bio 244 chapter 5 notes

8/9/2019 Bio 244 Chapter 5 Notes

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Microbial Metabolism

(Chapter 5)

Lecture Materials

for

Amy Warenda Czura, Ph.D.

Suffolk County Community College

Eastern Campus

Primary Source for figures and content:

Tortora, G.J. Microbiology An Introduction 8th, 9th, 10th ed. San Francisco: Pearson

Benjamin Cummings, 2004, 2007, 2010.

Metabolism = sum of all chemical reactions in

a living organism:

- Catabolic reactions: break complex organic

compounds into simper ones, usually via

hydrolysis, usually exergonic

- Anabolic reactions: build complex molecules

from simpler ones, usually via dehydration

synthesis, usually endergonic

*Catabolic reactions provide the energy (ATP)

and building blocks to drive anabolic

reactions (cell growth and repair)

(handout)

Metabolic pathway= series of steps to

perform a chemical reaction in living

organisms, requires a new enzyme at eachstep

Pathways used by an organism depend on

enzymes encoded by the DNA: what types

of reactions any one organism can perform

is determined by its genetic makeup

Enzymes

- biological catalysts, catalytic proteins

- speed up reactions by lowering activation

energy, orient molecules to favor reaction

- can increase reaction rates up to 10 billion X

faster than random collisions allow

Turnover number= maximum number ofsubstrate molecules an enzyme converts to

product each second,

different for different enzymes

Each enzyme has a unique 3D shape: it will

bind only its specific substrate(s) at the

active site and catalyze only one specific

reaction resulting in particular product(s)

All cellular reactions performed by enzymes:

cells require thousands of different enzymes

all encoded by the DNA to carry out all

reactions required for life

The majority of proteins in a cell are enzymes

Amy Warenda Czura, Ph.D. 1 SCCC BIO244 Chapter 5 Lecture Notes


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Enzyme Nomenclature

-most end in - ase

-6 classes based on type of reaction:

1. Oxidoreductase

oxidation/reduction reactions

2. Transferase

transfer functional groups

3. Hydrolase

hydrolysis

4. Lyase

removal of atoms without hydrolysis

5. Isomerase

rearrangement of atoms in a molecule

6. Ligase

joining of two molecules

- typically named for reaction catalyzed and

substrate acted upon:

e.g. DNA ligase: functions to join two pieces

of DNA together

Enzyme Components:

Most enzymes have two parts:1.Apoenzyme= protein part, inactive by itself

2. Cofactor= non-protein part, usually a metal

ion, turns the apoenzyme on

Coenzyme = organic cofactor

apoenzyme + cofactor = holoenzyme

(whole active enzyme)

Metal ion cofactors form a bridge between

enzyme and substrate to facilitate the

reaction

Coenzymes accept/donate atoms or carry

electrons to transfer to other molecules

Two most important coenzymes:

- NAD+

(nicotinamide adenine dinucleotide) Carries electrons in catabolic reactions

- NADP+

(nicotinamide adenine dinucleotide phosphate)

Carries electrons in anabolic reactions

Both are derived from the B vitamin nicotinic

acid

Mechanism of Enzyme Action

(on handout)

1. The substrate contacts the active site

2. The enzyme-substrate complex is formed.

3. The substrate molecule is altered

atoms are rearranged,

or the substrate is broken into smaller parts,

or the substrate is combined with another molecule

4. Product(s) is/are released from the active site.

5. The enzyme is unchanged and can catalyze a new reaction.

Each enzyme acts on only one substrate, but

any one substrate can be acted upon by

multiple enzymes



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Enzymes must be controlled to maintain

homeostasis: two ways to control:

1. level of synthesis (amount produced)

2. level of activity (control cofactors, restrict

access to substrate)

Factors that influence enzyme activity:

1. Temperature

!temp = !reaction rate

until denaturation

-Enzymes have an optimal

temperature = temp at

which the enzyme

catalyzes the reaction at

its maximum rate

-above this they become denatured

denatured = unfolded, enzyme no longer fits

substrate, cannot catalyze the reaction

2. pH

-enzymes have an optimal

pH that favors the native

conformation (correct

folding)

-pH that is too acidic or too

basic will denature the enzyme

3. Substrate concentration

!substrate conc = !rxn rate

until saturation

-each enzyme has a

maximum turnover

number = top speed for

converting substrate into

product

-at saturation, the active site is always full: the

enzyme works at maximum speed

-addition of more substrate beyond the

saturation point will not increase the

reaction rate

saturation

4. Inhibitors

inhibitor = a substance that

blocks enzyme functionThree types:

A. Competitive inhibitors

-block the active site

-same shape as the substrate

-competes for the active site

thus blocking enzyme

reaction with the substrate

-some bind permanently thus

killing the enzyme =

irreversible competitive inhibitor-some bind reversibly and just

slow the reaction rate =

reversible competitive inhibitor

B. Noncompetitive inhibitors

-does not bind the active site

-binds elsewhere

= the allosteric site

-binding of inhibitor to the allosteric site

causes a shape change in the whole enzyme

such that substrate no longer fits in theactive site = allosteric inhibition

-a reversible allosteric inhibitor will slow the

reaction rate

-an irreversible allosteric inhibitor will kill theenzyme permanently

C. Enzyme poisons

-bind up metal ion cofactors thus preventing

formation of the holoenzyme



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Usually there are many steps in a metabolic

pathway to convert substrate to final

product

Each step requires a different enzyme

Feedback inhibition / End product inhibition:

