Al-Farabi Kazakh National University

Faculty of Medicine and Healthcare

Higher School of Medicine
Department of Fundamental Medicine

Physiology and
biochemistry of
bacteria I

Almaty, 2022
1
 Learning outcomes
1. Describe in a broad range the metabolic and physiological diversity among bacteria
2. Consider the main physiological differences among the domains Eukarya, Archaea and Bacteria
3. Define aerobic and anaerobic respiration and various intermediary mechanisms involved, oxidative
phosphorylation
4. Describe conceptual role of enzymes in physiology and biochemistry of bacteria
5. Explain the importance of the nitrogen and carbon cycles, and the role of microbes in
their maintenance.
6. Describe the different phases of the bacterial growth curve.
7. List the types of bacterial growth requirements with examples
8. Characterize the various ways bacterial growth is measured, and explain the advantages and
disadvantages of each method.
9. Predict the effect of different environmental conditions on microbial growth and death curves.
10. Discuss the diverse nutritional needs that support the growth of bacteria.
11. Draw neat labeled diagram of bacterial growth curve
12. Explain the factors affecting bacterial growth curve
Introduction
Metabolism: The chemical traffic of cell metabolism can be compared
to a busy highway going in all directions, with on ramps and off ramps,
intersections, side streets, green lights, and stop signs, all producing a
constant flurry of change—but in the case of metabolism the changes
are to the biochemical structure of cells
Metabolism

Features of bacteria metabolism:

1) the variety of substrates used;
2) the intensity of metabolic processes;
3) the focus of all metabolic processes on providing reproduction
processes;
4) the predominance of decay processes over processes synthesis;
5) the presence of exo- and endoenzymes of metabolism.
Metabolism (metabolism and energy):
• anabolism - (assimilation, constructive or plastic metabolism) - the
synthesis of high molecular weight compounds for the formation of
cellular structures
• catabolism - (dissimilation, energy metabolism) - the breakdown of
various substrates in order to obtain energy
Catabolism + anabolism  metabolism
Enzymes
BY LOCALIZATION:
Endoenzymes secret in the environment.
Exoenzymes function only inside cells, catalyze reactions of biosynthesis and
energy exchange
BY THE MECHANISM OF GENETIC CONTROL:
1) constitutive - enzyme synthesis occurs constantly; substrate availability always
contains in the cell at certain concentrations;
2) inducible - the synthesis of the enzyme depends on the presence of an
appropriate substrate in the environment.
Types of enzymes
• OXIDOREDUCTASES - catalyze reactions oxidation-reduction.
• TRANSFERASES - catalize transfer reactions various groups from
donor to acceptor.
• LIAZES - catalyze relationship in substrate without joining water or
oxidation.
• HYDROLAZES - catalyze relationship in substrates with water
joining.
• ISOMERASES - catalize transformations in limits of one molecule
(intromolecular rebuilding).
• LIGASES - catalyze join two molecules using energy phosphate
communications.
 The Role of Microbial Enzymes in Disease
Microorganism Enzymes Effect

Streptococcus Streptokinase throat and skin infections

pyogenes

Streptococcus streptolysin damages blood cells and tissues.

pyogenes
Pseudomonas elastase and collagenase respiratory and skin pathogen
aeruginosa

Clostridium spp. botulinum and tetanus toxins prevent cell vesicles containing
neurotransmitters from releasing
their contents and thus block nerve
transmission to muscles
Bacteria can be placed into 2 groups
based on how they obtain energy:
AUTOTROPHS – can synthesize all their organic compounds by
utilizing atmospheric CO2 and N2. No medical importance
HETEROTROPHS – unable to synthesize their own metabolites and
depend on performed organic compounds. All pathogens
Types of Autotrophs
• Photoautotrophs – organisms that use energy from sunlight to
convert CO2 & water to carbon compounds (green plants, algae and
cyanobacteria).

