BIO 208 Unit 2 Review of General Metabolism Concepts
Review - Important Concepts for Lectures over Metabolism
I assume that you have had an introduction to the basics of metabolism in an introductory biology course. The metabolism you learned was probably entirely focused on the types of metabolism that animal (maybe plant) cells carry out -aerobic respiration; perhaps you were exposed to lactic acid fermentation (When muscles are working very hard, they may be temporarily depleted of oxygen, muscle cells can perform lactic acid fermentation for a short period of time. The lactic acid end products are secreted by the muscle cells into your tissues, and you feel the lactic acid as muscle soreness). The microorganisms are tremendously more diverse and complex in metabolic patterns than are Eucarya and I want to spend our time emphasizing what microbes can do, not just covering what you have already had in other courses.
So, if you do not remember the basics of metabolism you will need to review. The following pages should serve as a reminder. If it doesn’t all come back to you then read Chapter 5 in the text. If you have not had chemistry you will also need to read
Chapter 2.
Review of oxygen tolerance:

Obligate anaerobe – does not require O
2
.

Aerotolerant anaerobe – does not require O
2
for .

Microaerophile – needs a little O
2
for metabolism, but less than amount present in the atmosphere.

Facultative anaerobe – can switch its metabolism based on whether or not O
2
is present.

Aerobe (obligate aerobe) – requires O
2
for metabolism.
Review of nutritional patterns:
Source of energy Source of carbon
Chemicals organic
CO
2
(used by autotrophs)
Organic molecules (-C-C-C-) (used by heterotrophs) inorganic
Light
Most common combinations of Energy gaining strategy plus Carbon gaining strategy
Chemoorgano heterotrophs
Chemolitho autotrophs
Photo autotrophs
Photo heterotrophs

BIO 208 Unit 2 Review of General Metabolism Concepts
You should also know
Definitions of metabolism, anabolism, and catabolism
That ATP (Adenosine Tri Phosphate) is made to store energy and used to release energy – it is the energy “currency” for the cell.
Pyruvate is a key intermediate molecule in many catabolic pathways.
Should understand basics of oxidations - reductions
Remember - A l oss of an e lectron is called an o xidation; a g ain of an e lectron is called a r eduction (remember as: LEO the lion says GER).
In biological molecules it is usually the entire H atom (electron and proton) that is lost or gained, but not always. Sometimes the electrons are separated from the proton and only the electrons are lost or gained; and sometimes it may be one H atom + 1 electron (from a second H atom) that are lost or gained.
In any pair of molecules you can distinguish which is the oxidized and which is the reduced:
Oxidized state Reduced state:
Contains more oxygen atoms OR fewer hydrogen atoms AND therefore has fewer electrons and is less negative or more positive
Example pairs:
Contains fewer oxygen atoms OR more hydrogen atoms AND therefore has more electrons and is more negative or less positive
Glucose
C
6
H
12
O
6
Pyruvate
C
3
H
4
O
3
NAD +
Sulfate
SO
4
NADH
Hydrogen sulfide
H
2
S

BIO 208 Unit 2 Review of General Metabolism Concepts
All cells need:
1. A source of carbon for making cellular molecules.
There are two strategies for obtaining carbon: a. Recycle the C already present in some organic (-C-C-) molecule b. Use CO
2
from the atmosphere
2. A source of energy for performing all cellular work (building molecules, transport across the plasma membrane, locomotion, etc.)
Energy is created by harvesting the electrons present in: a. Organic molecules.
(specifically the electrons in the H atoms in the molecules)
Hydrogen – showing the proton and electron like a sugar or an amino acid
OR b. Inorganic molecules. electrons in molecules like ammonia hydrogen sulfide
The more electrons a molecule has, the more energy the molecule is capable of yielding – so look at glucose compared to hydrogen sulfide – which molecule should yield the most energy? (glucose – 12 H vs. 2 in H
2
S)

