FGD 1: Chemical and Genetic Aspects of
Microorganisms Carbohydrates and the different categories
[ THE BIOCHEMICAL BASIS OF LIFE ]
GROUP 1
QUESTION #1:
What do you think is the importance of studying
the biochemical makeup of microorganisms?
(Also, try to discuss the four main categories of
biomolecules)
The importance of studying the
biochemical makeup of microorganisms will help
us understand all life on this planet. The study of
microbes is pivotal to understanding all living
things.
Biochemistry
o is the science of studying chemical processes
in living organisms.
o it examines it structure, function, and
interactions of biomolecules like proteins,
nucleic acids, carbohydrates, and lipids,
along with the metabolic pathways and
regulatory mechanisms of cells.
4 main categories of biochemistry
 Carbohydrates
 Lipids
 Proteins
 Nucleic acids
The carbohydrates, lipids, proteins, and
nucleic acids are 4 main categories of
biochemistry, it's because of their fundamental
roles in living organisms and their abundance
in biological systems.
QUESTION # 2:
according to the number of carbon atoms:
Carbohydrates
o are organic compounds composed of
carbon, hydrogen, and oxygen, with a
hydrogen: oxygen ratio of 2:1. They
serve as a primary energy source for
living organisms and are essential for
various physiological processes.
Carbohydrates can be broadly categorized
based on the number of carbon atoms they
contain:
 Triose: (3 carbon atoms)
 Tetrose: (4 carbon atoms)
 Pentose: (5 carbon atoms)
 Hexose: (6 carbon atoms)
QUESTION # 3
Classification of Carbohydrates
 Monosaccharides
-are simple sugar
-it cannot be degraded into simpler
products via hydrolysis reaction
-examples of monosaccharides are
glucose, fructose, and galactose
 Disaccharides
-contains two monosaccharides
covalently bonded to each other
-examples of disaccharides are sucrose,
lactose, and maltose
 Oligosaccharides
- contains 3-10 monosaccharides
covalently bonded
 - examples of oligosaccharides are sucrose,
maltose, and cellobiose
 Polysaccharides
-have many monosaccharides units
covalently bonded
-examples of polysaccharides are starch,
glycogen, and cellulose
QUESTION # 4
The similarities and differences between a
dehydration synthesis reaction and a hydrolysis
reaction and the examples of these reactions in
biochemistry.
Dehydration synthesis reactions
o build molecules up and generally require
energy
Hydrolysis reactions
o break molecules down and generally release
energy.
Carbohydrates, proteins, and nucleic acids
are built up and broken down via these types of
reactions, although the monomers involved are
different in each case.
Similarities:
1. Both dehydration synthesis and hydrolysis
are chemical reactions that involve the
breaking and forming of chemical bonds.
2. They are both involved in the metabolism of
biomolecules and play crucial roles in
maintaining the balance of molecules within
living organisms.
3. Both reactions are catalyzed by specific
enzymes that facilitate the reactions.
Differences:
1. Dehydration synthesis is a reaction that
involves the formation of a new molecule by
removing a water molecule. It is a
condensation reaction where two smaller
molecules combine to form a larger
molecule. On the other hand, hydrolysis is a
reaction that involves the breakdown of a
larger molecule into smaller molecules by
the addition of a water molecule.
Example in biochemistry:
Dehydration synthesis is involved in the
formation of complex carbohydrates like
glycogen. When individual glucose
molecules combine through dehydration
synthesis, a glycosidic bond is formed,
resulting in the formation of glycogen.
Hydrolysis, on the other hand, is involved in
the breakdown of glycogen into individual
glucose molecules when the body needs
energy.
2. Dehydration synthesis reactions are
anabolic, meaning they build larger
molecules from smaller ones, requiring
energy input. Hydrolysis reactions are
catabolic, meaning they break down larger
molecules into smaller ones, releasing
energy.
Example in biochemistry:
Dehydration synthesis is involved in the
formation of proteins from amino acids.
 When amino acids combine through
dehydration synthesis, a peptide bond is
formed, resulting in the formation of a
protein. Hydrolysis, on the other hand, is
involved in the breakdown of proteins into
individual amino acids during digestion.
3. Dehydration synthesis reactions are
endergonic, meaning they require energy to
proceed. Hydrolysis reactions are exergonic,
meaning they release energy.
Example in biochemistry:
Dehydration synthesis is involved in the
formation of lipids from glycerol and fatty acids.
When glycerol and fatty acids combine through
dehydration synthesis, ester bonds are formed,
resulting in the formation of lipids. Hydrolysis, on
the other hand, is involved in the breakdown of
lipids into glycerol and fatty acids for energy
utilization.
These are just a few examples of how
dehydration synthesis and hydrolysis reactions
are involved in biochemistry. They are essential
processes that help maintain the balance and
functionality of biomolecules within living
organisms.
QUESTION # 5
Differentiate Covalent bond, Glycosidic and
Peptide bond.
Covalent Bond
o sharing of electrons between atoms.
o In biomolecules, the covalent bonds found
in the backbone of DNA and RNA are
PHOSPHODIESTER BONDS. These bonds
create a stable structure that forms the
genetic code.
Glycosidic Bond
o Link sugar molecules by sharing an
oxygen atom.
o In carbohydrates, such as starch or
glycogen, glycosidic bonds connect
individual unit, forming larger, complex
structures.
o This linkage is vital for energy storage
and release.
Peptide Bond
o A peptide bond forms when the
carboxyl group of one amino acid reacts
with the amino group of another.
o This linkage repeats to create a
polypeptide chain, the foundation of
proteins.
o The unique sequence of amino acids in
a protein determines its structure and
function.
o This bond shapes the structure of
proteins, and different sequences of
these bonds make different proteins
with specific jobs in our bodies.
Biomolecules & Bond Types
Carbohydrates–Glycosidic bonds, linking
sugar molecules.
Proteins–Composed of peptide bonds,
linking amino acids.
Lipids–Ester Bond especially triglycerides
that are crucial for energy storage.
Ester Bond–An ester bond is a type of
chemical linkage formed between a
 carboxylic acid group and an alcohol group.
It's like a zipper that holds together two
parts in a molecule.
–act like tiny locks in the chemistry of fats.
Nucleic Acid–The backbone of DNA and
RNA consists of phosphodiester bonds.
QUESTION # 6
Try to discuss the basic definition of lipid.
Then ask volunteers who will discuss the
following types of lipids: FAs, waxes and oil,
phospholipids, glycolipid, and steroids.
Lipids
o An organic compound found in living
organisms.
o Soma lipids are most insoluble in water
but in soluble in fat solvent.
Two types
 Saturated - single bond
 Unsaturated - double bond
Unsaturated consist:
 Monounsaturated - one carbon-
carbon double bond is present.
 Poly unsaturated - two or more
carbon-carbon double bonds are
present.
Waxes
o Consistent of saturated fatty acid
with higher molecular weight
alcohols
Fat
o In a solid state, semi solid at room
temperature
o Source: animals

