"Bacterial metabolism: Fueling life's processes in tiny powerhouses." Use of bacterial metabolism in biotechnology, biofuels, and other industries Examples of how bacterial metabolism is harnessed for beneficial purposes "Metabolism: the sum of chemical reactions in an organism, supporting growth, energy production, and vital functions." "Bacterial Metabolism and Life: Pervading every aspect of life, shaping ecosystems, and influencing our world." Bacterial metabolism refers to the collective chemical reactions and processes that occur within bacterial cells, enabling them to maintain life, grow, and reproduce. These metabolic activities involve a complex network of biochemical pathways that facilitate the conversion of nutrients into energy, biomolecules, and essential compounds necessary for bacterial survival. Metabolic processes in bacteria include catabolic pathways that break down complex molecules (such as sugars) to release energy and anabolic pathways that build complex molecules (such as proteins, nucleic acids) using energy. Bacteria utilize various metabolic strategies based on their energy and carbon sources, including aerobic and anaerobic respiration, fermentation, and photosynthesis in photosynthetic bacteria. The primary goals of bacterial metabolism are to obtain energy, synthesize necessary cellular components, regulate chemical processes, and adapt to changing environmental conditions. The understanding of bacterial metabolism is crucial for various fields, including medicine, agriculture, biotechnology, and environmental science, as it allows us to develop strategies to combat harmful bacteria, harness their metabolic capabilities for beneficial applications, and study their role in ecological systems.

1. BACTERIAL
METABLOSM
UNIT-3
AYUSHI SHARMA (FACULTY)
DEPARTMENT OF MICROBIOLOGY
M.J.P ROHILKHAND UNIVERSITY

2. ENZYMES
And its Action

3. INTRODUCTION
• The human body is composed of different types of cells, tissues and other complex organs.
For efficient functioning, our body releases some chemicals to accelerate biological processes
such as respiration, digestion, excretion and a few other metabolic activities to sustain a
healthy life. Hence, enzymes are pivotal in all living entities which govern all the biological
processes.
• Enzymes are proteins that help speed up metabolism, or the chemical reactions in our
bodies. They build some substances and break others down. All living things have enzymes.
Our bodies naturally produce enzymes. But enzymes are also in manufactured products and
food.
• STRUCTURE OF ENZYMES -Enzymes are a linear chain of amino acids, which give rise
to a three-dimensional structure. The sequence of amino acids specifies the structure, which in
turn identifies the catalytic activity of the enzyme. Upon heating, the enzyme’s structure
denatures, resulting in a loss of enzyme activity, which typically is associated with
temperature.
• It is compared to its substrates, enzymes are typically large with varying sizes, ranging from
62 amino acid residues to an average of 2500 residues found in fatty acid synthase.
• Only a small section of the structure is involved in catalysis and is situated next to the
binding sites. The catalytic site and binding site together constitute the enzyme’s active site.
• A small number of ribozymes exist which serve as an RNA-based biological catalyst. It reacts
in complex with proteins.

6. • “Enzymes can be defined as biological polymers that catalyze biochemical reactions.”
• The majority of enzymes are proteins with catalytic capabilities crucial to perform
different processes. Metabolic processes and other chemical reactions in the cell are
carried out by a set of enzymes that are necessary to sustain life.
• The initial stage of metabolic process depends upon the enzymes, which react with
a molecule and is called the substrate. Enzymes convert the substrates into other
distinct molecules, which are known as products.
• The regulation of enzymes has been a key element in clinical diagnosis because of
their role in maintaining life processes. The macromolecular components of all
enzymes consist of protein, except in the class of RNA catalysts called ribozymes.
The word ribozyme is derived from the ribonucleic acid enzyme. Many ribozymes
are molecules of ribonucleic acid, which catalyze reactions in one of their own
bonds or among other RNAs.
• Enzymes are found in all tissues and fluids of the body. Catalysis of all reactions
taking place in metabolic pathways is carried out by intracellular enzymes. The
enzymes in the plasma membrane govern the catalysis in the cells as a response to
cellular signals and enzymes in the circulatory System regulate the clotting of
blood. Most of the critical life processes are established on the functions of
enzymes.

