Learning objectives

Understand the ways in which organisms capture energy from the

environment and convert it to usable forms
Light energy
Energy released by breaking chemical bonds
How organisms are classified based on their sources of energy and
carbon
Be able to explain the differences between aerobic respiration,
anaerobic respiration, and fermentation
Be able to explain how glycolysis and the Krebs cycle (TCA cycle)
provide precursors for synthesis of new cell material
Be able to describe some of the metabolic pathways unique to
microorganisms

What I expect you to remember from general chemistry and intro. biology
(review Ch. 10 Intro. to metabolism, pg. 210-219)
G'

= standard free energy change at pH 7

= maximum amount of energy from a reaction that is available to do useful
work
G' is negative for reactions that release energy (exergonic)
G' is positive for reactions that require an input of energy (endergonic)

Energy for doing cellular work can be stored as:

ATP and certain other phosphorylated compounds that have a phosphate
transfer potential, e.g. GTP, phosphoenolpyruvate, 1,3-bisphosphoglycerate)
An ion gradient across a cellular membrane (aka membrane potential or, for
H+, the proton motive force)
Redox reactions
A compound that loses an electron (e-) is oxidized (OIL)
A compound that gains an electron (e-) is reduced (RIG)
Basic concept of an electron transport chain and how the movement of e- from one
component of the electron transport chain to the next is coupled to
movement of H+ across a membrane

Overview of metabolism:
the reactions needed to make 2 cells from 1 cell

Carbon
source
+ energy
source

Fueling
rxns

Biosynthesis

N S
Fueling
Products

precursor metabolites
ATP
membrane potential
NAD(P)H

Polymerization of
monomers
Building
blocks

amino acids
nucleotides
fatty acids
sugars, etc.

Assembly

Macromolecules

Proteins
DNA and RNA
phospholipids
LPS
peptidoglycan

Cellular
Structures

http://en.wikipedia.org/wiki/Primary_nutritional_groups
The Wiki form is correct and graphically helpful

Fig 11.1

Nester et al., Microbiology 6 ed Fig. 6.1

 1 gallon of gasoline: approx 6.3 pounds

1 gallon of gasoline when burned
produces approx. 20 pounds of CO 2
What is the explanation?

Nester et al., Microbiology 6 ed Fig. 6.6

7th ed Fig. 9.1

Metabolic Fuel
Respiration and Fermentation

Amazon.com

Chemoorganotrophic Fueling
Chemoorganotrophs oxidize organic energy sources
These sources lose electrons
Two major pathways for fueling
Respiration
Electrons are transferred to an exogenous electron
acceptor
Electron transfer is through a membraneembedded electron transport chain
Electron transfer results in a membrane
potential we call proton motive force (PMF)
Fermentation
Electrons are transferred to an endogenous
electron acceptor

Respiration
Aerobic respiration
02 is the electron acceptor
Anaerobic respiration
Electron acceptors include NO3-, SO42-, CO2,
Fe3+, SeO42 As electrons pass through the electron transport
chain to the final electron acceptor, a proton
motive force (PMF) is generated and used to
synthesize ATP
Process known as oxidative phosphorylation
(ox phos)

Respiration requires an electron transport chain

to generate Proton Motive Force (PMF)

Fig. 11.2 top

PMF = proton motive force

ox phos = oxidative phosphorylation
SLP = substrate level phosphorylation

Electrons go directly to endogenous acceptors in

fermentation (no PMF involvement)
SLP = substrate level phosphorylation

Fig. 11.2 bottom

Three stages of aerobic respiration

Large nutrient molecules broken down to their
constituent parts
Proteins to amino acids
Polysaccharides to monosaccharides
Lipids to glycerol + fatty acids
Constituent parts further oxidized/degraded
Metabolites include acetyl-coenzyme A and
pyruvate
Partially oxidized products are fully oxidized to
CO2 to produce NADH, FADH2 and a large yield
of ATP

Organizing principles for respiration

A wide variety of molecules get funneled into a
few metabolic intermediates
The product of one reaction serves as substrate
for the next
Catabolic pathways degrade many nutrients to a
few metabolic intermediates
Increases efficiency and flexibility
Reversibility in the system enables
macromolecular synthesis
Amphibolic pathways can be used
catabolically or anabolically

Large nutrients
broken down
Further
oxidation/degrada
tion

Complete
oxidation

7th ed Fig. 9.3 more informative

than 9th ed Fig. 11.3

Glycolysis
Glycolytic pathways break down sugars into
pyruvate and related intermediates
Prescott considers three major pathways
Embden-Meyerhof (most common)
Hexoses to pyruvate
Pentose phosphate/hexomonophosphate
(also common)
Generally used for biosynthesis
Entner-Doudoroff (microbial)
Alternative hexose to pyruvate

Large nutrients
broken down
Further
oxidation/degrada
tion

Complete
oxidation

7th ed Fig. 9.3 more informative

than 9th ed Fig. 11.3

Glycolysis yields ATP by substrate level

phosphorylation
Substrate level phosphorylation
Phosphorylation of ADP to ATP
Breakage of a high energy bond in a
phosphorylated substrate enables transfer of
the substrates phosphate to ADP
Ebden-Meyerhof pathway yields 2 pyruvate and
2 ATP
Glucose + 2ADP + 2Pi +2 NAD+ ->
2 pyruvate + 2ATP + 2 NADH + 2H+
(Pyruvate product yields additional NADH and
FADH to make ATP through respiration)

