Chapter Title - Blackboard Media Content Portal BIO 186 Fall 2014...Figure 5.18 One possible arrangement of an electron transport chain. Bacterium Exterior Cytoplasmic ... •Called

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PowerPoint® Lecture

Presentations prepared by

Mindy Miller-Kittrell,

North Carolina State University

C H A P T E R

© 2015 Pearson Education, Inc.

Microbial

Metabolism

5


Basic Chemical Reactions Underlying

Metabolism

• Metabolism

• Collection of controlled biochemical reactions that take

place within a microbe

• Ultimate function of metabolism is to reproduce the

organism



Metabolism • Metabolic Processes Guided by Eight Statements

• Every cell acquires nutrients

• Metabolism requires energy from light or catabolism of

nutrients

• Energy is stored in adenosine triphosphate (ATP)

• Cells catabolize nutrients to form precursor metabolites

• Precursor metabolites, energy from ATP, and enzymes are

used in anabolic reactions

• Enzymes plus ATP form macromolecules

• Cells grow by assembling macromolecules

• Cells reproduce once they have doubled in size © 2015 Pearson Education, Inc.

Metabolism: Overview

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Metabolism

• Catabolism and Anabolism

• Two major classes of metabolic reactions

• Catabolic pathways

• Break larger molecules into smaller products

• Exergonic (release energy)

• Anabolic pathways

• Synthesize large molecules from the smaller products of

catabolism

• Endergonic (require more energy than they release)


Figure 5.1 Metabolism is composed of catabolic and anabolic reactions.



Metabolism

• Oxidation and Reduction Reactions

• Transfer of electrons from an electron donor to an

electron acceptor

• Reactions always occur simultaneously

• Cells use electron carriers to carry electrons (often in

H atoms)

• Three important electron carriers

• Nicotinamide adenine dinucleotide (NAD+)

• Nicotinamide adenine dinucleotide phosphate (NADP+)

• Flavin adenine dinucleotide (FAD)


Figure 5.2 Oxidation-reduction, or redox, reactions.

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Oxidation-Reduction Reactions



Metabolism • ATP Production and Energy Storage

• Organisms release energy from nutrients

• Can be concentrated and stored in high-energy

phosphate bonds (ATP)

• Phosphorylation – inorganic phosphate is added to substrate

• Cells phosphorylate ADP to ATP in three ways

• Substrate-level phosphorylation

• Oxidative phosphorylation

• Photophosphorylation

• Anabolic pathways use some energy of ATP by breaking a

phosphate bond



Metabolism

• The Roles of Enzymes in Metabolism

• Enzymes are organic catalysts

• Increase likelihood of a reaction


Enzymes: Overview

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Metabolism


• Naming and classifying enzymes

• Six categories of enzymes based on mode of action

• Hydrolases

• Isomerases

• Ligases or polymerases

• Lyases

• Oxidoreductases

• Transferases




Metabolism


• The makeup of enzymes

• Many protein enzymes are complete in themselves

• Apoenzymes are inactive if not bound to nonprotein

cofactors (inorganic ions or coenzymes)

• Binding of apoenzyme and its cofactor(s) yields

holoenzyme

• Some are RNA molecules called ribozymes


Figure 5.3 Makeup of a holoenzyme.

Inorganic cofactor Active site

Coenzyme (organic cofactor)

Apoenzyme (protein)

Holoenzyme

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© 2015 Pearson Education, Inc. © 2015 Pearson Education, Inc.

Figure 5.4 The effect of enzymes on chemical reactions.

Reactants

Activation energy without enzyme

Activation energy with enzyme

Products


Figure 5.5 Enzymes fitted to substrates.

Active sites similar to substrate's shape

Substrate

Enzyme Enzyme-substrate complex; active sites become exact shape of substrate


1

Enzyme-

substrate

complex

Enzyme

(Fructose-1,6- bisphosphate aldolase)

Substrate

(Fructose 1,6-bisphosphate)

Dihydroxyacetone-P Glyceraldehyde-3P

Products

2

3

4

Figure 5.6 The process of enzymatic activity.

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Enzymes: Steps in a Reaction



Metabolism • The Roles of Enzymes in Metabolism

• Enzyme activity

• Many factors influence the rate of enzymatic reactions

• Temperature

• pH

• Enzyme and substrate concentrations

• Presence of inhibitors

• Inhibitors block an enzyme's active site

• Do not denature enzymes

• Three types


Figure 5.7 Representative effects of temperature, pH, and substrate concentration on enzyme activity.


