. Oxaloacetate (4C) is regenerated with one decarboxylation step to yield 1 CO2 +
three dehydrogenation steps to yield 2 NADH and 1 FADH2 + one substrate-level
phosphorylation step to yield 1 ATP
- Per acetyl CoA: 2 CO2 + 3 NADH + 1 FADH2 + 1 ATP → Per glucose (x2)...
- Electrons and protons originally from glucose molecule have now been
transferred to electron carriers NAD+ (NAD+ + 2H+ + 2e- NADH + H+) and FAD
(FAD + 2H+ + 2e- FADH2)
- All the carbon in glucose has been lost as CO2 (1x2 in link, 2x2 in Krebs)

Oxidative Phosphorylation (cristae, inner mitochondrial membrane)
- NADH and FADH2 from previous processes take part in oxidative phosphorylation
- Mechanism where exergonic reoxidation of reduced coenzyme molecules
NAD+ and FAD by O2 is coupled to formation of ATP, with electrochemical
proton gradient as an intermediate
- Crista is highly infolded to increase surface area to accommodate many electron
transport chains (ETC), series of electron carriers (mainly proteins) with increasing
electronegativity + many ATP synthases (stalked particles), enzyme complexes
involved in ATP synthesis
- Each electron carrier has a lower energy level than the one preceding it

- Electron carriers undergo reduction and oxidation as they accept and
donate electrons respectively
- Only occurs in the presence of oxygen
Functions of NAD+ & FAD
- Coenzymes NAD+ and FAD, reduced to form NADH and FADH2, serve as mobile
electron carriers to carry electrons and protons from oxidation of organic mol. in
glycolysis, link reaction and K rebs cycle to ETC on cristae of mitochondria
- NADH and F ADH2 r educe electron carriers of ETC and are r eoxidized
- [Steps 2 to 4 of Oxidative Phosphorylation] → H+ liberated in reoxidation of NADH
and FADH2 establishes p roton gradient
- Each NADH entering ETC yields 3 ATP and each FADH2 yields 2 ATP through
oxidative phosphorylation
- Regeneration of coenzymes NAD+ and FAD → Allows them to pick up more
electrons and protons from g lycolysis, link reaction and K rebs c
ycle
Process of Oxidative Phosphorylation
1. NADH and FADH2 from glycolysis, link reaction and Krebs cycle donate electrons
to (reduce) electron carriers of the ETC and are reoxidized in the process
a. NADH → NAD+ + 2e- (ETC) + H+ (matrix)
2. Electrons are p assed down electron carriers of increasing electronegativity
3. Energy released is coupled to pumping of H+ from matrix into intermembrane
space through electron carriers of ETC to generate proton gradient across cristae
a. Crista is impermeable to H+ → H+ accumulates in intermembrane space →
Proton-motive force
4. As H+ diffuses down its concentration gradient through ATP synthase back into
matrix, A DP is p
hosphorylated with inorganic Pi to form A TP via chemiosmosis
5. O2 acts as final electron acceptor at end of ETC, where it combines with
electrons and H+ to form water; ½O2 + 2e- + 2H+ → H2O (catalyzed by
cytochrome oxidase)


- Phospholipid bilayer of mitochondrial membranes is impermeable to H+ ions →
ATP passes through ATP synthase → Proton gradient generated across crista
- 90% of ATP produced via chemiosmosis (oxidative p) of aerobic respiration


Functions of Oxygen
1. Oxygen is final electron acceptor at end of ETC, where it combines with electrons
and p
rotons to form w ater (½O2 + 2e- + 2H+ → H2O)
2. By removing electrons, oxygen reoxidizes electron transport chain so that NADH
and FADH2 can continue to donate their electrons to the ETC → Allows oxidative
phosphorylation to c ontinue to produce ATP via chemiosmosis
3. This allows regeneration of coenzymes NAD+ and FAD → Allows them to pick up
more electrons and protons from g lycolysis, link reaction and K
rebs cycle
+
4. Reduction of O2 to water removes H from mitochondrial matrix → Helps create
proton gradient across cristae, needed for oxidative phosphorylation

Functions of ETC
- Generates proton-motive force to produce ATP + regeneration of coenzymes
NAD+ and FAD allows them to pick up more electrons and protons from…
Outline two of the functions of the protein complexes in the ETC. [2]
- ATP synthase couples diffusion of H+ down its conc. gradient from intermembrane space
into m
atrix via c
hemiosmosis to phosphorylation of ADP with inorganic Pi to form ATP
- Electron carriers that alternate between reduced and oxidized states as they accept and
donate electrons respectively → Flow of electrons in ETC in oxidative phosphorylation