• Chemoautotrophs – organisms that make organic molecules from

CO2 using energy from chemical reactions (some Bacteria and ▶
Archaea, such as methanogens).
Types of Heterotrophs :
• Chemoheterotrophs – organisms that must take in organic molecules
for both energy & carbon (animals, fungi, protists and most
bacteria).

• Photoheterotrophs – organisms that are photosynthetic but need

organic compounds as a carbon source (some ▶ Bacteria).
Releasing Energy

-Bacteria, like all organisms, release energy through cellular

respiration, fermentation, or both.

Cellular respiration – process that releases energy by breaking

down glucose & other food molecules in the presence of
oxygen (O2).

Fermentation – process by which cells release energy in the

absence of O2.
According to the type of respiration, the following
groups of microorganisms are distinguished:
• Obligatory aerobes - grow and multiply only in the presence of oxygen. Oxygen is
used to generate energy by oxidative phosphorylation. Subdivided into:
• a) strict aerobes - grow at a partial pressure of the atmosphere;
• b) microaerophiles - grow at low partial pressure.
• Obligatory anaerobes - do not use oxygen for growth and reproduction. They get
energy by substrate phosphorylation. Subdivided into:
• a) strict anaerobes - molecular oxygen is toxic for them: it kills microorganisms or
restricts their growth;
• b) aero-tolerant - can exist in an oxygen atmosphere without using it to generate
energy.
• Facultative anaerobes - able to grow and multiply both in the presence of oxygen, and
in its absence. They have a mixed type of metabolism.
 Obligate aerobes vs. anaerobes
-Organisms that require a constant supply of oxygen
in order to live are called obligate aerobes,
e.g. Mycobacterium tuberculosis .
-Organisms that must live in the absence of oxygen
are called
obligate anaerobes (oxygen would kill them), e.g.
Clostridium botulinum.
-Organisms that can survive with or without oxygen
are called facultative anaerobes, e.g. E. coli.
-Anaerobes perform fermentation to release energy &
aerobes perform cellular respiration to release
energy.
 Bacterial Growth & Reproduction
-Growth in bacteria is directly
related to availability of food &
production of waste products.
Some divide every 20 minutes.

Reproduction can occur by :

1. Binary fission – asexual reproduction in

which an organism replicates it’s DNA
& divides in half, producing 2 identical
daughter cells.
2. Conjugation – sexual reproduction in
which an organism exchanges genetic
information.
• Budding
This type of reproduction is analogous to that in budding
fungi, such as brewer’s yeast (Saccharomyces cerevisiae). .
Generation times for various bacteria
• E.coli = 20 min (most common • Theoretically 1 bacteria in 24
pathogens) hours can produce 1021 progeny
• M.tuberculosis = 20 hours amounting to 4000 tones!
• M.leprae = 20 days • But practically because of
limited nutrients, accumulation
of toxic metabolites and other
factors the actual the number of
progeny is less
Bacterial growth
• Lag Phase - is the period when the bacteria are adjusting to the environment
(synthesis of ribosomes, enzymes and other proteins).
• Log Phase - rapid exponential growth. Generation time - time it takes one cell to
divide into two. This is determined during log phase.β-Lactam drugs, such as
penicillin, act during this phase because the drugs are effective when cells are
making peptidoglycan (i.e., when they are dividing).
• Stationary Phase - nutrients used up. Toxic products like acids and alkali begin
to accumulate. Number of new cells equals the number of dying cells.
• Death phase is characterized by an exponential decrease in the number of living
cells.
Microbial Physiology
Microbial Nutritional Requirements

