Microbial Metabolism
BIOL 318 Clinical Microbiology
Dr. David E. Fulford, Ph.D.
Department of Biology and Health Services
Edinboro University of Pennsylvania
Basic Principles
All cells acquire nutrients from their environment
All cells require energy in the form of light or the breakdown of nutrients (catabolism)
The energy is stored in the form of ATP
With the help of enzymes, precursor molecules and ATP larger molecules are produced by the cell (anabolism) The larger molecules are referred to as macromolecules
The cells put the macromolecules together to form larger structures such as plasma membranes, cell walls, ribosomes, etc..
Oxidation/Reduction Reactions
Oxidation/reduction reactions are very important
A reducing agent is capable of releasing electrons
A oxidizing agent is capable of picking up electrons
In the cell electrons often are released and picked up by electron carries such as NAD+, NADP+ or FAD+
These molecules serve as coenzymes and are not the terminal electron acceptors
click
here for illustration
Energy and ATP all living organisms require energy and this energy is usually
supplied in the form of chemical energy the energy stored in chemicals is in the chemical bonds
(potential energy). As energy is needed for cellular activity the bond energy is
released when the chemical bonds are broken (kinetic energy). chemical reactions fall into two major types based on whether
energy is released or stored in the reaction: exergonic reactions release energy endergonic reactions require energy (they store energy)
when chemical reactions occur there is transitional state that
the chemical must go through in order for the reaction to occur. The higher the transition energy, the less likely the reaction
will occur. Enzymes lower the transition energy and therefore increase the
reaction rate
Why ATP?
The energy in nutrients often needs to be concentrated before it can be useful
ATP is a good molecule because it takes quite a bit of energy to form the phosphate bonds
Energy is stored in the phosphate bonds
adenosine triphosphate (ATP) is a high energy molecule that supplies energy to enzymes and other molecules as needed.
bacterial cells use ATP:
for binary fission
for protein synthesis
for carbohydrate breakdown
for flagellar motion
for spore formation
other chemical and physical activities
if a cell cannot generate ATP it will die
cells do not store energy in the form of ATP, but rather they store energy as carbohydrate or fat and occasionally as things such as polyphosphates (metachromatic granules) and Poly(3-hydroxybutyrate) Granules or PHA
ATP can be produced using several different mechanisms:
Substrate level phosphorylation
Oxidative phosphorylation
Photophosphorylation
Enzymes
There are hundreds of chemical reactions
Most of these require catalysts in order to occur
These biological catalysts are called enzymes
Enzymes are proteins
enzyme names are derived from the reactions they catalyze:
enzyme names end in -ase
there are groups of enzymes that have similar functions
hydrolases
oxidases
transferases
kinases,
isomerases
ligases
oxidoreductases
exoenzymes are released from the cell, they help to digest large extracellular molecules
endoenzymes are found inside cells and for the most part involved in metabolic pathways
constitutive enzymes are enzymes that are always found in the cell
induced enzymes are enzymes that are only present under certain situations like when the substrate is present
enzyme activity is highly specific
specific substrate is the molecule(s) that interacts with the enzyme
the product is the molecule(s) that is released once the chemical reaction has occurred
the substrate binds to the active site
The active site is produced by the folding of the protein into a very specific three dimensional structure.
These sites are often the targets of inhibitors
the reactions catalyzed by enzymes are for the most part reversible
Some enzymes require cofactors and coenzymes:
enzymes that require cofactors are referred to as apoenzymes.