Suggest how the structure of the ATP synthase allows it to carry out its function and to be
embedded onto the membrane. [2]
- ATP synthase has a specific EAS to catalyze phosphorylation of ADP with inorganic
phosphate to form ATP / It has a hydrophilic pore which allows protons to diffuse across
the cristae during chemiosmosis for phosphorylation of ADP with inorganic Pi to form
ATP
- Non-polar, hydrophobic R-groups form hydrophobic interactions with hydrophobic core of
the phospholipid bilayer of cristae → Allow it to be embedded; Polar, hydrophilic R-groups
interact with h ydrophilic phosphate heads of phospholipid bilayer of cristae

Explain how cyanide inhibition on cytochrome c oxidase affects oxidative phosphorylation. [2]
- Cyanide prevents reoxidation of electron carriers (electron carriers remain reduced)
- This prevents flow of electrons down ETC → No generation of proton gradient → No
chemiosmosis to produce ATP

ATP per Glucose
- Each NADH entering the ETC can yield 3 A TP; each FADH2 can yield 2 ATP
- FADH2 enters the ETC at a lower energy potential (passes its electrons to protein
further down the chain) → Electrons ‘fall’ down smaller energy difference → Less
energy released to pump H+ across crista → Fewer ATP produced
NADH FADH2 CO2 ATP
Glycolysis 2 - - 4-2 = 2
Link Reaction 2 - 2 -
Krebs Cycle 6 2 4 2
Oxidative Phosphorylation - - - 10(3)+2( 2) = 3

4

Total 10 2 6 38

- Depending on cell type, less than 38 ATP per glucose molecule may be produced
as mitochondrial membrane is impermeable to NADH generated by glycolysis
- Electrons and protons of NADH passed to either NAD+ or FAD in mitochondrion
via a shuttle system → If passed to FAD, only 2 ATP produced instead of 3
- 2ATP (glycolysis) + 2ATP (Krebs cycle) formed via substrate-level
phosphorylation
- 10NADH and 2FADH2 enter ETC to produce 34ATP via oxidative phosphorylation

Explain how the rate of glycolysis may be regulated by PFK. [3]
- When A TP levels are h igh, it binds to allosteric site of PFK
- This alters 3D conformation of EAS, such that its substrate is no longer complementary
in shape and charge to EAS → This stabilizes inactive conformation of PFK, which has a
lower affinity for substrate
- This results in a d ecrease in rate of glycolysis due to end-product inhibition

Is there a net change in concentrations of NAD+ and NADH in the whole process of respiration?
[3]
- No net change: NAD+ is reduced to NADH when it accepts electrons and protons during
glycolysis, l ink reaction, and Krebs cycle
- During oxidative phosphorylation, NADH is oxidized to regenerate NAD+ as it donates
electrons to e lectron transport chain

Mitochondria contain DNA and ribosomes. State the significance of their presence. [4]
- DNA carries genetic information for p roteins to be synthesized in mitochondria
- Ribosomes are site for translation, so that essential proteins like respiratory enzymes and
electron carriers of ETC can be produced
- DNA allows m itochondria to replicate independently of nucleus

Anaerobic Respiration ( cytosol)
- In the absence of oxygen, there is no final electron acceptor to accept electrons
from the ETC, so oxidative phosphorylation; NADH and FADH2 can no longer
donate electrons to the ETC
Explain how aerobic respiration may be affected by a decrease in oxygen availability. [2]
- Less aerobic respiration: Oxygen is the final electron acceptor at the end of the electron
transport chain (ETC) → Decrease in oxygen → Decrease in oxidative phosphorylation
- Decrease in regeneration of NAD+, FAD+; decrease in glycolysis, link reaction, Krebs cycle

-In absence of oxygen, anaerobic respiration takes place in cytosol, with glycolysis
followed by fermentation (alcohol, lactic acid)
- Fermentation regenerates NAD+ from NADH → Ensures steady supply of
NAD+ for g
lycolysis to continue to produce 2
ATP per glucose
- Since O2 is absent, ethanal/p
yruvate becomes the final electron acceptor
+
to regenerate NAD via alcohol/lactic acid fermentation respectively
Functions of Anaerobic Respiration
- Produce a small yield of energy: Glycolysis produces 2 ATP per glucose molecule
→ 1/19 the amount of ATP generated in aerobic respiration

- Regenerate NAD+ from NADH: In glycolysis, oxidation of glucose to yield 2 ATP
reduces NAD+ to NADH; for glycolysis to continue, processes in alcohol and lactic
acid fermentation regenerate NAD+

Alcohol Fermentation
➢ Occurs in yeast and certain bacteria; used in wine and beer production
1. Pyruvate decarboxylase reduces pyruvate (3C) to ethanal/acetaldehyde (2C) via
decarboxylation with the release of CO2
2. NADH produced during glycolysis has to be regenerated to NAD+ for glycolysis to
continue to produce 2 ATP each round
3. Alcohol dehydrogenase reduces ethanal, the final electron acceptor, to ethanol,
while removing H+ from NADH to r egenerate NAD+
- End products are 2 ATP and 2 ethanol per glucose molecule

