Chapter 6
Metabolism: Fueling Cell Growth
Overview
Harvesting energy is essential for
the life and functioning of cells. In this chapter the principles of
metabolism are
presented. Enzymes are described and their role in metabolism is discussed.
Specific
metabolic pathways are described with an emphasis
on energy transformation. Respiration and
fermentation are
discussed. Photophosphorylation and carbon fixation also are presented.
Anabolic
pathways are
summarized.
Learning Objectives
After studying the material in this
chapter, you should be able
to:
1. Differentiate between the two components of
metabolism—catabolism and anabolism.
2. Distinguish between exergonic and endogonic
reactions.
3. Define enzyme and describe how enzymes
function.
4. Describe how enzymes are controlled by
inhibition (allosteric regulation).
5. Describe the role of cofactors and
coenzymes in enzyme function.
6. List and explain the factors influencing
enzymatic activity.
7. Distinguish between competitive and
noncompetitive inhibition.
8. Describe how the following types of
organisms harvest energy:
• Chemolithoautotrophs
• Chemoorganoheterotrophs
• Photoautotrophs
• Photoheterotroph
9. Define oxidation-reduction reactions.
10. Describe the
role of electron carriers.
11. Define
reducing power and explain how it is used.
12. List and
describe the three ways that ATP can be produced in a cell.
13. Define
metabolic pathway and list its components.
14. Define each
of the following and describe what occurs in each:
• Glycolysis
• Pentose phosphate pathway
• Transition step (oxidative decarboxylation
of pyruvate)
• Tricarboxylic acid cycle
• Oxidative phosphorylation
15. Define cell
respiration and describe where it occurs in the eukaryotic cell and in the
prokaryotic cell.
16.
Differentiate between aerobic and anaerobic respiration on the basis of
terminal electron acceptors.
17. Define
fermentation.
18. Describe
precisely where ATP is made.
19. Explain why
38 ATPs can be theoretically produced from the oxidation of one molecule of
glucose in
the prokaryotic
cell whereas only 36 ATPs may be produced from the same process in the
eukaryotic
cell.
20. Explain how lipid catabolism and protein catabolism can be integrated with carbohydrate metabolism.
21. Define photosynthesis.
22. Differentiate
among the following:
• Cyclic photophosphorylation
• Non-cyclic photophosphorylation
• Calvin cycle
23. Describe how the following compounds can be
synthesized through anabolic reactions:
• subunits oflipids
• amino acids
• nucleotides
24. List the four
nutritional types of microorganisms and give the energy and carbon sources for
each.
Key Concepts
1.
Metabolism is all the chemical reactions that occur in a cell.
2. Cells break down (catabolize) nutrients in a
controlled manner in order to (1) obtain energy that can
be used for cellular
activity and (2) obtain the biochemical units to build new molecules for use in
the
cell.
3. Cells build up (anabolism) new molecules in
order to (1) store energy and (2) to make new molecules
used in cellular
metabolic pathways or in cell structure.
4. Nutrients are broken down by the central
metabolic pathways which are: (1) glycolysis, (2) the
pentose-phosphate
pathway and (3) the TCA (Krebs) cycle.
5. The electron transport chain is a series of
electron carrier molecules that sequentially pass electrons
from one to another in
order to produce a proton motive force used to fuel the synthesis of ATP which
is the immediate
source of energy used in cell activities.
6. In aerobic respiration the terminal electron
acceptor is oxygen, while in anaerobic respiration the
terminal electron
acceptor is an inorganic compound other than oxygen. Aerobic respiration
results in
a greater ATP yield
than does anaerobic respiration.
7.
Fermentation is a process in which the terminal electron acceptor is an
organic molecule. The TCA
cycle and electron
transport chain are not used.
8. Enzymes (biological catalysts) are used to
catalyze chemical reactions in the cell.
9. Bacteria vary in the kinds and numbers of
enzymes that they use to synthesize various products.
Specific enzymes and
products can be used in the identification of bacterial species.
10. Bacteria vary in
the sources they use for energy and carbon.
Summary Outline
I.
Principles of metabolism
A. Catabolism
encompasses those processes that transform and release energy.
