MİCROBİAL METABOLİSM

METABOLISM is defined as the sum

of all chemical reactions occurring
within a living organism.
Metabolism = Anabolism +
Catabolism
Metabolism
 Catabolism

■ The breakdown of complex organic

molecules into simpler molecules
usually by hydrolysis
■ Generally hydrolytic
■ Exergonic, energy releasing
(produce energy)-energy stored in
chemical bonds is released.
■ The chemical processes of
digestion typically occur by this
route.
 Anabolism
■ The synthesis of complex organic
molecules from simpler molecules
usually by condensation
■ Generally dehydration synthesis
reactions (release water)
■ Endergonic, energy-requiring (consume
energy)
■ The energy for anabolic reactions is
provided by catabolic reactions; they
are ALWAYS LINKED.
■ Energy is ultimately stored in the form
of the energy -rich molecule, ATP.
 Energy Classes of Microbes

Microbes nedd three things to grow

■ Energy source
■ Nutrients
■ Suitable environmental conditions
■ Carbon source
– Heterotrophy: biomass generated
from organic carbon
– Autotrophy: biomass generated from
CO2
■ Energy source
– Phototroph (light)
– Chemotroph(chemicals)
 Chemoorganotroph(gain energy
from breaking organic chemical
bonds)
 Chemolithoautotroph(gain energy

from breaking inorganic chemical

■ Autotrophs:is an organism that
produces complex organic
compounds from simple
inorganic molecules using
energy from light or inorganic
chemical reactions.

■ Heterotrophs(Organotrophs):O
rganic compounds serve both
as energy source and carbon
source.
■ Photoautotrophs or Phototroph :
Phototrophs are organisms
(commonly plants) that carry out
photosynthesis to acquire energy

■ Chemotroph: Chemotrophs are

organisms that obtain energy by
the oxidation of electron donating
molecules in their environments.
These molecules can be organic
(organotrophs) or inorganic
(lithotrophs; such as NH4, NO2, H2S,
Fe2 or H2 ).
 Photoheterotrophs (or
photoorganotrophs)
■ organisms which use light for
energy, but cannot use carbon
dioxide as their sole carbon
source. They use compounds such
as carbohydrates, fatty acids and
alcohols as their organic "food“.
■ Chemoheterotroph:
Most chemoheterotrophs derive
energy from organic molecules like
glucose.
 HIGH ENERGY
COMPOUNDS
ATP is the energy currency of the cell
High energy released when
phosphate is hydrolized
(ATD,ADP,AMP)
Acetyl phosphate
Acetyl coenzyme A
Phospho-enol pyruvate
■ Energy is conserved in the
form of phosphate bonds
■ Energy is stored in ATP
 ROLE OF ATP İN
METABOLİZM
■ ATP (adenosine triphosphate)
stores the energy generated
by catabolic reactions and
makes it available for anabolic
reactions
■ ATP generated in exergonic
reactions and use to drive
endergonic reactions
HOW İS ATP GENARETE?
■ Substrate-level
phosphorylation
is the
production of
ATP from ADP
by a direct
transfer of a
high-energy
phosphate
group from a
phosphorylated
intermediate
metabolic
compound in an
exergonic
II. Electron-transport
phosphorylation:
Membrane-
associated
mechanism where
ATP formation is
coupled with
flow of electrons
from donor to
acceptor. Occurs
in respiratory
chain and in
photosynthetic
reaction
sequences.
 Energetics
■ Energetics 
■ Gibbs Free-Energy (G)
■ Reaction has a free-energy
change
– Negative: exergonic
– Positive: endergonic
– Zero: equilibrium
■ Standard concentrations—tables of
ΔGf°’
■ Calculation of reaction energetics 
■ First, must write balanced equation
– E.g., 2H2 + O2 → 2H2O
■ Calculation of ΔG°’ for a reaction
– ΔG°’ = ΔGf°’products - ΔGf°’reactants
– ΔG°’ = 2 x (-237.2 kJ/mol) – (2 x 0 +
0)
■ Calculation of ΔG for a reaction
– ΔG = ΔG°’ + RT x ln(k)
■ Energy is defined as the ability to
do work.
■ Chemical energy is the energy
released when organic or inorganic
compounds are oxidized.
■ Chemical energy is derived from
the energy stored in chemical
bonds. When bonds are made or
broken there is a quantifiable
amount of energy expended.
 FREE ENERGY
■ The energy (i.e., the work needed
to transport ions against a
concentration gradient) comes
from the internal energy that is
released during the rxn.
■ The energy available to do work is
free energy (ΔG)
■ if ∆G is negative, reaction is
spontaneous and energy yielding
= exergonic
■ if ∆G is positive, reaction is non-
spontaneous and energy requiring
= endergonic
 Summary of Redox and e-
Carriers,Reduction and
Oxidation