Lactic Acid Fermentation
➢ Occurs in mammals when muscle contracts → High demand for ATP → Increased rate of
glycolysis depletes limited supply of NAD+ → Oxidative phosphorylation cannot replenish
NAD+ fast enough → Anaerobic respiration is additional system to regenerate NAD+
(occurs concurrently); used in cheese and yoghurt production
➢ Significance: Muscle contraction can take place in the absence of O2: Oxidative
phosphorylation c annot occur, but glycolysis can to meet additional ATP demand
1. Lactate dehydrogenase reduces pyruvate, the final electron acceptor, to lactic
acid/lactate, while removing H+ from NADH to r egenerate N AD+
- End products are 2 ATP and 2 lactate per glucose molecule → No CO2 produced
as no decarboxylation involved, unlike alcohol fermentation

- During strenuous exercise, lactic acid accumulates in muscles faster than it can be
removed → Excessive accumulation of lactic acid → Muscle fatigue
- Lactate still contains large part of the energy originally in glucose → Carried from muscle
cells to liver in blood → Converted back into pyruvate by liver cells → Enter link reaction
and Krebs cycle of aerobic respiration to produce more ATP

- Liver cells contain large number of mitochondria as they require large amounts of

energy due to numerous metabolic processes taking place
- In presence of O2, pyruvate is transported into mitochondria and oxidized to CO2 and
water; In a
bsence of O2, pyruvate remains in cytosol and is reduced to lactate

Compare the fate of pyruvate in anerobic respiration in yeast and mammalian cells. [4]
- In yeast, alcohol fermentation where pyruvate is reduced to ethanol via ethanal; while in
mammalian cells, lactic acid fermentation where pyruvate is reduced to l actic acid
- In yeast, pyruvate undergoes decarboxylation step to produce 1 molecule of CO2 before it
is reduced; while in mammalian cells, pyruvate does not undergo decarboxylation step
- In yeast, alcohol dehydrogenase reduces ethanal to ethanol; while in mammalian cells,
lactate dehydrogenase reduces p yruvate to lactic acid
- Similarity: In both alcohol and lactic acid fermentation, NADH is reoxidized to regenerate
NAD+ to allow glycolysis to continue to generate more ATP

Explain how ATP is produced in lactic acid-producing bacteria when oxygen is absent. [3] /
Explain how ATP is formed in the absence of oxygen.
- Pyruvate is reduced by l actate dehydrogenase to form lactate
- H+ removed from NADH → N AD+ is regenerated to allow glycolysis to c ontinue
● ATP is produced by substrate-level phosphorylation in glycolysis → Net gain of 2
ATP per glucose

*Explain the small yield of ATP under anaerobic conditions in yeast and mammals. [8]
- Anaerobic respiration took place in the a bsence of oxygen;
- Oxygen serves as the f inal electron acceptor in electron transport chain
- Without oxygen, oxidative phosphorylation, link reaction and Krebs cycle
subsequently stop, so bulk of ATP is not produced
- NAD+ c annot be regenerated from N ADH in mitochondrion
- Anaerobic respiration takes place in cytosol via g lycolysis and fermentation
➢ Initial investment of 2 ATP per glucose molecule during phosphorylation of
glucose to fructose 1,6-bisphosphate by phosphofructokinase (PFK)
➢ Total yield of 4 ATP per glucose molecule when 1,3-bisphosphoglycerate is
dephosphorylated to form pyruvate in s ubstrate-level phosphorylation
➢ Net of 2 ATP produced via substrate-level phosphorylation in glycolysis per
glucose molecule oxidized
● In yeast, pyruvate is reduced by pyruvate decarboxylase to ethanal, with release
of CO2 in decarboxylation, which is further reduced by alcohol dehydrogenase to
ethanol with r egeneration of NAD+
● In mammals, pyruvate is reduced by lactate dehydrogenase to lactate with
regeneration of NAD+
- NAD+ regenerated in both processes ensures steady supply of NAD+ for glycolysis
to c ontinue

Explain why less glucose is required to maintain cell metabolism under aerobic conditions than
under anaerobic conditions. [3]
- Under aerobic conditions, complete breakdown of glucose produces 38 ATP per glucose
as compared to 2 ATP per glucose under a naerobic conditions

- Under aerobic conditions, link reaction and Krebs cycle produce NADH that will be
oxidized and regenerated by electron transport chain during oxidative phosphorylation,
generating additional ATP
- Under anaerobic conditions, glycolysis only produces net 2 ATP for each glucose oxidized
and NAD+ is only regenerated through fermentation to allow only g lycolysis to continue

