Metabolic Processes

Energy In the Cell

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

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There are 2 types:

  1. Potential Energy(Ep)

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

  1. Kinetic Energy (Ek)

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

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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

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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.

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

  • Cell Respiration
  • Photosynthesis

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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.

  1. 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.

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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.^^

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Cell Respiration

Main goals:

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

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Cell Respiration occurs in 25-30 steps.

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It occurs in 4 steps:

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

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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^^)^^

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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).^^

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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^^

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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.^^

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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^^

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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^^

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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^^

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Cellular respiration total ATP: 36-38 ATP

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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.^^

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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.^^

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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.

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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.

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Lactic acid fermentation in muscle cells:

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

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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

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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

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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

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

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

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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)

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

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

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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)

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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.

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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.%%

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%%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.

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%%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.%%

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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.%%

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Chlorophyll B:

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

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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.%%

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

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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

Anatomy of a Leaf (EnchantedLearning.com)

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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.

    C4 photosynthesis cycle. Biodiffrences.com

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.

    CAM photosynthesis pathway. Botanicacuriosa.com

Factors affecting photosynthesis (PS)

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

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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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