When the apoenzyme binds its cofactor(s), the whole complex is referred to as a holoenzyme
cofactors – non-protein, inorganic ions that the enzymes requires to function properly - iron, magnesium, calcium,, zinc
coenzymes – non-protein organic molecules required by enzymes to function properly - NAD, FAD, coenzyme A
Enzymes catalyze chemical reactions by:
Decreasing the energy of activation
Increasing the thermal energy
Increasing the local concentration of substrates
Adding a catalyst
enzyme activity is disrupted by a variety of chemical and physical parameters:
temperature - heat will often denature enzymes
alcohol and phenol - precipitate proteins
iodine - iodinates amino acids in enzymes and alters their structure
antibiotics - some interfere with enzyme production
enzymes can be virulence factors and enhance a bacteria's ability to cause infection
Many of these enzymes are considered to be toxic to the host:
streptokinase - digests blood clots
collagenase - breaks down collagen
lipases - degrade lipids
penicillinase - degrades penicillin
enzymes can be regulated in a number of ways:
competitive inhibition - molecules similar in structure to the substrate compete for the active site with the substrate
non-competitive (allosteric inhibition) - a molecule other than the substrate binds to a regulatory site other than the active site
feedback inhibition - an end product can inhibit the activity of the enzyme the production of an enzyme can be suppressed or induced as the need arises
Usually an end product builds up and represses the synthesis of the enzyme, whereas the presence of substrate often induces the synthesis of the enzyme
Carbohydrate Catabolism
is similar for most organisms:
one mole of glucose (180 grams) contains 690,000 calories of energy
a typical bacteria captures about 277,400 calories of energy from a mole of glucose in the form of 38 moles of ATP
the pathway that leads to the release of energy is referred to as respiration
There are two types of respiration, aerobic and anareobic
the formula for aerobic respiration is:
C6H12O6 + 6 O2 + 38 ADP +38 P -----> 6 CO2 + 6 H2O + 38 ATP
Glycolysis
the best known pathway is the Embden-Meyerhof pathway. In this pathway glucose is converted into a 3-carbon molecule called pyruvate.
A net of two ATP are produced by this pathway.
high energy electrons are removed from glucose during the pathway along with protons. These are picked up by NAD + (nicotinamide adendine dinucleotide).
no oxygen is used during glycolysis
Kreb Cycle (Citric Acid Cycle)
the first thing that must happen to the pyruvate from glycolysis is that it must release one carbon in the form of carbon dioxide and the remaining two carbon molecule combine with coenzyme A (CoA) to form acetyl-CoA.
Acetyl-CoA combines with oxaloacetate to form citric acid and the cycle begins.
during the Krebs Cycle the remaining carbons are released as carbon dioxide, ATP is produced
high energy electrons and protons are picked up by NAD+ and FAD+ (flavin adenine dinucleotide).
These high energy electrons enter the final step of the aerobic respiratory pathway, the electron transport chain
Oxidative Phosphorylation
electrons released from glucose during glycolysis and the Kreb Cycle are passed down a series of molecules called cytochromes.
During this process the electrons give up some of their energy which is used to put phosphate groups onto ADP molecules
the actual mechanism for the formation of ATP is called chemiosmosis and is powered by the movement of protons against a concentration gradient.
As the electrons move down the cytochrome pathway, protons are excluded from the cell and build a high concentration outside the cell.
Eventually proton channels open up and the protons rush back into the cell
This force drives the ATP synthetase to make ATP out of ADP and P
Anaerobic Respiration
is a process where oxygen is not used as the terminal electron acceptor. An oxidative phosphorylation process takes place, but molecles other than oxygen accept the electrons:
these pathways occur in the absence of oxygen
inorganic molecules usually are used as electron acceptors
E. coli
reduced nitrate to nitrite
Desulfovibrio
Methanobacterium reduces carbon dioxide to methane click here
Fermentation
occurs when an organic molecule is used as an electron acceptor
The organic molecule is usually an intermediate in the catabolic pathway
A variety of products can be made by the fermentation of pyruvate:
butyric acid Clostridium
propionic acid Propionibacterium
butanediol Enterobacter
acetic acid Acetobacter
mixed acid (acetic, lactic, succinic and formic) E. coli
Other Aspects of Catabolism
Catabolism of other carbohydrates: a variety of mono-, di- and polysaccharides can be catabolized by bacteria.
These compounds are usually converted into glucose or an intermediate of the glycolytic pathway or Krebs cycle.
Catabolism of proteins and fats (fats are a better source of energy than proteins):
proteins are initially broken down into amino acids which are deaminated to form components of the various catabolic pathways
alanine converts into pyruvate
aspartic acid converts into oxaloacetic acid
fats are broken down into fatty acids and glycerol
glycerol is converted into DHAP and enters glycolysis
fatty acids are broken down into 2 carbon units that are converted into acetyl-CoA and enter the Krebs cycle