Figure 5.8 Denaturation of protein enzymes.

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Competitive inhibitor

Substrate

Enzyme

Reversible competitive inhibitor

Substrate

Increase in substrate concentration

Enzyme

Figure 5.9 Competitive inhibition of enzyme activity.


Enzymes: Competitive Inhibition


Active site Enzyme

Allosteric site

Allosteric (noncompetitive) inhibition

Distorted, nonfunctional active site

Allosteric

inhibitor

Distorted active site

Substrate

Active site becomes

functional

Allosteric activator Allosteric site

Allosteric activation

Substrate

Figure 5.10 Allosteric control of enzyme activity.


Enzyme-Substrate Interaction: Noncompetitive

Inhibition

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Figure 5.11 Feedback inhibition.

Substrate

Pathway

shuts down

Bound end-product (allosteric inhibitor)

Enzyme 1

Allosteric site

Pathway

operates

Feedback inhibition Intermediate A

Enzyme 2

Intermediate B

End-product

Enzyme 3 © 2015 Pearson Education, Inc.

Carbohydrate Catabolism

• Many organisms oxidize carbohydrates as primary

energy source for anabolic reactions

• Glucose is most common carbohydrate used

• Glucose is catabolized by two processes

• Cellular respiration

• Fermentation


Glucose

2 Pyruvic acid

Electrons

KREBS

CYCLE

Acetyl-CoA

Final electron acceptor

Formation of fermentation end-products

Pyruvic acid (or derivative)

G

L

Y

C

O

L

Y

S

I

S

Fermentation Respiration

Figure 5.12 Summary of glucose catabolism.



• Glycolysis

• Occurs in cytoplasm of most cells

• Involves splitting of a six-carbon glucose into two three-

carbon sugar molecules

• Substrate-level phosphorylation – direct transfer of

phosphate between two substrates

• Net gain of two ATP molecules, two molecules of

NADH, and precursor metabolite pyruvic acid

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Glycolysis: Overview



• Glycolysis

• Divided into three stages involving 10 total steps

• Energy-investment stage

• Lysis stage

• Energy-conserving stage


Figure 5.13 Glycolysis.


Glycolysis: Steps

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Figure 5.14 Example of substrate-level phosphorylation.

Phosphoenolpyruvate (PEP)

Holoenzyme

Pyruvic acid

Phosphorylation



• Cellular Respiration

• Resultant pyruvic acid is completely oxidized to produce

ATP by series of redox reactions

• Three stages of cellular respiration

1. Synthesis of acetyl-CoA

2. Krebs cycle

3. Final series of redox reaction

(electron transport chain)


Figure 5.15 Formation of acetyl-CoA.




• Synthesis of acetyl-CoA

• Results in

• Two molecules of acetyl-CoA

• Two molecules of CO2

• Two molecules of NADH

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• The Krebs cycle

• Great amount of energy remains in bonds of acetyl-CoA

• Transfers much of this energy to coenzymes NAD+ and

FAD

• Occurs in cytosol of prokaryotes and in matrix of

mitochondria in eukaryotes




• The Krebs cycle

• Six types of reactions in Krebs cycle

• Anabolism of citric acid

• Isomerization

• Redox reactions

• Decarboxylations

• Substrate-level phosphorylation

• Hydration reaction


Figure 5.16 The Krebs cycle.


Krebs Cycle: Overview

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Krebs Cycle: Steps




• The Krebs cycle

• Results in

• Two molecules of ATP

• Two molecules of FADH2

• Six molecules of NADH

• Four molecules of CO2




• Electron transport

• Most significant production of ATP occurs from series of

redox reactions known as an electron transport chain

(ETC)

• Series of carrier molecules that pass electrons from one to

another to final electron acceptor

• Energy from electrons is used to pump protons (H+) across

the membrane, establishing a proton gradient

• Located in cristae of eukaryotes and in cytoplasmic

membrane of prokaryotes


Respiration Fermentation

Path of

electrons

Final electron

acceptor

Figure 5.17 An electron transport chain.