Other Substrates in Respiration

Photosynthesis

Photosynthesis
- Conversion of light energy to chemical energy that is stored in glucose and other
organic compounds
- Photoautotrophs (energy source is light, carbon source is inorganic CO2)
- Light-Dependent Reaction: Photochemical events where energy from visible light
is converted to high energy intermediates (NADPH) + ATP, used to drive reactions
in light-independent reaction (Calvin cycle) of photosynthesis
- Light-Independent Reaction: Carbon fixation (fixing C in form of CO2 into sugar
mol) using NADPH + ATP from light-dependent reaction → Continues so long as
products of light-dependent reactions have not run out
- ATP (adenosine triphosphate): Highly mobile energy carrier, can easily release
energy via single-step hydrolysis, can easily be reformed from ADP + Pi
- Simplified equation: 6CO2 + 6H2O → (light energy) C6H12O6 + 6O2
- Significant to life on earth as a source of organic carbon + oxygen for aerobic
respiration

Leaf: Location of Photosynthesis
- Palisade mesophyll cells contain 3 to 5 times as many chloroplasts as spongy
mesophyll cells + they are closer to the upper epidermis where more sunlight is
received → Efficient use of light for photosynthesis

- Leaf is thin for CO2 to diffuse quickly through intercellular air spaces of spongy
mesophyll layer into palisade mesophyll cells, which have large SA for efficient
gaseous exchange
- Long axis of palisade mesophyll is perpendicular to leave surface to minimize
amount of light scattered and absorbed by cell wall before it reaches chloroplasts
- Chloroplasts in peripheral cytoplasm of palisade + spongy mesophyll cells move
via cytoplasmic streaming (circular flow of cytoplasm) for optimal capture of light

Chloroplast: Site of Photosynthesis

- Chloroplast: Plastid (membrane-bound org.) containing photosynthetic pigments
- Chloroplast envelope (double membrane) separates inside of chloroplast from
cytoplasm of cell
- Inner membrane encloses stroma, a concentrated solution of enzymes, including
those required for carbohydrate synthesis
- Stroma surrounds internal membrane system of thylakoids, which are fluid-filled
membranous sacs → Contains photosynthetic pigments (chlorophyll, carotenoids)
- Stacks of thylakoids form grana (sing. granum), which are linked by intergranal
lamellae (sing. lamella)

Light-Dependent Reaction (thylakoid membrane)
- Photosynthesis makes use of only visible light → Not all wavelengths (e.g. green
is reflected off leaf surfaces, making them appear green)
Photosynthetic Pigments
- Each type of photosynthetic pigment on thylakoid membranes in chloroplasts has
a certain molecular structure to absorb light strongly at specific wavelengths
- Chlorophyll a (most abundant) exists as several forms (P700, P680) with
different absorption peaks → Only pigment that participates directly in
photosynthesis
- Chlorophyll b is an accessory pigment that channels light energy absorbed to
chlorophyll a → Participates indirectly in photosynthesis

- Carotenoids are a class of accessory pigments (e.g. carotene, xanthophylls) →

Participate indirectly in photosynthesis + absorb and dissipate excess light energy
in p
hotoprotective role + add color to fruits, flowers to help in dispersal, pollination
- Spectrophotometer measures ability of pigment to absorb different wavelengths
of light (directs beams of light of diff wavelengths through solution of pigment +
measures fraction of light transmitted at each wavelength)


Absorption & Action Spectra

- Absorption Spectrum: Graph showing a pigment’s l ight absorption vs wavelength
- Action Spectrum: Graph showing effectiveness of different wavelengths of light in
stimulating photosynthesis, indicated by r ate of photosynthesis
- Each pigment has its own specific spectrum
+ different number, height, breadth of peaks
+ hardly absorb any green light wavelengths
- Action spectrum is similar in wavelengths of
peaks + trough, but does not exactly match
absorption spectrum for chlorophyll a
- Chlorophyll b, carotenoids broaden spectrum
of wavelength over which photosynthesis
can occur by channeling energy absorbed to
chlorophyll a

Photosystems

- Chlorophyll molecules cluster together to form photosystems located on
thylakoid membrane of chloroplast; a photosystem consists of…
- A reaction center, a protein complex containing 2 special chlorophyll a
molecules + a molecule called the primary electron acceptor…
- surrounded by a number of light-harvesting complexes, each consisting of
photosynthetic pigments (chloro a, b, carotenoids) bound to particular
proteins → Allow light to be harvested over wider range of wavelengths
- Photosystem II (PSII) and photosystem I (PSI) function sequentially with PSII first,
in light-dependent reactions of photosynthesis
- PS II contains 2 P680 special chlorophyll a molecules in its reaction center
that most effectively a bsorb light of wavelength 6 80nm
- PS I contains 2 P700 special chlorophyll a molecules in its reaction center
that most effectively a bsorb light of wavelength 700nm
- P680 and P700 identical: Association with different proteins in thylakoid
membrane affects electron distribution = Diff light-absorbing properties
Light-Dependent Reaction: Non-cyclic / Cyclic → Non-cyclic LDR is p redominant route



