Metabolic Processes

Energy In the Cell

Energy- the ^^ability to work or cause change^^ (chemical reactions)

\ There are 2 types:

1. Potential Energy(Ep)

^^Energy stored^^, causes change in the ^^future^^.

2. Kinetic Energy (Ek)

^^Energy of motion^^ causing change ^^now^^.

\ Free Energy(G)- ^^energy that is converted into a useful form^^ (released OR stored). ^^Available energy^^ in a system.

Entropy(S)- ^^energy that is lost as non-useful heat^^

Enthalpy(H)- ^^total energy^^ in a system

\ 1st Law of Thermodynamics:

^^Energy cannot be created or destroyed, only converted^^ from one form to another.

2nd Law of Thermodynamics:

^^Energy is loss during transformation^^. As energy is converted, entropy increases until no energy is left to do work.

\ Bioenergetics- the ^^study of energy transfer^^ in the cell

• Cell Respiration
• Photosynthesis

\ 2 Types of Metabolism

1. Catabolism

Degradation/^^breakdown of biological molecules so energy is released.^^ Therefore it is ^^exergonic^^ and tend to be ^^oxidation^^. Eg. $Cell Respiration.$

2. Anabolism

The ^^build up of biological molecules so energy is stored^^. Therefore it is ^^endergonic^^ and tends to be ^^reduction^^. Eg. $Photosynthesis$.

$Energy Input is needed for Anabolism.$

\ Simple Oxidation - a ^^one step chemical reaction that requires high temperature and releases large amounts of heat.^^

$Body Cells cannot do simply oxidation.$

^^Body cells use oxidative phosphorylation^^. It is a controlled oxidation. A ^^series of reactions.^^

\ \

Cell Respiration

Main goals:

1. Break 6C glucose into a 6CO2
2. More hydrogen to form 6H2O
3. Trap free energy to form ATP

\ $Cell Respiration occurs in 25-30 steps.$

\ It occurs in 4 steps:

1. Glycolysis
2. Pyruvate Oxidation
3. Krebs Cycle
4. Electron Transport Chain and chemiosmosis

\

STAGE 1: GLYCOLYSIS

Where? In the ^^cytoplasm^^.

What does it start with? ^^Glucose^^

What does it produce?

• ^^2 pyruvates(Krebs)^^
• ^^2 NADH(ETC)^^
• ^^4 ATP (^^$2 used, 2 left$^^)^^

\ Summary of Glycolysis:

1. ^^2 ATP used to prepare 6C glucose for splitting into two 3C^^ molecules. Substrate level phosphorylation is used.
2. ^^6C glucose splits into two 3C molecules.^^
3. ^^G3P is oxidated. It releases H+ and e- which are captured by NAD+→NADH^^. NADH moves on to the ETC.
4. ^^ATP is produced by removing the phosphates and producing 2 pyruvates (3C).^^

\

STAGE 2: PYRUVATE OXIDATION

Where? In the ^^matrix of the mitochondria.^^

What does it start with? ^^2 pyruvates^^.

What does it produce?($per cycle)$

• ^^1 Acetyl CoA^^
• ^^1 CO2^^
• ^^1 NADH^^

\ Summary of Pyruvate Oxidation:

1. ^^Pyruvate enters the mitochondria^^ from the cytoplasm.
2. ^^One carbon is removed with a release of CO2.^^
3. ^^Hydrogen is removed by NAD+→NADH.^^
4. ^^A CoA (coenzyme) becomes attached^^ to the remaining carbons which ^^creates Acetyl CoA.^^

\

STAGE 3: KREBS CYCLE

Where? In the ^^matrix of the mitochondria.^^

What does it start with? ^^Oxoloacetate (OAA) and Acetyl CoA^^

What does it produce? ($Per cycle)$

• ^^2 CO2^^
• ^^2 CoA^^
• ^^3 NADH^^
• ^^1 FADH^^
• ^^1 ATP^^

\ Summary of Krebs Cycle:

