BIO 208 Unit 2 Patterns of Metabolism
This outline is intended to facilitate your preparation for lecture. This web outline will NOT
substitute for regular lecture attendance.
While we will be covering the topics outlined in Chapter 5 of your text, we will be doing it in a
very different manner from how it is presented in the text. Please be prepared to take careful
notes in class.
III. Patterns of Metabolism in the Microbial World (a.k.a. how do microbes make a living –
and who cares?)
A. The Basics: background info
Metabolism = sum of all chem. rxns occurring within a living organism
All cells need a source of energy for:
Catabolism- breaking bonds in molecules –
Ex. glucose to carbon dioxide and water
Anabolism – creating bonds -
1
BIO 208 Unit 2 Patterns of Metabolism
2
The coupling of catabolism and anabolism is made possible through adenosine triphosphate (=ATP.
ADP stands for adenosine diphosphate)
During catabolism – ATP  ADP + Pi + energy
Pi = inorganic phosphate
During anabolism – ADP + Pi + energy  ATP
ATP can be formed in 3 ways:
1. by substrate level phosphorylation – the simplest, oldest and least-evolved way to make ATP a high energy phosphate is removed from a substrate and is added to ADP to make ATP.
Ex. C-C-C~P + ADP  C-C-C + ATP
2. by oxidative phosphorylation aka electron transport phosphorylation – electrons are transferred
from organic compounds to electron carrier molecules and then to final electron acceptor molecules.
The transfer of electrons releases energy that is used to convert ADP  ATP.
3. by photophosporylation – occurs in photosynthetic cells only. Light energy is converted to ATP.
We will see examples of #1 and #2 as we continue our discussion
BIO 208 Unit 2 Patterns of Metabolism
Oxidation-Reduction Reactions
Electrons (e-) in molecules contain energy.
Oxidation – removal (loss) of e- Reduction – addition (gain) of e- Oxidation and reduction reactions are always coupled-
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 entire atom plus 1 additional electron (from a
second H atom) that are lost or gained.
In any pair of molecules you can distinguish which is in the oxidized state and which is reduced:
Oxidized state:
Contains more oxygen atoms OR
fewer hydrogen atoms AND
therefore has fewer electrons and is
less negative (or more positive)
Reduced state:
Contains fewer oxygen atoms OR
more hydrogen atoms AND
therefore has more electrons and is
more negative (or less positive)
Glucose
C6H12O6
2 Pyruvate
2 C3H4O3
NAD+
NADH
Sulfate
SO4
_____
Hydrogen sulfide
H2S
_____
________________________
3
BIO 208 Unit 2 Patterns of Metabolism
4
B. Patterns of Energy Production
1. Basic information
Patterns among Eukaryotes:
 alcohol fermentation (yeast)
 lactic acid fermentation (muscle cells, neutrophils)
 aerobic respiration (mold, protozoa, animals)
 oxygenic photosynthesis (algae, plants)
Prokaryotes do all the above plus:
 anaerobic respiration: uses inorganic molecules other than 02 as a final electron acceptor
 lithotrophy: use of inorganic substances as sources of energy
 photoheterotrophy: use of organic compounds as a carbon source during bacterial photosynthesis
 anoxygenic photosynthesis: photophosphorylation in the absence of O2
 methanogenesis: uses H2 as an energy source and produces methane
 light-driven nonphotosynthetic photophosphorylation: converts light energy into chemical energy
There are 2 initial sources of usable energy:
1. sunlight –
2. chemical bonds of molecules Heterotrophs - energy is created by breaking bonds in a molecule and harvesting the electrons
released from the H atoms in:
a. Organic molecules b. Inorganic molecules –
The more electrons a molecule has, the more energy it is capable of releasing. This initial
molecule is called the electron donor.
Ex. glucose (C6H12O6) has a lot of H atoms (12) and therefore a lot of electrons, its oxidation will
release a lot of electrons. Glucose is a high energy electron donor.
BIO 208 Unit 2 Patterns of Metabolism
The electrons have to go somewhere - they get passed from the initial donor of released electrons
(electron donor) to intermediate electron carrier molecules.