Photoactivation (thylakoid membrane)
1. When a photon of light at 680 and 700nm is absorbed by an accessory pigment
molecule in light-harvesting complex of PS II/I, one of its electrons is excited to a
higher energy state
2. As excited electron returns to its ground state, energy released is passed on to the
next pigment molecule and excites another electron in it
3. This resonance transfer of energy occurs until it reaches one of the two special
chlorophyll a molecules (P680, P700) in the reaction center of p hotosystem II/I
4. An excited electron is emitted from the special chlorophyll a molecule (P680,
P700), leaving an electron “hole” in P680/P700 of PS II/I * [non-cyclic]
5. This electron is c aptured by the primary electron acceptor in the r eaction center
If an isolated solution of chlorophyll is exposed to
UV light, fluorescence is seen. If chloroplast extract
is exposed, fluorescence is not seen.
- Excited electron is captured by PEA in RC,
which is only present in chloroplast extract
- Excited electron is lost and does not return
to ground level → No fluorescence

Non-Cyclic LDR (PS II & PS I, thylakoid membrane)

- Light drives synthesis of ATP + NADPH (reduced NADP+) → Nicotinamide
adenine dinucleotide phosphate, a coenzyme that acts as a high energy electron
carrier
Photoactivation at PS II
Photolysis of Water
6. *[non-cyclic] Water is split by an enzyme (H2 O → 2e- + 2H+ +½O2) in presence of
light → Donates its e- one by one to P680 chlorophyll a molecules + releases O2 as
byproduct + r eleases H+ that accumulates in thylakoid space (proton gradient)
First ETC from PS II to PS I
1. Each excited electron is passed down electron carriers of increasing
electronegativity along the electron transport chain (ETC) from PS II to PSI
2. Energy released in redox reactions along ETC is coupled to pumping of H+ from
stroma into t hylakoid space to establish proton gradient across thylakoid mem.
Concurrently, Photoactivation at PS I
6. *[non-cyclic] Electrons from PS II that have reached the end of the first ETC fill the
electron “hole” in P 700 of PS I
Second ETC from PSI to NADP+
1. Splitting of water by an enzyme releases H+ → H+ diffuses down its concentration
gradient through A TP synthase from thylakoid space to stroma
2. Electrons from PS I are passed down a second ETC and transferred to NADP+,
which combines with H+ to form NADPH (NADP+ + 2e- + H+ → NADPH) in stroma
→ This reduction is catalyzed by NADP+ reductase
3. NADP+ is the final electron acceptor in the n on-cyclic light dependent reaction

*Role of NADP+ & NADPH in Photosynthesis
- NADP+ is a c oenzyme which carries both p rotons and high energy electrons
+
- NADP is final electron acceptor in non-cyclic LDR in thylakoid membrane →
Reduced to NADPH
- Electrons carried in NADPH are used in the Calvin cycle in the stroma of the
chloroplast to r educe glycerate phosphate (GP) to triose phosphate (TP)
- ATP [from LDR] is required in reduction stage of Calvin cycle
- When GP is reduced to TP, NADP+ is regenerated to carry out its role as a mobile
electron carrier from the light dependent reactions




Cyclic LDR (PS I, thylakoid membrane)

- Cyclic LDR only produces ATP as Calvin cycle uses more ATP than NADPH
- Electrons from PS I are passed to 1st ETC instead of 2nd ETC when ratio of NADPH
to NADP+ is too high → too little NADP+ to accept electrons or when high ATP req.
Photoactivation at PSI
6. Each excited electron is transferred to middle and passed down electron carriers
of i ncreasing electronegativity along the (ETC from P S II to PSI
7. Electron flow is cyclical, passing from PS I (P700 is electron donor) to ETC and
going back to PS I (P700 is electron acceptor)

Photophosphorylation
➢ Process of generating ATP from ADP and Pi via proton-motive force generated across
thylakoid membrane of chloroplast using light energy absorbed during light dependent
reactions of photosynthesis
1. Energy released in redox reactions along ETC is coupled to pumping of H+ from
stroma into thylakoid space → Establish proton-motive force (gradient) across
thylakoid membrane
2. As H+ diffuses down its concentration gradient through ATP synthase back into
stroma, ADP is phosphorylated with inorganic phosphate (Pi) to form ATP via
chemiosmosis

Proton Gradient
- Photolysis: Splitting of water → Accumulation of H+ in thylakoid space
- Reduction of NADP+ to NADPH by NADP+ reductase: Uptake of H+ from stroma →
Accumulation of H+ in thylakoid space
ATP Synthase: Couples diffusion of H+ down its conc. gradient from thylakoid space into
stroma via c
hemiosmosis to p hosphorylation of A DP with i norganic Pi to form A
TP

What would happen to pH of thylakoid space and stroma if you shine/turn off light?
- Shine Light: pH in thylakoid space drops (more H+), pH in stroma increases
- Turn Off Light: pH gradient is abolished
If thylakoid membrane is disrupted and permeable to H+, how would ATP synthesis be affected?
- H+ cannot accumulate in thylakoid space → Proton gradient x established across
thylakoid membrane → No diffusion of H+ back into stroma through ATP synthase → No
ATP
If ATP can be generated through LDRs, why do plant cells require chloroplasts and mitochondria?
- ATP produced by photophosphorylation in chloroplasts sufficient for Calvin cycle alone →
More ATP produced by respiration in mitochondria to fulfil other energy needs of cell