9. Classification of Enzymes
• Oxidoreductases
• These catalyze oxidation and reduction reactions, e.g. pyruvate dehydrogenase, catalysing
the oxidation of pyruvate to acetyl coenzyme A.
• Transferases
• These catalyze transferring of the chemical group from one to another compound. An
example is a transaminase, which transfers an amino group from one molecule to another.
• Hydrolases
• They catalyze the hydrolysis of a bond. For example, the enzyme pepsin hydrolyzes peptide
bonds in proteins.
• Lyases
• These catalyze the breakage of bonds without catalysis, e.g. aldolase (an enzyme in glycolysis)
catalyzes the splitting of fructose-1, 6-bisphosphate to glyceraldehyde-3-phosphate and
dihydroxyacetone phosphate.
• Isomerases
• They catalyze the formation of an isomer of a compound. Example: phosphoglucomutase
catalyzes the conversion of glucose-1-phosphate to glucose-6-phosphate (phosphate group is
transferred from one to another position in the same compound) in glycogenolysis (glycogen
is converted to glucose for energy to be released quickly).

10. • Ligases
• Ligases catalyze the association of two molecules. For example, DNA ligase
catalyzes the joining of two fragments of DNA by forming a
phosphodiester bond.
• Cofactors
• Cofactors are non-proteinous substances that associate with enzymes. A
cofactor is essential for the functioning of an enzyme. An enzyme without
a cofactor is called an apoenzyme. An enzyme and its cofactor together
constitute the holoenzyme.
• There are three kinds of cofactors present in enzymes:
• Prosthetic groups: These are cofactors tightly bound to an enzyme at all
times. FAD (flavin adenine dinucleotide) is a prosthetic group present in
many enzymes.
• Coenzyme: A coenzyme binds to an enzyme only during catalysis. At all
other times, it is detached from the enzyme. NAD+ is a common
coenzyme.
• Metal ions: For the catalysis of certain enzymes, a metal ion is required at
the active site to form coordinate bonds. Zn2+ is a metal ion cofactor used
by a number of enzymes.

11. • Examples of Enzymes :-
• Following are some of the examples of enzymes:
• Beverages
• Alcoholic beverages generated by fermentation vary a lot based on many factors.
Based on the type of the plant’s product, which is to be used and the type of enzyme
applied, the fermented product varies.
• For example, grapes, honey, hops, wheat, cassava roots, and potatoes depending
upon the materials available. Beer, wines and other drinks are produced from plant
fermentation.
• Food Products
• Bread can be considered as the finest example of fermentation in our everyday life.
• A small proportion of yeast and sugar is mixed with the batter for making bread. Then
one can observe that the bread gets puffed up as a result of fermentation of the sugar
by the enzyme action in yeast, which leads to the formation of carbon dioxide gas.
This process gives the texture to the bread, which would be missing in the absence of
the fermentation process.
• Drug Action
• Enzyme action can be inhibited or promoted by the use of drugs which tend to work
around the active sites of enzymes.

12. Mechanism of Enzyme Reaction
• Any two molecules have to collide for the reaction to
occur along with the right orientation and a sufficient
amount of energy.
• The energy between these molecules needs to overcome
the barrier in the reaction. This energy is called activation
energy.
• Enzymes are said to possess an active site. The active site
is a part of the molecule that has a definite shape and the
functional group for the binding of reactant molecules.
• The molecule that binds to the enzyme is referred to as
the substrate group. The substrate and the enzyme form
an intermediate reaction with low activation energy
without any catalysts.

13. BIOLOGICAL CATALYST
• Catalysts are the substances which play a significant role in the chemical
reaction. Catalysis is the phenomenon by which the rate of a chemical
reaction is altered/ enhanced without changing themselves. During a
chemical reaction, a catalyst remains unchanged, both in terms of quantity
and chemical properties.
• An enzyme is one such catalyst which is commonly known as the
biological catalyst. Enzymes present in the living organisms enhance the
rate of reactions which take place within the body.
• Biological catalysts, enzymes, are extremely specific that catalyze a single
chemical reaction or some closely associated reactions. An enzyme’s exact
structure and its active site decide an enzyme’s specificity. Substrate
molecules attach themselves at the active site of an enzyme.
• Initially, substrates associate themselves by interactions to the enzymes
which include ionic, hydrogen bonds and hydrophobic interactions.
Enzymes reduce the reactions and activation energy to progress towards
equilibrium quicker than the reactions that are not catalyzed. Both
eukaryotic and prokaryotic cells usually make use of regulation to respond
to fluctuations in the state inside the cells.
• The nature of enzyme action and factors affecting the enzyme activity are
discussed below.

