Chapt08 lecture

Microbial Metabolism: The Chemical Crossroads

of LifeChapter 8

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Metabolism

• Catabolism

• Anabolism

• Energy

• ATP

• Gradients

Glucose CATABOLISMANABOLISM

ANABOLISM

ANABOLISMR

elat

ive

com

ple

xity

of

mo

lecu

les

+

Bacterialcell

Macromolecules

Nutrients fromoutside or frominternal pathways

PyruvateAcetyl CoAGlyceraldehyde-3-P

Amino acidsSugarsNucleotidesFatty acids

ProteinsPeptidoglycanRNA + DNAComplex lipids

GlycolysisKrebs cycleRespiratory chainFermentation

Yields energy

Buildingblocks

Precursormolecules

ATP

NADH

Uses energy Uses energy Uses energy;some assembly reactions

occur spontaneously.

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Enzymes

• Biological catalysts critical for life

• Nearly always proteins

• Active site

• Substrate(s)

• Cofactors

E

Products

Substrate (S)

Enzyme (E) Doesnot fit

ES complex


Reaction Energetics

• Activation energy

• Lowered by enzyme

• Exergonic releases energy – catabolism

• Endergonic uses energy – anabolism E

ne

rgy

Sta

te o

f R

ea

cti

on

Energy of activation in theabsence of enzymeEnergy of activation in thepresence of enzyme

Progress of Reaction

Final state

Products

Initialstate

Reactant


Enzyme Pathways

• Linking products to substrates

• Sequential modifications

• Results in energy – catabolism

• Results in biosynthesis - anabolism

A

B

C

D

E

U

V

W

X

Z

Y

O2

O

O1

M

N

P

Q

R

M

A

B

C

N

X

Y

Z

Multienzyme Systems

Linear Cyclic

Example:Glycolysis

Example:Krebs cycle

Tinput

S product

Example:Amino acidsynthesis

Convergent

Branched

Divergent


Strategy of Metabolism

• Use catabolism to

• Release energyCapture electrons

• Liberate building blocks

• Drive anabolism by

• Spending energy

• Using electrons

• Using building blocks

O

HO

H

CH2OH6

H

OH H

H

OH

C

CO2

C

C

C

C

C

5

4

3 2

13

H OH

En

erg

y L

evel

Of

Ch

emic

al C

om

po

un

d

O

1

2

The energy in electrons andhydrogens is captured andtransferred to ATP. ATP is spentto drive the thousands of cellfunctions.

ATPused to perform

cellular work

Hydrogen ionswith electrons


ATP

Progress of Energy Extraction over Time

These reactions lower theavailable energy in each successivereaction, but they effectively routethat energy into useful cell activities.

Low

High


Glucose

2H+ + 2e– O2

H2O

O

1–2

+

End products

Final electronacceptor

Glucoseis oxidizedas it passesmetabolic pathways,resulting in the removalof hydrogens and theiraccompanying electrons.During part of these pathways, theglucose carbon skeleton is alsodismantled, giving rise to the end productCO2.

―― ――

Oxidation of glucose by means

of enzyme-catalyzed pathways

4In aerobic metabolism,the electrons and hydrogenions generated by therespiratory pathwayscombine with oxygen toproduce another rendproduct, water.


Key Intermediates (building blocks)

• Glucose 6-Phosphate 6-Carbon Glycolysis

• Fructose 6-Phosphate 6-Carbon Glycolysis

• Triose Phosphate 3-Carbon Glycolysis

• 3-Phosphoglycerate 3-Carbon Glycolysis

• Phosphoenolpyruvate 3-Carbon Glycolysis

• Pyruvate 3-Carbon Glycolysis

• Acetyl CoA 2-Carbon Krebs cycle

-Ketoglutyrate 5-Carbon Krebs cycle

• Succinyl CoA 4-Carbon Krebs cycle

• Oxaloacetate 4-Carbon Krebs cycle

• Ribose 5-Phosphate 5-Carbon Pentose phosphate

• Erythrose 4-Phosphate 4-Carbon Pentose phosphate

Concept Check

What type of chemical reaction is illustrated here?