BIO 208 Unit 2 Review of General Metabolism Concepts
The electrons that are released when bonds are broken have to go somewhere, so they get passed from the donor
(the molecule that you started with that had all the electrons) to intermediate electron carriers.
NAD + is a soluble carrier present in the cytoplasm. It is lacking
1 electron (1 H) and so it can accept 1 electron
(1 H). As it accepts the electron, it is reduced to NADH.
Oxidized state fewer H, fewer emore positive (NAD + )
Reduced state more H, more e-

BIO 208 Unit 2 Review of General Metabolism Concepts
NAD + is in limiting quantities in the cell and it must be regenerated if energy production is to continue.
There are 2 ways to regenerate NAD + from NADH :
1.
NADH passes the electron to an organic molecule like pyruvate – this process is called fermentation - as NADH loses the electron it becomes oxidized to NAD + again.
As pyruvate accepts the electron it becomes reduced to acetic acid or to ethanol, etc., which are excreted from the cell, carrying waste electrons with them. Acetic acid, ethanol, etc. still have electrons, so potential energy is lost in the fermentation strategy.
2. NADH travels to the cytoplasmic Fig. 5.16 membrane and passes the electron off to the electron transport chain. This process is called respiration .
(NADH then becomes
NAD + ) electrochemical gradient - energy pH 8.5

BIO 208 Unit 2 Review of General Metabolism Concepts
The electrons are passed along the chain, generating two types of usable energy along the way – electrochemical gradient and ATP - until they reach a final electron acceptor, an inorganic molecule which can be: a. oxygen ( aerobic respiration ) As oxygen accepts electrons it will become reduced to H
2
O
OR b. some other inorganic molecule ( anaerobic respiration ) like nitrate or sulfate becomes reduced to nitrite (NO
2
) becomes reduced to hydrogen sulfide (H
2
S)
Note – fermentation is NOT anaerobic respiration. By definition respiration requires both an electron transport chain and an inorganic terminal electron acceptor. Fermentation does not employ an electron transport chain and the terminal electron acceptor is an organic molecule. Fermentation takes place in the absence of oxygen, it can occur in anoxic and anaerobic environments, but it is not respiration!

BIO 208 Unit 2 Review of General Metabolism Concepts
Comparison of Respiration vs Fermentation in Chemoorganotrophs
Initial electron donor : examples:
Respiration organic molecule carbohydrates, amino acids, lipids
Fermentation organic molecule carbohydrates, amino acids, lipids
Intermediary electron carrier(s):
Final electron acceptor examples: final electron acceptor reduced to:
NADH, FADH
2
, carriers in the electron transport chain
H inorganic
O
2
2
O
molecule
CO
CH
2
4
, NO
, NO
3
2
, SO
, H
2
4
S example organisms
Potential net ATP yield :
Mitochondria,
E. coli ,
Pseudomonas,
S. aureus
Methanogens,
E. coli,
Pseudomonas ,
Sulfate-reducing bacteria as many as 38 if starting with 1 glucose by aerobic respiration with an electron transport chain containing all the cytochromes – but often far fewer than 38 - but still more than 2.
NADH organic molecule pyruvate lactic acid, acetic acid, ethanol, etc.
Bifidobacterium,
Lactobacillus, E. coli,
Clostridium,
Bacteroides
2

BIO 208 Unit 2 Review of General Metabolism Concepts
Comparison of Respiration in Chemoorganotrophs vs Chemolithotrophs
Initial electron donor : examples:
Electron donor oxidized to :
Final electron acceptor examples:
Chemoorganotroph organic (-C-C-) molecule carbohydrates, amino acids, lipids
CO
2
O
2 inorganic molecule
(aerobic respiration)
CO
2
, NO
3
, SO
4
(anaerobic respiration)
Chemolithotroph inorganic molecule hydrogen gas, ammonia, nitrate, hydrogen sulfide water, nitrate, nitrite, sulfuric acid inorganic molecule
O
2
(aerobic respiration) electron acceptor reduced to:
H
2
O CH
4
, NO
2
, H
2
S H
2
O example organisms
Mitochondria,
E. coli ,
Pseudomonas,
S. aureus
Methanogens,
E. coli,
Pseudomonas ,
Sulfate-reducing bacteria
Alcaligenes,
Nitrosomonas,
Nitrobacter,
Thiomargarita