B. Anabolism
includes the processes that utilize energy to synthesize and assemble the
building
blocks of a cell.
C. Harvesting energy
1. Energy is the ability to do work.
2. The first law of thermodynamics states
that the energy in a system can never be created
or destroyed.
3. The
second law of thermodynamics states that entropy
always increases.
4. Phototrophs
harvest the energy of sunlight, using it to power the synthesis of organic
compounds.
5. Chemoorganotrophs
transform energy by organic compounds.
6. Free energy is the amount of energy that
can be gained by breaking the bonds of a
chemical.
a) Exergonic
reactions release energy.
b) Endergonic
reactions utilize energy.
D. Components of metabolic pathways
1. A
specific enzyme facilitates each step of a metabolic pathway by lowering the
activation energy of a reaction that
converts a substrate into a product.
2. ATP
is the energy currency of the cell.
a) Substrate
level phosphorylation uses the chemical energy released in an
exergonic reaction to
add P; to ADP.
b) Oxidative
phosphorylation harvests the energy
of proton motive force to do the
same thing.
3. The energy source is oxidized to release
its energy; this oxidation-reduction reaction
reduces an electron carrier.
4. NAD+, NADP+, and FAD are electron carriers. Their reduced form functions as
reducing power. NADH
and FADHz are used to provide electrons for the generation of
proton motive force.
NADPH is used in biosynthesis.
5. Precursor
metabolites are building blocks that
can be used to make the subunits of
macromolecules, but
they can also be oxidized to release energy.
E. Scheme of metabolism
1. The central metabolic pathways are:
a) Glycolysis
b) The
pentose phosphate pathway
c) The
tricarboxylic acid cycle (TCA cycle)
2. Glycolysis
oxidizes glucose to pyruvate, producing ATP, reducing power and precursor
metabolites.
3. The pentose
phosphate pathway also oxidizes glucose to pyruvate, but its primary
role is the production
of precursor metabolites and reducing power essential for
biosynthesis.
4. The transition
step forms acetyl CoA, which then
enters the tricarboxylic acid cycle
(TCA) cycle.
5. Respiration
uses the reducing power accumulated in the central metabolic pathways to
generate ATP by
oxidative phosphorylation.
a) Aerobic
respiration uses 02 as a terminal
electron acceptor. .
b) Anaerobic
respiration uses an inorganic
molecule other than 02 as a terminal
electron acceptor.
6. Fermentation
uses pyruvate or a derivative as a terminal electron acceptor rather than
oxidizing it further
in the TCA cycle; this recycles the reduced electron carrier NADH.
II.
Enzymes
A. Enzymes
function as biological catalysts,
which are not permanently changed during a
reaction.
B. The enzyme substrate binds to the active site or catalytic site to form a
temporary
intermediate called an
enzyme-substrate complex.
C. Allosteric
regulation uses an effector that
binds to the allosteric site of the enzyme which in
turn alters the
relative affinity of the enzyme for its substrate.
D. Cofactors
and coenzymes act in conjunction
with enzymes
E. Environmental
factors that influence enzyme
activity include
1. Temperature
2. pH
3. salt concentration
F. Enzyme inhibition
1. Competitive
inhibition occurs when the inhibitor
competes with the normal substrate
for the active binding
site.
2. Non-competitive
inhibition occurs when the inhibitor
and the substrate act as different
sites on the enzyme.
III.
Catabolic pathways that fuel aerobic growth ofchemoorganotrophs
A. Glycolysis
is a nine-step pathway that converts one molecule of glucose into two molecules
ofpyruvate; the
theoretical net yield is two ATP, two NADH + I-T and six different precursor
metabolites.
B. Pentose
phosphate pathway can generate some ATP, but its greatest significance is
that it
forms NADPH and two
different precursor metabolites.
C. Transition
step results in the decarboxylation
and oxidization ofpyruvate, and joins the
resulting acetyl group
to coenzyme A forming acetyl-Co A. This produces NADH + H~ and
one precursor
metabolite.
D. Tricarboxylic
acid cycle completes the oxidation of glucose; the theoretical yield is
6
NADH + 6H+, 2FADH2, 2ATP and three different
precursor metabolites.
