Biology Unit 3 Test

Biochemistry (metabolism, respiration, photosynthesis, lipid metabolism)

Laws of Thermodynamics

1. Conservation of energy, not created or destroyed but transferred

2. Energy transfers increase randomness (∆S)

∆G= …

∆H-T∆S

-∆G

• exergonic

• spontaneous

• favorable

• ex: ice melting

+∆G

• endergonic

• nonspontaneous

• unfavorable

• ex: climbing up

-∆H

• exothermic

• net loss in release

• ex: burn CH4

+∆H

• endothermic

• net gain in consumption

• ex: ice in water

-∆S

> organized

ex: synthesis

+∆S

> randomness

ex: break down

ATP and Energy Coupling

ATP hydrolysis is thermodynamically favored so it is paired with endergonic reactions to drive those reactions forward

ATP+ H2O —> ADP + Pi (∆G = -7.3 kcal/mol)

ex: Glucose + ATP → Glucose-P + ADP (-7.3 kcal/mol) →Glucose-P + Fructose →Sucrose + Pi. (+ 6.5 Kcal/mol)

Factors affecting enzymes

1. temperature (affects 3-D shape)

2. pH (affects 3-D shape)

3. salt concentration (affects 3-D shape)

4. cofactors (activates enzymes)

5. Substrate concentration (enzyme needs right substrate for rxn)

Vmax

highest velocity of the enzyme (maximum rate of reaction). Achieved when all the enzyme active sites are filled with the substrate

Km

is the substrate concentration at which the rate of reaction is half its maximum. indicates the [S] at which half the enzyme active sites are filled with substrates

Regulation of enzyme activity

1. Activators (+) and inhibitors (-)

2. Allosteric regulation

3. Feedback regulation

4. Chemical modification (chemically modified by themselves or by other enzymes to make them active or inactive)

Activators

bind to the enzyme, changing its conformation with a positive effect on its activity

Inhibitors

binds to the enzyme and changing their conformation, resulting in a reduced enzyme activity

Competitive inhibitors

compete with the substrate for the same active site on the enzyme. In the case of a competitive inhibitor, a higher concentration of the substrate can be added to overcome the competition

Km increases

Non-competitive inhibitor

binds to the protein at some place other than the active site, change the conformation of an enzyme and make it less active or inactive. Adding more of the substrate does not overcome the inhibition.

Vmax decreases

Uncompetitive inhibitor

Bind to the active site after the substrate binds to the enzyme

lowers Vmax and increases Km

Allosteric regulation

• complex enzymes with separate catalytic (binding to substrate) and regulatory (binding to activator or inhibitor) subunits

• An activator or inhibitor binds to the enzyme and changes its conformation to an active or an inactive form, respectively

• They respond to the substrate concentration in a sigmoid (s) fashion.

feedback regulation

The end product of a biosynthetic pathway or an intermediate of another but related pathway inhibits an earlier enzyme and stops the whole pathway

Keq= [products]/[reactants] when…

∆G = 0

what are examples of exergonic reactions?

respiration and passive transport

what are examples of endergonic reactions?

photosynthesis and active transport

glycolysis: place, inputs, outputs, key steps, key enzymes, # of ATP made (SLP or OP)

1. cytoplasm

2. Glucose, ADP pi, and NAD⁺

3. 2 Pyruvate, 2 ATP, 2 NADH

4. Steps 1 (G+ATP→GP+ADP) and 3(F6P+ATP→FI6BP+ADP)

5. Hexokinase (step 1) and Phosphofructokinase (step 3)

6. 2 ATP made by substrate level phosphorylation

Summary of glycolysis

Net inputs: Glucose, ADP pi, and NAD⁺

comes from: food, ATP hydrolysis, oxidative phosphorylation

net outputs: pyruvate, ATP, NADH

Go to: acetyl CoA formation, used in cytoplasm, goes to oxidative Phosphorylation via Electron shuttle

Acetyl CoA formation: place, inputs, outputs, key steps, key enzymes, # of ATP made (SLP or OP)

1. Mitochondrial membrane

2. CoA, 2 NAD⁺, 2 Pyruvate

3. 2 NADH, 2 Acetyl CoA, 2 CO2

4. none

5. pyruvate dehydrogenase

6. none

what happens when there is too much Acetyl CoA?