1. An ^^Acetyl CoA(2C) molecule joins a Oxaloacetate(4C) molecule to produce Citrate(6C).^^
2. ^^Isocitrate(6C) is oxidized into an Alpha-ketogluterate(5C) and then into Succenyl CoA(4C)^^ while ^^producing 2 NADH and 2 CO2.^^ All original carbons have been released at this point.
3. ^^Succenyl CoA(4C) is converted into succinate(4C) while producing an ATP and losing a CoA.^^
4. ^^Succinate(4C) converts to Fumerate(4C) and makes FADH2^^
5. ^^Fumerate(4C) is converted into Malate(4C) and then is converted back into Oxaloacetate(4C) while producing NADH.^^

STAGE 4: ÉLECTRON TRANSPORT CHAIN AND CHEMIOSMOSIS

Where? In the ^^cristae folds, the matrix and the inner membrane space of the mitochondria.^^

What does it start with? ^^NADH and FADH^^

What does it produce? ^^36-38 ATP^^

\ Summary of the ETC+C:

1. ^^NADH is oxidized in the matrix. High energy e- are released into the ETC.^^
2. ^^e- from NADH moves down ETC and use energy to pump H+ ions across the membrane^^. (3 pumps)
3. After the third pump the ^^e- is accepted by oxygen to form H2O.^^ This ^^allows for more e- to flow^^ down the chain.
4. ($CHEMIOSMOSIS$).The ^^high [H+] in the inner membrane are moved through ATP synthesis back into the matrix, low [H+]. This movement creates the energy needed to form ATP from ADP and Pi.^^

$Note: FADH produces 2 ATP because it only goes through 3 pumps whereas NADH produces 3 because it travels through all 3 pumps.$

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Summary of C.R

$Remember: NADH creates 3ATP, FADH creates 4ATP$

ATP YEILD

Glycolysis:

• -2 for activation
• +4 from substrate phosphorylation
• +4-6 (2NADH) from ETC (G3P→BPG)

^^Total: 6-8 ATP^^

Pyruvate and Krebs Cycle:

• +6 (2NADH) from Pyruvate→ Acetyl CoA
• +6 (2NADH) Isocitric→Alpha-Ketoglutaric
• +6 (2NADH) Alpha-Ketoglutaric→ Succinyl CoA
• +2 Succinyl CoA → Succinate
• +4 (2FADH) Succinate→Fumarate
• +6 (2NADH) Malate → Oxaloacetate

^^Total: 30 ATP^^

\

$Cellular respiration total ATP: 36-38 ATP$

\ What do we use the ATP for?

^^ATP is used immediately^^ to do things like; ^^make protein, muscle fibrils contractions, DNA+RNA assembly, nerve impulse trahissions, active transport and chemical reaction activation.^^

\ The Final Equation:

$C6H12O6 + 6O2 + 6H2O → 6CO2 + 12H2O + 36-38 ATP + Heat$

• ^^6O2 supplies 12O- at ETC^^
• ^^6H2O from krebs^^
• ^^6Co2 from pyruvates^^
• ^^24H+ and 24e- from NADH and FADH2^^
• ^^24H + 12O- → 12H2O at the end of ETC.^^

\

Fermentation (C.R)

What happens when no O2 is present?

1. ^^No O2= no final e- acceptor^^
2. ^^E- cannot move through 3rd pump (ETC)^^
3. No e- from carrier #2. Therefore ^^no e- movement in ETC, no [H] gradient, no ATP^^
4. ^^Prevent oxidation of NADH and FADH2^^ which limits reaction due to NAD+ and FAD not being available.

\ Alcohol fermentation in yeast

• the reduction of acetaldehyde into enthalpy allows the oxidation of NADH→NAD+
• The NAD+ produced is used in glycolysis, produces minimal ATP.

\ Lactic acid fermentation in muscle cells:

• reduce pyruvate to make lactic acid. Therefore NAD+ becomes available, glycolysis can continue.