A. Exergonic

B. Endergonic

C. Spontaneous

D. Anabolic

En

erg

y S

tate

of

Rea

ctio

n

Energy of activation in theabsence of enzymeEnergy of activation in thepresence of enzyme

Progress of Reaction

Final state

Products

Initialstate

Reactant


ATP

• Adenosine triphosphate

• Components

• Base (adenine)

• Sugar (ribose)

• Phosphate (3)

• Energy stored in the phosphate bonds

2H

2e:

N

NH2

O

H

C

C C

CC

C

P

P

N

H

C

C C

CC

C

O

P

P

H H+

Oxidizednic otinamide Reducednic otinamide

NAD

From substrate

Adenine

Ribose

NH2

NADH + H+


Substrate Level Phosphorylation

• ATP can be used to drive reactions

Glucose + ATP Glucose-6-phosphate + ADP

• Some compounds can be used to make ATP

Phosphoenolpyruvate + ADP pyruvate + ATP

• This is called substrate level phosphorylation

Oxidation/Reduction

• Oxidation is losing electrons

• Reduction is gaining electrons

• Oxidation is always linked to reduction

2 8 1 2 82 8 7 2 8 8

1 2

Reducedanion

ClNaClNa

Reducing agentgives up electrons.

Oxidizing agentaccepts electrons.

Oxidizedcation


NAD

• Nicotinamide adenine dinucleotide

• Electron acceptor

• Limited amount in the cell

• Must be re-oxidized from the reduced form

2H

2e:

N

NH2

O

H

C

C C

CC

C

P

P

N

H

C

C C

CC

C

O

P

P

H H+

Oxidizednic otinamide Reducednic otinamide

NAD

From substrate

Adenine

Ribose

NH2

NADH + H+


Glycolysis (Stage 1)

Glucose Glucose 6-Phosphate

A A

Fructose 6-Phosphate

A A

Fructose 1,6-Biphosphate

Energy is spent in the front end to get more later.



Fructose 1,6-Biphosphate PGAL &

DHAP

+

1,3 Bisphospho-glycerate

2X

2 NAD+

2 NADH + 2H+2

Splitting into two molecules doubles the reactants.



1,3 Bisphospho-glycerate

2X

2X

2X

AA2X

3 PGA

2X

2 PGA

Break-even point using substrate-level phosphorylation.


2X

Phosphoenolpyruvate


2 PGA

2X

2XAA

2X

2X

Pyruvate

The payoff - a net yield of ATP by substrate level phosphorylation


Concept Check

How many net ATP are formed in glycolysis?

A. One

B. Two

C. Three

D. Four

Glycolysis Summary

• One glucose is used

• Partial oxidation of the sugar

• Two NADH are reduced

• 2 ATP are consumed

• 4 ATP total are made

• Net of 2 ATP produced

• 2 pyruvates are end products

The Kreb’s Cycle• Complete oxidation to CO2

C

CH2

HC

HO CH2

CO2

C

C

H+

COO–

CH2

CH2

C O

COO–

COO–

CH2

HO

NAD+

CO2

C H2

C

C

C

O

O S

O

C S

C H3

C

C H2

C

C H2

Acetyl CoA

Isocitric acid

8

8

1

2

3

4

5

5

6

7

7

6

3

2

PO4–3

C

O

C H3

O

C

CoA

CH2

C

C H

HC

C

C

C H

C

C

C

C H2

OC

O–

O–

+

H++

H++

H++

C

C

CH2

HC

CO2

ATPADP

Succinyl CoA

CoA

CO2

NAD H

NAD+

An additional NADHis formed when malicacid is converted tooxaloacetic acid, whichis the final product toenter the cycle again, byreacting with acetyl CoA.

Fumaric acidreacts withwater to formmalic acid.

Succinic acid loses 2Hand 2e–, yieldingfumaric acid andgenerating FADH2.

Succinyl CoA isconverted to succinicacid and regeneratesCoA. This releasesenergy that iscaptured in ATP.

a-ketoglutaric acidloses the secondCO2 and generatesanother NADH+

plus 4C succinyl CoA.

Isocitric acid isconverted to 5Ca-ketoglutaricacid, whichyields NADHand CO2.

Citrate changes thearrangement of atomsto form isocitric acid.

The 2 Cacetyl CoAmolecule combineswith oxaloacetic acid,forming 6C citrate, andreleasing CoA.

a-ketoglutaric acid

NAD H

NAD+

OO–

OO–

Citric acid

CoA

OO–

OO–

OO–

CoA

Pyruvic acid

From glycolysis

NAD H

Oxaloacetic acid

OO–

OO–

H2O

Malic acid

OO–

HO

OO–

NAD+

NAD H

Krebs Cycle

OO–

OO–

FADH2

FAD

OO–

OO–

Fumaric acid

Succinic acid

AEROBIC RESPIRATION ANAEROBIC RESPIRATION FERMENTATION

Glycolysis Glycolysis Glycolysis

Glucose Glucose Glucose

ATPNADH

ATP

NADHATP

NADH2pyruvate(3C)

(6C)

2pyruvate 2pyruvate

(6C)

(3C) (3C)

(6C)

CO2CO2

Acety lCoA Acetyl CoA Fermentation

FADH2

NADH

ATP

Krebs CO2

Electrons

Electron transport

ATP produced = 38

O2 is final electronacceptor.

