BIO 420 Lecture 3

Microbial Metabolism

▪ All cells need to accomplish two fundamental tasks

• Synthesize new parts
• Cell walls, membranes, ribosomes, nucleic acids
• Harvest energy to power reactions
• Sum total of chemical reaction in a cell is called
metabolism
• Implications of microbial metabolism
• Biofuels-made from plants or organic waste
• Food production
• Important in laboratory
• Invaluable models for study
• Unique pathways potential
drug targets
Principles of Microbial Metabolism

▪ Can separate metabolism into two

parts
• Catabolism
• Processes that degrade compounds
to release energy
– Cells capture to make ATP
– Generate precursor metabolites
• Anabolism
• Biosynthetic processes
– Use ATP to drive reactions
– Assemble subunits of
macromolecules
• Processes interconnected
ATP is the energy currency of the cell

Adenosine triphosphate → immediate donor of free energy

phosphate groups
P P P P + P P

adenine

ribose
+ energy

ATP is
• produced by the cells during catablism
• spent by the cells during anabolism
The Role of ATP in Coupling Anabolic and Catabolic
Reactions
ATP
▪ Role of ATP
• Adenosine triphospate (ATP) is energy currency of the cell
• Composed of ribose, adenine, three phosphate groups
• Adenosine diphospate (ADP) acceptor of free energy
• Cells produce ATP by adding Pi to ADP using energy
• Release energy from ATP to yield ADP and Pi
▪ Three processes to generate ATP
• Substrate-level phosphorylation
• Exergonic reaction:
starting compounds have more free energy
than the products
• Oxidative phosphorylation
• Proton motive force
• Photophosphorylation
• Sunlight used to create proton
motive force
Metabolic Pathways

▪ A metabolic pathway is a sequence of

enzymatically catalyzed chemical reactions in a cell
▪ Metabolic pathways are determined by enzymes
▪ Enzymes are encoded by genes
Enzymes
Cellular reactions are mediated by enzymes

Reaction Activation
without enzyme energy
without
enzyme

Reaction Activation
with energy
enzyme with
Reactant enzyme

Initial energy level

Final energy Products

level

Enzymes lower the energy requirements of a chemical reaction

Enzyme Components

Coenzyme Substrate

Apoenzyme Cofactor Holoenzyme

(protein portion), (nonprotein portion), (whole enzyme),
inactive activator active
The Mechanism of Enzymatic Action

Substrate Active site Products

Enzyme Enzyme–substrate
complex
Factors Influencing Enzyme Activity

▪ Temperature
▪ pH
▪ Substrate concentration
▪ Inhibitors
Enzyme Inhibitors

Normal Binding of Substrate Action of Enzyme Inhibitors

Substrate Competitive
inhibitor
Active site

Enzyme
Enzyme Inhibitors

Normal Binding of Substrate Action of Enzyme Inhibitors

Altered
Substrate active site
Active site

Enzyme

Noncompetitive
inhibitor Allosteric
site
Feedback Inhibition
Substrate

Pathway
Operates

Pathway
Shuts Down

Enzyme 1

Allosteric site
Intermediate A Bound
end-product

Enzyme 2

Feedback Inhibition
Intermediate B

Enzyme 3

End-product
Energy Production
Oxidation-Reduction Reactions

▪ Electrons move from molecules with low electron affinity (A, electron
donor=energy source) to molecules with high electron affinity (B,
terminal electron acceptor)
▪ The greater the energy difference between molecules A and B, the more
energy is released during the reaction
▪ Oxidation (A): removal of electrons
▪ Reduction (B): gain of electrons
▪ Redox reaction: an oxidation reaction paired with a reduction reaction
Oxidation-Reduction Reactions

▪ In biological systems, the electrons are often

associated with protons (e-+H+=H atom)
▪ Biological oxidations are often dehydrogenations
Reduction

H+
H (proton)

Organic molecule NAD+ coenzyme Oxidized NADH + H+ (proton)

that includes two (electron carrier) organic (reduced electron
hydrogen atoms (H) molecule carrier)

