bsc 2010 - exam i lectures and text pages i. intro to biology (2-29) ii. chemistry of life –...

BSC 2010 - Exam I Lectures and Text Pages• I. Intro to Biology (2-29)

• II. Chemistry of Life

– Chemistry review (30-46)

– Water (47-57)

– Carbon (58-67)

– Macromolecules (68-91)

• III. Cells and Membranes

– Cell structure (92-123)

– Membranes (124-140)

• IV. Introductory Biochemistry

– Energy and Metabolism (141-159)

– Cellular Respiration (160-180)

– Photosynthesis (181-200)

Cellular Respiration• ALL energy ultimately comes from the SUN

• Catabolic pathways Yield energy by oxidizing organic fuels

• All the primary organic molecules can be consumed as fuel

• We’ll only examine the most common fuel = sugar (C6H12O6)

• Exergonic rxn: ∆G = -686 kcal/mol of Glucose (the energy will be used to generate ATP)

Energy ultimately comes from the Sun

• Energy

– Flows into an ecosystem as sunlight and leaves as heat Light energy

ECOSYSTEM

CO2 + H2O

Photosynthesisin chloroplasts

Cellular respiration

in mitochondria

Organicmolecules

+ O2

ATP

powers most cellular work

Heatenergy

Figure 9.2

Catabolic Pathways and Production of ATP

• The breakdown of organic molecules is exergonic (releases energy)

• Catabolic pathways yield energy by oxidizing organic fuels

Catabolic Pathways

• One catabolic process, fermentation

– Is a partial degradation of sugars that occurs without oxygen

– Involves Glycolysis

– Yields 2 ATP/Glucose molecule

Catabolic Pathways• Cellular respiration

– Is the most prevalent and efficient catabolic pathway

– Consumes oxygen and organic molecules such as glucose

– Involves Glycolysis

– Yields up to 38 ATP/Glucose molecule

• To keep working

– Cells must regenerate ATP

Cellular Respiration

Redox rxns = oxidation-reduction rxns

• Transfer of electrons (e-) releases energy stored in organic molecules this energy is ultimately used to generate ATP

• Oxidation = loss of e- from one substance

• Reduction = addition of e- to another substance

• Na + Cl Na+ + Cl-

• Na is the reducing agent (donates an e- to CL)

• Cl is the oxidizing agent (removes an e- from Na)

Cellular RespirationRespiration is a redox rxn:

• By oxidizing glucose, energy stored in glucose is liberated to make ATP

– Happens in a series of enzyme-catalyzed steps

– Coenzyme (NAD+) acts as e- shuttle

• Electron transport chains (ETC) - breaks the energetic fall of e- into several energy-releasing steps (not one big explosive rxn), fig 9.5

– Consists of mostly proteins embedded in the inner mitochondrial membrane

• Overview of Respiration: (fig 9.6)

Redox Reactions: Oxidation and Reduction

• Catabolic pathways yield energy

– Due to the transfer of electrons

The Principle of Redox• Redox reactions

– Transfer electrons from one reactant to another by oxidation and reduction

• In oxidation

– A substance loses electrons, or is oxidized

• In reduction

– A substance gains electrons, or is reduced

Examples of redox reactions• Examples of redox reactions

Na + Cl Na+ + Cl–

becomes oxidized(loses electron)

becomes reduced(gains electron)

Some redox reactions• Do not completely exchange electrons

• Change the degree of electron sharing in covalent bonds

CH4

H

H

HH

C O O O O OC

H H

Methane(reducingagent)

Oxygen(oxidizingagent)

Carbon dioxide Water

+ 2O2 CO2 + Energy + 2 H2O

becomes oxidized

becomes reduced

Reactants Products

Figure 9.3

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Oxidation of Organic Fuel Molecules During Cellular Respiration

• During cellular respiration

– Glucose is oxidized and oxygen is reduced

C6H12O6 + 6O2 6CO2 + 6H2O + Energy

becomes oxidized

becomes reduced

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Stepwise Energy Harvest via NAD+ and the Electron Transport Chain

• Cellular respiration

– Oxidizes glucose in a series of steps

– Allows the cell to use the energy harvested from sugar to power work rather than losing it in one explosive reaction.

