Download Introductory Microbiology Chap. 5 Chapter Outlines/Notes I

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Introductory Microbiology
Chap. 5
Chapter Outlines/Notes
I.
II.
III.
IV.
V.
VI.
VII.
VIII.
IX.
X.
XI.
Catabolic and Anabolic Reactions
Enzymes
Energy Production
Carbohydrate Metabolism
Lipid and Protein Catabolism
Biochemical Tests and Bacterial Identification
Photosynthesis
A Summary of Energy Production Mechanisms
Metabolic Diversity among Organisms
Metabolic Pathways of Energy Use
The Integration of Metabolism
Introduction
What basic things do living organisms have to acquire in order to live?
What determines what molecules or energy sources a specific species needs or is able to use?
All living cells’ energy ‘currency’:
Slide 1
Term: Phosphorylation
Note: Cells use only two kinds of energy: 1) light energy: trapped and used by plants, algae, and some bacteria for
photosynthesis and 2) chemical energy: the energy held in the bonds of various chemicals. Cells do not use thermal
or electrical energy because they don't have thermal or electrical converters. Thermal potential (that is, temperature)
affects the rate of chemical reactions, but does not provide any energy. What about the electrical signals of nervous
impulses? The cells use energy in the form of ATP to generate electric potentials in the membrane of nerve cells and
fibers. Those electrical signals are not ‘used’ by the cell to perform other work.
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Most metabolic processes are ‘similar’ in all cells, but not all. Microbes can do
things we cannot do! Crazy things, like eat petroleum or radioactive materials and
things that are waste products to us. On the other hand, there are microbes that
cannot live in our environment, such as those that are killed by oxygen.
I. Catabolic and Anabolic Reactions
A.
METABOLISM :


Two categories of Chemical Processes: Catabolic and Anabolic Reactions
Metabolic ‘Pathways’
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B. Molecules and Energy- intertwined….
Role of ATP
Fig. 2.18 on p. 49
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II. Enzymes: How they function and what can affect them
Enzymes increase the rate of chemical reactions by decreasing the activation energy required for
that specific reaction.
A. Collision Theory
SLIDE 2
B. Enzymes and Chemical Reactions
SLIDE 2
Catalysts
Substrate(s)
Product(s)
Decrease activation energy
C. Enzyme Specificity and Efficiency
Specificity
The turnover number is generally 1 to 10,000 molecules per second
D. Naming Enzymes
See Table 5.1 p. 116 Enzyme Classification Based on Type of Chemical Reaction Catalyzed
E. Enzyme Components
Slide 3 Fig. 5.3
Apoenzyme (protein portion)
Cofactor (nonprotein portion)
Haloenzyme
F. The Mechanism of Enzymatic Action: The sequence of events in enzyme action on the
reactant(s), the enzyme’s substrate(s).
Lock and Key Model
SLIDE 4 Fig. 5.4
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G. Factors Influencing Enzyme Activity
SLIDE 5, 6 Fig. 5.7
End of Chap. ‘Study Questions’ Review #2 a-c & Critical Thinking #2
1. Example of Competitive Inhibition and its use in Medicine: Sulfa Drugs
All cells require folic acid for growth. Folic acid (vitamin B9) in food diffuses or
is transported into human cells. However, folic acid cannot cross bacterial cell walls by
diffusion or active transport. For this reason bacteria must synthesize folic acid from paminobenzoic acid (PABA). (Find folic acid Table 5.2 p. 117). Folic acid is a vitamin
that functions as an enzyme cofactor in the synthesis of nucleotide nitrogen bases. p. 120
Sulfa drugs are chemically similar (chemical analogues) to the chemical PABA.
See reactions below for normal functioning (top reaction) and enzyme inhibition when sulfa
drugs are used (bottom reaction).
When sulfa drugs
are present:
Since sulfa drugs
are chemically
similar to
(analogues of)
PABA, they may
“trick” the
enzyme into
using the sulfa
drug to produce
folic acid instead
of PABA. In
effect, the sulfa
drug competes
with the PABA.
When the enzyme is ‘tricked’, the folic acid in the bacterial cell will not produce nitrogen bases.
It there is a shortage of nitrogen bases, DNA cannot be replicated, and therefore, growth stops
(no binary fission). The bacterial cell has been ‘inhibited’.
