IB Biology HL: Topic 8

8.1 METABOLISM
METABOLIC PATHWAY
Metabolism: total sum of reactions that happen in an organism

INCLUDES

ANABOLIC REACTIONS:
- building molecules
- requires energy
- condensation reaction
- eg photosynthesis

CATABOLIC REACTIONS
- Breaking molecules down
- hydrolysis
- releases energy
- cellular respiration

METABOLIC PATHWAY: The sequence showing the intermediate steps of metabolic

reaction

- Most metabolic reactions require ENZYMES and carried out in the compartment of
cell where the necessary enzymes are located
eg photosynthesis occurs in chloroplast

INDUCED FIT MODEL = conformation change

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ACTIVATION ENERGY

ENDERGONC REACTION
- requires energy
- products have more energy than
reactants
- eg photosynthesis
- probably anabolic
(enzymes lower the activation energy)

EXERGONC REACTION
- releases energy
- products have less energy that
reactants
- eg cellular respiration
- probably catabolic

Enzymes LOWER activation energy by placing molecules in favourable and

weakening bonds - making it more likely reaction take place

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MECHANISM OF ENZYME ACTION
1. Surface of substrate makes contact with active site of enzyme
2. Conformational change of active site
3. Formation of temporary complex called enzyme substrate complex
4. The citation energy is lower substrate is altered
5. product gets released from active site
6. unchanged enzyme is free to work on other substrate molecule

INHIBITION
The act of decreasing/eliminating the effect of an enzyme

COMPETITIVE INHIBITION
• A molecule that is shaped similarly to substrate sits in the active sites and blocks
the substrate from binding with enzyme
• Can be reversed
• Can be overcome by increasing substrate concentration

EXAMPLE:
Antibiotics
If we take a medicine that destroys bacteria (living cell) it is destroying all living cells
We don’t it to kill our own cells and so instead we inhibit some of the enzymes the
bacteria needs

• Bacteria have enzyme that produce folic acid which they need for building cell
wall
• Sulphanilamide are drugs that block active sites of enzyme - unable to
procure folic acid
• Because humans don’t use enzyme it doesn’t harm us

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NON-COMPETITIVE INHIBITION (Allosteric inhibitors)
• Something that binds to enzyme not near the active site
• This changes shape of Active Site - making it on functional
• Could be reversed

EXAMPLE:
MERCURY
- Binds easily to proteins including enzymes (very bad)
- Causes a change in shape, making enzymes unable to bind to substrate and
catalyse reactions
- BIOACCUMULATION (Building up of mercury from fish)

END PRODUCT INHIBITION

• Prevents cell from making more of something when it already has sufficient
amount; example fo Negative feed back loop in cells
• When end product reaches a certain concentration, that end product binds to
allosteric site of first enzyme, stopping metabolic pathway.

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EXAMPLE:
E-COLI BACTERIA
- Need 5 enzymes to produce the amino acid isoleucine from the amino acid
called threonine
- If Isoleucine is already present in high amounts, it inhibits the first enzyme an
process stops

ENZYME KINETICS

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8.2 CELL RESPIRATION
REDOX REACTIONS
• Oxidation - Loss of electrons (and energy)
• Reduction - gain of electrons (and energy)
• Happen simultaneously
• Electron carriers easily accept and give electrons
- NAD
- NADP
- FAD

AEROBIC AND ANAEROBIC RESPIRATION

CELL RESPIRATION OVERVIEW

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1) GLYCOLYSIS
o -2 ATP spent
o +4 ATP produced
o NET GAIN: 2 ATP
o CYTOPLASM

STARTS with 6 carbon glucose

ENDS with 2 NADH and net gain
of 2 ATP

• Starting with 6c glucose

molecule
• to get glycolysis started we need
to invest in energy (ATP)
1. Phosphorylation: steal two
phosphates one from each ATP
and attach them to the ends of
the glucose molecule; it makes
the molecule unstable
2. Lysis: Splitting the glucose
molecule in half
3. An inorganic phosphate group
attaches onto the ends of each
split glucose molecule
4. Oxidation: (reduction is
happening at the same time -
REDOX); steal energy/
electrons from the split glucose
(NOT phosphates at end) to
reduce NAD to NADH + H; also
use the left over phosphates at
each end to re phosphorylate
the 2 ADP into 2 ATP
5. We have now made pyruvate