Redox reactions
Oxidation - Reduction,
Oxidant – Reductant,
Reduction potential E0,
Half reactions,
Use of the Electron Towers
■ All organisms obtain energy by
transferring electrons from an
electron donor to an electron
acceptor.
■ Electron acceptor  gains electrons 
Reduced
■ Electron donor  gives up electrons
 Oxidized
■ Electron donor understood as energy
source, but it’s the reaction that
generates energy
■ The generally accepted convention is
keep the electrons on the left side of
the reaction
■ Electrons are transferred by oxidation-
a) An atom becomes more reduced when
it undergoes a chemical reaction in
which it

Gains electrons
By bonding to a less
electronegative atom
And often this occurs when the
atom becomes bonded to a
hydrogen

Oxidant + e-  reduced form

 b) An atom becomes more
oxidized when it undergoes a
chemical reaction in which it

■ Loses electrons
■ By bonding to a more

electronegative atom
■ And often this occurs when the

atom becomes bonded to an

oxygen

Reductant – e-  oxidized form

a) In metabolic pathways, we are
often concerned with the oxidation
or reduction of carbon.
b) Reduced forms of carbon (e.g.
hydrocarbons, methane, fats,
carbohydrates, alcohols) carry a
great deal of potential chemical
energy stored in their bonds.
c) Oxidized forms of carbon (e.g.
ketones, aldehydes, carboxylic
acids, carbon dioxide) carry very
little potential chemical energy in
their bonds.
■ REDUCED OXIDIZED OXIDIZED REDUCED

■ AH2 + B → A + BH2
■ AH2 - dehydrogenation, i.e., the
ELECTRON DONOR
■ B - the ELECTRON ACCEPTOR in
respiration is “external” and may be
O2 or
an oxidized form of N, S, C, Fe, Mn, etc.
■ In fermentation, the electron acceptor
is
“internal” and is often an organic
compound
■ No free electrons are present.
■ The reactions must be added to make
a complete reaction.
■ The generally accepted convention is
keep the electrons on the left side of
the reaction.
■ Reduction and oxidation always occur
together.
■ All redox reactions are coupled half
reactions.
■ Amount of energy generated is based
on the nature of both the electron
donor and electron acceptor (drop in
tower)
 Half Reactions
■ Often split redox reactions in two:
– oxidation half rxn  e- leaves left, goes
right
■ Fe2+  Fe3+ + e-
– Reduction half rxn  e- leaves left, goes
right
■ O2 + 4 e-  2 H2O
■ SUM of the half reactions yields the
total redox reaction
4 Fe2+  4 Fe3+ + 4 e-
O2 + 4 e-  2 H2O