-the product controls its own rate of formation

-occurs when the final

product can inhibit one

of the enzymes in the

pathway

-when product

accumulates, the

pathway is shut

down to prevent

over-production

-common to

anabolic pathways

-usually functions

by reversible

allosteric inhibition of the first enzyme

Energy Production In A Cell

(notes on typed handout)

Metabolism overview

play Metabolism.mpg

Glycolysis

Decarboxylation

Krebs Cycle



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Electron Transport Chain Summary of aerobic respiration

Fermentation Catabolism of organics for energy production



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Photosynthesis: light-dependent reactions

e.g. green and purple non-sulfur bacteria

e.g. plants, algae, cyanobacteria

Light-independent reactions

Summary of energy production Biochemical tests

-each organism produces a unique set of

enzymes that determine what type ofmetabolic reactions it can carry out

-often a microbe can be identified based on the

substrates it can metabolize and the

products it generates

e.g.EscherichiaandEnterobacterboth

catabolize glucose butEscherichiawill

produce mixed acids andEnterobacter

will produce butanediol (neutral)

Escherichiacan ferment lactose into

acid plus gas, Salmonellacannotferment lactose

-results from lab assays can be compared to

known metabolic profiles (in Bergeys

Manual) to identify unknowns

In the environment, often one organisms

waste serves as anothers fuel



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Metabolic Diversity

Organisms classified by nutritional patterns:

Energy source:

Phototrophs = light

Chemotrophs = redox rxns

Carbon source:

Autotrophs = carbon dioxide

Heterotrophs = organic molecules

(handout)

Photoautotrophs

-light for energy

(non-cyclic photophosphorylation)

-CO2for carbon

(Calvin-Benson cycle)

-e.g. most photosynthetic bacteria, algae,

plants

- can be:

Oxygenic: H from H2O used to reduce

CO2producing O2as waste e.g.

Cyanobacteria, algae, plants

Anoxygenic: no O2produced, other

molecules like H2S used to reduce CO2e.g. green and purple sulfur bacteria

Photoheterotrophs

-light for energy

(cyclic photophosphorylation)

- organics for carbon (respiration)

- e.g. green and purple non-sulfur bacteria

- always anoxygenic

Chemoautotrophs

- electrons from inorganics for energy (redox)

- CO2for carbon (Calvin-Benson cycle)- compounds used for oxidative

phosphorylation: H2S, S, NH3, NO2-, H2,

Fe2+, CO

(electron acceptor in respiration)

- e.g. Few bacteria, e.g. Pseudomonas

Chemoheterotrophs

- electrons from H in organics for energy

(redox reactions)

- C from same organics for carbon(respiration)

- compounds used for oxidative

phosphorylation: O2, organics, inorganics

- classified based on source of organics:

saprophytes - dead organics

parasites - nutrients from living host

- e.g. most bacteria, all fungi, all protozoa, all

animals (including humans)

energy production = catabolic reactions to

generate ATP

biosynthesis = anabolic reactions use ATP andbuilding blocks to generate new organic

molecules

Biosynthesis

Autotrophs: fix CO2via Calvin-Benson cycle

Heterotrophs: need organics to supply Carbon

Polysaccharide Biosynthesis

- catabolism/hydrolysis of carbohydrates,

lipids and amino acids can provide carbonfor glucose synthesis

-glucose is bonded into polysaccharides via

dehydration synthesis with ATP

- carbs used for: glycocalyx, cell walls,

complex molecules (e.g. glycoproteins),

and energy storage



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Lipid Biosynthesis

-many different lipids, different structures

-e.g. triglyceride (fat) = glycerol + 3 fatty

acids

- glycerol derived from a 3-carbon glycolysis

intermediate

- fatty acids = hydrocarbon chains, built by

linking acetyl molecules (via dehydration

synthesis with ATP)

- lipids used for: cell membranes, cell walls,

energy storage, parts of complex

molecules

Amino Acid and Protein Biosynthesis

- protein = peptide bonded amino acids

- some organisms must ingest amino acids

- some synthesize them from glucose and

inorganic salts or Krebs cycle

intermediates (amination)

-some perform amino acid conversion

(transamination)

- amino acids are peptide bonded together via

dehydration synthesis with ATP- polypeptides self-fold into the native

conformation of the protein

- proteins used for: enzymes (metabolism,

regulation), transport, structure

Nucleic Acid Biosynthesis

(nucleotides for DNA and RNA synthesis)

A, G = purines, double ring structureT, C, U = pyrimidines, single ring structure

- ring structures generated from amino acids:

aspartic acid, glycine, and glutamine

- ring attached to sugar and phosphate to

create nucleotide

Nucleotide = pentose sugar + phosphate +

base (purine or pyrimidine)

Nucleotides are bonded via dehydration

synthesis with ATP to form DNA and

RNA-DNA & RNA used for information storage

Integration of Metabolism

Amphibolic pathways - can function in both

anabolic and catabolic reactions- e.g. Krebs Cycle:

catabolism - ATP production

anabolism - intermediates used to

synthesize amino acids

Am Warenda C ra Ph D 8 SCCC BIO244 Chapter 5 Lect re Notes

bio 244 chapter 5 notes

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