Microbial Metabolism Sofronio Agustin Professor Sofronio Agustin Professor LECTURES IN MICROBIOLOGY...

Microbial MetabolismMicrobial Metabolism

Sofronio Agustin

Professor

Sofronio Agustin

Professor

LECTURES IN MICROBIOLOGYLECTURES IN

MICROBIOLOGY

LESSON 6LESSON 6

2

Lesson 6 TopicsLesson 6 Topics

Metabolism Energy Pathways Biosynthesis

3

MetabolismMetabolism

Catabolism

Anabolism

Enzymes

4

CatabolismCatabolism

Breakdown of complex organic molecules in order to extract energy and form simpler end products.

Enzymes are involved.

5

Metabolism ModelMetabolism Model

6

EnzymesEnzymes

Function Structure Enzyme-substrate interaction Cofactors Action Regulation

7

Enzyme StructureEnzyme Structure

Simple enzyme - primarily protein Conjugated enzyme

- protein and nonproteinThree-dimensional features:

Specificity -”lock-and-key”Active site or catalytic site

8

Conjugated EnzymesConjugated Enzymes

Conjugated enzymes contain a metallic cofactor, coenzyme, or both in order for it to function as a catalyst.

9

Active SiteActive Site

Specific active sites are folded regions of the protein molecule and contain specific amino acids in its microenvironment.

10

Enzyme-Substrate InteractionEnzyme-Substrate Interaction

Substrates specifically bind to the active sites on the enzyme:

-“lock-and-key” style

-Induced fit

Once the reaction is complete, the product is released and the enzyme reused.

11

Lock-and-Key ModelLock-and-Key Model

Specificity of enzyme-substrate reactions and induced fit.

12

Coenzymes Coenzymes

Function as transient carriers

Alter a substrate by removing a

chemical group from it and adding it

to another. Ex. NAD, FAD and CoA

13

Coenzyme ActivityCoenzyme Activity

Carrier function of

coenzymes

A coenzyme

transfers chemical

groups from one

substrate to another.

14

Enzyme ActionEnzyme Action

ExoenzymesEndoenzymesConstitutive

Induction or repressionTypes of reactions

15

Enzyme LocationEnzyme Location

Exoenzymes are inactive while inside the cell, but upon release from the cell they become active.

Endoenzymes remain in the cell and are always active.

16

Constitutive and Regulated EnzymesConstitutive and Regulated Enzymes

Constitutive enzymes are present in constant amounts.

Regulated enzymes are either induced or repressed.

17

Types of ReactionsTypes of Reactions

Condensation

Hydrolysis

Transfer reactions

18

Synthesis and Hydrolysis Synthesis and Hydrolysis

Condensation reactions are associated with anabolic reactions, and hydrolysis reactions are associated with catabolic reactions.

19

Transfer Reactions Transfer Reactions

Transfer of electrons from one substrate to

another.

Ex: Oxidoreductase - oxidation-reduction

reactions.

Transfer of functional groups from one molecule

to another.

Ex: Aminotransferases - transfer of amino group.

20

Sample Enzymes Sample Enzymes

Examples of enzymes, their substrates, and their reactions.

21

RegulationRegulation

Metabolic pathways

Direct control

Genetic control

22

Patterns of Metabolism Patterns of Metabolism

Metabolic pathways

follow stepwise

patterns.

These are regulated

by enzymes that

catalyze these

reactions.

23

Enzyme Control Mechanisms Enzyme Control Mechanisms

Competitive inhibition and noncompetitive inhibition are forms of direct control (regulation) of the enzyme action.

24

Genetic ControlGenetic Control

Repression - end products stop the expression of genes that encode for proteins (enzymes) which are responsible for metabolic reactions.

Induction - substrate initiates and enhances the expression of genes for proteins (enzymes) that drive metabolic reactions.

25

RepressionRepression

Repression as a type of genetic control of enzyme synthesis

26

Enzyme CharacteristicsEnzyme Characteristics

27

BioenergeticsBioenergetics

Cell energetics- Exergonic reactions

- Endergonic reactions

Redox reaction Electron carriers Adenosine Triphosphate (ATP)

28

Energy Machinery of the Cell Energy Machinery of the Cell

The general scheme associated with metabolism of organic molecules, the redox reaction, and the capture of energy in the form of ATP.

29

Redox ReactionRedox Reaction

Oxidation - removal or loss of electrons

Reduction - addition or gain of electronsThese are coupled reactions

Biological redox reactions involve transfer of

electrons and protons (hydrogens) =

dehydrogenationDehydrogenases - catalyze these reactions

30

Electron CarriersElectron Carriers

Electron carriers - transfer electrons (and

protons) from donor to acceptor molecules.

Coenzymes:

Ex: Nicotinamide adenine dinucleotide (NAD)

Respiratory chain (ETC) carriers:

Ex: Cytochromes (protein+porphyrin)

31

Adenosine TriphosphateAdenosine Triphosphate

Temporary energy repository (“cellular battery”)

Breaking of pyrophosphates bonds will release

free energy for cellular work.