Electrons from organic compounds• Are usually first transferred to NAD+, a

coenzyme

NAD+

H

O

O

O O–

O

O O–

O

O

O

P

P

CH2

CH2

HO OHH

HHO OH

HO

H

H

N+

C NH2

HN

H

NH2

N

N

Nicotinamide(oxidized form)

NH2+ 2[H]

(from food)

Dehydrogenase

Reduction of NAD+

Oxidation of NADH

2 e– + 2 H+

2 e– + H+

NADH

OH H

N

C +

Nicotinamide(reduced form)

N

Figure 9.4

NADH, the reduced form of NAD+

• Passes the electrons to the electron transport chain

• So it is an electron shuttle and moves electrons to the ETC from both glycolysis and from the citric acid cycle.

If electron transfer is not stepwise• If electron transfer is not stepwise

– A large release of energy occurs

– As in the reaction of hydrogen and oxygen to form water

(a) Uncontrolled reaction

Fre

e en

ergy

, G

H2O

Explosiverelease of

heat and lightenergy

Figure 9.5 A

H2 + 1/2 O2

The electron transport chain (ETC)

• Passes electrons in a series of steps instead of in one explosive reaction

• Uses the energy from the electron transfer to form ATP

Electron Transport Chain

2 H 1/2 O2

(from food via NADH)

2 H+ + 2 e–

2 H+

2 e–

H2O

1/2 O2

Controlled release of energy for synthesis of

ATP ATP

ATP

ATP

Electro

n tran

spo

rt chain

Fre

e en

ergy

, G

(b) Cellular respiration

+

Figure 9.5 B

An overview of cellular respiration

Figure 9.6

Electronscarried

via NADH

GlycolsisGlucos

ePyruvate

ATP

Substrate-levelphosphorylation

Electrons carried via NADH and

FADH2

Citric acid cycle

Oxidativephosphorylation:

electron transport and

chemiosmosis

ATPATP

Substrate-levelphosphorylation

Oxidativephosphorylation

MitochondrionCytosol

Three Stages of Cellular Respiration: A Preview

• Respiration is a cumulative function of three metabolic stages

– Glycolysis

– The citric acid cycle (Kreb’s Cycle)

– Oxidative phosphorylation (driven by the ETC)

Stages of Cellular Respiration1. Glycolysis

– Breaks down glucose into two molecules of pyruvate

– Produces net 2 ATP and 2 NADH

Conversion of pyruvate to acetyl CoA yields 2NADH

2. The citric acid cycle

– Completes the breakdown of glucose

– Produces net 2 ATP, 6 NADH and 2 FADH2

from 2 Acetyl CoA

Stages of Cellular Respiration

3. Oxidative phosphorylation

– Is driven by the electron transport chain (receives electrons from NADH and FADH2)

– Generates 32 – 34 ATP

An overview of cellular respiration

Figure 9.6

Electronscarried

via NADH

GlycolsisGlucos

ePyruvate

ATP

Substrate-levelphosphorylation

Electrons carried via NADH and

FADH2

Citric acid cycle

Oxidativephosphorylation:

electron transport and

chemiosmosis

ATPATP

Substrate-levelphosphorylation

Oxidativephosphorylation

MitochondrionCytosol

Cellular Respiration• Glycolysis & Citric Acid Cycle = catabolic

pathways that breakdown glucose

• Glycolysis pyruvate + coenzymes + ATP

• CAC coenzymes + ATP

• ATP formed by substrate-level phosphorylation (fig 9.7) = enzyme transfers a phosphate group from an organic substrate to ADP to make ATP

• Oxidative Phosphorylation = ATP synthesis powered by ETC. Makes 90% of the 38 ATPs

Both glycolysis and the citric acid cycle• Can generate ATP by substrate-level

phosphorylation

Figure 9.7

Enzyme Enzyme

ATP

ADP

Product

SubstrateP

+

Glycolysis• Glycolysis harvests chemical E by oxidizing glucose to pyruvate

• Glucose Two 3-C sugars oxidized & rearranged Two pyruvates

• Two Major Phases of Glycolysis

• 1. E-investment phase (fig 9.9)

• Rearrange glucose + add phosphate groups (uses 2 ATP)

• Split 6-C sugar two 3-C sugar isomers

• Glyceraldehyde-3-phosphate form next phase

• 2. E-payoff phase (fig 9.9)

