Download ch5.2

Micrococcus luteus
on blood agar
A microbiologists
view of the periodic
table
Group
1
2
4
3
5
6
7
8
9
10
11
12
Period
1
2
3
4
5
6
Key:
Essential for all microorganisms
Essential cations and anions for most microorganisms
Trace metals, some essential for some microororganisms
Used for special functions
Unessential, but metabolized
Unessential, not metabolized
13
14
15
16
17
18
Colony morphology , A form of multicellularity?
Streaking for
singles.
Looking for single
colony forming units
Isolated colonies
at end of streak
Confluent growth at
beginning of streak
Enzymes lower
activation energy
Free energy
Activation
energy—
no enzyme
Substrates (A  B)
∆G0 = Gf0(C  D)
Gf0(A  B)
Activation
energy with
enzyme
Products (C  D)
Progress of the reaction
Enzymes are
recycled
Substrate
Glyceraldehyde-3-P
Fructose 1,6-bisphosphate
Dihydroxyacetone-P
Products
Active site
Enzyme–substrate complex
Free aldolase
Free aldolase
Enzymes are specific
for their substrates
3 dimensional structure determined by folding is dependent on side chain interactions
determined by charge and hydrophobicity.
ReDox - gaining electrons = reduction
losing electrons = oxidation
Leo the lion goes Gerrrrrr
Electron
donor
Electron-donating
half reaction
Electron-accepting
half reaction
Formation of water
Net reaction
Electron
acceptor
Some ReDox
potentials of ETC
E0 (V)
Redox couple
-0.60
-0.50
-0.40
-0.30
(1)
-0.20
-0.10
0.0
+0.10
(2)
+0.20
+0.30
+0.40
+0.50
+0.60
+0.70
(3)
+0.80
+0.90
(1) H2  fumarate2

(2) H2  NO3
(3) H2 
1
2
O2
succinate

2
∆G0  = –86 kJ
NO2 + H2O
∆G0  = –163 kJ
H2O
∆G0  = –237 kJ
Fig. 5-10-1
Redox couple
E0 (V)
-0.60
-0.50
-0.40
(1)
-0.30
-0.20
-0.10
0.0
+0.10
(1) H2  fumarate2
succinate2 ∆G0  = –86 kJ
Fig. 5-11
NADH  H
Reduced
Oxidized
NAD
Nicotinamide
Ribose
Ribose
Adenine
Phosphate added
in NADP
Fig. 5-12
Reaction 1.
Enzyme I reacts with electron
donor and oxidized form of
coenzyme, NAD+.
NAD+ binding Active site
site
Reaction 2.
Enzyme II reacts with electron
acceptor and reduced form of
coenzyme, NADH.
NADH binding
site
Active
site
Enzyme II
Enzyme I
NAD+ Electron donor
NADH
Electron acceptor
Enzyme
substrate
complex
NADH
Electron donor
oxidized
NAD+ Electron acceptor
reduced
Bond energies of
some important
compounds
Anhydride bonds
Ester bond
Ester bond
Anhydride bond
Adenosine triphosphate (ATP)
Phosphoenolpyruvate
Anhydride
bond
Thioester
bond
Acetyl
Coenzyme A
Acetyl-CoA
Acetyl phosphate
Glucose 6-phosphate
Fig. 5-13-1
Anhydride bonds
Ester bond
Anhydride bond
Adenosine triphosphate (ATP)
Phosphoenolpyruvate
Anhydride
bond
Thioester
bond
Acetyl
Coenzyme A
Acetyl-CoA
Acetyl phosphate
Using SLP to drive
thermodynamically
unfavorable
reactions
Intermediates in the
biochemical pathway
Energy-rich
intermediates
Substrate-level phosphorylation
Energized
membrane
Less energized
membrane
Oxidative phosphorylation
You must use energy to free energy