To date about 15,000 sulfonamide derivatives, analogues, and related compounds have been
synthesized.
Some disadvantages of sulfa drugs:
1) Only bacteriostatic, not bactericidal
2) Resistance
3) Hypersensitivity
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4) Crystallization in kidney of patient
2. Noncompetitive Inhibition See Fig. 5.7c p. 120
Allosteric site
H. Feedback Inhibition
Example: Production of the amino acid isoleucine
See Fig. 5.8 p. 121
I. Ribozymes
What are they and what chemical reactions do they catalyze?
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III. Energy Production
A. Oxidation-Reduction Reactions
Provide
energy
for…
SLIDE 7, 8, 15, 17
End of Chapter ‘Study Questions’ Multiple Choice #1
Removal and Gain of
B. The Generation of ATP: Phosphorylation of ADP to ATP
Energy is then in…
SLIDE 9, 10
1. Substrate-level phosphorylation
SLIDE 10, 11, 14, 17
2. Oxidative phosphorylation
SLIDE 10, 12, 20
3. Photophosphorylation
SLIDE 10, 13
End of Chapter ‘Study Questions’ Review #5
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C. Metabolic Pathways of Energy Production
In the cell, there are many series of enzymatically catalyzed chemical reactions that store energy
and release energy from organic molecules- carbohydrates, proteins, and lipids. Catabolic
reactions with these molecules release energy for ATP production and anabolic reactions use the
energy in those ATPs primarily to synthesize large forms of these molecules.
IV. Carbohydrate Metabolism
A. Glycolysis
SLIDE 14-17
Fig. 5. 11 Foundation Figure: An Overview of Respiration and Fermentation
Fig. 5.12 Outline of the reactions of glycolysis



Biochemical pathway (10 reactions) in which ONE molecule of GLUCOSE is
OXIDIZED to form 2 molecules of PYRUVIC ACID.
NAD (nicotinamide adenine dinucleotide, an important electron carrier) is reduced
ATP is required in the first stage of glycolysis and formed in the later stage of glycolysis
B. Alternatives to Glycolysis
Text discussion p. 125, 127
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After glycolysis…
NEXT: Either Cellular Respiration or Fermentation
C. Cellular Respiration
1. Aerobic respiration
Define respiration: p. 127
a. Glycolysis
b. Preparing for the Kreb cycle
SLIDE 18 Fig. 5.13 p. 128
c. Krebs cycle
SLIDES 19 Fig. 5.13
d. Electron transport chain/ Chemiosmosis/ADP Phosphorylation
Electron transport chain: A series of electron carriers are oxidized (lose
electrons) & other electron carriers are reduced (gained electrons) as
electrons are passed from one electron carrier to another.
NADH and FADH2 will donate their electrons to electron carriers located
in the prokaryotic plasma membrane. Eukaryotes- occur in the
mitochondria.
Oxygen is the final electron acceptor in aerobic respiration.
Before continuing, turn the page and draw the electron transport chain. Then come back!
Info:
 Some electron carriers pick up one electron, others pick up more than one electron.
 Some electron carriers carry hydrogen atoms (1e-, 1p+); others ONLY CARRY
ELECTRONS (THE PROTON IS SEPARATED FROM THE ELECTRON IN THE H
ATOMS).
 In the electron transport system, FADH2 donates its electrons after NADH.
 There also is anaerobic respiration (p. 12 this document) where the final electron acceptor
is NOT oxygen. Less common & doesn’t produce as much ATP.
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SLIDE 20 Fig. 5.16 ETC and chemiosmotic generation of ATP
Electron Transport Chain
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Chemiosmosis
Fig. 5.15 p. 130, Fig. 5.16 p. 131
1) Occurs simultaneously with the electron transport chain (they are coupled) to transfer the
energy to form ATP from ADP and phosphate (ADP phosphorylation).
2) At certain points along the electron transport chain, the hydrogen atom is ‘split’; the electron
and the proton are separated.
Remember, some electron carriers carry hydrogen atoms (1e- & 1p+), others only carry e-. So
what happens to the protons in the H atoms when an electron carrier only picks up the e-?
3) The protons are pumped out of the cell (through the plasma membrane) & the electron is then
passed to other electron carriers.
4) This creates a situation where there are more protons on the external side of the plasma
membrane than are on the internal side of the plasma membrane; in other words, a gradient is
formed.