E. Oxidative
phosphorylation
1. The reducing
power accumulated in glycolysis and the TCA cycle is used to
drive the
synthesis of ATP.
2. The electron
transport chain sequentially passes electrons, and, as a result, ejects
protons; this
mechanism generates the chemiosmotic
gradient called the proton
motive force.
3. ATP
synthetase harvests the energy
released by the electron transport chain as it
allows protons to move
back across the membrane, driving the synthesis of ATP.
IV. Catabolic pathways
that fuel anaerobic growth ofchemoorganotrophs
A. Glycolysis
and the pentose phosphate pathways are
used anaerobically to oxidize glucose
to pyruvate.
B. Anaerobic
respiration—respiration in which an
inorganic molecule other than molecular
oxygen acts as a
terminal electron acceptor.
C. Fermentation
is used by organisms that cannot respire, either because a suitable inorganic
terminal electron
acceptor is not available or because they lack an electron transport chain.
V.
Catabolism of organic compounds other than glucose
A. Hydrolytic enzymes break down
macromolecules into their respective subunits.
B. Polysaccharides
1. Amylases digest starch, releasing glucose
subunits.
2. Cellulases degrade cellulose.
3. The sugar subunits can enter glycolysis
to be oxidized to pyruvate.
C. Lipids
1. Fats are hydrolyzed by lipase, releasing
glycerol and fatty acids.
2. Glycerol is converted to the precursor
metabolite glyceraldehyde 3-phosphate; fatty
acids are degraded by
beta-oxidation, generating reducing power and the precursor
metabolite acetyl-CoA.
D. Proteins
1. Proteins are hydrolyzed by proteases.
2. Deamination removes the amino group; the
remaining carbon skeleton is then
converted into the
appropriate precursor molecule.
VI.
Chemolithotrophs are
autotrophs; they do not require an external source of organic carbon because
they can fix carbon dioxide.
VII. Phototrophs harvest the energy of sunlight and use it to
drive the synthesis of ATP.
A. The role ofphotosynthetic pigments
1. Chlorophylls are the primary pigments
used to harvest solar energy.
2.
Carotenoids are accessory pigments that absorb wavelengths of light not
absorbed by
the
chlorophylls and then transfer that energy to the chlorophylls.
B.
Photophosphorylation—light
energy excites an electron, which is passed along an electron transport chain,
generating proton motive force.
C. Electron source
1. Oxygenic
phototrophs extract electrons from
water.
2. Anoxygenic
phototrophs extract electrons from
reduced compounds other than water.
VIII. Carbon fixation—Calvin cycle is used to incorporate 002
into organic carbon.
IX. Anabolic pathways—synthesizing subunits from precursor molecules
A. Amino acid synthesis
B. Nucleotide synthesis
Terms You Should
Know
Activation energy
Active
site
Aerobic
respiration
Allosteric site
Anabolism
Anaerobic
respiration
Biosynthesis
Catabolism
Chemiosmotic theory
Chemoautotrophs
Chemoheterotrophs
Chemolithotrophs
Chemoorganotrophs
Coenzymes
Cofactors
Competitive inhibition
Electron carrier
Electron
donor
End product
Endergonic
Energy
Energy source
Entner-Doudoroff pathway
Entropy
Enzyme
Enzyme-substrate
complex
Exergonic
Feedback inhibition
Fermentation
Free energy
Glycolysis
Intermediates
Kinetic energy
Metabolic pathway
Metabolism
Non-competitive
inhibition
Oxidation-reduction reactions
Oxidative phosphorylation
Pentose phosphate pathway
Photophosphorylation
Photosynthesis
Phototrophs
Potential energy
Precursor metabolites
Products
Reactants
Substrate
Substrate level phosphorylation
Terminal electron acceptor
Transition step
Tricarboxylic acid cycle
Chapter 11 The
Diversity of Prokaryotic
Microorganisms
Overview
This chapter presents a survey of the prokaryotic
microorganisms with an emphasis on 1) patterns of
metabolism and 2)
ecophysiology. These organisms are extremely diverse and exist under a great
variety of conditions.