STAGE I: PREPARATORY
REACTIONS
Glucose
Hexokinase
Isomerase
Glucose-6-
Fructose-6-
Phosphofructokinase
Fructose-1,6Aldolase
STAGE II: MAKING ATP
AND PYRUVATE
Glyceraldehyde-3-
2
Glyceraldehyde-3-P
dehydrogenase
2
1,3-Bisphosphoglycerate
2
2 NAD+
Electrons
2 NADH
To
Stage III
Phosphoglycerokinase
2 3-Phosphoglycerate
2 2-Phosphoglycerate
Enolase
2 Phosphoenolpyruvate
STAGE III: MAKING
FERMENTATION
PRODUCTS
Pyruvate kinase
2 Pyruvate
NADH
To Stage II
NAD+
Lactate
Pyruvate
dehydrogenase decarboxylase
Pyruvate:Formate lyase
Acetate formate
Lactate
Acetaldehyde
Alcohol
dehydrogenase
Formate
hydrogenlyase
H2  CO2
NADH
NAD+
Ethanol
CO2
To Stage II
Fig. 5-15-1
STAGE I: PREPARATORY
REACTIONS
Glucose
Hexokinase
Isomerase
Glucose-6-
Fructose-6-
Phosphofructokinase
Fructose-1,6-
Investment and
return on investment
Aldolase
STAGE II: MAKING ATP 2 Glyceraldehyde-3AND PYRUVATE
Glyceraldehyde-3-P
dehydrogenase
2
2
Electrons
1,3-Bisphosphoglycerate
Phosphoglycerokinase
2 3-Phosphoglycerate
2 2-Phosphoglycerate
Enolase
2 Phosphoenolpyruvate
2 NAD+
2 NADH
To
Stage III
Fig. 5-15-3
STAGE III: MAKING
FERMENTATION
PRODUCTS
Pyruvate kinase
2
Pyruvate
NADH
To Stage II
NAD+
Lactate
dehydrogenase
Pyruvate
decarboxylase
Pyruvate:Formate lyase
Acetate formate
Lactate
Acetaldehyde
Alcohol
dehydrogenase
Formate
hydrogenlyase
H2  CO2
NADH
NAD+
Ethanol
CO2
To Stage II
Iron-sulfur clusters : a motif for electron transfer
R-Cysteine
Cysteine-R
R-Cysteine
Cysteine-R
R
Cysteine
R
Cysteine
R
Cysteine
Cysteine
R
Fig. 5-20
E0 (V)
–0.22
0.0
Complex II
Fumarate
Succinate
CYTOPLASM
0.1
0.36
0.39
ENVIRONMENT
E0 (V)
chemiosmosis
F1/Fo ATP synthase
and the proton
gradient
F1
In
b2
Membrane
C12
Fo
Out
The Balance sheet:
The bottom line
Pyruvate (three carbons)
Key
C2
C4
C5
C6
Acetyl-CoA
Oxalacetate2
Citrate3
Energetics Balance Sheet for Aerobic Respiration
(1) Glycolysis: Glucose  2NAD  2 ATP
(a) Substrate-level phosphorylation
2 ADP  Pi
2 ATP
(b) Oxidative phosphorylation
2 NADH
6 ATP
2 Pyruvate  4 ATP  2 NADH
 4 ADP
to CAC
to Complex I
8 ATP
Aconitate3
(2) CAC: Pyruvate  4 NAD  GDP  FAD
Malate2
Isocitrate3
Fumarate2
Succinate2
–Ketoglutarate2
3 CO2  4 NADH  FADH
to Complex I
(a) Substrate-level phosphorylation
1 GDP  Pi
1 GTP
1 ATP  1 GDP
1 GTP  1 ADP
(b) Oxidative phosphorylation
4 NADH
12 ATP
1 FADH
2 ATP
Succinyl-CoA
(3) Sum: Glycolysis plus CAC
15 ATP ( 2)
38 ATP per glucose
GTP
to Complex II
Fig. 5-22b
Energetics Balance Sheet for Aerobic Respiration
(1) Glycolysis: Glucose  2NAD  2 ATP
(a) Substrate-level phosphorylation
2 ATP
2 ADP  Pi
(b) Oxidative phosphorylation
6 ATP
2 NADH
(2) CAC: Pyruvate  4 NAD  GDP  FAD
2 Pyruvate  4 ATP 2 NADH
 4 ADP
to CAC
to Complex I
8 ATP
Key
C2
C4
C5
C6
3 CO2  4 NADH  FADH  GTP
to Complex I to Complex II
(a) Substrate-level phosphorylation
1 GTP
1 GDP  Pi
1 GTP  1 ADP
1 ATP  1 GDP
(b) Oxidative phosphorylation
4 NADH
12 ATP
1 FADH
2 ATP