14. CO FACTORS
• Cofactors can be metals or small organic molecules, and their primary function is
to assist in enzyme activity. They are able to assist in performing certain,
necessary, reactions the enzyme cannot perform alone. They are divided into
coenzymes and prosthetic groups.
•
Cofactor-dependent enzymes exhibit extremely useful synthetic utility. However,
the high cost and low availability of enzyme cofactors preclude their use in
amounts.
• As a result, various cofactor regeneration strategies have been developed that
serve to regenerate the required cofactor, while simultaneously driving the
reaction equilibrium toward the desired products. Cofactor regeneration systems
have been demonstrated using chemical, electrochemical, and photochemical
methods.
• However, enzymatic methods continue to dominate regeneration processes due
to stringent requirements for selectivity and compatibility with the reaction of
interest. The most notable recent developments in cofactor regeneration have
been the use of multienzyme regeneration systems and enzyme immobilization.
• These recent developments have enabled the increasingly widespread use of
cofactor-dependent enzymes at industrial scale.

15. TRACE ELEMENTS
• A trace element, also called minor element, is a chemical
element whose concentration is very low. They are
classified into two groups: essential and non-essential.
• Essential trace elements are needed for many physiological
and biochemical processes in both plants and animals.
• Trace elements (or trace metals) are minerals present in
living tissues in small amounts.
• Some of them are known to be nutritionally essential, others
may be essential (although the evidence is only suggestive
or incomplete), and the remainder are considered to be
nonessential.

17. BIOCHEMISTRY OF
METHANOGENES
• The biochemistry of methanogenesis involves the following coenzymes and cofactors:
F420, coenzyme B, coenzyme M, methanofuran, and methanopterin. . Coupling of the
coenzyme M thiyl radical (RS) with HS coenzyme B releases a proton and re-reduces Ni(II)
by one-electron, regenerating Ni(I).
• Since fossil sources for fuel and platform chemicals will become limited in the near future, it
is important to develop new concepts for energy supply and production of basic reagents for
chemical industry.
• One alternative to crude oil and fossil natural gas could be the biological conversion of CO2
or small organic molecules to methane via methanogenic archaea.
• This process has been known from biogas plants, but recently, new insights into the
methanogenic metabolism, technical optimizations and new technology combinations were
gained, which would allow moving beyond the mere conversion of biomass. In biogas plants,
steps have been undertaken to increase yield and purity of the biogas, such as addition of
hydrogen or metal granulate.
• Furthermore, the integration of electrodes led to the development of microbial
electrosynthesis (MES). The idea behind this technique is to use CO2 and electrical power to
generate methane via the microbial metabolism. This review summarizes the biochemical and
metabolic background of methanogenesis as well as the latest technical applications of
methanogens.
• As a result, it shall give a sufficient overview over the topic to both, biologists and engineers
handling biological or bioelectrochemical methanogenesis.

18. • Methanogens are spherical or rod shaped archaebacteria that
produce methane as metabolic byproduct in low oxygen
environment. Methanogens are especially common in marshlands or
wetlands and even in the intestine of humans and ruminant
mammals
• Methanogenes are present as endosymbionts in many free-living
marine and freshwater anaerobic protozoa, where they are often
closely associated with hydrogenosomes, organelles that produce
H2, CO2, and acetate from the fermentation of polymeric substrates.
The products of the hydrogenosomes are substrates
for mthanogenesis.
• It is conceivable that the methanogens have a synergistic role by
lowering the H2 partial pressure to create a favorable
thermodynamic shift in the protozoan’s fermentation reaction. Also,
evidence suggests that excretion of undefined organic compounds
by the methagen provides an advantage to the protist host.
• Endosymbiont are also found in flagellates and ciliates that occur in
the hindgut of insects, such as termites, cockroaches, and tropical .
Although rumen ciliates do not harbor endosymbionic methanogens,
many have ectosymbionic methanogens that may have an analogous
function.