\

Alternative Pathways (C.R)

Energy from proteins:

Eg. Alanine (amino acid)

• proteins must be digested into amino acids.
• The amino group is removed, this is called “deamination” and occurs in the liver.
• The amino group is converted into urea(urine) and is excreted.
• The carbon chain that you are left with is inserted into C.R pathway as pyruvate.
• $1 molecule of Alanine creates 15ATP$

\ Energy from fats:

Eg. Triglycerides

• Digested into fatty acids and glycerol.
• Glycerol goes into C.R pathway
• F.A are broken down for entry into pathway by using B-Oxidation.
• F.A are broken into 2C subunits
• Each cut made produces 5 ATP (1NADH, 1FADH)
• 2C carbons enter C.R as Acetyl CoA
• 6C F.A can produce 44ATP

\ How does 6C F.A produce 44ATP?

• 2 cuts =10ATP
• 1 Acetyl CoA: 3NADH, 1FADH and 1ATP = 12ATP. 12ATP x 3 (due to 3 Acetyl CoAs) = 36 ATP
• 36+10=46 ATP
• But remember you need 2 ATP to commence the breakdown of glucose in glycolysis
• Therefore: 46-2=44
• $44 ATP$

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Photosynthesis

Overall Results:

• %%Anabolic%% process(put things together)
• %%Chloroplast%%(site of photosynthesis)
• %%Light energy converted into chemical energy%% (potential energy)
• %%Enzymes and intermediate molecules%% to complete process

\ Light is converted into glucose in approximately 2 minutes after the leaf is exposed to light.

\ $6CO2 + 12H2O → light → C6H12O6 + 6O2 + 6H2O$

\ Co2: in through %%stomata%% (gas exchange)

H2O: %%roots, xylem%% (water transport cells)

Glucose: %%CO2 combined H+%% ions from water

O2: from %%water%%

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Chloroplast(PS)

\ Thylakoid: %%pigment molecules in bilayer. Traps light.%%

Stroma: %%enzymes for making glucose%%. %%Ribosomes for making proteins/enzymes. DNA that can duplicate on their own.%%

\ Thylakoid Membrane:

• %%traps light.%%
• Composed of a %%phospholipid bilayer.%%
• %%Protein pigment complex%%→proteins and pigment molecules embedded in the membrane that %%trap various wave lengths of light.%%
• Main pigment in plants is green due to chlorophyll(absorbs all but green light).
• Other pigment→carotenoids, xanthophylls (absorb different wave lengths)

\ Photosystem:

• %%Groups of 40-500 pigment protein molecules in the thylakoid membrane.%%
• %%Absorbs various wavelengths to make glucose.%%
• Half the molecules are chlorophyll, other half are pigment molecules called Accessory Pigments.

\ Chlorophyll:

• %%Primary light absorber.%%
• %%Porphyrin ring Containing Mg atom%%→similar to the heme ring structure of hemoglobin and cytochromes except they contain Fe.
• %%Long hydrocarbon tail called the phytol tail.%%

\ %%Both A and B chlorophyll are embedded in the thylakoid bilipid layer by the phytol tail%% being buried inside. The %%phytol tail is hydrophobic and the porphyrin ring is hydrophilic.%%

$Both types absorb red and blue-violet light, they reflect green wavelengths.$

\ %%Many double bonds alternate with single bonds. This allows the molecules to absorb light.%% It %%allows extra electrons of the double bonds to be excited%% when light photons hit them. This %%occurs in the porphyrin ring.%%

\ Chlorophyll A:

• %%Contains a CH3%% group
• Absorbs more %%violet light%%
• %%Main trap pigment. Only it can pass light energy onto another molecule that can store it as potential energy.%%

\ Chlorophyll B:

• %%Contains aldehyde%% group
• Absorbs more %%blue wavelengths%%
• Is an %%accessory%% pigment
• %%Absorbs light and passes it on to Chlorophyll A.%%

\ $There is normally 3x more chlorophyll A than B.$

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Light Reactions (PS)

1. Light dependant reactions

• %%light energy strikes the chlorophyll.%%
• Occurs in the %%thylakoid membrane.%%
• Involve %%photosynthesis%%→groups of chlorophyll molecules and accessory pigments.
• Use %%light energy to excite e- and create ATP and NADPH%% to power the production of glucose.