TCA cycle fully oxidizes fuel

Tricarboxylic acid cycle = citric acid cycle =
Krebs cycle
Pyruvate converted to Acetyl-CoA (Acetylcoenyzme A)
Acetyl-CoA can be obtained by catabolism
of amino acids and fatty acids
For each Acetyl-CoA oxidized:
2 CO2, 3 NADH, 1 FADH2, 1 GTP
Consider GTP energetically equivalent to ATP

Can run cycle in reverse for biosynthesis

Large nutrients
broken down
Further
oxidation/degrada
tion

Complete
oxidation

7th ed Fig. 9.3 more informative

than 9th ed Fig. 11.3

7th ed.

TCA cycle enzymes are widely

distributed among prokaryotes
and eukaryotes
Mitochondrial location in eukaryotes
Cytoplasmic location in prokaryotes

http://nobelprize.
org/nobel_prizes/m
edicine/laureates/
1953/

Fig. 11.8

Electron transport and

oxidative phosphorylation
4 ATP equivalents (2 ATP and 2 GTP) are
synthesized directly from oxidation of glucose to
CO2
Most ATP is made when NADH and FADH2
(formed during glucose oxidation) are
themselves oxidized by the electron transport
chain (ETC)
The ETC generates PMF which is used to
drive ATP synthesis
Process is called oxidative phosphorylation

The electron transport chain

Series of electron carriers that operate
together
Transfer electrons from NADH and FADH2
to a terminal electron acceptor
Electrons flow from carriers with more
negative E0 (standard reduction potential) to
carriers with more positive E0
Localization
Prokaryotic plasma membrane
Eukaryotic mitochondrial membrane

The electron transport chain: principle of operation

Fig. 11.9

E0 = standard reduction potential

Large nutrients
broken down
Further
oxidation/degra
dation

Complete
oxidation

7th ed Fig. 9.3 more informative

than 9th ed Fig. 11.3

Fig. 11.8

The electron transport chain

Series of electron carriers that operate
together
Transfer electrons from NADH and FADH2
to a terminal electron acceptor
Electrons flow from carriers with more
negative E0 (standard reduction potential) to
carriers with more positive E0
Localization
Prokaryotic plasma membrane
Eukaryotic mitochondrial membrane

Fig. 11.9

E0 = standard reduction potential

Mitochondrial electron transport chain

avin mononucleotide; Cyt, cytochrome; FeS, Iron sulfur

Fig 11.11

Amazon.com

Fig. 11.15

http://nobelprize.or
g/nobel_prizes/chemi
stry/laureates/1978/

Mitochondrial electron transport chain

FMN, flavin mononucleotide; Cyt, cytochrome; FeS, Iron sulfur

Fig. 11.11

http://nobelpr
ize.org/nobel_
prizes/chemist
ry/laureates/1
997/

Fig. 11.16a

Fig. 11.16b

http://nobelprize.org/nobel_priz
es/chemistry/laureates/1997/walk
er-lecture.pdf

http://www.res.titech.ac.jp/~seibutu/

Rotation of the gamma subunit of thermophilic F1-ATPase was observed directly

with an epifluorescent microscope. The enzyme was immobilized on a coverslip
through His-tag introduced at the N-termini of the beta subunit. Fluorescently
labeled actin filament was attached to the gamma subunit for the observation.
Images of the rotating particles were taken with a CCD camera attached to an
image intensifier, recorded on an 8-mm video tape and now can be viewed by just
clicking on the figures below. (Noji et al. Nature 386 299-302 1997)

Proton motive force drives ATP synthesis

From John Walkers research interests:
In eubacteria, chloroplasts and mitochondria, the synthesis of ATP is
carried out by a highly complex molecular machine known as ATP
synthase. Our aim is to understand how this machine works.it uses the
transmembrane proton motive force (pmf) generated by the oxidation of
nutrients as a source of energy for making ATP. The pmf across the
[membrane] is coupled to the chemical synthesis of ATP from ADP and
phosphate by a rotary mechanism illustrated in the Figure. During ATP
synthesis, the central rotor turns in the direction shown about 150 times
every second. In order to provide energy to sustain our lives, every day,
each one us produces a quantity of ATP by this mechanism that is
approximately equal to our body weights

http://www.mrc-mbu.cam.ac.uk/research/atp-synthase

http://www.mrc-mbu.cam.ac.uk/research/atp-synthase

Total aerobic yield: 36-38 ATP

Fig. 11.17

E. coli
electron
transport
chain

Fig. 11.13

Paracoccus denitrificans aerobic respiration

FP, Flavoprotein; MD, methanol dehydrogenase

Fig. 11.12

Anaerobic respiration
The exogenous final electron acceptor is not
O2
Anaerobic respiration generally yields less
energy
E0 of final electron acceptor is generally
less positive than E0 of O2
Electron acceptors include NO3-, SO42-,
CO2, Fe3+, SeO42-

Paracoccus denitrificans anaerobic respiration

FP, Flavoprotein; Nar, nitrate reductase; Nir, nitrite reductase;

Nor, nitric oxide reductase; Nos, nitrous oxide reductase

Fig. 11.18