FADH2

NADHKrebs

ATP

CO2

Electrons

Electron transport

ATP produced = 2 to 36 ATP produced =2

Lactic acidAcetaldehyde

Ethanol

Or other alcohols,acids, gases

An organic molecule is finalelectron accept or (pyruvate,acetaldehyde etc.).

Non oxygen electron acceptors(examples: SO4

2–, NO3–,

CO32– )

1

4


Kreb’s Cycle Summary

Pyruvate 1

• 3 CO2

• 4 NADH

• 1 FADH2

• 1 ATP

Pyruvate 2

• 3 CO2

• 4 NADH

• 1 FADH2

• 1 ATP• Each glucose has now been completely oxidized

to carbon dioxide• Electrons are temporarily on carrier molecules• 4 ATP total made by substrate level

phosphorylation

Regenerating NAD+

• From one glucose…

• Glycolysis = 2 NADH

• Kreb’s cycle = 8 NADH & 2 FADH2

• There is a limited amount of NAD in the cell, so it must be regenerated for reuse later.

Concept Check

What is the process of making ATP from the degradation of phosphoenolpyruate called?

ADP + Pi + PEP Pyruvate + ATP

A. Oxidative phosphorylation

B. Oxidative decarboxylation

C. Photophosphorylation

D. Substrate level phosphorylation

Fermentation

• Performed by anaerobic microorganisms

• Primary purpose: Regenerate NAD for reuse

• The electron acceptor is an organic molecule

• Secondary purpose: Generate additional energy

• Energy yields are very small

• As a consequence the growth rates are slower

Fermentation

• NADH oxidized

• Organic molecule reduced

• Many possible end products

• Lactic acid

• Ethanol

• Vinegar

• Acetone

C C

OO

C

H

H

H

OHC C

H

H

H

H

H

C C

O

H

H

H

H

CC C

H

H

H

H

O HO

OH

System: Homolactic bacteria;human muscleGlucose

System: Yeasts

Glycolysis

Lactic acidEthyl alcohol

Pyruvic acid

OH

NADH

NAD HNADH

NAD

NAD

CO2

Acetaldehyde

O2 is final electronacceptor.

ATP produced = 38 ATP produced = 2 to 36 ATP produced = 2

Non oxygen electron acceptors (examples: SO4

2–, NO3–, CO3

2– )

An organic molecule is finalelectron accept or (pyruvate,acetaldehyde, etc.).

AEROBIC RESPIRATION

Glycolysis

Glucose

ATP

NADH

2pyruvate (3C)

(6C)

CO2

Acety lCoA

FADH2

NADH

ATP

Krebs CO2

Electrons

Electron transport

ANAEROBIC RESPIRATION

Glycolysis

Glucose

ATP

NADH

2pyruvate (3C)

(6C)

CO2

Acety lCoA

FADH2

NADH

ATP

Krebs CO2

Electrons

Electron transport

FERMENTATION

CO2

Glycolysis

Glucose

ATP

NADH

2pyruvate

Lactic acid

Ethanol

Or other alcohols,acids, gases

Acetaldehyde

(6C)

(3C)


Redox Potential Energy

• Molecules differ in their affinity for electrons

• Moving from a good donor to a good acceptor is favorable and releases energy

• NADH is a good donor

• Oxygen is the best acceptor

• Want to couple this to do work

Electron Transport System

• NADH oxidized

• Electrons pass through membrane carriers

• Protons pumped out (work is done)

• Electrons accepted by an inorganic molecule

H

H

HH

H

HH

H

H

H

HH

H

HH

H

H

H

H

H

Cell wall

Cytochromes

Cytoplasm

Cell membranewith ETS

ATP

ADP

ATP synthase


Anaerobic Respiration

• The electron acceptor is not oxygen

• Examples: nitrate, nitrite, and sulfate

• These are mediocre acceptors – not as good as oxygen

• Yields other inorganic molecules upon reduction

• Less favorable reactions pump out fewer protons

Concept Check

Which of these is the best electron acceptor?

