Chapter 8

Microbial
Metabolism

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 Catabolic and Anabolic Reactions
• Metabolism: the sum of the _________ reactions in
an organism
– Catabolism: provides energy and building blocks for
anabolism
– Anabolism: uses energy and building _____ to build large
molecules
 Catabolic and Anabolic Reactions
• A metabolic pathway is a sequence of
_________ catalyzed chemical reactions in a cell
• Metabolic pathways are determined by enzymes
• Enzymes are encoded by ________________
I. The Activation E Barrier
A. activation E (EA)
1. E needed to ______ bonds into position for a reaction
2. can be ________________
3. determines the rate of the reaction
a. e.g. if EA is low enough then rate will be
relatively high
 Collision Theory
• The collision theory states that chemical
reactions can occur when atoms, ions, and
molecules _____________________
• Activation energy is needed to disrupt
electronic configurations
• Reaction rate is the frequency of collisions
with enough energy to bring about a reaction
• Reaction rate can be increased by enzymes or
by increasing _________________ or pressure
 Enzyme Components
• Apoenzyme: ________________
• Cofactor: nonprotein component
– Coenzyme: organic cofactor ( Coenzyme A, NAD+,
FAD+, NADP+)
• Holoenzyme: apoenzyme plus _____________
The _____________ of enzymatic action.
Factors Influencing Enzyme Activity
Factors that influence enzymatic activity, plotted for a hypothetical enzyme, pages 322-323.

(a) Temperature. The enzymatic activity (rate of reaction catalyzed by the

enzyme) increases with increasing temperature until the enzyme, a protein, is
denatured by heat and inactivated. At this point, the reaction rate falls steeply.
Factors that influence enzymatic activity, plotted for a hypothetical enzyme.

(b) pH. The enzyme illustrated is most active at about pH 5.0.

Factors that influence enzymatic activity, plotted for a hypothetical enzyme.

(c) Substrate concentration. With increasing concentration of

substrate molecules, the rate of reaction increases until the active sites
on all the enzyme molecules are filled, at which point the maximum rate
of reaction is reached.
Enzyme _______________________.

Normal Binding of Substrate Action of Enzyme Inhibitors

Substrate Competitive
inhibitor
Active site

Enzyme
_________________________
Enzyme inhibitors.

Normal Binding of Substrate Action of Enzyme Inhibitors

Altered
Substrate active site
Active site

Enzyme

Noncompetitive
inhibitor Allosteric
site
_______________________ inhibition.
Substrate

Pathway
Operates

Pathway
Shuts Down

Enzyme 1

Allosteric site
Intermediate A Bound
end-product

Feedback Inhibition
Enzyme 2

Intermediate B

Enzyme 3

End-product
 ATP Production and Energy Storage
• Organisms release ______ from nutrients; can be
concentrated and stored in high-energy phosphate
bonds of ATP
• Phosphorylation – organic phosphate is added to
substrate
• Cells phosphorylate ADP to ATP in three ways
– ________-level phosphorylation
– Oxidative phosphorylation
– Photophosphorylation

• Anabolic pathways use some energy of ATP by

breaking a phosphate bond
Substrate ______ Phosphorylation
• ATP made during glycolysis is a result of substrate-level
phosphorylation. One of the two enzymatic reactions in the
energy payoff phase of Embden Meyerhof-Parnas glycolysis
that produce ATP in this way is shown here.
 Oxidation-Reduction Reactions
• Oxidation: __________________ of electrons
• Reduction: ____________ of electrons
• Redox reaction: an oxidation reaction paired
with
a reduction reaction
 Oxidation-Reduction Reactions
• In biological systems, the electrons are often
associated with hydrogen atoms
• Biological oxidations are often dehydrogenations

ANIMATION Oxidation-Reduction Reactions

 Carbohydrate Catabolism
• The breakdown of carbohydrates to release
energy
– Glycolysis
– Krebs cycle
– Electron
transport chain
Glycolysis
 The energy investment phase of the Embden-Meyerhof-Parnas ________
pathway uses two ATP molecules to phosphorylate glucose, forming two
glyceraldehyde 3-phosphate (G3P) molecules. The energy payoff phase
harnesses the energy in the G3P molecules, producing four ATP
molecules, two NADH molecules, and two pyruvates.