Variegation: Absence of chloroplasts/photosynthetic pigments causing white/lighter patches on
leaf where no photosynthesis occurs → Lower potential to fix CO2 on sugars → Grow more slowly

*Functions of Thylakoid Membrane in Photophosphorylation
- Provides large SA to embed many photosynthetic pigments for light absorption + many
electron carriers in ETC and ATP synthase for ATP production
- Maintains sequential arrangement of photosystems and electron carriers of ETC in
increasing electronegativity f or flow of electrons
- Maintains proton gradient for ATP synthesis since hydrophobic core is impermeable to H +
- Allows ATP synthase to be embedded in correct orientation for H+ to diffuse down its
concentration gradient from thylakoid space to stroma via chemiosmosis

Cyclic vs. Non-Cyclic Photophosphorylation
Cyclic Non-Cyclic
Products Produces only ATP Produces ATP, NADPH and O2
Photosystem Involves only PS I Involves PS II and PS I
Source of Electron donor is P700 in PS I; does x Electron donor is water; involves
Electrons involve splitting of water by enzyme splitting of water by enzyme
Pathway of Electron flow is cyclical (from PS I Electron flow is in one direction (from
Electrons through 1st ETC back to PS I) water through 2 ETC to NADP+)
Final Electron
P700 in PS I NADP+
Acceptor

Describe how photophosphorylation differs from oxidative phosphorylation.



State the similarities between ATP production in mitochondria and chloroplasts and suggest why
these similarities exist. [5]
- ATP production via oxidative phosphorylation in mitochondria and photophosphorylation
in chloroplasts both take place on m embranes (cristae in m, thylakoid membranes in c)
- Energy released from flow of e along ETC used to generate proton gradient
-
- ATP synthase on both organelles couple diffusion of H+ down its concentration gradient
to p
hosphorylation of ADP with i norganic Pi to ATP via chemiosmosis
- Presence of series of electron carriers in ETC pump H+ to form proton gradient across
membranes of both organelles
- According to endosymbiotic theory, they have prokaryotic origins → Circular DNA, 70S
ribosomes, A TP synthase, similar e lectron carriers

Light-Independent Reaction: Calvin Cycle (stroma)
- Prerequisites: NADPH + ATP [products of LDR] + CO2 → Reduces CO2 to carbs

Carbon Dioxide Fixation
1. Inorganic carbon dioxide combines with ribulose bisphosphate (RuBP, 5C) to
form an unstable 6C intermediate that immediately splits to form 2 glycerate
phosphate (GP, 3C) molecules
2. This reaction is catalyzed by R uBP carboxylase/oxygenase (RuBisCO)
Reduction
1. NADPH [fr LDR] is r educing power used to r educe GP to triose phosphate (TP)
2. ATP [fr LDR] is source of energy required
3. Triose phosphate (TP, 3C) is first sugar formed in photosynthesis and end product
of Calvin cycle
Regeneration of RuBP
1. 5 TP molecules are used to regenerate 3 RuBP for carbon dioxide fixation cycle to
continue → This requires 3 ATP [from LDR]
- The net synthesis of 1 TP molecule requires 3 CO2 to be fixed (6+3 ATP, 6 NADPH)
- 2 TP molecules are used to form 1 glucose molecule (hexose sugar)


Similarities between Krebs & Calvin Cycle

1. Involves regeneration of the initial compound: Oxaloacetate in Krebs cycle and ribulose
bisphosphate (RuBP) in Calvin cycle
2. Involves redox (oxidation-reduction) reactions
3. Involves coenzymes as electron and proton carriers: NAD+ and FAD in Krebs cycle and
NADPH in Calvin cycle

LDR vs. LIR of Photosynthesis
Light-Dependent Reactions Calvin Cycle
Location Thylakoid membranes of chloroplast Stroma of chloroplast
Reactions - Requires light for photoexcitation of e- - Does not require light
- (Non-)cyclic photophosphorylation - Requires RuBisCO for carbon fixation
- Reduction
Reactants H2O, NADP+, ADP, Pi NADPH, ATP, CO2
Products NADPH, ATP TP (G3P)
Byproducts O2 -