TAKE PYRUVATE INTO KREBS CYCLE

But we have to go through the link reaction to get to the Krebs cycle

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2) LINK REACTION
Pyruvate gets DECARBOXYLATED
o removing a carbon
o releases carbon dioxide
o MITROCHONDIRA MATRIX
-STARTS with 2 pyruvate (3c)

-ENDS with 2 Acetyl-CoA (2c); 2 CO2; 2 NADH

1) 3 carbon pyruvate - if we release one carbon it turns into CO2, now we have 2
carbons.
2) Whenever you break bond between 2 carbons it releases energy; use that
energy to reduce NAD to NADH - pyruvate getting oxidised and NAD is getting
reduced.
3) We attach CO enzyme A (Co-A) to the 2 carbons left to make ACETL-CoA

Now the Acetyl-CoA can now enter into the KREBS CYCLE

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3) KREBS CYCLE
o MITROCHONDRIA MATRIX
STARTS with 2 ACetyl-CoA
ENDS with 4 CO2; 6 NADH; 2 FADH2; 2 ATP

1) the acetylecoa is going to get picked up by a 4c compound (oxaloacitate)

2) When the 4c Compound picks up the two carbons from acetyl CoA it becomes a
6c Compound; CoA comes off
3) Decarboxylation: Release 1 carbon from 6 carbon compound (to make co2) to
have 5c compound (oxidation)
4) when you you decarboxylate something, that is going to break a bond =
oxidation - So that mean we can reduce NAD to NADH
5) AGAIN decarboxylate to form CO2 - now left with 4c compound + NAD reduced
to make NADH
6) The 4c compound goes back into the cycle as we have used up all the Carbons
from the glucose
• As it re-enters back to the beginning of cycle it can again be oxidised
however it loses electrons but NOT carbon which then we can reduce NAD
to NADH+
• We can further reduce another electron carrier to FAD to FADH2
• Further reduce ADP to ATP
THIS CYCLE HAPPENS TWICE AS WE WERE ABLE TO MAKE 2 AcetlyCoA

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4) ELECTRON TRANSPORT CHAIN & CHEMIOSMOSIS

o HAPPENS IN CRISTAE of MITOCHONDRIA

o The NADH and the FADH2 are then going to come to the electron transport
chain that is embedded into the membrane
o STARTS with NADH; FADH2; OXYGEN
o ENDS with H2O + 34 ATP

1. They are going to donate their electrons; NADH = oxidised - donating to one of
the protein carriers which gets reduced
2. The protein is then going to donate the electron to the next one in chain and so
on
- Every time the protein receives the electron it is getting reduced and the
one that passed it on is getting oxidised (series of REDOX reaction)
- When its getting passed on to carrier to carrier not all the energy
associated with that electron will be passed on
- Some energy will be lost in transport chain
- Some is going to be used to pumped actively hydrogen ions from
matrix to inter membrane space - very small and so we can produce
a high amount of H ions really quickly
- then allow the H ions aka protons to diffuse passively through ATP
synthase (enzyme)

3. This part of enzyme acts as a turbine as H ions diffusing into it and that kinetic
energy is enough to catalyse the ADP into ATP
4. NAD and FADH2 donate their electrons to electron transport chain it passes
through carrier to carrier and releases enough energy to pump H ions.

5. At end of chain oxygen is that final electron accepter it is electronegative

(accepts any electrons). - now that it has this extra electron it is enough to
form some covalent bonds. so in the matrix you have all these H ions we can
now combine it to oxygen = H2O

OXYGEN IS REDUCE MOLECULE


GLUCOSE OXIDISED

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Inter membrane space

2
1
3
MATRIX

FEATURES OF MITOCHONDRIA
Contain the electron transport chain
and ATP synthase for that step we call
oxidised phosphorylation.

Skinny - so we can
accumulate high con. of H ions
and building con. to get them
to passively diffuse back into
ATP synthase.

