Introductory Microbiology Chap. 5 Chapter Outlines/Notes

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Introductory Microbiology
Chap. 5
Chapter Outlines/Notes
Introduction
What are you and microbes and all living things made of, i.e., what forms the structures in a
living cell, and what performs living functions?
What do living cells have to do to obtain the things they need to form the above structures and
perform the above functions?
What molecules allow organisms to acquire the things they need for life processes at the time
they need them?
How does the (above answer) function to do that?
So cells need
and
.
What determines what molecule source or energy source a specific species can use?
Both are central to METABOLISM. Define.
Slide 1, 2
All living cells’ energy ‘currency’:
Note: Cells use only two kinds of energy: 1) light energy: trapped and used by plants 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? They 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.
1
Chemical reactions are central to LIFE: Catabolic and Anabolic Reaction Pathways Slides 3 & 4
Chapter 5 Microbial Metabolism p. 113
Most processes are the same/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.
Online Site http://www.aw-bc.com/microplace/
 Pretest #1-10, 14-16
I. Catabolic and Anabolic Reactions p. 114 Slides 3 & 4
A.
METABOLISM : Two categories of Chemical Processes/Reactions

Catabolic and Anabolic Reactions

Metabolism and Metabolic Pathways Slide 4
2
Chapter 5 Microbial Metabolism
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 (not on exam)
Photosynthesis
A Summary of Energy Production Mechanisms
Metabolic Diversity among Organisms
Metabolic Pathways of Energy Use
The Integration of Metabolism
Online Site http://www.aw-bc.com/microplace/
 Pretest #1-10, 14-16
I. Catabolic and Anabolic Reactions
A.
SLIDES 3 & 4
METABOLISM : Two categories of Chemical Processes/Reactions
1. Catabolic and Anabolic Reactions
2. Metabolism and Metabolic Pathways
3
B. Molecules and Energy- intertwined….
See Text Fig. 5.1
Role of ATP
See similar Fig. 2.18 on p. 49
Textbook Online Site http://www.aw-bc.com/microplace/ Metabolism Overview Animation with Quizzes
4
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 5
B. Enzymes and Chemical Reactions
Catalysts
Substrate
Decrease activation energy
C. Enzyme Specificity and Efficiency
SLIDE 6
Specificity
Turnover number
D. Naming Enzymes
See Table 5.1 p. 116 Enzyme Classification Based on Type of Chemical Reaction Catalyzed
E. Enzyme Components
Slide 7 Fig. 5.3 p. 116
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 8 Fig. 5.4 p. 118
5
G. Factors Influencing Enzyme Activity
End of Chap. ‘Study Questions’ Review #2 a-c
SLIDE 9, 10 Fig. 5.6 p. 119
1. Example of Competitive Inhibition and its use in Medicine: Sulfa Drugs
SLIDE 11 Fig. 5.7 p 120
End of Chap. ‘Study Question’ Critical Thinking #2
SLIDES 12-14
Structure: Sulfa drugs are chemically similar (chemical analogues) to the chemical
PABA (para-aminobenzoic acid) which is required by microbes to produce folic acid.
Folic acid is a vitamin that functions as an enzyme cofactor in the synthesis of nucleotide
nitrogen bases. p. 120
Normal functioning when no sulfa drugs are present:
PABA is used by bacteria to produce folic acid. (Table 5.2 p. 117)
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 is defective and 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.
Some disadvantages of sulfa drugs:
1) Only bacteriostatic, not bactericidal
2) Resistance
3) Hypersensitivity
4) Crystallization in kidney of patient
6
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?
See Learning Objectives p. 115 and Check Your Understanding p. 121
7
III. Energy Production
A. Oxidation-Reduction Reactions
SLIDE 15 & 16
SLIDES 20-23 Fig. 5.9 p. 122
Come back to this in a minute…
End of Chapter ‘Study Questions’ Multiple Choice #1
Removal and Gain of
B. The Generation of ATP: Phosphorylation of ADP to ATP
SLIDE 17
1. Substrate-level phosphorylation
SLIDE 18
2. Oxidative phosphorylation
SLIDE 24
3. Photophosphorylation
SLIDE 19
End of Chapter ‘Study Questions’ Review #5
See Learning Objectives p. 121 and Check Your Understanding pp. 122, 123
Textbook Online Site http://www.aw-bc.com/microplace/

Energy Production
o Animations with Quizzes: Oxidation-Reduction Reactions
o Interactive Tutorials: Oxidation-Reduction
8
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 25
SLIDE 26-32
Fig. 5.12, Text p. 126