All living protoplasm contains six major chemical elements: carbon,

hydrogen, oxygen, nitrogen, phosphorus, and sulfur.
– Combinations of these and other elements make up vital macromolecules of
life, including carbohydrates, lipids, proteins, and nucleic acids.
Materials that organisms are unable to synthesize, but are required for
building macromolecules and sustaining life, are termed essential
nutrients (e.g., certain essential amino acids and essential fatty acids).
Chemical Analysis of the Microbial
Cytoplasm
• Water – 70% of all components
• Proteins
• Organic compounds – 97% of dry cell weight
• Elements CHONPS – 96% of dry cell weight
• Most chemical elements available to the cell as compounds and not
as pure elements
• Only a few types of nutrients needed to synthesize over 5,000
different compounds
Other Important Nutrients
Sodium (Na): important for certain types of cell transport
Calcium (Ca): stabilizer of cell wall and endospores of bacteria
Magnesium (Mg): component of chlorophyll and a stabilizer of
membranes and ribosomes
Iron (Fe): important component of the cytochrome proteins of cell
respiration
Zinc (Zn): essential regulatory element for eukaryotic genetics
How microbes eat:
Transport Mechanisms
• Transport of necessary nutrients occurs across the cell membrane,
even in organisms with cell walls.
• The driving force of transport is atomic and molecular movement.
• Diffusion: the phenomenon of molecular movement, in which atoms
or molecules move in a gradient from an area of higher density or
concentration to an area of lower density or concentration
The movement of water: osmosis

• Osmosis: the diffusion of water through a selectively, or

differentially, permeable membrane
- Has passageways that allow free diffusion of water, but block certain
other dissolved molecules
- When the membrane is placed between solutions of differing
concentrations of solute and the solute cannot pass through the
membrane, water will diffuse at a faster rate from the side that has
more water to the side that has less water.
- This will continue until the concentration of water is equalized on both
sides of the membrane.
Active Transport
• Active transport:
- The transport of nutrients against the diffusion gradient or in the same
direction as the natural gradient, but at a rate faster than by diffusion alone
- The presence of specific membrane proteins (permeases and pumps)
- The expenditure of energy
• Examples of substances transported actively: monosaccharides,
amino acids, organic acids, phosphates, and metal ions
Endocytosis:
Eating and Drinking By Cells
• Endocytosis:
- Cell encloses the substance in its membrane
- Simultaneously forms a vacuole and engulfs the substance
• Phagocytosis:
- Accomplished by amoebas and white blood cells
- Ingest whole cells or large solid matter
• Pinocytosis:
– Ingestion of liquids such as oils or molecules in solution
Biochemical Cycling & Energy Flow
• Biochemical Cycles
– Cyclical paths elements take as they flow through living
(biotic) and non-living (abiotic) components of
ecosystem
– Fixed and limited amount of elements available
• Carbon and nitrogen particularly important
– Stable gaseous forms CO2 and N gas enter atmosphere
– Global impacts
– Elements continually cycle in ecosystem
• Energy does not, must be continually added to fuel life
Biochemical Cycling
• Elements - three general purposes
– Biomass production
• Incorporated into cell material
– All organisms require nitrogen to produce amino acids
– Energy source
• Reduced form of element is used to generate energy – ATP
• Energy yielding reactions oxidize the energy source
– Chemoorganotrophs use reduced carbon compounds – sugar, lipids
and amino acids
– Chemolithotrophs use reduced inorganic molecules – H2S, ammonia
(NH3) and hydrogen gas (H4)
Biochemical Cycling
– Terminal electron acceptor
• Electrons from energy source transferred to an
oxidized form of element during respiration
– Aerobic conditions
» O2 is terminal electron acceptor
– Anaerobic conditions some prokaryotes use
» Nitrate (NO3), nitrite (NO2), sulfate (SO4)and
CO2
 Oxygen Cycle

• During photosynthesis
cyanobacteria, algae and
green plants produce
oxygen from water. The
oxygen is utilized via
respiration.
– The level of oxygen in the
atmosphere is maintained
by chemical reactions in
the upper atmosphere,
aerobic respiration and
photosynthesis
Carbon Cycle
• Carbon
– Carbon enters producers during photosynthesis or
chemosynthesis
– In turn enters consumers via consumption of the
producers.
– Carbon returned to the atmosphere in the form of CO2 by
respiration and the actions of decomposers consuming
dead or decaying waste.
• Oxygen has profound influence on cycle
– Allows degradation of certain compounds
– Helps determine the types of carbon containing gases produced
– Aerobic decomposition
– Great deal of OC2 formed through aerobic respiration
– (CH2O)n + (O2)n CO2 + H2O
Carbon Cycle
– Low oxygen (wet soils, marshes, swamps, etc.)
» Degradation is incomplete
» Generate CO2 and other gases