1. Light independent reactions

• %%Calvin cycle%%
• Occurs in the %%stroma%% of chloroplast.
• Involves a series of steps that %%combines CO2 into a glucose molecules.%% It %%uses ATP and NADPH from light dependant reactions.%%

\ Light dependant summary:

 1. %%Light strikes PS2 and excited e-%% in pigment molecules.  2. %%Excited e- are ejected from chlorophyll A to plastoquinone%% (e carrier).  3. %%PQ moves e- to the B6F%% complex which %%pulls H+ across the membrane.%%  4. %%e- move from B6F complex to plastocyanin%% (e carrier) and %%into PS1.%%  5. The %%H+ ions are moved through ATP synthase to create ATP.%%  6. %%E- lost from PS2 are replaced when Z enzyme splits water%%, releasing H+, O and e-.  7. %%PS1 absorbs light energy e- are excited.%%  8. %%e- move to ferredoxin%% (e carrier) %%then to NADP reductase%%. E- are %%used to reduce NADP to NADPH.%%  9. %%E- from PS2 replenish e- lost in PS1%%

10. %%ATP and NADPH move to the Calvin cycle%% to produce glucose.

\ Calvin Cycle summary:

1. Carbon Fixation

• %%CO2 is fixed to RuBP and produces 3PG%%. $Rubisco$ is the enzyme needed for this reaction.

1. Reduction

• %%3PG is reduced using ATP from light reactions to produce 1,3BPG.%%
• %%1,3BPG is reduced using NADPH from light reaction to produce G3P.%%
• $Some G3P is released from the cycle to make glucose.$

1. Regeneration

• %%Most G3P will react with ATP to regenerate the RuBP%% molecules the cycles started with.

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Cyclic and NonClycic(PS)

Noncyclic: electron flow generates a proton gradient for chemiosmotic ATP synthesis and NADPH. Normal light reaction.

Cyclic: e- excited in PS1 are taken back to the B6F complex by ferridoxin to pump H+ ions across the membrane. These ions can then be used to make ATP. PC recycles the e- back to PS1 and the cycle can continue.

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The Leaf and Photorespiration (PS)

Light energy transfers through the upper cuticle.

H2O transported by veins.

CO2 enters through lower cuticle/stomata

O2 leaves through lower cuticle/stomata

H2O(some) diffuses through lower cuticle/stomata

\ Photorespiration

• on hot days the stomata will close to help preserve H2O. That causes [CO2] to decrease and [O2] to increase.
• Rubisco likes CO2 when its present but will react with O2 if CO2 levels drop.
• When Rubisco reacts with O2 it creates a set of reactions that results in CO2 being released.
• Some plants lose up to 50% of their fixed carbon during Photorespiration.
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Alternative Pathways (PS)

C3, normal plants.

C4 Pathway (Hot/dry/tropical)

Uses Z locations

1. Mesophyll cells (photosynthetic cells)
2. Bundle Sheath Cells (area for Calvin cycle)

• uses special enzymes that only reacts with CO2. Pepcarboxylose.

CAM plants (cactus)

Uses different times of day.

• At night, the stomata opens, CO2 diffuses into plant.
• During the day, stomata closes and light reactions occur and create energy for Calvin cycle.

Factors affecting photosynthesis (PS)

• Light intensity
• Light wavelength
• Tempurature
• [CO2]
• [O2]
• Plant type

\ How can we measure the rate of photosynthesis?

Net CO2 uptake= CO2 taken in during photosynthesis - CO2 released during during mito respiration - CO2 released into a plant during photorespiration.

Bibliography

The Leaf and Photosynthesis

Anatomy of a leaf diagram. https://www.enchantedlearning.com/subjects/plants/leaf/

Alternative Pathways

C4 pathway diagram. https://biodifferences.com/difference-between-c3-c4-and-cam-pathway.html

CAM pathway diagram. https://www.botanicacuriosa.com/blog/crassulacean-acid-metabolism-cam-the-other-photosynthesis

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