Three part molecule:Nitrogen base - AdeninePentose sugar - Ribose)Chain of three phosphate groups

32

Energy CaptureEnergy Capture

The phosphate groups

capture the energy

derived from metabolism

as pyrophosphate bonds

within the ATP molecule.

ATP and its partner

compounds ADP and

AMP.

33

PhosphorylationPhosphorylation

ATP can be used

to phosphorylate

an organic

molecule such as

glucose during

catabolism.

Phosphorylation -

catalyzed by

phosphorylases(e.g. hexokinase)

34

Substrate-level PhosphorylationSubstrate-level Phosphorylation

ATP can be synthesized by substrate-level

phosphorylation.

A phosphate group from an intermediate is transferred to ADP to regenerate ATP.

35

Catabolic PathwaysCatabolic Pathways

Embden-Meyerhoff-Parnas (EMP) Pathway or Glycolysis

Kreb’s or Tricarboxylic Acid (TCA) Cycle

Electron Transport or Respiratory Chain

Alternate pathways

Fermentation

36

Glucose MetabolismGlucose Metabolism

Overview of the

location, flow, end-

products of cellular

(aerobic)

respiration.Glucose is catabolized to harness energy.

37

Cellular Respiration Cellular Respiration

Glycolysis

Kreb’s Cycle

Electron Transport Chain

38

Glycolysis Glycolysis

Glucose (6-carbon sugar) splits into two pyruvates (3-carbon molecules).

Glucose is oxidized and coenzyme NAD is reduced to NADH.

Energy investment phase:- Phosphorylation of intermediates using 2 ATP molecules

Energy yielding phase:- Substrate-level-phosphorylation of ADP to produce 4 ATPs.

39

Glycolytic StepsGlycolytic Steps

40

Kreb’s CycleKreb’s Cycle

Each pyruvic acid is processed to enter the Kreb’s Cycle as Acetyl CoA.

CO2 is generated -decarboxylation

reactions. Coenzymes NAD and FAD are reduced to

NADH and FADH2

Net yield of two ATPs per molecule of

glucose.

41

Steps in Kreb’s CycleSteps in Kreb’s Cycle

42

Electron Transport ChainElectron Transport Chain

•NADH and FADH2 from glycolysis and Kreb’s Cycle donate electrons to the electron carriers (ETC).•Membrane bound carriers transfer electrons by redox reactions.•Oxygen (final electron acceptor) completes the terminal step.

43

Electron Transport ChainElectron Transport Chain

The Electron Transport Chain and Chemiosmosis driven by the Proton Motive Force

44

Location of ETCLocation of ETC

Eukaryotes - Inner Mitochondrial

Membrane

Prokaryotes- Cytoplasmic Membrane

45

ATP YieldATP Yield

Glycolysis - 2Kreb’s Cycle - 2ETC- 34

Total Yield: 38

NADH yield - 2 in Glycolysis

8 in Kreb’s CycleFADH2 yield- 2 in Kreb’s Cycle

46

Anaerobic RespirationAnaerobic Respiration

Similar to aerobic respiration,

except nitrate or nitrite is the

final electron acceptor

47

FermentationFermentation

Glycolysis only

NADH from glycolysis is used to reduce the glucose

Organic compounds as the final electron acceptors (not O2)

Low ATP yields per glucose molecule compared to cellular respiration

48

FermentationFermentation

Chemistry of

fermentation:

Production of

ethyl alcohol or

lactic acid and

release of CO2

49

Types of FermentersTypes of Fermenters

Facultative anaerobes

Fermentation in the absence of oxygenRespiration in the presence of oxygen

Ex. Escherichia coli

Strict fermenters No respirationEx. yeast

50

Fermentation ProductsFermentation Products

Alcoholic fermentation

Acidic fermentation

Mixed acid fermentation

51

Mixed Acid FermentationMixed Acid Fermentation

Mixed acid fermentation and related products synthesized from pyruvate

52

BiosynthesisBiosynthesis

Amphibolic

Gluconeogenesis

Beta oxidation

Amination

Transamination

Deamination

Macromolecules

53

Amphibolic SynthesisAmphibolic Synthesis

Integration of the catabolic and anabolic

pathways (Coupled Reactions)

Intermediates serve multiple purposes

54

Amphibolic SynthesisAmphibolic Synthesis

Intermediates serve as precursors to synthesize amino acids, carbohydrates and lipids.

55

GluconeogenesisGluconeogenesis

Pyruvate (intermediate) is converted back to

glucose

Occurs when the glucose supply is low

56

Beta OxidationBeta Oxidation

Metabolism of fats into acetyl, which can

then enter the Kreb’s cycle as acetyl CoA.

57

Amino Acid SynthesisAmino Acid Synthesis

58

MacromoleculesMacromolecules

Cellular building blocks:MonosaccharidesAmino acidsFatty acidsNitrogen basesVitamins