» Some CO2 used by methanogens (ex:

Archaea) as terminal electron acceptor
generating methane (CH4)
» 4H2 + CO2 CH4 + H2O
» Methane entering atmosphere is oxidized by
UV light and chemical ions to CO and CO2
Nitrogen Cycle
• Nitrogen
– Most important constituent of proteins and
nucleic acids
– Consumers obtain required nitrogen from
ingested plants and animals and use it to
build biomass
• Prokaryotes – diverse in use of nitrogen
compounds
– Some use oxidized compounds like nitrate and nitrite
– Some use reduced nitrogen compounds like ammonium
• All of these metabolic activities represent steps in
the N cycle
Nitrogen Cycle
– Nitrogen Fixation
• Nitrogen gas reduced to form ammonium
– Ammonium can be incorporated into cellular material
– Atmosphere 79% N2
» Relatively few organisms use atmospheric (gaseous)
nitrogen – rely on prokaryotes to convert
atmospheric nitrogen into a useable form
– Nitrogenase
» Enzyme complex that mediates nitrogen fixation and
is readily inactivated by oxygen
» Nitrogen fixing aerobes must have a mechanism for
protection
Nitrogen Cycle
– Nitrogen fixing prokaryotes (diazotrophs)
• Free living
– Azotobacter - hief suppliers of fixed nitrogen in
grasslands & similar ecosystems
– Cyanobacteria - most significant nitrogen fixer in aquatic
environments
.
– Clostridium spp - dominant free-living anaerobes in
soils
• Symbiotic - significant in benefiting plant growth
– Found in association with all leguminous plants including
alfalfa, clover, peas, beans, peanuts and vetch
– Rhizobium
– Synthetic nitrogen compounds
Nitrogen Cycle
– Denitification
• Process to convert nitrate to gaseous nitrogen
• Nitrate represents fully oxidized nitrogen
– Pseudomonas spp. can use nitrate as terminal electron acceptor
» Anaerobic respiration
– Nitrate reduced to gaseous nitrogen compounds – nitrous oxide and
molecular nitrogen
– Release to atmosphere represents a loss of nitrogen and contributes
to global warming
– Benefit – waste water treatment processes to remove nitrate
– Anammox
• Brocadia anamoxidans oxidizes ammonium anaerobically
• Potential benefit in waste water treatment
Sulfur Cycle
• Sulfur
– Occurs in all living things
– Key steps of cycle rely on prokaryotes
• Some use reduced form of H2S, some elemental S
• Others use sulfate
Sulfur Cycle
• Hydrogen sulfide is toxic to lining things
– Under aerobic conditions, H2S oxidizes spontaneously to
sulfur and is then converted to sulfate (SO42-) (its most
readily utilized form) by sulfur bacteria
– Under anaerobic conditions sulfate-reducing bacteria
reduce sulfate to hydrogen sulfide
• Oxidation of hydrogen sulfide to sulfate carried out
principally by nonphotosynthetic autotrophs,
Thiobacillus, Thiothrix and Beggiatoa and less commonly
by photosynthetic autotrophs (green and purple
sulfur bacteria)
Phosphorus Cycle

• Involves movement of phosphorus between inorganic

and organic forms
– Microorganisms play three major roles in phosphorus
transformations
• Mineralize organic phosphorus
• Convert insoluble forms of inorganic phosphorus to soluble forms
• Immobilize inorganic phosphorus
Phosphorus Cycle
• Overall Transformations of Phosphorus
– Soil Organisms
• Break down organic phosphate into to inorganic
phosphates
• Then convert inorganic phosphates to
orthophosphate (PO43-)
– Orthophosphate is water soluble and readily used by
most plants and microorganisms
• When plants & animals die decomposers convert
organic phosphate back into inorganic phosphate
– Phosphorus is often the limiting nutrient in
many environments