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Figure 5.12 An outline of the reactions of glycolysis (Embden-Meyerhof pathway).

1 Glucose enters the cell and is phosphorylated. A

molecule of ATP is invested. The product is glucose 6-phosphate.

Glucose 6-phosphate 2 2 Glucose 6-phosphate is rearranged to form fructose

6-phosphate.

Fructose 6-phosphate 3 The P from another ATP is used to produce fructose 1,6-

diphosphate, still a six-carbon compound. (Note the total

investment of two ATP molecules up to this point.)

Fructose 1,6-diphosphate 4 An enzyme cleaves (splits) the sugar into two three-carbon
molecules: dihydroxyacetone phosphate (DHAP) and
glyceraldehyde 3-phosphate (GP).

Glyceraldehyde 3-phosphate (GP) 5 DHAP is readily converted to GP (the reverse action may also occur).

6 The next enzyme converts each GP to another three-carbon compound,

1,3-diphosphoglyceric acid. Because each DHAP molecule can be
converted to GP and each GP to 1,3-diphosphoglyceric acid, the result is
two molecules of 1,3-diphosphoglyceric acid for each initial molecule of
glucose. GP is oxidized by the transfer of two hydrogen atoms to NAD + to
1,3-diphosphoglyceric acid
form NADH. The enzyme couples this reaction with the creation of a high-
energy bond between the sugar and a P . The three-carbon sugar now has
two P groups.

3-phosphoglyceric acid 7
The high-energy P is moved to ADP, forming ATP, the first ATP
production of glycolysis. (Since the sugar splitting in step 4, all products are
doubled. Therefore, this step actually repays the earlier investment of two ATP
2-phosphoglyceric acid molecules.)

8
An enzyme relocates the remaining P of 3-phosphoglyceric acid to
form 2-phosphoglyceric acid in preparation for the next step.
Phosphoenolpyruvic acid (PEP) 9 By the loss of a water molecule, 2-phosphoglyceric acid is

converted to phosphoenolpyruvic acid (PEP). In the process, the

phosphate bond is upgraded to a high-energy bond.

10 This high-energy P is transferred from PEP to ADP, forming ATP. For

each initial glucose molecule, the result of this step is two molecules of ATP
and two molecules of a three-carbon compound called pyruvic acid.
 Alternatives to Glycolysis
• ________________ phosphate pathway
– Uses pentoses and NADPH
– Operates with glycolysis
• ________________-Doudoroff pathway
– Produces NADPH and ATP
– Does not involve glycolysis
– Pseudomonas, Rhizobium, Agrobacterium
Alternatives to Glycolysis

Green = ED

Blue = PPP

Red = Glycolysis
The __________________ cycle.
1 A turn of the cycle begins
as enzymes strip off the CoA
portion from acetyl CoA and
combine the remaining two-
carbon acetyl group with
oxaloacetic acid. Adding the
acetyl group produces the six-
carbon molecule citric acid.

2 – 4 Oxidations generate
6 – 8 Enzymes rearrange
NADH. Step 2 is a
chemical bonds, producing three
rearrangement. Steps 3 and 4
different molecules before
combine oxidations and
regenerating oxaloacetic acid. In
decarboxylations to dispose of
step 6, an oxidation produces
two carbon atoms that came
FADH2. In step 8, a final oxidation
from oxaloacetic acid. The
generates NADH and converts
carbons are released as CO2,
malic acid to oxaloacetic acid,
and the oxidations generate
which is ready to enter another
NADH from NAD+. During the
round of the Krebs cycle.
second oxidation (step 4), CoA
is added into the cycle,
forming the compound
succinyl CoA.
5 ATP is produced by substrate-
level phosphorylation. CoA is
removed from succinyl CoA,
leaving succinic acid.
Coenzyme A

 CoA does not enter the ________________ Cycle

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 The Electron Transport Chain
• A series of carrier molecules that are, in turn,
oxidized and reduced as electrons are passed
down the chain.
• Energy released can be used to produce a proton
gradient that can be used to generate ATP. This
process is called ______________________
An electron transport chain (system).

