Microbial Metabolism
Microbiology 2314
Why Study Bacterial
Metabolism?
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For Interest
Treatment of Disease
Productive Use of Bacteria
Unity of Biochemistry
Inexpensive
Easy to Grow and Study
Energy
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Capacity to Do Work
Calories / Joules
Defined in Terms of What It Does
1 calorie = 4.184 Joules
Cells Require Energy
• Phototrophs  Light
• Chemolithotrophs  Inorganic Chemicals
• Chemoorganotrophs  ?
Types of Energy
• Kinetic
- Energy of Motion
- Light, Heat, Mechanical
• Potential
- Stored Energy
- Battery, Molecular Bonds, Reservoir
Water Behind Dam
Metabolism
Metabolism is the sum total of all the
chemical reactions within a living organism.
Metabolism = Anabolism + Catabolism
Anabolism
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Make New Molecules
Simple to Complex
Assimilative
Biosynthetic
Endergonic/Endothermic
Catabolism
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Used to Obtain Energy
Complex to Simple
Degradative
Dissimulative
Exergonic/Exothermic
The energy of catabolic reactions is used to drive anabolic
reactions. Energy is typically stored as ATP.
ATP
The universal energy carrying molecule
in living organisms.
• 1 Adenine
• 3 Phosphates
• Ribose
Energy Flows One-Way Through a System
The Earth’s Energy Comes From the Sun
Rules of Metabolism
• Concerned with Acquiring and Using Energy.
• Efficient Energy Users Survive and
Reproduce Their Genes. Their Advantage is
Passed On.
• Not Magic. Follows Simple Physical Laws.
• To Understand Metabolism – Must
Understand the Components of Metabolism.
Regulation
• Living Organisms are Very Complicated.
• Life Requires a High Level of Regulation
• Regulation is Achieved Via Molecular
Recognition
• Recognition  Preprogrammed Response
The Principle of Molecular
Recognition
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Specialized Cells
Receptors are Binding Sites
Ligands are Docking or Attaching Sites
Binding by Ligands to Receptors
Message Transfer to the Cell’s Interior
Control Center Initiates a Response
Information About Enzymes
• Enzymes
– Proteins Produced by Living Cells
– Catalyze Chemical Reactions
– Lower the Activation Energy
• Enzymes as Proteins
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Globular Proteins
Efficient
Operate at Low Temperatures
Subject to Cellular Control
Information About Enzymes
• Enzymes are the Tools of Life
– Performs Functions Necessary for Life
– Has Only One Job
– Do Everything in the Cell
• Chemical Nature of Enzymes
– Determined by the Chemical Characteristics of
the Amino Acids that Compose it
– Influenced by the Arrangement of the Amino
Acids
Amino Acids
• 20 Amino Acids
• Arranged in Chain During the Process of
Translation
• Strong Covalent Peptide Bonds
• Proteases Break Bonds
Types of Amino Acids
1. Hydrophobic
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Repelled by Water
Only Associate with One Another
2. Basic
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Bind Protons / Positively Charged
Attracted by Water
3. Acidic
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Negatively Charged
Attracted by Water
4. Polar-Nonionizable
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No Charge
Attracted by Water
Naming Enzymes
• End in ASE
• Named According to Substrate or Type of
Reaction they Catalyze
• Six Classes of Enzymes
Enzyme Components
CoFactor Compostion
• Metal Ion
- Fe, Cu, Mg, Mn, Ca, Zn
• Coenzyme
- NAD, NADP, FAD, Coenzyme A
• Vitamins are Organic Cofactors
• Minerals are Inorganic Cofactors
Enzyme Characteristics
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Organic Catalysts
Renewable
Large
Work Quickly
Stable and Long Lasting
Unique Functional Structure
Enzymes serve as Catalysts. Catalysts lower the
activation energy making it easier for reactions to occur.
The Mechanism of Enzymatic
Action
• An enzyme attracts substrates to its active site,
catalyzes the chemical reaction by which
products are formed, and then allows the
products to dissociate—i.e., separate from the
enzyme surface.
• The combination formed by an enzyme and
its substrates is called the enzyme–substrate
complex.
• When two substrates and one enzyme are
involved, the complex is called a ternary
complex; one substrate and one enzyme are
called a binary complex.