Oxidation
 e-
Electron Carriers
▪ Electron Carriers
• Energy is harvested in stepwise process. The electron carriers are NOT the
terminal electron acceptors, but an intermediate step
• Molecules that can easily accept and easily transfer electron/proton pairs
• reducing power: their capacity to transfer electrons to chemicals with higher
affinity for electrons
– Raise energy level of recipient molecule
• NAD+/NADH, NADP+/NADPH, and FAD/FADH2 different biological roles
Catabolism of Glucose
 An Overview of Respiration and Fermentation
Respiration Fermentation
Glycolysis produces ATP and reduces
NAD+ to NADH while oxidizing glucose to 1 Glycolysis
pyruvic acid. In respiration, the pyruvic acid Glucose
is converted to the first reactant in the
Krebs cycle, acetyl CoA.
NADH ATP

The TCA cycle (Krebs cycle)

Pyruvic In fermentation, the
produces some ATP by acid
substrate-level pyruvic acid and the
phosphorylation, reduces the 2 electrons carried by
electron carriers NAD+ and NADH from glycolysis are
Acetyl CoA Pyruvic acid
FAD, and gives off CO2. (or derivative)
NADH incorporated into
Carriers from both glycolysis fermentation end-
and the Krebs cycle donate products.
NADH
electrons to the electron
Kreb’s
transport chain. FADH2 Formation of brewer’s yeast
cycle
fermentation
end-products

In the electron transport NADH &

FADH2 CO2
chain, the energy of the
ATP
electrons is used to
produce a great deal of 3 Electrons
ATP by oxidative
phosphorylation.
ATP
Electron
transport O2
chain and
chemiosmosis
H2O
Overview of Cellular Respiration
▪ Cellular respiration
e- e-
glycolysis Krebs cycle electron transport chain

terminal electron
glucose acceptor

Through electron carriers, electrons are taken from glucose to the

electron transport chain which ultimately carries them to the
terminal electron acceptor
• Aerobic respiration
– O2 is terminal electron acceptor
• Anaerobic respiration
– Molecule other than O2 as terminal electron acceptor
– Also use modified version of Krebs (TCA) cycle
• Electron transport chain generates proton motive force
• Harvested to make ATP via oxidative phosphorylation
Aerobic vs. Anaerobic Respiration

▪ Aerobic respiration: the final electron acceptor

in the electron transport chain is molecular
oxygen (O2)
▪ Anaerobic respiration: the final electron
acceptor in the electron transport chain is NOT
O2
• Yields less energy than aerobic respiration because
only part of the Krebs cycle operates under anaerobic
conditions Electron Acceptor Products

NO3– NO2–, N2 + H2O

SO4– H2S + H2O

CO32 – CH4 + H2O

Oxydative phosphorylation

▪ Electron transport chain

is membrane-embedded
electron carriers
• Pass electrons
sequentially, eject
protons in process
• A proton gradient is
created
• ATP synthase allows
protons to re-enter the
cell down gradient
• The released energy
drives ATP synthesis
The Electron Transport Chain—Generating Proton
Motive Force
▪ Electron transport chain is membrane-embedded
electron carriers
• Energy gradually released
• Release coupled to ejection
of protons
• Creates electrochemical
gradient (H+)

• Prokaryotes can also power

transporters, flagella
• Prokaryotes: in cytoplasmic membrane
• Eukaryotes: in inner mitochondrial membrane
Electron transport and the chemiosmotic generation of ATP
Cell Periplasmic Plasma Outer Inner
wall space membrane membrane membrane

Intermembrane space
Mitochondrial matrix

Cytoplasm
Bacterium Mitochondrion

Periplasmic space of prokaryote or

intermembrane space of eukaryote

Prokaryotic
plasma
membrane
or eukaryotic
inner
mitochondrial
membrane

Cytoplasm of
prokaryote or
mitochondrial
matrix of
eukaryote
Respiration (Eukaryotes vs. Prokaryotes)

Pathway Eukaryotes Prokaryotes

Glycolysis Cytoplasm Cytoplasm

Intermediate step Cytoplasm Cytoplasm

Krebs cycle Mitochondrial matrix Cytoplasm

ETC Mitochondrial inner Plasma membrane

membrane
Respiration (Eukaryotes vs. Prokaryotes)

▪ Prokaryotic cells: Produce 38 ATP, 10 NADH

and 2 FADH2 per molecule of glucose

▪ Eukaryotic cells: Slightly less total ATP in

eukaryotic cells
• NADH from glycolysis in cytoplasm transported
across mitochondrial membrane to enter electron
transport chain requires ~1 ATP per NADH generated
Fermentation: Another Catabolic Pathway
Overview of Fermentation