NAD (Nicotinamide Adenine Dinucleotide) -
accepts 2 e- (and 1 proton) and becomes reduced to
+
NAD
NADH
PROBLEM: NAD+ is present in limited amounts in the cell and could be depleted; it must be
regenerated if energy production in the cell is to continue.
5
BIO 208 Unit 2 Patterns of Metabolism
2. Example – generation of energy via carbohydrate catabolism – specifically glucose
Glycolysis (= Embden-Meyerhof pathway) – occurs in the cytoplasm – electron donor is glucose
Glucose + 2 ATP
C6H12O6
2 Pyruvate + 4 ATP
2 C3H4O3
net ATP production = 2 ATP
6
BIO 208 Unit 2 Patterns of Metabolism
End of glycolysis - 2 ATP and 2 Pyruvate (C3H4O3) and 2 NAD+ converted to 2 NADH
Need to regenerate NAD+
Fermentation – occurs in the cytoplasm - pass e- from NADH to an organic molecule,
regenerates NAD+
Ex.
2 C3H4O3
2 NADH + 2H+
2 C3H6O3
(lactic acid)
2 NAD+
Inefficient –
End of fermentation - 2 ATP and some fermentation end products and 2 NAD+ regenerated
7
BIO 208 Unit 2 Patterns of Metabolism
8
Alternative (to fermentation) strategy:
Respiration – pass e- along a series of electron carrier molecules, ultimately to a final (or
terminal) electron acceptor molecule, regenerates NAD+
Step 1 – Tricarboxylic acid (TCA) cycle (also known as citric acid cycle or Krebs cycle) – occurs in
the cytoplasm - harvests the energy stored in pyruvate but transfers an even larger number of e- to
NAD+ (which converts it to NADH).
At this point following TCA:
For each pyruvate (C3H4O3)  1 ATP + 3 CO2 + 4 NAD  NADH and 1 FAD  FADH2
For each glucose  2 ATP + 6 CO2 + 8 NADH+ 2 FADH2
BIO 208 Unit 2 Patterns of Metabolism
Step 2 – Electron Transport Chain – the soluble NADH and FADH2 carry e- from the cytoplasm
to the cytoplasmic membrane and pass them off to a series of membrane associated electron
carriers (NAD+ is regenerated when NADH passes the e-), ending with the final or terminal
electron acceptor.
This final electron acceptor may be oxygen –
Electron acceptor (oxidized state)
½ O2
becomes reduced to
H20
aerobic respiration
1 molecule of C6H12O6 oxidized completely to CO2 coupled to reduction of oxygen to water
(aerobic respiration) can yield up to a max of 38 ATP.
9
BIO 208 Unit 2 Patterns of Metabolism
OR
This final electron acceptor is something other than oxygen –
Examples of final e- acceptors for anaerobic respiration:
Electron acceptor (oxidized state)
becomes reduced to:
Fe3+
ferric iron
Fe2+
Iron respiration
NO3nitrate
NO2-, N2O, N2
Nitrate respiration
SO42sulfate
HS-
Sulfate respiration
CO2
carbon dioxide
CH4
methane
Methanogenesis
S0
sulfur
HS-
Sulfur respiring
yield of ATP is greater than 2 but fewer than 38 ATP
10
BIO 208 Unit 2 Patterns of Metabolism
C. Some Exciting Implications of Microbial Activity:
1. Metabolism of the Human Intestinal Community
a. Where does your gut microbial community come from?
At birth
Progression of your gut community if you were a breast-fed baby
Day 1 - First colonizer was Escherichia coli


facultative anaerobe
chemoorgano heterotroph (both C and E from organic)
Where did E. coli come from?
What organic cmpd does E. coli use as a C and E source?
How does E. coli get C and E from lactose?
