Microbial Metabolism

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Microbial Metabolism
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• Metabolism change, pertains to all
  chemical
• reactions and physical workings
• of the cell
• or all the
  biochemical reactions that
• take place in a cell
• metabolism of most living things are similar
• but there are some differences, depending on
  the
• organism

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Ex. Metabolic tasks required to double
cell mass 1. Bringing nutrients into the
cell 2. Catabolism 3. Biosynthesis (or
Anabolism) 4. Polymerization 5. Assembly
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Catabolism degrade, break bonds,
convert large molecules into smaller
component often
produce energyAnabolism synthesis of
cell molecules and structures
usually requires the input of energyMetabolites
compounds given off by the complex
networks of metabolism

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Enzymes Catalyzing the chemical reactions
of life

• How do enzymes work?
• Energy of activation

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Enzyme structure

• simple enzymes consist of protein alone
• conjugated enzyme (or haloenzyme)
• contain protein (apoenzyme) and
• nonprotein molecules (cofactors)

active site the site that accepts a
substrate
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• Cofactors supporting the work of
  enzymes
• organic molecules coenzyme (e.g.
  vitamin)
• perform a necessary alteration of
  a substrate

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• inorganic elements metal ions (Fe,
  Cu,
• Mg, Mn, Zn, Co, Se etc.) help bring the
• active site and substrate close together

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Allosteric enzymes have 2 types of specific
binding sites
active site
allosteric site
binding
effectors
- change the conformation of enzyme at active
site - results in a corresponding inhibition
(activation) of enzyme activity
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Inhibitors prevent or slow down enzyme
reactions by binding to the enzyme
competitive
structure resemble the normal substrate
non-competitive
structure not relate e.g. CN-, Hg, As
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pH affects the charge characteristics of a.a.
comprising the structure of enzyme
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Temperature affects enzyme activity in the same
manner as in other chemical reactions
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Coupled reactions

• most common in biological systems oxidation-
• reduction or redox reactions
• substances differ in their abilities to donate
  or accept
• electrons
• ability of a substance to donate or accept
  electrons
• redox potential (E0)
• Ex. Fe 2 Fe3 e- (0.77V)
• 1/2 O2 2H 2e- H2O (0.82V)

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Electron carriers
transfer electrons from electron donors to
electron acceptors
Electron carriers themselves are oxidized and
reduced
e.g. NAD NADH H FAD FADH2
free energy change
liberation of energy (ATP)
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High-Energy Compounds

• have large negative free energy change (gt-7
  kcal/mole)

• many have one or more high-energy phosphate bonds

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ATP Synthesis

• m.o. use three mechanisms to generate ATP

- oxidative phosphorylation
e- (reduced chemicals)
- photophosphory- lation
e- (reduced chlorophyll molecules)
- substrate-level phosphorylation
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Pi org.cpd. intermediate
Pi
ADP
Ex. glyceraldehyde-3-phosphate
1,3-diphosphoglycerate
Pathways involving substrate-level phosphorylation

• Carbohydrates common energy sources for m.o.

• proteins, lipids, nucleic acids also can be
  used

• Carbohydrates compounds with large
  quantities of
• electrons to donate during oxidation

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Chemoheterothroph obtain energy from CHO by two
basic processes
fermentation
respiration
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Glucose oxidation

• glycolytic or
• Embden-Meyerhof
• pathway

• net production
• 2 ATP 2 NADH H

• other glycolytic pathways

- Entner-Doudoroff
- Pentose phosphate
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Entner-Doudoroff pathway
ATP
NADPH H
NADP
ADP
Glucose
6-phosphogluconate
Glucose-6-phosphate
2-keto-3-deoxy-6-phosphogluconate
NADH H
NAD
Glyceraldehyde-3-phosphate
ATP
ADP
ATP
ADP
Pyruvate
phosphoenolpyruvate
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Pentose Phosphate pathway
NADPH H
NADP
ATP
ADP
Glucose
6-phosphogluconolactone
Glucose-6-phosphate
6-phosphogluconate
Ribose-5-phosphate
NADP
NADPH H
Ribulose-5-phosphate
Xylulose-5-phosphate
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Pyruvate
fermentation
Escherichia
Enterobacter
Saccharomyces
Propionibacterium
Lactobacillus
Clostridium
Ethanol lactate acetate succinate
carbon dioxide hydrogen formate
Ethanol 2,3-butanediol formate lactate
carbon dioxide hydrogen
Lactate
Ethanol carbon dioxide
propionate carbon dioxide hydrogen
acetate
Butyrate butanol isopropanol acetone
carbon dioxide
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Oxidative Phosphorylation
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Malate
Isocitrate
Fumarate
?-ketogutarate
Succinate
Succynyl CoA
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Electron Transport Chain
plasma membrane procaryotes
inner mitochondrial membrane eucaryotes
proton electron carriers pyridine
nucleotides (NADH H), flavoprotein (FAD,
FMN), quinones (coenzyme Q)
electron carriers iron-sulfur protein
(ferredoxin), cytochromes (a, b, c)
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E0(V)
Substrate
-0.40
-0.30
NAD/NADH H
ADP Pi
-0.20
0.27 V 12.4 kcal
Flavoprotein
-0.10
ATP
Coenzyme Q
0.0
Cytochrome b
0.10
ADP Pi
0.22 V 10 kcal
0.20
Cytochrome c
ATP
0.30
Cytochrome a
0.40
0.50
ADP Pi
0.5 V 24 kcal
0.60
ATP
0.70
O2
0.80
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Chemiosmosis
proton motive force
or