Suggest reasons for changes in quantities of GP and RuBP in Fig. 2A, resulting from change from
light to dark conditions. [6] → W hy RuBP↓ while GP↑ + difference in magnitude of change
- In the dark, light-dependent r eaction does not occur → ATP and N ADPH n
ot produced
- Carbon fixation continues as it does not require ATP or NADPH → Amount of RuBP
decreases as it is carboxylated and converted to GP
- GP is not reduced to TP due to lack of ATP and NADPH → Lack of TP for regeneration of
RuBP → RuBP regeneration is slowed
- GP is not reduced to TP due to lack of ATP and NADPH → GP accumulates in the dark
- QD: Increase in GP is t wice the decrease in RuBP as 2 GP is formed from every 1 RuBP
In Fig. 2B, when CO2 concentration is reduced from 1% to 0.003%, explain why (i) the quantity of
RuBP increases. [2]
- At low CO2 concentration, less RuBP is used in carbon fixation as CO2 acceptor → RuBP↑
- GP is reduced to T P, which is regenerated to form RuBP → A ccumulation of RuBP [input]
(ii) the quantity of GP decreases. [2]
- GP, using ATP and NADPH, is reduced to T P and eventually to RuBP → GP↓
- Less RuBP is f ixed due to low CO2 concentration → Less GP replacement [input]


Limiting Factors of Photosynthesis

- The rate of a chemical process is limited by the factor nearest its minimum value,
which d
irectly affects the process if its magnitude is changed

Light Intensity: Low

- In the light-dependent reactions of photosynthesis, light excites electrons in
photosynthetic pigments to higher energy state through photoactivation
- In low light intensities, rate of photosynthesis increases linearly with increasing
light intensity; rate of increase decreases as other factors become limiting
- Light intensity is rarely limiting during daylight hours (not major limiting factor)
- Light on clear summer’s day is ~100,000 lux, whereas light saturation for
photosynthesis is reached at ~10,000 lux
- At light compensation point, photosynthetic rate equals respiration rate, with no
net change in O2 and CO2 → CO2 given out during respiration is equivalent to CO2
fixed during carbon fixation in Calvin cycle of photosynthesis → No net gain in dry
mass and no growth
- Unique to plants as they photosynthesize and respire at same time; higher light
compensation point = higher light intensity req. for photosynthesis
- Light Quality: Rate of photosynthesis is high under wavelengths of light of about
700 nm (red light) and about 4 70 nm (blue light), Light Duration (photoperiod)

Explain why the CO2 assimilation rate levels off at higher light intensity. [3]
- At higher light intensity, photosynthesis is occurring at maximum rate
- Chloroplasts are s aturated with light
- Light is n o longer a limiting factor and other factors like temperature are limiting factor


Explain why the CO2 assimilation rate is negative at the lowest light intensity. [3]
- At lowest light intensity, l ow photosynthesis occurs
- There are fewer photons of light for photoactivation of chlorophyll molecules in LDRs of
photosynthesis → Less ATP and NADPH produced for Calvin cycle
- Respiration occurs at a h igher rate than photosynthesis (more CO2 produced than used)
- This is occurring b elow the l ight compensation point

CO2 Concentration: Low
- In Calvin cycle, CO2 is used in carbon fixation of RuBP, catalyzed by RuBisCO
- As atmospheric concentration of CO2 is low at 0.03% to 0.04%, while optimum
concentration is 0.1% to 0.5%, CO2 is a (major) limiting factor of photosynthesis
- Increasing CO2 concentration increases rate of photosynthesis
- Increases frequency of effective collisions b/w CO2, RuBP and RuBisCO →
Increases rate of formation of enzyme-substrate complex → Increases
rate of carbon fixation → Increases rate of Calvin cycle

Temperature: Low
- Both LDR and to a larger extent, Calvin cycle, are enzyme-controlled
- Rate of reaction doubles for every 10ºC rise in temperature until ~35ºC; beyond
40ºC, enzymes start to denature, decreasing rate of photosynthesis
- Increasing temperature increases rate of photosynthesis
- Increases kinetic energy of CO2, RuBP and RuBisCO → Increases
frequency of effective collisions between them → Increases rate of
formation of enzyme-substrate complex → Increases rate of carbon
fixation → Increases rate of Calvin cycle

Other Factors: O2 Concentration (NOT limiting factor)
- When CO2:O2 ratio is low, RuBisCo accepts O2 as competitive inhibitor
➢ Both O2 and CO2 are complementary in conformation to EAS, so O2 binds to
RuBisCO and b locks its EAS → CO2 c annot bind → Lower rate of c arbon fixation
➢ At higher light intensity, more O2 is produced by the light-dependent reactions,
further increasing inhibition by O2 of Calvin cycle
- Bright, hot, dry days → Stomata on leaf close to restrict water loss → Less CO2
enters leaf, [CO2] decreases + More photosynthesis, [O2] increases
- Oxygenase function of RuBisCO splits RuBP into GP (3C) and glycolate (2C); the
2C compound is exported to peroxisomes and mitochondria, where it is broken
down into CO2 in photorespiration, which does not generate ATP


e.g. Planning: How 3 Factors (light, CO2, temp.) affect Rate of Photosynthesis

+ +
Role of NAD and NADP


EYA Corrections

Multiple Choice Questions




Open-Ended Questions

Describe how the mitochondrion aids in the reproductive cycle of HIV.
- It synthesizes energy in the form of ATP during aerobic respiration for the translation of
viral proteins + for the m
ovement of vesicles/membrane
Explain how genetic changes led to the formation of the HIV strain in humans.
- From the chimpanzee, mutations of the SIV genome led to changes in the conformation of
gp120 → gp120 has more precise binding site for C D4 receptor of T-helper cell
- Antigenic shift allows virus to jump from chimpanzee to human host