11
BIO 208 Unit 2 Patterns of Metabolism
12
BIO 208 Unit 2 Patterns of Metabolism
Day 3 – added 2 more bacteria
Enterococcus
obligate but aerotolerant anaerobes
chemoorgano heterotrophs
obligate fermentative metabolism
Bifidobacterium
Lactic acid bacteria (named from their final fermentation end product)
e1 Glucose
NAD+
2 Pyruvate
eNADH
glycolysis
2 ATP
fermentation
NAD+ regenerated
2 Lactic acid
(excreted waste)
Soon after added:
Enterobacter
Clostridium
facultative anaerobe
obligate (aerotolerant) anaerobe
fermentative metabolism
Butanediol fermenters (named from their final fermentation end product)
e1 Glucose
NAD+
2 Pyruvate
eNADH
glycolysis
2 ATP
fermentation
ethanol
acetic acid
Acetoin
lactic acid
2,3-Butanediol + CO2
CO2 + H2
NAD+ regenerated
succinic acid
all of these are excreted waste products
13
BIO 208 Unit 2 Patterns of Metabolism
Community of breast-fed infant from 1 week to ~ 3.5 months:
E. coli
Enterococcus
Bifidobacterium
Enterobacter
Clostridium
3.5 months to weaning
99% Bifidobacterium infantis –another lactic acid fermenter
When meat is introduced:
Gram-negative anaerobes:
Bifidobacterium
Clostridium
Fusobacterium
Eubacterium
Ruminococcus
Peptococcus
Peptostreptococcus
Bacteroides – 30% of total adult community
Bacteroides
obligate anaerobe
extremely oxygen sensitive
fermenter
14
BIO 208 Unit 2 Patterns of Metabolism
b. What are the benefits of a stable, mature gut community?
1) Nutrition
2) Prevents colonization by pathogens
3) Trains the immune system
1) Nutrition
Complex polysaccharides are converted to volatile fatty acids (vfa)
Bacteroides is the key player
Host and dietary carbohydrates – complex carbs, starch, cellulose
saccharolases
hydrolases
fermentation
volatile short-chain fatty acids*
acetic acid
butyric acid
propionic acid
reabsorbed through the large intestine
used by you as an energy source
provide a significant proportion of your daily energy requirement (540 kcal)
* These products in brown are good for your health metabolic by-products
15
BIO 208 Unit 2 Patterns of Metabolism
Dietary fats
Liver
Bile acids
Absorbed by small intestine
----------------------------------------------------------------------------------------------------
If fats and bile acids are not reabsorbed by small intestine but make it to colon
deconjugated
deoxycholic acid
lithocholic acid
intermediate products
Bacteroides thetaiotomicron
ethyl ester
*These products in purple are mutagenic, carcinogenic products; they can induce cancer –
bad for your health products
16
BIO 208 Unit 2 Patterns of Metabolism
17
Dietary protein
Peptides
Amino acids
Absorbed by small intestine
---------------------------------------------------------------------------------------------------Combined activity of the
colonic microbial community
If peptides are not reabsorbed by small intestine but make it to colon
Amino acids
R
+
H3N – C – C – OH–O
deamination
decarboxylation
aromatic
amino acids
sulfur
amino acids
reduced to
phenolic
compounds
SO4
H2S gas
anaerobic respiration by
sulfate-reducing bacteria
fermentation
by many microbes
ammonia
H2
branched chain
fatty acids
volatile
fatty acids
CO2
reduced to
CH4 gas
anaerobic respiration by Methanogens (which are Archaea)
brown and purple as explained before. red are final electron accepts in anaerobic respiration
BIO 208 Unit 2 Patterns of Metabolism
We’ve seen aerobic respiration, fermentation, and anaerobic respiration in chemoorgano
heterotrophs. Now let’s bring in some chemolitho autotrophs and look at the effects of their
metabolism!
All microbes need:
a source of energy (electrons = ATP)
a source of C to build macromolecules (-C-C-)
Heterotrophs that we have talked about already– get C to make –C-C- by recycling the C
contained in organic molecules (like sugars or amino acids). (all heterotrophs get energy
(electrons and therefore ATP) to make –C-C- from breaking chemical bonds)
**Autotrophs – get C to make –C-C- from CO2
But there are 2 sources of energy that can be used to turn CO2  -C-C- and the source defines 2
groups of autotrophs:
1. Photo autotrophs
energy from sunlight (C from CO2) (I’ll leave this for Botany, but lots of microbes do this too)
2. Chemolitho autotrophs
energy is generated from inorganic chemicals (C from CO2)
Many different inorganic chemicals can serve as electron donors to provide the energy for
microorganisms via aerobic respiration (notice the presence of O2 as final electron acceptor in
all the equations following – therefore all chemolitho autotrophs are obligate aerobes):
a. Hydrogen gas as an electron donor
e- donor
H2
+
e- acceptor
1/2 O2

reduced to
H2O
Hydrogen bacteria
Ex. Alcaligenes faecalis (from Lab 8)
b. Sulfur compounds as electron donors
e- donor
2S + 2H2O
e- acceptor
+ 3O2

reduced to
2H2SO4
Ex. Sulfur bacteria like Thiomargareta namibiensis or the bacteria that form snot-tites in
caves.