▪ Organisms that cannot

respire

• No Krebs cycle
• No electron transport chain
• Does not require oxygen
• Uses an organic molecule as
the final electron acceptor
Overview of Fermentation

glycolysis
ATP is only
produced at
2 ADP+ 2Pi this stage of
e- e- fermentation
pyruvate

glucose
2NAD+ 2NADH+2H+ Pyruvate acts as terminal
electron acceptor and is
reduced

Depending on the NADH is oxidized back to

organism, the end NAD+ so glycolysis can
product changes continue

e.g. lactic acid in humans

ethanol in yeast
Overview of Fermentation

▪ Fermentation
• If cells cannot respire, will run out of carriers available to
accept electrons
• Glycolysis will stop
• Fermentation uses pyruvate or derivative as terminal
electron acceptor to regenerate NAD+
• Glycolysis can continue
Overview of Fermentation
▪ Fermentation used when respiration not an option
• E. coli is facultative anaerobe
• Aerobic respiration, anaerobic respiration, and fermentation
• Streptococcus pneumoniae lacks electron transport chain
• Fermentation only option
• ATP-generating reactions are only those of glycolysis
• Additional steps consume excess reducing power
– Regenerate NAD+

▪ Fermentation end
products varied
Catabolism of Organic Compounds
Other than Glucose
Catabolism of Organic Compounds Other than Glucose

▪ Microbes can use variety

of compounds
• Convert to precursor
metabolites
• Enter appropriate
metabolic pathways
Photosynthesis
Photosynthesis

nCO2 + nH2O + photons→(CH2O)n+ nO2

▪ Photo: conversion of light energy into chemical

energy (ATP)
• Light-dependent (light) reactions → O2, ATP and
NADPH
▪ Synthesis:
• Carbon fixation: fixing carbon into organic molecules
• Light-independent (dark) reaction: Calvin-Benson
cycle (still occurs in light but isn’t dependent on it)→
carbohydrates using CO2 and products of light reaction
Photosynthesis
▪ Photosynthesis
• Oxygenic
• Anoxygenic
Cyclic Photophosphorylation
Photophosphorylation: sunlight energy is used to
phosporylate ADP to ATP

Electron
transport Energy for
chain production
Light
Excited of ATP
electrons

Electron carrier

Excited electrons return to

In Photosystem I chlorophyll producing a proton-
(a) Cyclic photophosphorylation motive force
Noncyclic Photophosphorylation
Two-stage process involving
Electron
two different chlorophyll transport
photosystems chain
Light Energy for
Excited production
electrons of ATP
+ 2H+ + 2e-
+ H+

In Photosystem I
Light Excited
electrons
Net production of :
• ½ O2
• ATP
In Photosystem II
• NADPH
H+ + H+
1.H2O is 1
broken down 2
A Simplified Version of the Calvin-Benson Cycle
1 From atmosphere
Input

RuBP
1. Incorporation of the
Ribulose diphosphate 3-phosphoglyceric acid 2
CO2 into an organic
compound
From light
2. Reduction of the 1,3-diphosphoglyceric acid reactions
resulting molecule Calvin-Benson cycle

3. Carbohidrate
formation 4
Glyceraldehyde Glyceraldehyde
4. Regeneration of the 3-phosphate 3-phosphate
starting compound PGAL
Output

Glyceraldehyde 3-phosphate
3
Glyceraldehyde 3-phosphate
Photosynthesis overview
Anabolic Pathways
Anabolic Pathways—Synthesizing Subunits from
Precursor Molecules
▪ Prokaryotes remarkably similar in biosynthesis

• Synthesize subunits using central metabolic pathways

• If enzymes lacking, end product must be supplied

• Fastidious bacteria require many growth factors
Anabolic Pathways—Synthesizing Subunits from
Precursor Molecules
Nucleotide
synthesis
DNA, RNA
initially
synthesized as
ribonucleotides

Glycerol: dihydroxyacetone
phosphate from glycolysis
Purines: atoms added to ribose 5-
phosphate to form ring (A, G)

Pyrimidines: ring made, then

attached to ribose 5-phosphate
Can be converted to other
nucleobases of same type (C, U, T)

Fatty acids: 2-
Lipid synthesis requires fatty acids and carbon units
glycerol added to
acetyl group
from acetyl-
CoA