Biochemical pathway (10 reactions) in which ONE molecule of GLUCOSE is
OXIDIZED to form 2 molecules of PYRUVIC ACID.
NAD (nicotinamide adenine dinucleotide) is reduced: Important electron carrier
ATP is used and formed
B. Alternatives to Glycolysis
Text discussion p. 125, 127
SLIDE 30
9
NEXT: Either Cellular Respiration or Fermentation
C. Cellular Respiration
1. Aerobic respiration
Define respiration: p. 127
a. Glycolysis
b. Intermediate Step after Glycolysis
SLIDE 31 Fig. 5.13 p. 128
c. Krebs cycle
SLIDES 32, 33 Fig. 5.13
d. Electron transport chain/ Chemiosmosis/ADP Phosphorylation
2.
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 where the final electron acceptor is NOT oxygen. Less
common, doesn’t produce as much ATP.
10
Electron Transport Chain
11
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+). So what happens to the
protons in the H atoms?
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. Surrounding those channels is 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:
SLIDES 34-37 Fig. 5.15 p. 130 and Fig. 5.16 p. 131
Overview: Electron Transport Chain & Chemiosmotic Generation of ATP
SLIDE 38 Comparing Eukaryotes and Prokaryotes: Where in the cell?
SLIDE 39 Carbohydrate Catabolism – Number of ATPs generated from aerobic respiration
through Substrate-Level Phosphorylation Only
SLIDE 40 Carbohydrate Catabolism – Number of ATPs generated from aerobic respiration
through Substrate-Level and Oxidative Phosphorylation
12
Overall Summary Reaction of Aerobic Respiration:
13
Anaerobic Respiration.
SLIDE 41, 42
What takes the place of oxygen?
The amount of energy generated varies depending on the electron acceptor.
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.
14
D. Fermentation
Definition SLIDE 43
Steps of Fermentation SLIDE 44 Fig. 5.18 p. 134
Two Primary Categories of Fermentation
SLIDE 45 Fig. 5.18 p. 134
SLIDE 46 Fig. 5.19 p. 136
Examples of Types & Importance of Fermentation
SLIDE 47 Table 5.4 p. 137
SLIDE 48 Table 5.4 p. 137
Table 5.5 p. 137 Aerobic Respiration, Anaerobic Respiration, and Fermentation Compared
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
Textbook Online Site http://www.aw-bc.com/microplace/
 Microflix 3-D Animation Cellular Respiration
 Carbohydrate Catabolism
o Animations with Quizzes
 Glycolysis #3-5
 Electron Transport Chain Overview #1-5
 Electron Transport Chain The Process #1 & #4
o Interactive Tutorials: Fermentation
See Learning Objectives p. 124 and Check Your Understanding pp. 127, 132
15
V. Lipid and Protein Catabolism
Learning Objective p. 136
SLIDE 32
Summary of the interrelationships of carbohydrate, lipid and protein catabolism
Fig. 5.21 p. 138
16
VI. Biochemical Tests and Bacterial Identification (not on exam)
Lab- Your Unknown
VII. Photosynthesis p. 140
SLIDES 50-53
Textbook Online Site http://www.aw-bc.com/microplace/
 Photosynthesis
o Animations with Quizzes
 Overview
 Comparing Prokaryotes and Eukaryotes
Learning Objective 5-20 & 5-21 and Check Your Understanding p. 140
VIII. A Summary of Energy Production Mechanisms
p. 141
See Requirements for ATP (energy sources, electron carriers, final electron acceptors)
Fig. 5.27 p. 143
Recap what is required for ATP Production
End of Chapter ‘Study Questions; Multiple Choice #3
Learning Objective and Check Your Understanding p. 141
17
IX. Metabolic Diversity among Organisms p. 142
Metabolic Classification: Nutritional Patterns
SLIDE 54 Fig. 5.28 p. 143 (old Slides 55 & 56 combined)
Nutritional Classifications of all organisms: Energy Source (see below)
Nutritional Classifications of all organisms: Carbon Source (see below)
Put Energy and Chemical Requirements together to classify organisms by their nutritional needs
SLIDE 55 Summary Table of Fig. 5.28 p. 143
End of Chapter ‘Study Questions’ Review #7
Learning Objective p. 142
X. Metabolic Pathways of Energy Use p. 146
Now you have ATP, what are you going to do with it?
Describe the major types of anabolism and their relationship to catabolism.
18
XI. The Integration of Metabolism p. 147
SLIDE 56, 57 Fig. 5.33 p. 149
Amphibolic pathways: Metabolic pathways that have both catabolic and anabolic functions
Learning Objectives: pp. 146 and 147 and Check Your Understanding 5-24 p. 147
19
SLIDE 58
Metabolism The Big Picture
End of Chapter ‘Study Questions’ Review #1h
Textbook Online Site http://www.aw-bc.com/microplace/



Concept Map (left side column): Metabolism
Step 2
o MP3 Tutor Session
o Integration of Metabolism
o Animations with Quizzes
 Metabolism: The Big Picture
Step 3: Test Yourself
o Multiple Choice #1, 9, 11, 12, 13, 15, 18, 19, 20
o Fill in the Blank #1-4, 6, 9, 10
o True/False #3, 4, 8, 9
o Foundation Figure Quiz #1-4
o Microbe Review #2 & 3
o Post-Test #1-3, 5, 6, 8-14, 18, 20
20
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