18
BIO 208 Unit 2 Patterns of Metabolism
c. Nitrogen compounds as electron donors
Nitrifying Bacteria
2 groups of Nitrifying Bacteria:
1) 2NH3 + 3O2  NO2 + 2H2O + 2H+
Ex. Nitrosomonas
2) 2NO2 + 2O2  2NO3 + 2H+
Ex. Nitrobacter
d. iron as an electron donor
Fe2+ + 1/2 O2 + 2H+ Fe3+ + H2O
Iron bacteria like Ferroplasma
Two scenarios where chemolitho autotrophs are very important:
Metabolism of Wastewater Treatment
How do we go from toilet water to treated water? (stay tuned, we will discuss this in Unit 4  )
19
BIO 208 Unit 2 Patterns of Metabolism
Metabolism of the Deep - What? No photosynthesis???
Deep sea hydrothermal vents – provide all the necessary chemicals
 Black smokers – vent hydrogen, sulfur, iron (electron donors for energy), and CO2 (for
carbon) from the Earth’s core
 Sea water contains dissolved oxygen (electron acceptor for aerobic respiration)
 Everything that is needed for chemolithoautotrophs to grow.
Chemolithoautotrophic metabolism turns CO2 and inorganic chemicals into bacterial biomass,
with excess energy to spare!
Animals (chemoorganoheterotrophs)
Giant tube worms
with endosymbiotic chemolithoautotrophs
Giant mussels
Brittle stars
Limpets
Worms
Crabs
Vent fish
Sharks
Assignment
Read Chapter 5
Review 4, 5b,c, 6,7,9
MC 1,4,6
CT 1,3,5
20
BIO 208 Unit 2 Patterns of Metabolism
Supplemental Information – For your information (FYI) only
How can 2 people eat the same foods, 1 person gains weight and the other stays lean?
colonization of gut by microbes increases
glucose uptake in the intestine
↓
microbial fermentation
↓
resulting in substantial elevations in serum
glucose and insulin
results in production of short-chain fatty acids
both
stimulate lipogenesis in the liver
↓
triglycerides into the circulation
↓
taken up by adipocytes (fat cells)
The composition and operation of your gut microbiota influences your energy balance.
Relatively high-efficiency gut microbial communities would promote energy storage (weight
gain), whereas lower efficiency communities would promote leanness.
Small but long-term differences between energy intake and expenditure can, in principle,
produce major changes in body composition.
Ex. if energy intake exceeds energy expenditure by +12 kcal/day, >1 lb of fat could be gained in
a year; this is the average annual weight gain experienced by Americans between ages 25 and 55.
2). Prevents colonization by pathogens – pathogens like Salmonella, Shigella, Campylobacter,
the pathogenic strains of E. coli, etc. that cause intestinal disease. If we have time…
a. competition for attachment sites – the gut epithelium is so densely colonized by normal
microbiota, nowhere for pathogens to attach.
b. competition for nutrients – if pathogens do attach, they have to fight normal microbiota for a
share of nutrients
c. antimicrobial chemicals – and then the normal microbiota secrete antimicrobial chemicals
that kill pathogens.
Ex. E. coli – produces a chemical called colicin
21
BIO 208 Unit 2 Patterns of Metabolism
3) Trains the immune system
The primary barrier between the outside world and you is a single layer (1 cell thick) of gut
epithelium. This barrier is tight, but not impenetrable.
Microvilli – where adsorption takes place
Epithelium
Submucosa
Muscle
The surface of the intestinal epithelium is protected by your immune system – the antibody
IgA, the white blood cells called T and B lymphocytes, and phagocytic macrophages.