• The substrates are attracted to the active site
by electrostatic and hydrophobic forces
Lock and Key Paradigm
1. Interaction Between Enzyme and Substrate
2. Initiates a Preprogrammed Reaction
3. Causes Substrate Transformation
Denaturation
Factors Influencing Enzymatic Activity
1. Temperature
2. pH
3. Concentration
Inhibition
• Competitive Inhibitors
- Compete with the normal substrate for
active site of the enzyme
- Mimic the true substrate
• Noncompetitive Inhibitors
- Act on other parts of the apoenzyme
or on the cofactor and decrease the
enzymes ability to combine with the normal
substrate
Inhibition
Feedback Inhibition / Estrogen
Production
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Hypothalamus Secretes Gonadotrophin
Gonadotrophin goes to Pituitary
Causes Pituitary to release LH and FSH
LH and FSH act on the Overies
Overies release Estrogen
Estrogen goes to the Hypothalamus
Knowing What We Do About Enzymes, Explain Why a
Siamese Cat is Colored the Way They Are.
Glycolysis
• Glycolysis is the metabolic pathway that
converts glucose C6H12O6, into pyruvate,
CH3COCOO− + H+.
• The free energy released in this process is
used to form the high-energy compounds
ATP (adenosine triphosphate) and NADH
(reduced nicotinamide adenine
dinucleotide).
Glycolysis is a
metabolic
pathway found in
the cytosol of
cells in all living
organisms both
aerobic and
anaerobic.
• When oxygen is present, acetyl-CoA is
produced from the pyruvate molecules
created from glycolysis.
• Once acetyl-CoA is formed, two processes
can occur, aerobic or anaerobic respiration.
• When oxygen is present, the mitochondria
will undergo aerobic respiration which leads
to the Krebs cycle.
• However, if oxygen is not present,
fermentation of the pyruvate molecule will
occur.
Kreb’s
Cycle
• In the presence of oxygen,
when acetyl-CoA is
produced, the molecule
then enters the Krebs cycle
inside the mitochondrial
matrix, and gets oxidized
to CO2 while at the same
time reducing NAD to
NADH. NADH can be
used by the electron
transport chain to create
further ATP as part of
oxidative phosphorylation.
Summary
Step
coenzyme yield
Glycolysis preparatory phase
ATP yield
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4
Glycolysis pay-off phase
Oxidative decarboxylation of
pyruvate
2 NADH
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2 NADH
6
2
Krebs cycle
6 NADH
2 FADH2
Total yield
18
4
36 ATP
Source of ATP
Phosphorylation of glucose
and fructose 6-phosphate uses
two ATP from the cytoplasm.
Substrate-level
phosphorylation
Oxidative phosphorylation Each NADH produces net 2
ATP due to NADH transport
over the mitrochondrial
membrane
Oxidative phosphorylation
Substrate-level
phosphorylation
Oxidative phosphorylation
Oxidative phosphorylation
From the complete oxidation
of one glucose molecule to
carbon dioxide and oxidation
of all the reduced coenzymes.
No Oxygen?
• Without oxygen, pyruvate (pyruvic acid) is not
metabolized by cellular respiration but undergoes
a process of fermentation.
• The pyruvate is not transported into the
mitochondrion, but remains in the cytoplasm,
where it is converted to waste products that may
be removed from the cell.
• This serves the purpose of oxidizing the
electron carriers so that they can perform
glycolysis again and removing the excess
pyruvate.
• This waste product varies depending on the
organism. In skeletal muscles, the waste
product is lactic acid. This type of
fermentation is called lactic acid
fermentation.
• In yeast, the waste products are ethanol and
carbon dioxide.
• This type of fermentation is known as
alcoholic or ethanol fermentation.
• The ATP generated in this process is made
by substrate-level phosphorylation, which
does not require oxygen.
Efficiency?
• Fermentation is less efficient at using the energy
from glucose since 2 ATP are produced per
glucose, compared to the 38 ATP per glucose
produced by aerobic respiration.
• This is because the waste products of
fermentation still contain plenty of energy.
Ethanol, for example, can be used in gasoline
solutions.
Chemiosmotic Model of ATP
Generation
• Chemiosmosis is the movement of ions
across a selectively-permeable membrane,
down their electrochemical gradient.
• More specifically, it relates to the
generation of ATP by the movement of
hydrogen ions across a membrane during
cellular respiration.