Energy
Electron Transport Chain
 Note that FADH2 gives up its electrons to _________________

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Electron transport and the chemiosmotic generation of ATP.
Cell Periplasmic Plasma Outer Inner
wall space membrane membrane membrane

Intermembrane space
Mitochondrial matrix

Cytoplasm
Bacterium Mitochondrion

Periplasmic space of prokaryote

or intermembrane space of
eukaryote

Prokaryotic
plasma
membrane
or eukaryotic
inner
mitochondrial
membrane

Cytoplasm of
prokaryote or
mitochondrial
matrix of
eukaryote
Figure 8.155 Chemiosmosis.

High H+ concentration

Membrane

Low H+ concentration
 A Summary of Respiration
• Aerobic respiration: the final electron
acceptor in the electron transport chain is
molecular oxygen (O2)
• Anaerobic respiration: the final electron
acceptor in the electron transport chain is
_____________________________
– Yields __________ energy than aerobic respiration
because only part of the Krebs cycle operates
under anaerobic conditions
 Anaerobic Respiration
Electron Acceptor Products
NO3– NO2–, N2 + H2O

________________________________ H2S + H2O

CO32 – CH4 + H2O

 Carbohydrate Catabolism
• ATP produced from complete oxidation of one
glucose using aerobic respiration

By Oxidative Phosphorylation
Pathway By Substrate-Level
Phosphorylation
From NADH From FADH

Glycolysis 2 6 0

_________________ 0 6 0

Krebs cycle 2 18 4

Total 4 30 4
 Fermentation
• Any spoilage of food by microorganisms
(general use)
• Any process that produces _______ beverages
or acidic dairy products (general use)
• Any large-scale microbial process occurring
with or without air (common definition used
in industry)
 Fermentation
• Scientific definition:
– Releases energy from oxidation of organic
molecules
– Does __________ require oxygen
– Does _______ use the Krebs cycle or ETC
– Uses an organic molecule as the
final electron acceptor
Fermentation.
A fermentation test.
Lipid catabolism.

Lipase

Beta-oxidation

Krebs
cycle
Catabolism of various organic food molecules.

Krebs
cycle

Electron
transport
chain and
chemiosmosis
 Protein Catabolism
Urease
____ NH3 + CO2
BIOCHEMICAL TESTS

Human Tuberculosis – Dallas, Texas

Figure A: An identification scheme for selected species of slow-growing mycobacteria.

 Photosynthesis
• Oxygenic:

• ___________________________:

ANIMATION: Photosynthesis: Comparing Prokaryotes and Eukaryotes

 Photosynthesis
• Photo: conversion of ________ energy into chemical
energy (ATP)
– Light-dependent (light) reactions
• Synthesis:
– Carbon fixation: fixing carbon into organic molecules
– Light-independent (dark) reaction: _____________ cycle

ANIMATION Photosynthesis: Overview

Cyclic Photophosphorylation
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A simplified version of the Calvin-Benson cycle.

Input

Ribulose bisphosphate 3-phosphoglyceric acid

1,3-diphosphoglyceric acid

Calvin-Benson cycle

Glyceraldehyde Glyceraldehyde
3-phosphate 3-phosphate

Output

Glyceraldehyde 3-phosphate

Glyceraldehyde 3-phosphate
Calvin Cycle

 Ribulose bisphosphate carboxylase = __________

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Table 5.6 Photosynthesis Compared in Selected Eukaryotes and Prokaryotes
 Metabolic Diversity among Organisms p 319
Nutritional Type Energy Source Carbon Source Example

Photoautotroph Light CO2 Oxygenic:

Cyanobacteria, plants
Anoxygenic: Green
bacteria, purple
bacteria

Photoheterotroph Light ______________ Green bacteria, purple

nonsulfur bacteria

Chemoautotroph Chemical CO2 Hydrogen-, sulfur-,

nitrogen-, Iron-, and
carbon monoxide
oxidizing bacteria
Chemoheterotroph Chemical Organic Fermentative bacteria
compounds Animals, protozoa,
fungi, bacteria