Some of these organisms are beneficial to human life, others have no direct
effect
and still others cause
disease.
Learning Objectives
After studying
the material in this chapter,
you should be able to:
1.
Define
• Anaerobe
• Chemolithotrophs
• Chemoorganotrophs
2. List the types ofprokaryotic microorganisms
that are found in the following groups:
• Anaerobic chemolithotrophs
• Anaerobic chemoorganotrophs—anaerobic
respiration
• Anaerobic chemoorganotrophs—fermentative
3. Define:
• Anoxygenic phototrophs
• Oxygenic phototrophs
4. List and describe the types of prokaryotic
microorganisms that are found the in the following
groups:
• Anoxygenic phototrophs
• Oxygenic phototrophs
5. Define:
• Aerobic chemolithotrophs
• Aerobic chemoheterotrophs
6. List and describe the kinds of
microorganisms included in
• Aerobic chemolithotrophs
• Aerobic chemoheterotrophs
7. List the kinds of bacteria that:
• Form endospores
• Produce cysts
• Produce fruiting bodies
• Form conidia at the end of hyphae
8. List and describe the kinds of prokaryotic
microorganisms that live in an aquatic environment.
9. List and describe the kinds of prokaryotic
microorganisms that use animals as their habitat.
10. List and describe the kinds of prokaryotic microorganisms that live
under extreme conditions.
Key Concepts
1.
Prokaryotic organisms are extremely diverse and live under a wide
variety of conditions.
2. Some prokaryotic organisms can derive
energy from the oxidation of compounds (chemotrophs)
while others derive
energy from sunlight (phototrophs).
3. Chemotrophs can be divided into two groups:
those that obtain energy by oxidizing organic
chemicals
(chemoorganotrophs) and those that obtain energy by oxidizing inorganic compounds
(chemolithotrophs).
4.
Methanogens oxidize hydrogen gas, using C02 as a terminal
electron acceptor, to generate methane.
5. Sulfur- and sulfate-reducing bacteria
oxidize organic compounds, with sulfur compounds serving as
terminal electron
acceptors, to generate hydrogen sulfide (H2S).
6. The lactic acid bacteria oxidize organic
compounds, with an organic compound serving as a
terminal electron
acceptor.
7. Phototrophs harvest energy from sunlight
and can be divided into two groups: anoxygenic and
oxygenic. Anoxygenic
phototrophs, unlike oxygenic phototrophs, do not generate oxygen because
they do not use water
as a source of electrons.
8. Obligate aerobes can generate energy only
through aerobic respiration. Facultative anaerobes prefer
to use aerobic
respiration to generate energy, but can use fermentative metabolism if oxygen
is
unavailable.
9. Bacillus and Clostridium species produce endospores. These dormant forms are
very resistant to
heat and drying and
enable these bacteria to survive adverse conditions.
10. Agrobacterium and Rhizobium derive nutrients from plants, although the former are
plant pathogens
and the latter benefit
the plant.
11. Prokaryotic
microorganisms have a variety of mechanisms that help them to live in aquatic
habitats.
These include
production of sheaths; production of prosthecae, which are extensions that
maximize
the absorptive surface
area; bioluminescence; preying upon other bacteria; using unusual methods
of locomotion such as
axial filaments or magnetic crystals to move to more desirable locations; and
storage granules.
12. Some prokaryotic
organisms use animals, including humans, as their habitat; these include
Staphylococcus species, that live under dry, salty conditions; Bacteroides, Bifidobacterium
species,
Campylobacter species and Helicobacter
species that live in the gastrointestinal tract; Neisseria
species, mycoplasma
and spirochetes that inhabit other mucous membranes; and Rickettsia,
Orientia, Ehrlichia, Coxiella and Chlamydia species
which are obligate intracellular parasites.
13. Archaea inhabit
extreme environments that include conditions of excess salinity, heat, acidity
and
alkalinity.
Summary Outline
I. Metabolic diversity
A. Anaerobic
chemoorganotrophs—anaerobic respiration
1. Chemoorganotrophs
oxidize organic compounds to obtain energy.