The gut epithelium tests the contents of the
gut lumen (open cavity) and can directly
sense the antigens of microbes using “pattern
recognition receptors” (PRRs) – the
epithelium recognizes conserved structures
of bacteria and viruses and then alerts the
host to the potential of infection.
Normal microbiota of the gut and dietary
antigens in food are tolerated (should not
stimulate an immune response).
22
BIO 208 Unit 2 Patterns of Metabolism
c. How does what you eat influence your gut community and in turn your health? –So very cool!!
1). Over stimulation of microbial growth and metabolism
Ex. Lactose intolerance
In babies, the enzyme human lactase is secreted by the small intestine and will break milk
lactose into glucose and galactose. By the age of weaning, humans stop secreting human
lactase.
After the age of weaning if lactose is consumed in dairy, it will pass undigested to the large
intestine. In the large intestine E. coli will secrete the enzyme -galactosidase, which will
now break lactose in to glucose and galactose. The E. coli will use the glucose as a carbon
and energy source to support rapid population growth.
As a result of their fermentative metabolism on this bounty of glucose, E. coli will produce a
lot of 3 carbon fermentation end products, and a lot of CO2 gas. The 3 C end products
increase the osmotic pressure in the large intestine, which combined with the CO2 will results
in the symptoms of bloating and diarrhea
Adult lactose intolerance is the normal state for humans. People who as adults can tolerate
lactose had ancestors that acquired a mutation that allows them to continue to secrete human
lactase in to adulthood.
2). Diet can upset immune system training – if we have time…
The gut immune system has the challenge of responding to disease-causing microbes but not
responding to food antigens and the normal gut microbial community.
In developed countries like the U.S., this discriminatory ability appears to be breaking down.
High-fat, high-sugar, low-fiber diet changes gut community composition, which upsets
immune training resulting in allergies and/or chronic inflammation
Ex.1. Allergies
Children w/ allergies have a higher chance of having bad Clostridium difficile and
Staphylococcus aureus and lower prevalence of good Bacteroides and Bifidobacteria in their
gut.
Ex. 2. Chronic inflammation
Crohn's disease and ulcerative colitis (UC)
? breakdown in tolerance to Bacteroides initiates an autoimmune reaction?
Experimental txt - whipworms
23
BIO 208 Unit 2 Patterns of Metabolism
3). Diet can promote abnormal cell growth – i.e., cancer
Examples of suggested links between microbial metabolism and cancer:
1. High fat diet – go back and look at diagram of what happens to fat in the gut

conjugated secondary bile acids – are carcinogens
2. High protein diet – go back and look at protein diagram again




protein fermentations may be sources of systemic toxins
Heterocyclic amines (HCA) are converted into carcinogens.
phenolics from aromatic amino acids may enhance production of mutagens.
reduced sulfur compounds (like H2S) may be toxic to the colonic epithelium.
3. Alcohol consumption

acetaldehyde toxicity
Look again at diagram of lactose utilization by E. coli. See where ethanol is produced by
mixed acid fermentation? An intermediate molecule in the pathway Acetyl CoA  ethanol is
a toxin called acetaldehyde
Acetyl CoA  acetaldehyde  ethanol
Part of this pathway also runs in the reverse direction:
oxidation
mitochondria in the liver cells
ethanol

acetaldehyde (bad)

alcohol dehydrogenase
aldehyde dehydrogenase
acetic acid (good)
If there is a lot of ethanol being converted to acetaldehyde, the hepatic mitochondrial enzyme
aldehyde dehydrogenase cannot keep up, and acetalydehyde levels build in the liver and
blood. This causes symptoms of hangover in the short term, in the long term the acetaldehyde
causes mutations in DNA that can lead to cancer.
Prebiotics are complex carbohydrates that you cannot digest, such as fructo oligosaccharides
(FOS). They pass to the intestines where they stimulate the growth and activity of intestinal
bacteria that secrete beneficial metabolic end products. Fruits and vegetables contain
oligosaccharides; bananas and artichokes are especially high.
Probiotics are living bacteria from genera that produce favorable end products, such as
Bifidobacterium and Lactobacillus.
24