4 Fe2+ + O2  4 Fe3+ + 2 H2O

POTENTIAL ENERGY (E ) 0

■ The reduction potential

 Electron Tower
■ Oxidation / Reduction
Pairs
■ first in pair is oxidizer
(accepts e-)
■ second in pair is reduced
(donates e-)
■ Due to energy required
to build molecules,
strong e- donors are
found at the top of
tower, while strong e-
acceptors are found at
the bottom of tower.
■ As electrons are donated
from the top of the tower
, they can be caught by
acceptors at various
levels. The farther the
electron fall before they
are caught, the greater
the difference in
reduction potential
■ To determine which direction
the reactions go, see which is
“higher”
on the e- tower
 ELECTRON CARRIERS
Reduction/oxidation is mediated
by
electron carriers in the cell
• Electron carriers can be
divided into those that are
freely diffusable and those that
are fixed
• Fixed = cytochromes
associated with the cytoplasmic
membrane
■ These are electron plus proton
carriers transporting 2e- and
2H+ at a time (-0.32V)
■ NAD is used in energy
generation
(catabolic reactions). NADP is
used in biosynthetic reactions
(anabolic)
■ NAD and NADP are coenzymes
that are recycled
Microbes, e- flow
■ Catabolism –
breakdown of any
compound for
energy
■ Anabolism –
consumption of that
energy for
biosynthesis
■ Transfer of e-
facilitated by e-
carriers, some bound
1. Enzymatic Pathways for
Metabolism
– Metabolic reactions take place
in a step-wise fashion in which
the atoms of the raw materials
are rearranged, often one at a
time, until the formation of the
final product takes place.
– Each step requires its own
enzyme.
– The sequence of enzymatically-
catalyzed steps from a starting
raw material to final end
products is called an enzymatic
 Membrane bound electron
carriers
■ Membrane bound electron
carriers have 2 basic functions:
■ 1) Accept electrons and
transfer them
■ 2) Conserve energy released
for synthesis of ATP
■ Enzymes involved in oxidation
reduction reactions:
■ NADH dehydrogenase
■ Flavoproteins (FMN & FAD)
■ Iron-sulphur proteins
■ Cytochromes (heme) iron
■ Lipid soluble quinones
■ Cytochromes:
– Transport electrons ONLY
– Different cytochromes have different
reduction potentials (cyt a, cyt b, etc)
Nonheme iron-sulfur proteins
■ Only carry electrons
Quinones
– Accepts both protons and electrons but
only donates the electrons
■ NADH dehydrogenase
Found on cytoplasmic face of membrane
Accepts e- and H+
■ Flavoproteins (FMN & FAD)
■ Prosthetic group derived from vitamin
B2
■ Accepts e- and H+, but only transfers
e-
 MODES OF ENERGY
PRODUCTION
■ Microorganisms oxidize
carbohydrates as their primary
source of energy
■ Glucose - most common energy
source
■ Energy obtained from Glucose by:
– Respiration
– Fermentation
Cellular Respiration
Cellular Energy
•The Stages of Cellular Respiration Cellular
respiration has two stages.
•Glycolysis The first stage of cellular respiration
is called glycolysis.
•Aerobic and Anaerobic Respiration The second
stage of cellular respiration is either aerobic
respiration (in the presence of oxygen) or anaerobic
respiration (in the absence of oxygen). A large
amount of ATP is made during aerobic respiration.
NAD+ is recycled during the anaerobic process of
fermentation.
Aerobic Cellular Respiration
■ 4 subpathways

■ 1. Glycolysis
■ 2. Transition Reaction
■ 3. Kreb’s Cycle
■ 4. Electron Transport System
1. Glycolysis (splitting of sugar)

■ Oxidation of Glucose into 2

molecules of Pyruvic acid
■ Embden-Meyerhof Pathway

■ End Products of Glycolysis:

– 2 Pyruvic acid
– 2 NADH2
– 2 ATP
2. Transition Reaction
■ Connects Glycolysis to Krebs Cycle

■ End Products:
– 2 Acetyl CoEnzyme A
– 2 CO2
– 2 NADH2
 3. Krebs Cycle (Citric Acid
Cycle)
■ Series of chemical reactions that
begin and end with citric acid

■ Products:
–2 ATP
–6 NADH2
–2 FADH2
–4 CO2
 4. Electron Transport
System
■ Occurs within the cell membrane
of Bacteria

■ Chemiosomotic Model of Mitchell

– 34 ATP
Total ATP production for the complete
oxidation of 1 molecule of glucose in
Aerobic Respiration
■ ATP
■ Glycolysis 2
■ Transition Reaction 0
■ Krebs Cycle 2
■ E.T.S. 34

■ Total 38 ATP
 Anaerobic Respiration
■ Electrons released by oxidation are
passed down an E.T.S., but oxygen
is not the final electron acceptor

■ Nitrate (NO3-) ----> Nitrite (NO2-)