- UV triggers switch from lysogenic to lytic cycle
- Prophage e xcised from bacterial host genome and phage genes activated
- Phage synthesizes enzymes and p hage components after induction event
- Host cell l ysis to release new phages

In the Warburg Effect, cancer cells exhibit increased rate of glycolysis, but do not progress to
oxidative phosphorylation even when oxygen is abundant. This results in overproduction of
Molecule X, which leads to acidification of the extracellular environment of the tumor.
(i) Identify Molecule X. Explain its formation and how it leads to acidification.
- Lactic Acid: Glucose undergoes glycolysis to produce p yruvate
- In lactic acid fermentation, pyruvate is reduced to lactic acid by lactate dehydrogenase
to regenerate NAD+ from NADH for glycolysis to c ontinue
(ii) Suggest why cancer cells require more glucose than non-cancer cells.
- Glycolysis generates net 2 ATP per glucose molecule while oxidative phosphorylation,
which does not occur in cancer cells, generates 3 6 ATP per glucose molecule
- Cancer cells need more glucose to obtain the same amount of ATP + need more ATP to
undergo u ncontrolled cell division

Explain the ratios of (C+T)/(A+G) for maize and humans.
- The ratios are approximately 1:1: A and G are purines while C and T are pyrimidines →
There is complementary base pairing between a purine and a pyrimidine
Suggest why the (A+T)/(C+G) ratios are different between maize and humans.
- Maize and humans are different organisms with different DNA sequences

Suggest an advantage of using E. coli in the experiment.
- Reproduces rapidly + Easy to g row in culture + Easy to e xtract DNA



5-methylcytosine in the coding region of a gene does not change the structure of the encoded
protein. Suggest a reason for this.
- Modification does not modify DNA nucleotide sequence → There is still complementary
base pairing between DNA and free ribonucleotides during transcription → Same mRNA
codon sequence → No effect on amino acid sequence/p rimary structure of protein


Biology: Energy & Equilibrium: Respiration

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Respiration​ ​Photosynthesis​ ​EYA Corrections

Biology: Energy & Equilibrium

By Jermaine Wong (2020)

- NADH: R ​ educed ​nicotinamide​ adenine dinucleotide

By Jermaine Wong (2020)

By Jermaine Wong (2020)

By Jermaine Wong (2020)

By Jermaine Wong (2020)

By Jermaine Wong (2020)

Glycolysis 2 - - 4-2 = ​2

Oxidative Phosphorylation - - - 10​(3)+​2(​ 2) = 3

By Jermaine Wong (2020)

Total 10 2 6 38

By Jermaine Wong (2020)

By Jermaine Wong (2020)

- Liver cells contain large number of mitochondria as they require ​large amounts of

By Jermaine Wong (2020)

By Jermaine Wong (2020)

By Jermaine Wong (2020)

- Carotenoids are a class of accessory pigments (e.g. carotene, xanthophylls) →

By Jermaine Wong (2020)

Absorption & Action Spectra

By Jermaine Wong (2020)

By Jermaine Wong (2020)

Non-Cyclic LDR​ (​PS II & PS I​, thylakoid membrane)

By Jermaine Wong (2020)

By Jermaine Wong (2020)

Cyclic LDR​ (​PS I​, thylakoid membrane)

By Jermaine Wong (2020)

Products Produces only ATP Produces ATP, NADPH and O​2

Photosystem Involves only PS I Involves PS II and PS I

By Jermaine Wong (2020)

By Jermaine Wong (2020)

Similarities between Krebs & Calvin Cycle

Location Thylakoid membranes of chloroplast Stroma of chloroplast

Reactants H​2​O, NADP​+​, ADP, P​i NADPH, ATP​, CO​2

Products NADPH, ATP TP (G3P)

By Jermaine Wong (2020)

Limiting Factors of Photosynthesis

By Jermaine Wong (2020)

By Jermaine Wong (2020)

By Jermaine Wong (2020)

By Jermaine Wong (2020)

By Jermaine Wong (2020)

By Jermaine Wong (2020)

By Jermaine Wong (2020)

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Respiration Photosynthesis EYA Corrections

- NADH: R educed nicotinamide adenine dinucleotide

Glycolysis 2 - - 4-2 = 2

Oxidative Phosphorylation - - - 10(3)+2( 2) = 3

- Liver cells contain large number of mitochondria as they require large amounts of

Non-Cyclic LDR (PS II & PS I, thylakoid membrane)

Cyclic LDR (PS I, thylakoid membrane)

Products Produces only ATP Produces ATP, NADPH and O2

Reactants H2O, NADP+, ADP, Pi NADPH, ATP, CO2