• 2 NAD+ 2 NADH & a phosphate group added to each of 2 3-C sugars

• 4 ATP produced by substrate-level phosphorylation

• Rearrangement of remaining phosphate group and the 3-C substrate

Final Products from 1 Glucose = 2 ATP + 2 pyruvate + 2NADH

Glycolysis

• Glycolysis harvests energy by oxidizing glucose to pyruvate

• Glycolysis

– Means “splitting of sugar”

– Breaks down glucose into pyruvate

– Occurs in the cytoplasm of the cell

Glycolysis

• Glycolysis consists of two major phases

– Energy investment phase

– Energy payoff phase

Glycolysis Citricacidcycle

Oxidativephosphorylation

ATP ATP ATP

2 ATP

4 ATP

used

formed

Glucose

2 ADP + 2 P

4 ADP + 4 P

2NAD+ + 4 e- + 4H + 2 NADH + 2 H+

2 Pyruvate + 2 H2O

Energy investment phase

Energy payoff phase

Glucose 2 Pyruvate + 2 H2O

4 ATP formed – 2 ATP used 2 ATP

2NAD+ + 4e– + 4H +2NADH + 2H+

Figure 9.8

Dihydroxyacetonephosphate

Glyceraldehyde-3-phosphate

HH

H

HH

OHOH

HO HO

CH2OHH H

H

HO H

OHHO

OH

P

CH2O P

H

OH

HO

HO

HHO

CH2OH

P O CH2O CH2 O P

HOH HO

HOH

OP CH2

C OCH2OH

HCCHOHCH2

O

O P

ATP

ADPHexokinase

Glucose

Glucose-6-phosphate

Fructose-6-phosphate

ATP

ADP

Phosphoglucoisomerase

Phosphofructokinase

Fructose-1, 6-bisphosphate

Aldolase

Isomerase

Glycolysis

1

2

3

4

5

CH2OHOxidative

phosphorylation

Citricacidcycle

Figure 9.9 A

A closer look at the energy investment phase

Uses 2 ATP. Produces 2 Glyceraldehyde-3-phosphates to feed into energy payoff phase.

2 NAD+

NADH2+ 2 H+

Triose phosphatedehydrogenase

2 P i

2P C

CHOH

O

P

O

CH2 O

2 O–

1, 3-Bisphosphoglycerate2 ADP

2 ATP

Phosphoglycerokinase

CH2 O P

2

C

CHOH

3-Phosphoglycerate

Phosphoglyceromutase

O–

C

C

CH2OH

H O P

2-Phosphoglycerate

2 H2O

2 O–

Enolase

C

C

O

PO

CH2

Phosphoenolpyruvate2 ADP

2 ATP

Pyruvate kinase

O–

C

C

O

O

CH3

2

6

8

7

9

10

Pyruvate

O

Figure 9.8 B

A closer look at the energy payoff phase

Produces 4 ATP, 2 NADH (for ETC), and 2 pyruvates to be converted to Acetyl-CoA and fed into Citric Acid Cycle.

So, net of glycolysis is 2 ATP, 2 NADH, and 2 pyruvate.

Citric acid cycle

• Citric acid cycle completes the E-yielding oxidation of organic molecules

• Pyruvate enters mitochondrion via active transport converted to acetyl coenzyme A (acetyl CoA)

– Happens in 3 rxns catalyzed by a multienzyme complex

• Citric acid cycle (also = Krebs cycle)

• Citrate (ionized form of citric acid) = 1st molecule produced

• Acetyl CoA brings two C atoms to cycle recycles oxaloacetate C atoms leave cycle as CO2 (completely oxidized)

• Ultimately get CO2, NADH, FADH2, and ATP from the CAC.

Before the citric acid cycle can begin• Pyruvate must first be converted to acetyl CoA, which

links the citric acid cycle to glycolysis

• Happens in 3 rxns catalyzed by a multienzyme complex.

CYTOSOL MITOCHONDRION

NADH + H+NAD+

2

31

CO2 Coenzyme APyruvate

Acetyle CoA

S CoA

C

CH3

O

Transport protein

O–

O

O

C

C

CH3

Figure 9.10

Process yields 2 NADH (for ETC) from 2 pyruvate