Any excess acetyl CoA formed from the glycolysis of carbohydrates are converted to fats for storage

Krebs Cycle: place, inputs, outputs, key steps, key enzymes, # of ATP made (SLP or OP)

1. Mitochondrial Matrix

2. 6 NAD⁺, 2 FAD, 2ADP 2pi, 2Acetyl CoA

3. 6 NADH, 2 FADH, 2 ATP, 4CO2, 2 CoA

4. 1 (citrate synthesis) and 3 (Oxidative decarboxylation of isocitrate)

5. Citrate synthase (step 1) and Isocitrate dehydrogenase (step 3)

6. 2 ATP substrate level phosphorylation

Oxidative phosphorylation: place, inputs, outputs, key steps, respiratory poisons , # of ATP made (SLP or OP)

1. Mitochondrial matrix

2. NADH, FADH₂, ADP pi, O2

3. NAD⁺, FAD, ATP, H2O

4. none

5. CO cyanide, oligomycin, DNP

6. 32-34 ATP by oxidative phosphorylation

Alcohol Fermentation: place, inputs, outputs, # of ATP made (SLP or OP)

1. cytoplasm

2. Glucose and ADP Pi

3. 2 ATP, 2 CO2, 2Ethanol

4. 1 and 3

5. Hexokinase and phosphofructokinase

6. 2 ATP by substrate level phosphorylation

Acetate fermentation: place, inputs, outputs, # of ATP made (SLP or OP)

1. cytoplasm

2. glucose, 2ADP pi

3. 2 lactate, 2 ATP

4. 1 and 3

5. Hexokinase and phosphofructokinase

6. 2 by substrate level phosphorylation

phloem

transport sugars to other parts of the plant for use or storage

Xylem

transport water and minerals

Photophosphorylation

• Electron transfer through a series of thylakoid membrane proteins results in the generation of a proton gradient inside the thylakoid, which becomes acidic.

• When protons return to the stroma through ATP synthase, they help in the synthesis of ATP, as in the chemiosmosis of respiration.

cyclic light reaction

• Involves only PS I

• Electrons return to PS I reaction center

• ATP synthesized in PS I

• No NADPH made

• No O2 is evolved

• Electrons are recycled

• Occurs when NADPH level is high

noncyclic light reaction

• Use both PS I and PS II

• Electrons do not return to reaction center

• ATP synthesized in PS II

• Electrons are used to reduce NADP+ to generate NADPH

• O2 is evolved from the splitting of water

• The ultimate electron source is H2O

• Most common in plants

key enzyme in Calvin cycle:

ribulose bisphosphate carboxylase/oxygenase (rubisco)

RuBisCo is regulated by…

1. CO2 and O2 concentration

2. NADPH concentration

3. Mg⁺⁺ cofactor

4. pH (high in stoma and low in thylakoid)

Net inputs and outputs of Calvin Cycle

inputs: CO2, ATP, NADPH

outputs: CH2O (C6H12O6), ADP pi, NADP⁺

C3 plants: where does Calvin cycle occur, C4 pathway, examples

1. mesophyll

2. none

3. rice and wheat

C4 plants: where does Calvin cycle occur, C4 pathway, examples

1. bundle sheath

2. mesophyll

3. corn and sugarcane

CAM plants: where does Calvin cycle occur, C4 pathway, examples

1. day time

2. night time

3. cacti and pineapple

photosynthesis: place, inputs, outputs

1. chloroplasts

2. 6CO2 + 6H2O

3. C6H12O6 + 6O2

cyclic light reactions: place, inputs, outputs

1. thylakoid

2. light, ADP pi

3. ATP

noncyclic light reactions: place, inputs, outputs

1. Thylakoid

2. light, H2O, NADP⁺, ADP pi

3. O2, NADPH, ATP

Calvin cycle: place, inputs, outputs

1. mesophyll (c3 plants) or bundle sheaths (c4 plants)

2. CO2, ATP, NADPH

3. CH2O, ADP pi, NADP⁺

C4 pathway: place, inputs, outputs

1. mesophyll

2. CO2, ATP, NADPH

3. CH2O, ADP pi, NADP⁺

Fats: composition, precursor, key enzyme, break down

1. glycerol and fatty acids

2. acetyl CoA

3. acetyl CoA carboxylase

4. beta oxidation

Steroids: composition, precursor, key enzyme, break down

1. 4 fused rings

2. acetyl CoA

3. HMG CoA and HMG CoA reductase

4. Receptor mediated endocytosis

phospholipids: composition, precursor, key enzyme, break down

1. glycerol, fatty acids, and phosphates

2. G3-P, Acetyl CoA

3. Acetyl CoA carboxylase and phosphatidic acid

4. beta oxidation

carotenoids: composition, precursor, key enzyme, break down

1. hydrocarbons (40-c) and plastids

2. isoprene unites

3. NA

4. other pigments