A. Oxygen

B. Nitrate

C. Pyruvate

D. NAD

Aerobic Respiration

• The electron acceptor is an oxygen

• This is a very good acceptor

• Yields water upon reduction

• Because so much energy is released, the cell can pumps out about 10 protons

• Occurs in bacterial membrane and mitochondria of eukaryotes

Chemiosmosis

• Proton gradient is potential energy

• Allowing protons back into the cell can be coupled to work

• 3 protons entering drive the synthesis of 1 ATP

• Oxidative phosphorylation

H+

F0

e–

HH

O

O

H+

1 /2 O2

(c) The distribution of electric potential and the concentration gradient of protons across the membrane drive the synthesis of ATP by ATP synthase. The rotation of this enzyme couples diffusion of H+ to the inner compartment with the bonding of ADP and Pi. The final event of electron transport is there action of the electrons with the Hand O2 to form metabolic H2O. This step is catalyzed by cytochrome aa3.

H+

H+

H+

H+

H+

ATPADP + Pi

ATPsynthase

H+

Outercompartment

e–

Cytochromeaa3

H+H+

H+

H+

H+

H+ H+

H+

H+H+

H+

H+

Innercompartment


Aerobic Respiration Yield

• 1 Glucose 6 CO2

• 2 ATP from glycolysis

• 2 NADH from glycolysis 6 ATP

• 2 ATP from Krebs cycle substrate level

• 8 NADH from Krebs cycle 24 ATP

• 2 FADH2 from Krebs cycle 4 ATP

• Total 36-38 ATP per glucose

Amphibolism

CO2

H2O

Gly

coly

sis

An

abo

lism

Cat

abo

lism

Simpleproducts

Metabolicpathways

Building block

Macromolecule

Cellstructure

Chromosomes EnzymesMembranes

Cell wallStorage

MembranesStorage

LipidsFats

StarchCelluloseProteinsNucleic

acids

Nucleotides Amino acids Carbohydrates Fatty acids

Beta oxidationDeamination

GLUCOSE

Pyruvic acid

Krebscycle

Acetyl coenzyme A

NH3


Oxygenic Photosynthesis

• Chlorophyll pigments

• Thylakoid membrane

• Capture light energy

• Electron transport

• Photophosphorylation

• Makes NADH and ATP

• Oxygen produced

• Algae, plants, and cyanobacteria

½ O2

2e–

2H+

Pi

Ph

oto

lys

is

Elec

tron

carr

iers

Ca

lvin

Cyc

les

A B

D C

N N

N

Mg

N

H+

H+

H+

H+

H+H+H+

1

2

3

4

5

6

(a) A cell of the motile alga Chlamydomonas,with a single large chloroplast (magnifiedcut away view). The chloroplast containsmembranous compartments called granawhere chlorophyll molecules and thephotosystems for the light reactionsare located.

(b) A chlorophyll molecule,with a central magnesiumatom held by a porphyrin ring.

Flagellum

Nucleus

Cell wall

Chloroplast

Photons

Granum

Stroma

Thylakoid membrane

NADPH

ATP

ADP +

NADP

2e–

P700

Electroncarriers

Photosystem I2e–

P680

Photosystem IIH2OH2O

ATPATPsynthasesynthase

ProtonpumpProtonpump

Interior of granum

(c) The main events of the light reaction shown as an exploded view in one granum.

When light activates photosystem II, it sets up a chain reaction, inwhich electrons are released from chlorophyll.

1

2

3

4

5

6 Both NADPH and ATP are fed into the stroma for the Calvin cycle.

The final electron and H+ acceptor is NADP, which receives these fromphotosystem I.

Pumping of H+ into the interior of the granum produces conditions forATP to be synthesied.

The empty position in photosystem II is replenished photolysis ofH2O.Other products of photolysis are O2 and H+

These electrons are transported along a chain of carriers tophotosystem I.


Anoxygenic Photosynthesis

• Purple bacteria (similar to photosystem II)

• Make ATP

• Can’t make NADH

• No oxygen produced

• Green bacteria (similar to photosystem I)

• Make ATP

• Also make NADH

• No oxygen produced

Calvin Benson Cycle

• Fix carbon dioxide

• Autotrophs

• Reverse of glycolysis

• 6 CO2 Glucose

P P

PP

PP

P P

P P

PP

P

PH

H

Splitting

ADP

ATP × 2

ADP

ATP

Series of 7 Carbonand 5 Carbonintermediates

Ribulose-1,5-bisphosphate5Carbon

CO2

6 Carbonintermediate

NADPH × 2

NADP

Glyceraldehyde-3phosphate

Glucose

Fructose intermediates

1,3-bisphosphoglyceric acid

Calvin Cycle

3-phosphoglycericacid


Concept Check

Where does aerobic respiration occur in a yeast?

A. Nucleus

B. Cell membrane

C. Mitochondria

D. Ribosome

Education

Chapt08 lecture