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Electron Transport Chain: Overview




• Electron transport

• Four categories of carrier molecules

• Flavoproteins

• Ubiquinones

• Metal-containing proteins

• Cytochromes

• Aerobic respiration: oxygen serves as final electron

acceptor

• Anaerobic respiration: molecule other than oxygen serves

as final electron acceptor


Figure 5.18 One possible arrangement of an electron transport chain. Bacterium

Exterior

Cytoplasmic membrane

Intermembrane space

Matrix

Mitochondrion

Cytoplasm

Phospholipid membrane

NADH from glycolysis,

Krebs cycle, pentose phosphate

pathway, and Entner-Doudoroff pathway

FADH2 from

Krebs cycle

Cytoplasm of prokaryote

or matrix of mitochondrion

Exterior of prokaryote or intermembrane space

of mitochondrion

Ubiquinone

FMN

NADH FADH2

NAD+ Cyt c1

ATP synthase

Cyt b

H+

H+

2

1

e–

e–

e–

e–

H+ H

+

e–

e–

e– e

–

e–

e–

Cyt c Cyt a

Cyt a3

H+ H

+

e–

e–

H+ H

+

4

H+

H+

H+

H+

ADP

3

H2O

ATP

P + 1/2 O2

H+

H+ FAD +

+

H+


Electron Transport Chain: The Process

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Electron Transport Chain: Factors Affecting

ATP Yield




• Chemiosmosis

• Use of ion gradients to generate ATP

• Cells use energy released in redox reactions of ETC to

create proton gradient

• Protons flow down electrochemical gradient through ATP

synthases that phosphorylate ADP to ATP

• Called oxidative phosphorylation because proton gradient

is created by oxidation of components of ETC

• Total of ~34 ATP molecules formed from one molecule of

glucose



• Alternatives to Glycolysis

• Yield fewer molecules of ATP than does glycolysis

• Reduce coenzymes and yield different metabolites

needed in anabolic pathways

• Two pathways

• Pentose phosphate pathway

• Entner-Doudoroff pathway

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Figure 5.19 The pentose phosphate pathway.


Figure 5.20 Entner-Doudoroff pathway.

Glucose

Glucose 6-phosphate

6-Phosphogluconic acid

2-Keto-3-deoxy- 6-phosphogluconic acid

Glyceraldehyde 3-phosphate (G3P)

Pyruvic acid

Pyruvic acid

To Krebs cycle

or fermentation

Steps 6–10

of glycolysis



• Fermentation

• Sometimes cells cannot completely oxidize glucose by

cellular respiration

• Cells require constant source of NAD+

• Cannot be obtained simply by using glycolysis and Krebs

cycle

• Fermentation pathways provide cells with alternative source

of NAD+

• Partial oxidation of sugar (or other metabolites) to release

energy using an organic molecule from within the cell as

final electron acceptor © 2015 Pearson Education, Inc.

Figure 5.21 Fermentation.

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Figure 5.22 Representative fermentation products and the organisms that produce them.


Fermentation


Other Catabolic Pathways

• Lipids and proteins contain energy in their

chemical bonds

• Can be converted into precursor metabolites

• Serve as substrates in glycolysis and the Krebs cycle

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Figure 5.23 Catabolism of a fat molecule.

Fatty acid chains Glycerol

Lipase 3

Glycerol

+

Fatty acids

Hydrolysis

DHAP

To step 5 glycolysis

Fatty acid

To electron transport chain

Acetyl-CoA

To Krebs cycle

Shorter fatty acid

Beta-oxidation


Extracellular fluid

Protease

s

Polypeptide

Amino

acids

Cytoplasmic

membrane

Cytoplasm

Deamination

To Krebs

cycle

Figure 5.24 Protein catabolism.


Photosynthesis

• Many organisms synthesize their own organic

molecules from inorganic carbon dioxide

• Most of these organisms capture light energy and

use it to synthesize carbohydrates from CO2 and

H2O by a process called photosynthesis


Photosynthesis: Overview

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Metabolism


Photosynthesis

• Chemicals and Structures

• Chlorophylls

• Type of pigment molecule that photosynthetic organisms

use to capture light energy

• Composed of hydrocarbon tail attached to light-absorbing

active site centered on magnesium ion

• Active sites are structurally similar to cytochrome

molecules in ETC

• Structural differences cause absorption at different

wavelengths


Photosynthesis


• Photosystems

• Arrangement of molecules of chlorophyll and other

pigments to form light-harvesting matrices

• Embedded in cellular membranes called thylakoids

• In prokaryotes – invagination of cytoplasmic membrane

• In eukaryotes – formed from inner membrane of

chloroplasts

• Arranged in stacks called grana

• Stroma is space between outer membrane of granum and

thylakoid membrane © 2015 Pearson Education, Inc.