5) This gradient creates a force.
6) Chemiosmosis is the process of creating a proton gradient (by movement of protons across
the plasma membrane) and the subsequent movement of the protons back into the cell through
specific channels through the enzyme ATP synthase.
ATP Generation: ADP Phosphorylation
1) Bonding of a phosphate group to ADP to form ATP.
2) The energy required to bond the phosphate to ADP (and that is then stored in the resulting
bond) is provided by the movement of protons back into the cell during chemiosmosis.
3) When the protons rush back into the cell (due to the gradient), energy is released. This may
cause a CONFORMATIONAL (shape) change in the enzyme ATP synthase.
ATP synthase that then catalyzes the reaction:
SLIDE 21 Comparing Eukaryotes and Prokaryotes: Where in the cell do these processes occur?
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How many ATPs are generated from aerobic respiration through Substrate-Level
Phosphorylation only?
How many ATPs are generated from aerobic respiration through Substrate-Level and Oxidative
Phosphorylation?
Overview Fig. 5.17 Summary of aerobic respiration p. 133
Overall Summary Reaction of Aerobic Respiration:
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Anaerobic Respiration.
SLIDE 22, 23
What takes the place of oxygen?
The amount of energy generated varies depending on the electron acceptor (2-36 ATPs).
EXAMPLES:
a. Sulfate. In marine sediments this leads to large amounts of sulfate reduction - Sulfate
SO42- is converted (reduced) to hydrogen sulfide H2S - which some may be familiar with
as the rotten egg smell and black material that can be found just a few centimeters below
sediment surfaces.
b. Nitrate NO3-. which is converted (reduced) to nitrite NO21-, nitrous oxide N2O, or
nitrogen gas N2 in the process.
c. Metal ions. For example: Fe+2, Mn+2
d. Carbonate, CO32-. is converted (reduced) to methane, CH4. This is called
methanogenesis Very little energy is obtained from methanogenesis and vast amounts of
substrate need to be turned over to make a living.
What are these organisms?
Primarily live in
conditions.
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D. Fermentation
Definition
SLIDE 24
Overview
SLIDE 25 Fig. 5.18 b p. 134
Two Primary Categories of Fermentation
SLIDE 26 Fig. 5.19 p. 136
Examples of Types & Importance of Fermentation
SLIDE 27 Table 5.4 p. 137
SLIDE 28 Table 5.4 p. 137
See Table 5.5 Aerobic Respiration, Anaerobic Respiration, and Fermentation Compared p. 137
Fig. 5.11 p. 125 Foundation Figure An Overview of Respiration and Fermentation
End of Chapter ‘Study Questions’
Review #4 a and b
Multiple Choice #7-10
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V. Lipid and Protein Catabolism
SLIDE 29
Summary of the interrelationships of carbohydrate, lipid and protein catabolism
Fig. 5.21 p. 138
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VI. Biochemical Tests and Bacterial Identification: Directly relates to your ‘Unknown’
laboratory exercises
VII. Photosynthesis p. 140-1
VIII. A Summary of Energy Production Mechanisms
SLIDES 30, 31
p. 141
See Requirements for ATP (energy sources, electron carriers, final electron acceptors)
Fig. 5.27 p. 143
End of Chapter ‘Study Questions; Multiple Choice #3
IX. Metabolic Diversity among Organisms p. 142
Four Categories (Nutritional Patterns): Where do you get your energy and where do you get
your C for the organic molecules you need?
SLIDE 32 (See Fig. 5.28 p. 143)
End of Chapter ‘Study Questions’ Review #7
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X. Metabolic Pathways of Energy Use p. 146
Now you have ATP and Carbon (and some other basic stuff), what are you going to do with it?
Describe the major types of anabolism and their relationship to catabolism.
A. Polysaccharide Biosynthesis
B. Lipid Biosynthesis
C. Amino acid and Protein Biosynthesis
D. Purine and Pyrimidine Nitrogen base Biosynthesis
XI. The Integration of Metabolism p. 147
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Amphibolic pathways: Metabolic pathways that have both catabolic and anabolic functions
SLIDE 33, 34 Fig. 5.33 p. 149
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SLIDE 35
Metabolism The Big Picture
End of Chapter ‘Study Questions’ Review #1h
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