Has all the enzymes that we

need for things like Krebs Folds which increase
cycle surface areas to have
more electron transport
Contains transport proteins for being chains
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able to get pyruvate into mitochondria
in link reaction
OUTLINE THE PROCESS OF GLYCOLYSIS (6marks)
• occurs in cytoplasm
• Hexose is phophorlated using ATP
• Hexose phosphate is split into two triode phosphates
• Oxidation by removal of Hydrogen (DO NOT ACCEPT HYDROGEN IONS/
PROTONS)
• Conversion of NAD to NADH (+H)
• Net gain fo two ATP
• Pyruvate produced at the end of glycolysis

DESCRIBE THE PROCESS THAT OCCUR IN THE MITOCHONDRIA WHEN

OXYGEN IS PRESENT (8Marks)
• Pyruvate gets decarboxylated and that gives CO2 and reducing NAD to
NADH
• That two carbon mol (acetyl group) combines with CoA
• Acetyl CoA is what enter the Krebs cycle
• 2 CO2 molecule removed (as waste)
• NADH molecule is reduced
• for each turn of Krebs cycle produce: 3NADH and 1 FADH2
• 1 ATP formed per pyruvate each turn ( by substrate level phosphorylation)
• Reduced NAD/NADH and FADH2 enter electron transport chain
• Oxidative phosphorylation uses energy released by ETC to synthesis ATP
• As electron ,oves along ETC protons/H - ions move into inter membrane
space
• Create an area o high concentration
• ATP is synthesised by the passive movement of H ions back across
membrane through ATP synthase
• ATP synthesised by Chemiosmosis
• ETC reduces oxygen

EXPLAIN HOW CHEMICAL ENERGY FOR USE IN THE CELL IS GENERATED

BY THE ELECTRON TRANSPORT CHAIN (ETC)
• Chemical energy = ATP
• NAD and FAD get reduced
• NADH produce in glycolysis/link reaction/Krebs cycle
• ETC is in Mitochondria inner membrane (cristae)
• As the get passed from carrier to carrier it releases energy
• Electron from ETC at end is accepted by Oxygen
• Protein in inter membrane act as proton pumps
• Protons pumped into inter membrane space
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• Energy from electrons used pump protons into inter membrane space
• ATP Synthase is enzyme located in inner membrane space (cristae)
• Energy release as protons pass down the gradient through app synthase
• App synthase coverts ADpt o ATP
• Oxidation phosphorylation is ATP production using energy form oxidising foods

OVERVIEW OF SUBTOPIC 8.2

• Outline that cell respiration involves the oxidation and reduction of electron
carriers.
• State that phosphorylation of molecules makes them less stable.
• Outline that in glycolysis, glucose is converted to pyruvate in the cytoplasm.
• Explain how glycolysis gives a small net gain of ATP without the use of
oxygen.
• Explain how, in aerobic cell respiration, pyruvate is decarboxylated and
oxidised to form acetyl coenzyme A in the link reaction.
• Analyse diagrams of the pathways of aerobic respiration to deduce where
decarboxylation and oxidation reactions occur.
• Explain how, in the Krebs cycle, the oxidation of acetyl groups is coupled to
the reduction of hydrogen carriers, liberating carbon dioxide.
• State that energy released by oxidation reactions is carried to the cristae of the
mitochondria by reduced NAD and FAD.
• Explain how the transfer of electrons between carriers in the electron transport
chain in the membrane of the cristae is coupled to proton pumping.
• Explain how, in chemiosmosis, protons diffuse through ATP synthase to
generate ATP.
• Outline that oxygen is needed to bind with free protons to form water to
maintain the hydrogen gradient.
• Explain how the structure of the mitochondrion is adapted to the function it
performs.
• Outline that electron tomography can be used to produce images of active
mitochondria.
• Annotate a diagram of a mitochondrion to indicate the adaptations to its
function.

Youtube videos by Alex lee have helped me understand this topic! Go check
out his videos if your struggling :)

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8.3 PHOTOSYNTHESIS
Light energy turns into chemical energy
Cells synthesise organic molecules form inorganic molecules in the presence of
sunlight

Photosynthesis = 2 step process

- light dependent reaction converts light energy from the sun into chemical energy
(ATP)
- Light independent reactions use the chemical energy to synthesise organic
compounds (eg. carbohydrates)