(3) Sum: Glycolysis plus CAC
15 ATP ( 2)
38 ATP per glucose
Fig. 5-23
Fermentation
Organic compound
Electron transport/
Proton motive force
Electron
acceptors
S0
NO3–
SO42
CO2
Carbon flow in respirations
Organic e–
acceptors
Biosynthesis
O2
Aerobic respiration
Anaerobic respiration
Chemoorganotrophy
Inorganic compound
CO2
Electron transport/
Proton motive force
Electron
acceptors
S0
O2
NO3– SO42
Carbon
flow
Biosynthesis
Chemolithotrophy
Photoheterotrophy
Organic
compound
Carbon
flow
Biosynthesis
Phototrophy
Light
Electron
transport
Proton
motive
force
Photoautotrophy
CO2
Carbon
flow
Biosynthesis
Fig. 5-23ab
Organic compound
Fermentation
Carbon flow in respirations
Electron transport/
Proton motive force
Electron
acceptors
S0
NO3
–
SO42
Organic e–
acceptors
CO2
Biosynthesis
O2
Aerobic respiration
Anaerobic respiration
Chemoorganotrophy
Inorganic compound
Electron transport/
Proton motive force
Electron
acceptors
S0
O2
Chemolithotrophy
NO3– SO42
CO2
Carbon
flow
Biosynthesis
Fig. 5-23c
Photoheterotrophy
Organic
compound
Carbon
flow
Biosynthesis
Phototrophy
Light
Electron
transport
Proton
motive
force
Photoautotrophy
CO2
Carbon
flow
Biosynthesis
Fig. 5-25
-Ketoglutarate
Glutamate family
Proline
Glutamine
Arginine
Oxalacerate
Aspartate family
Asparagine
Lysine
Methionine
Threonine
Isoleuine
Pyruvate
Alanine family
Valine
Leucine
3-Phosphoglycerate
Serine family
Glycine
Cysteine
Chorismate
Aromatic family
Phenylalanine
Tyrosine
Tryptophan
Citric acid cycle
Glycolysis
Phosphoenolpyruvate
Erythrose-4-P
Fig. 5-26
-Ketoglutarate  NH3
Glutamate  NH3
Glutamate
Glutamate
dehydrogenase
Glutamine
synthetase
Glutamate  Oxalacetate
Glutamine
-Ketoglutarate  Aspartate
Transaminase
Glutamine  -Ketoglutarate
Glutamate
synthase
2 Glutamate
Fig. 5-27
Amino group
of aspartate
Formyl
group
(from folic
acid)
CO2
Glycine
Formyl
group
(from folic
Amide nitrogen acid)
of glutamine
Ribose-5-P
Inosinic acid
NH3
Aspartic acid
CO2
Orotic acid
Uridylate
Fig. 5-28
Acetyl-ACP
Malonyl-ACP
Acetoacetyl-CoA
Palmitate
(16 C)
4C
6C
14 C
8C
12 C
10 C
Control of pathways: feedback inhibition (noncompetitive inhibition)
The allosteric
enzyme
Starting substrate
Enzyme A
Intermediate I
Enzyme B
Intermediate II
Enzyme C
Intermediate III
Enzyme D
End product
Feedback
inhibition
Fig. 5-30
Enzyme
Allosteric site
End product
(allosteric effector)
INHIBITION:
Substrate cannot
bind; enzyme
reaction inhibited
Active site
Substrate
ACTIVITY:
Enzyme reaction
proceeds
Fig. 5-31
Erythrose
4-phosphate
Phosphoenol 
pyruvate
1
Initial
substrates
3
2
DAHP synthases
(isoenzymes 1, 2, 3)
DAHP
Chorismate
Tyrosine
Tryptophan
Phenylalanine
Glutamine synthetase, a paradigm of allosteric control
GS
GS–AMP6
GS–AMP12
Enzyme
activity
Glutamine
50
0
AMP
0
3
6
9
AMP groups added
Glutamine
Glutamine
concentration
Relative GS activity
100
12
The makings of a
microbe
also
Cofactors galore:
Take your vitamins!
Tab. 5-4
Thinking thermo!