20. NUCLEOTIDE SYNTHESIS
• Nucleotides are the fundamental building blocks essential for the synthesis of DNA and
RNA. Each nucleotide contains three functional groups: a sugar, a base, and phosphate.
• Nucleotides can be divided into two groups: pyrimidines and purines. The family of
pyrimidines includes thymine (T), cytosine (C), and uracil (U), which is only
incorporated into RNA. These compounds contain a single-ringed nitrogenous base that
pairs with a purine nucleotide counterpart.
• Thymine pairs with adenine forming two hydrogen bonds, in contrast to cytosine, which
pairs with guanine to form three hydrogen bonds. Purines, both guanine (G) and adenine
(A), are double-ringed structures and more difficult to break down in the body. As such,
the salvage pathway for purine metabolism is of importance.
• Nucleotide synthesis will be described below, but one of the fundamental requirements
of the synthesis of either purines or pyrimidines is the need for a five-carbon sugar
(ribose). This sugar is generated through glucose oxidation via the pentose phosphate
pathway.
• For purines synthesis, the base is synthesized and attached to the sugar, while for
pyrimidine synthesis, the sugar group is added after the base is produced. In either case,
ribose is the added sugar, and this must be converted to the deoxyribose form before the
bases can be used for DNA synthesis.

21. • Synthesis of purines
• Purines are composed of a bicyclic structure that is synthesized from carbon and nitrogen
donated from various compounds such as carbon dioxide, glycine, glutamine, aspartate, and
tetrahydrofolate (TH4). The synthesis of purines starts with the synthesis of
5ʼphosphoribosylamine from PRPP and glutamine.
• The enzyme glutamine phosphoribosylpyrophate amidotransferase (GPAT) catalyzes this
reaction and is the committed step in purine synthesis Synthesis continues for nine additional
steps culminating in the synthesis of inosine monophosphate (IMP), which contains the base
hypoxanthine.
• IMP is used to generate both AMP and GMP. The synthesis of both AMP and GMP requires
energy in the form of the alternative base (i.e., the synthesis of GMP requires ATP while AMP
synthesis requires energy in the form of GTP). The synthesis of AMP and GMP is regulated by
feedback inhibition This allows for the maintenance of nucleotides in a relative ratio that is
required for cellular processes.
• The generated nucleotide monophosphates can be converted to the di and triphosphate
forms by nucleotide specific kinases, which will transfer phosphate groups to maintain a
balance of the mono,di and triphosphate forms.
• Regulation of pyrimidine synthesis
• The reaction catalyzed by CSPII is the regulatory step in the pathway and is activated by PRPP
and ATP and inhibited by UTP.
•

23. NUCLEOTIDE DEGRADATION
• Normal nucleic acid degradation leads to an accumulation of purine nucleotides
that are broken down into adenosine (Ado) and deoxyadenosine (dAdo), and
guanosine (Guo) and deoxyguanosine (dGuo).
• ADA is present in all cells and converts Ado and 2′-dAdo molecules into inosine
(Ino) and 2′-deoxyinosine), respectively. PNP converts Ino and 2′-dIno to
hypoxanthine, to guanine.
• These molecules can enter the purine salvage pathway (shown in green in the
figure below) and are converted back to ATP and GTP that can be recycled into
new purines in preparation for cell division.
• Thus, are crucial for the recycling of elements of old purines into new purines,
particularly in tissues in which cell division occurs at a rapid pace (such as the bone
marrow, thymus, and lymph nodes).
• Without ADA/PNP function (red pathway in the figure), high levels of accumulate
and are metabolized to These molecules are toxic and induce breaks in DNA, block
normal DNA methylation, and interfere with de novo DNA synthesis such that cell
death is triggered. Rapidly proliferating cells such as T and B lymphocytes and NK
cells are most affected by dATP and dGTP accumulation, and ADA and PNP
mutations therefore result in a variable loss of these cell types and clinical
symptoms of SCID.

25. Thank
You