2. Anaerobes
use a terminal electron acceptor other than 02.
B. Anaerobic
chemoorganotrophs—fermentation
1. The end
products of fermentation include
a variety of acids and gases that are
generally
characteristic for a given species.
2.
Clostridium species
are Gram-positive rods
3.
The lactic acid bacteria are a
group of Gram-positive organisms
that produce lactic acid as their primary fermentation end-products.
4.
Propionibacterium species
are Gram-positive pleiomorphic
rods that produce
propionic acid as their primary fermentation end product.
C. Anoxygenic
phototrophs
1. Phylogenetically
diverse group of bacteria that harvest the energy of sunlight, using
photosynthesis to synthesize organic materials.
2. The
purple bacteria
a) The purple
bacteria are Gram-negative organisms that appear red, orange or
purple; the
photosynthetic apparatus is contained within the cytoplasmic
membrane.
b) The purple
sulfur bacteria preferentially use sulfur
as a source of reducing
power.
c) The purple
nonsulfur bacteria preferentially use organic
molecules as a
source of reducing power.
3. The
green bacteria
a) The green
bacteria are Gram-negative organisms that are typically green or
brownish in color.
Their light harvesting pigments are located in structures
called chlorosomes.
b) The green
sulfur bacteria use hydrogen sulfide as a source of reducing
power.
c) The green
nonsulfur bacteria are characterized by their filamentous growth;
metabolically, they
resemble the purple nonsulfur bacteria.
4. Other anoxygenic phototrophs
include a Gram-positive rod that forms endospores.
D. Oxygenic
phototrophs
1. The cyanobacteria
are a diverse group of Gram-negative bacteria that are essential
primary producers; unlike eukaryotic
photosynthesizers, they can fix nitrogen.
2. Genetic evidence indicates that chloroplasts of plants and algae
evolved from a
species of
cyanobacteria.
3. Nitrogen-fixing
cyanobacteria provide an available
source of both carbon and
nitrogen.
4. Filamentous
cyanobacteria may be involved in
maintaining the structure and
productivity of some
soils.
5. Some
species of cyanobacteria produce toxins that can be deadly to animals that
ingest heavily contaminated
water.
E. Aerobic
chemolithotrophs
1. Aerobic
chemolithotrophs generate energy by
oxidizing reduced inorganic
compounds using 02 as a terminal
electron acceptor.
2. Sulfur-oxidizing
bacteria are Gram-negative rods or spirals,
sometimes growing
in filaments.
3. The filamentous
sulfur-oxidizers Beggiatoa and Thiothrix live in sulfur springs,
sewage-polluted
waters, and on the surface of marine and freshwater sediments.
F. Nitrifiers—Ammonia oxidizers
convert ammonia to nitrite and include Nitrosomonas and
Nitrosococcus, nitrite oxidizers oxidize nitrite
to nitrate and include Nitrobacter
and
Nitrococcus.
G. Hydrogen-oxidizing bacteria are thermophilic
bacteria that are thought to be
among the
earliest bacterial
forms.
H. Aerobic
chemoorganotrophs oxidize organic compounds for energy using 02 as
a
terminal electron acceptor.
1. Obligate aerobes generate energy
exclusively by respiration.
a)
Micrococcus species
are Gram-positive cocci found in soil and on dust
particles, inanimate
objects, and skin.
b) Mycobacterium species are acid-fast.
c) Pseudomonas
species are Gram-negative rod-shaped bacteria that are
widespread in nature
and have extremely diverse metabolic capabilities.
d) Thermus aquaticus is the source
of Taq
polymerase, which is an essential
component in the polymerase chain reaction.
e) Deinococcus radiodurans can survive
high doses of gamma radiation.
2. Facultative
anaerobes
a) Corynebacteium species are Gram-positive
pleiomorphic rod-shaped
organisms that commonly inhabit the soil, water and the surface of plants.
3. Members of the family Enterobacteriaceae are Gram-negative rods that typically
inhabit the intestinal
tract of animals, although some reside in rich soil. Enterics that
ferment lactose are included in the
group called coliforms and are used
as indicators
of fecal pollution.