■ Sulfate (SO24-) ----> Hydrogen
Sulfide (H2S)
■ Carbonate (CO24-) -----> Methane (CH4)
■ Aerobic respiration
■ • Kreb’s cycle

Pyruvic acid CO2 + NADH + ATP

+ FADH
• Electron transport chain (ETC)
■ – Carrier molecules that
transport electrons resulting in a
step wise release of energy that
is used to for ATP
■ – Final electron acceptor is O2
which forms H2O
■ Anaerobic Respiration
• Final electron acceptor is an
inorganic molecule other that
oxygen
– Nitrate (NO3-)  Nitrite (NO2-)
– Sulfate (SO4-2)  Hydrogen
sulfide (H2S)
– Carbonate (CO3-2)  Methane
(CH4)
• Less ATP than aerobic
– All components of Kreb’s cycle
Fermentation
• Conversion of pyruvic acid to organic
• Product

• Does not require oxygen

• No part of Kreb’s cycle or ETC used
Lactic Acid Fermenation
Alcohol Fermentation
■ Both the electron donor and acceptor
are organic compounds and ATP is
generated solely via substrate-level
phosphorylation.
■ Fermentation releases little energy (2
ATP/molecule of glucose) and most of
Differences between Resp. and
Ferment.
■ • Fermentation: redox reaction occurring with
no
exogenous terminal electron acceptor
■ • Instead fermentation is coupled to reduction
of a
■ compound generated from the initial
substrate, no
■ external electron acceptor is supplied
■ • Respiration: redox reaction requiring an
exogenous
■ electron acceptor
■ • In aerobic respiration this is molecular
oxygen (O2), in
■ anaerobic respiration the electron acceptor
Embden-Meyerhof pathway-
■ Two more ADP and 2 NAD+
molecules are used to make
two molecules of NADH and
two more molecules of ATP.
This step also yields two
pyruvate molecules. The
pyruvate still have most of the
original energy that was found
in the original glucose
molecule and the point of the
of aerobic cellular respiration
will be to harvest as much of
that energy as possible!
Aerobic respiration happens in 3
stages:

Stage 1 – Glycolysis

glycol ysis

glucose splitting
 Stage 2 – Breakdown of
pyruvic acid
The pyruvic acid made in glycolysis
(stage1) still contains a lot of energy

It can only be broken down to release

the rest of the energy in the presence
of oxygen.
Stage 3 – Oxidative Phosphorylation
■ Requires the Electron Transport
Chain…

■ the Electron Transport Chain is a

collection of proteins, embedded in
the inner membrane, used to
transport the electrons from NADH
and FADH2
Krebs Cycle
■ Also called: Citric Acid Cycle or
Tricarboxylic Acid Cycle

■ Function: Oxidize pyruvic acid to

CO2

■ Produce: 3NADH, 1FADH2 and 1ATP

■ Location: Mitochondria matrix

■ Formation of Acetyl CoA:
Acetyl CoA is formed when the
pyruvate , from glycolysis,
combines with Coenzyme A…
this takes place in the matrix.
Requirements for Krebs Cycle
■ Pyruvic acid (3C acid)
■ Coenzyme A
■ 3 NAD+
■ 1 ADP
■ 1 FAD
■ Double this list for each
glucose.
 Results
■ Produces most of the cell's
energy in the form of NADH
and FADH2… not ATP
■ Does NOT require O2
FADH = 2 ATP
NADH = 3 ATP
 Electron Transport System
■The electron transport system
(ETS) is a chain of electron
carriers associated with the
cytoplasmic membrane in
prokaryotes and mitochondria
in eukaryotes.
■ This system transfers the
energy stored in NADH and
FADH into ATP. The chain
consists of electron carriers
such as flavin mononucleotide
(FMN), coenzyme Q, iron–sulfur
proteins, and cytochromes.
 Comparison of aerobic and
anaerobic respiration
Aerobic Anaerobic Respiration
respirati in animals in plants and
on yeast
Oxygen required? yes no no

Glycolysis occurs yes yes yes

ATP yield 38ATP 2ATP 2ATP

Glucose yes no no
completely
broke down?
End products Carbon Lactic acid Ethanol and
dioxide carbon
and water dioxide