LIGHT-DEPENDENT REACTIONS
Non-cyclic photophosphorylation - to produce ATP
- Happens in the thylakoids of inter membrane space
▪ Light absorbed by chlorophyll —> releases energised electrons that are used
to produce ATP (chemical energy)
▪ electrons donated to carrier molecules (NADP+), which is used (with ATP) in
the light independent reactions 
▪ electrons lost from chlorophyll are replaced by water, which is split (photolysis)
to produce oxygen and hydrogen
▪ Ultimate goal to make glucose

Excite
electron from Reaction
Chl. A

Stroma

ATP
ETC synthase

LUMEN
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Pigments
Photosystem II: (produces ATP requires ATP synthase)
- happens first: Light absorbed by photosystem II, and embedded in them are
pigments - light passes to each pigment to pigment until lands at reaction centre
- In reaction centre is the molecule chlorophyll A
- When photon hits chlorophyll A it is going to excite an electron from chlorophyll A
- That electron is passed down an electron transport chain and it is going to use the
energy from electron and pump H ions from stroma to lumen of thylakoid (high
con. h ions)
- Chlorophyl A lost electron is replaced by water, which is split (photolysis) to
produce Oxygen & Hydrogen ions (water splitting enzyme)

Photosystem I: (produce NADPH requires NADP reductase)

- Is going to absorb its own photon and passes through each pigment and reaches
the reaction centre
- Chlorophyl A molecule is excite by photon and this electron is going to move
down ETC
- and that electrons energy is going to be harvested by enzyme called NADP
reductase and reduces NADP to NADPH
- Chlorophyll A lost electron replaces electron by non cyclic photophosphoralation
- Using this energy in ETC to pump H-ions into thylakoid space
- These H-ions diffuses into ATP synthase (acting as protein channel and enzyme
as the turbines at the end turns and catalyses ADP to ATP)

PHOTOPHOSPHORALTION
Formation of ATP using light energy in the light dependent reaction of
photosynthesis
- Happens after PS II
- Non-cyclic (electron doesn’t return to PSII)

CALVIN CYCLE
Goal to produce glucose
We need 6 carbons; 6 hydrogens; 6 oxygens to make 1 molecule of glucose

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LIGHT-INDEPENDENT REACTIONS

STARTS:
RUBP - Ribulose Biphosphate
[it has 5 carbons]

- It is going to pick up CO2 molecule from air

- attaches to RUBP molecule (now we have 6c); This is catalysed by Rubisco -
ribulose biphosphate carboxyLASE (ENZYME) - carbon fixation
- This 6c compound is split into 3c = 12 glycerATE 3 phosphate/G3Ps
- These GPs are going to get reduce into triosephosphate (12TP)
- Reduction phase: However we need energy! = The NADPH (is spent) is going to
get oxidised to NADP and ATP is oxidised to ADP = the G3P is going to get
reduced to TP (this has a lot of energy because we just spent NADPH and ATP)
- 12TP = 2 of the TP’s they will leave cycle and they are going to form GLUCOSE
- 12TP - 2TP = 10TPS x 3 carbons = 30 carbons
- The 30 carbons go back to the beginning of the cycle because remember we
started with 6 RUBPS which has 5 carbons = 5x6 = 30 carbons!
- RUBP Regeneration: HOWEVER, we need to spend energy for this regeneration
process. We made ATP in the light dependent reaction so we have some to spend
(ATP reduces to ADP)

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 Clear - no need for
CHLOROPLAST pigment; STROMA =all
the enzymes need for
Calvin cycle
Contains the chlorophyll
(rejecting green light)

Evidence for
endosymbiosis (how
chloroplast and
mitochondria formed).
It was once its own living
thing. They also have a
loop of DNA which Flat thylakoid discs -
supports this theory, increases surface area for
membranes = small
space which allows
production of H-ions at
high conc.

Compare ATP generation in respiration and photosynthesis

Similarities

Both producing ATP Photosynthesis uses light energy (light

energy used to excite electron for the ETC
Both using ETC that contains enzyme ATP Respiration: electrons are donated from
synthase (NADH2) electron carriers that were
reduced when carbon compounds are
oxidised
Both rely on building up high conc. H-ions Photosynthesis H-ions pumped through
and have them diffuse passively through lumen and diffuse back out in stroma
ATP synthase
Respiration H-ions are pumped into the
inter membrane space and diffuse back into
the matrix

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 "
" " " "

•
thylakoid
e-

.
:* . .

Lamella

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