Figure 5.25 Photosynthetic structures in a prokaryote.

Photosystem embedded

in membrane (sectioned) Chlorophyll

Thylakoid

membrane

Active

site

Tail

(carbon

chain)

Thylakoid

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Photosynthesis


• Two types of photosystems

• Photosystem I (PS I)

• Photosystem II (PS II)

• Photosystems absorb light energy and use redox

reactions to store energy in the form of ATP and

NADPH

• Light-dependent reactions depend on light energy

• Light-independent reactions synthesize glucose from

carbon dioxide and water © 2015 Pearson Education, Inc.

Photosynthesis

• Light-Dependent Reactions

• As electrons move down the chain, their energy is used

to pump protons across the membrane

• Photophosphorylation uses proton motive force to

generate ATP

• Photophosphorylation can be cyclic or noncyclic


Acceptor

Light

Reaction center chlorophyll

Possible path of energy transfer

Photosystem:

reaction center

Figure 5.26 Reaction center of a photosystem.


Exterior of prokaryote

or thylakoid space of chloroplast

Cyclic photophosphorylation

Cytochromes

Cu Photosystem I

Fe Reaction center

Light Cytoplasm of

prokaryote

or stroma of

chloroplast

ATP synthase

Membrane of

prokaryote or

of thylakoid in

chloroplast

Membrane of

prokaryote or

of thylakoid in

chloroplast

ATP synthase

Photosystem I

Cytochromes

Fe

Light

Cytoplasm of

prokaryote

or stroma of

chloroplast

Light

Quinone

Reaction

center Reaction

center

Cu

Noncyclic photophosphorylation

Exterior of prokaryote

or thylakoid space

of chloroplast

To

Calvin-Benson

cycle

NADPase

Photosystem II

Figure 5.27 The light-dependent reactions of photosynthesis: Cyclic and noncyclic photophosphorylation.

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Photosynthesis: Light Reaction: Cyclic

Photophosphorylation


Photosynthesis: Light Reaction: Noncyclic

Photophosphorylation


Photosynthesis

• Light-Independent Reactions

• Do not require light directly

• Use ATP and NADPH generated by light-dependent

reactions

• Key reaction is carbon fixation by Calvin-Benson cycle

• Three steps

• Fixation of CO2

• Reduction

• Regeneration of RuBP

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Figure 5.28 Simplified diagram of the Calvin-Benson cycle.


Photosynthesis: Light-Independent Reaction


Other Anabolic Pathways

• Anabolic reactions are synthesis reactions

requiring energy and a source of precursor

metabolites

• Energy derived from ATP from catabolic reactions

• Many anabolic pathways are the reverse of

catabolic pathways

• Reactions that can proceed in either direction are

amphibolic


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Figure 5.29 The role of gluconeogenesis in the biosynthesis of complex carbohydrates.


Figure 5.30 Biosynthesis of fat, a lipid.


Figure 5.31 Examples of the synthesis of amino acids via amination and transamination.


Figure 5.32 The biosynthesis of nucleotides.

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Integration and Regulation of Metabolic

Function

• Cells synthesize or degrade channel and transport

proteins

• Cells often synthesize enzymes only when

substrate is available

• Cells catabolize the more energy-efficient choice if

two energy sources are available

• Cells synthesize metabolites they need, cease

synthesis if metabolite is available



Function

• Eukaryotic cells isolate enzymes of different

metabolic pathways within membrane-bounded

organelles

• Cells use allosteric sites on enzymes to control

activity of enzymes

• Feedback inhibition slows/stops anabolic

pathways when product is in abundance

• Cells regulate amphibolic pathways by requiring

different coenzymes for each pathway



Function

• Two types of regulatory mechanisms

• Control of gene expression

• Cells control amount and timing of protein (enzyme)

production

• Control of metabolic expression

• Cells control activity of proteins (enzymes) once produced


Figure 5.33 Integration of cellular metabolism (shown in an aerobic organism).

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Metabolism: The Big Picture

Documents

Chapter Title - Blackboard Media Content Portal BIO 186 Fall 2014...Figure 5.18 One possible arrangement of an electron transport chain. Bacterium Exterior Cytoplasmic ... •Called