• Hydrogen ions (protons) will diffuse from an
area of high proton concentration to an area of
lower proton concentration.
• Peter Mitchell proposed that an
electrochemical concentration gradient of
protons across a membrane could be harnessed
to make ATP.
• He linked this process to osmosis, the diffusion
of water across a membrane, which is why it is
called chemiosmosis.
• ATP synthase is the enzyme that makes
ATP by chemiosmosis.
• It allows protons to pass through the
membrane using the kinetic energy to
phosphorylate ADP making ATP.
• The generation of ATP by chemiosmosis
occurs in chloroplasts and mitochondria
as well as in some bacteria.
Compare/Contrast Aerobic and
Anaerobic Respiration
• Aerobic respiration requires oxygen.
• Anaerobic respiration does not require
oxygen
• Aerobic respiration tends to create more
ATP per glucose molecule and is thus more
efficient than anaerobic.
• Cellular respiration is an aerobic process that has
3 stages.
1. glycolysis is the anaerobic stage and does
not require oxygen.
2. the krebs cycle or the citric acid cycle and
chemiosmosis requires the use of oxygen.
When there is no oxygen present, the cell is able
to use only glycolysis and the process in which
the cell recycles the NAD+ required in glycolysis
to repeat glycolysis is called fermentation, an
anaerobic process.
• there are 2 types:
1. alcoholic fermentation
2. lactic fermentation
• Alcoholic fermentation makes the byproduct:
alcohol.
• Yeast and other prokaryotic organisms tend to
use this type of fermentation.
• Lactic fermentation makes
the byproduct: lactic acid,
hence the reason when you
run, your legs have a burning
sensation because your
muscles are using the process
of lactic fermentation and
acid burns.
**the lactic acid is ultimately
brought to the liver and
detoxified
Summary
• Aerobic = oxygen = more efficient (more
ATP)
• Anaerobic = no oxygen = less efficient (less
ATP)
• Aerobic = cellular respiration
• Anaerobic = fermentation
• Fermentation originally
referred to the foaming that
occured during the
manufacture of wine and
beer, a process at least
10,000 years old.
• That the frothing results
from the evolution of
carbon dioxide gas was
not recognized until the
17th century.
Fermentation
• Louis Pasteur in the 19th century used the
term fermentation in a narrow sense to
describe the changes brought about by yeasts
and other microorganisms growing in the
absence of air (anaerobically); he also
recognized that ethyl alcohol and carbon
dioxide are not the only products of
fermentation.
Ethanol Fermentation
• Ethanol fermentation, also referred to as
alcoholic fermentation, is a biological process
in which sugars such as glucose, fructose, and
sucrose are converted into cellular energy and
thereby produce ethanol and carbon dioxide as
metabolic waste products.
• Because yeasts perform this conversion in the
absence of oxygen, ethanol fermentation is
classified as anaerobic.
• The chemical equation below summarizes
the fermentation of glucose, whose
chemical formula is C6H12O6.
• One mole of glucose is converted into two
moles of ethanol and two moles of carbon
dioxide:
C12H22O11 +H2O + invertase → C6H12O6
C6H12O6 + Zymase → 2C2H5OH + 2CO2
• C2H5OH is the chemical formula for
ethanol.
Lactic Acid Fermentation
• Lactic acid fermentation is a biological
process by which sugars such as glucose,
fructose, and sucrose, are converted into
cellular energy and the metabolic byproduct
lactate.
• It is an anaerobic fermentation reaction that
occurs in some bacteria and animal cells,
such as muscle cells, in the absence of
oxygen.
• The process of lactic acid fermentation using
glucose is summarized below. In fermentation,
one molecule of glucose is converted to two
molecules of lactic acid:
C6H12O6 → 2 CH3CHOHCOOH
• Before lactic acid fermentation can occur, the
molecule of glucose must be split into two
molecules of pyruvate. This process is called
glycolysis.
Identifying Bacteria
• Fermenting bacteria have characteristic
sugar fermentation patterns, i.e., they can
metabolize some sugars but not others. For
example, Neisseria meningitidis ferments
glucose and maltose, but not sucrose and
lactose, while Neisseria gonorrhoea
ferments glucose, but not maltose, sucrose
or lactose.
• Such fermentation patterns can be used to
identify and classify bacteria