• Explains how ATP is synthesized during electron
  transport

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Anaerobic respiration
Some procaryotes have a variation of
respiration anaerobic respiration
Use a chemical compound other than O2 as terminal
electron acceptor
NO3- NO3- NO2- N2O N2 denitrificatio
n
SO42- SO42- H2S sulfate
reduction
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Anabolism
The main pathways of biosynthesis in procaryotic
cells
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Photosynthesis

• Occur in algae, plants, and several groups of
  procaryotes

• Consists of photophosphorylation (light reaction)
  and carbon dioxide fixation (dark reaction)

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• Both reactions are able to function independently

• Chlorophylls are photosynthetic pigments in
• phototrophic eucaryotes and cyanobacteria (a,
  b, c)

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• bacteriochlorophylls are the photosynthetic
  pigments
• in bacteria (a, b, c, d, e)

• Wavelengths ranging from 400 to 650 nm

Chlorophyll a
Bacteriochlorophyll a
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The Nature of Sunlight
Sunlight is electromagnetic energy it has
spectrum ranges from gamma rays ( lt 1
nm) to radio waves ( gt 1 km)
Wavelike property
Visible light is a small part of
electromagnetic spectrum it is most
important for photosynthesis
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Particlelike property
- photon - each photon has a fix amount of
energy (short wavelength high energy)
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The Light Reactions
Schematic of a Photosystem
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there are 2 separate photosystems in plants,
algae, and cyanobacteria
Photosystem I (P700)
Photosystem II (P680)
their chlorophyll molecules are the same, but
are surrounded by different proteins
in others bacteria have only Photosystem II
the photosystems are coupled by an electron
transport ATP and NADP NADPH H
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Non-Cyclic Electron Flow (Z-scheme)
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Photosystem in bacteria
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Cyclic Electron Flow
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The simplest pathway that involves only PS I
(P700)
Electrons that leave the P700 reaction center
chlorophyll cycle from Fd to the cytochrome
complex and return to reaction center
Produce ATP but not NADPH or O2
Cyclic electrons flow supplies the extra ATP
required in the Calvin Cycle
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How is the ATP made during the light reaction

• Chemiosmosis the coupling of exergonic
  electron
• flow down an ETC with endergonic ATP production

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• as electrons pass through the cytochrome
  complex,
• H ions are pumped into the thylakoid space

• this leads to 1000-fold difference in H ion
  conc.
• between the stroma and the thylakoid space

• ATP synthase uses the downhill diffusion of H
  ions
• across the thylakoid membrane to produce ATP

• in chloroplast, approx. 3 Hions must diffuse
• through ATP synthase to make 2 ATP molecule

Splitting of water
2 H ions
1.3 ATP
Movement of electrons
2 H ions
1.3 ATP
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6 MOLECULES OF
3 MOLECULES OF
6 MOLECULES OF
5 MOLECULES OF
6 MOLECULES OF
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Phase one
6 RuBP 6 CO2 12 3-Phosphoglycerate
6 H2O
rubisco
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Phase two

• phosphorylation followed by reduction

• Consumes 6 ATP and
• 6 NADPH to produce
• six glyceraldehyde
• 3-phosphate molecules

REDUCTION

• only one glyceraldehyde
• 3-phosphate molecules
• exits the cycle

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Phase three

• RuBP (a 5-carbon sugar)
• is regenerated

• requires 3 ATP molecules

• takes five glyceraldehyde
• 3-phosphate and
• rearranges them to make
• three 5-carbon sugars
• (RuBP)

6 CO2 18 ATP 12 NADPH
Fructose-6-phosphate 18 ADP 12 H
11 H2O 12 NADP 17 H3PO4
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