Example of fat solvent Oil

 Acetone o Liquid at room temperature

 Benzene o Source: plants and fish oil
 Ether
Phospholipid
 Chloroform
o Composed of glycerol
Types of Lipids
o The head of phospholipids is
Fatty Acids hydrophilic head and tail is
o These are essential components of many hydrophobic tail that consist of two
complex lipid molecules and serve as a fatty acid: saturated and
cellular energy source unsaturated.)
o Occurring naturally mono carboxylic acid. (Glycerol- is naturally occurring
(Mono carboxylic - Are one COOH alcohol)
functional group.)
 Two types
 Glycerophospholipid - most abundant lipid
in cell membrane
 Sphingolipids- are phospholipids that
contain 18 carbon alcohols called
sphingosine found in the brain and nerves.
Glycolipid
o Abundant in the brain and in the myelin
sheaths of nerve.
Two types
 Cerebroside -simple sphingoglycolipids
 Ganglioside- complex sphingoglycolipids.
Steroid
o Is an organic compound with four fused
rings arranged in a specific molecular
configuration.
o Steroids do is reduce redness and swelling.
QUESTION #7
Try to discuss the basic definition of a protein.
Then, ask the members what they think
whenever they hear the word 'protein'
Protein
o Is a large biomolecule composed of one or
more long chains of amino acids, which are
the building blocks of life.
o Play essential roles in various biological
processes, such as catalyzing biochemical
reactions, providing structural support to
cells and tissues, transporting molecules
within cells and throughout the body, and
serving as signaling molecules. They are
crucial for the functioning of organisms and
are found in every cell, tissue, and organ.
Amino acid
o molecules that combine to form
proteins.
Examples of proteins foods:
 eggs
 yogurt
 fish and seafood
 beans and other foods of proteins
Why are proteins important?
o required for the structure, function, and
regulation of the body's tissues and
organs.
QUESTION #8
Discuss the basics of protein structures
(primary, secondary, tertiary, quaternary)
Basics of Protein Structures
o Proteins are complex molecules essential for
the structure, function, and regulation of the
body's tissues and organs.
o The structure of a protein is crucial as it
determines its function.
o Proteins have four levels of structural
organization:
Primary Structure: QUESTION #9

o This level refers to the linear sequence of Define enzymes and discuss the roles of
amino acids that make up a protein. The
enzymes have in metabolism
sequence is determined by the genetic code
and plays a fundamental role in defining the Enzymes
protein's overall structure and function.
o are known as biologic catalysts.
Secondary Structure: o are proteins that catalyze (speed up or
accelerate) the rate of biochemical
o Refers to the local folding patterns within a
reactions.
protein chain.
o In some cases, the reaction will not
o The two main types of secondary structures
occur at all in the absence of the
are alpha helices and beta sheets, which are
enzyme. Thus, a complete definition of a
stabilized by hydrogen bonds between
biologic catalyst would be a protein that
amino acids along the chain.
either causes a particular chemical
Tertiary Structure: reaction to occur or accelerates.
o A particular enzyme can only catalyze
o Describes the three-dimensional
one particular chemical reaction.
arrangement of the entire protein
o In most cases, a particular enzyme can
molecule. It results from interactions
only exert its effect or act on one
between amino acid side chains, leading to
particular substance known as the
the formation of a complex 3D shape.
substrate for that enzyme.
o The unique three-dimensional shape of
Quaternary Structure:
the enzyme enables it to fit the
o Is the arrangement of multiple protein
combining site of the substrate, much
subunits (polypeptide chains) into a
like a key fit into a lock.
functional, biologically active protein
complex.
o This level of organization is seen in
QUESTION #10
proteins composed of more than one
polypeptide chain. “What makes an enzyme active? What
components of enzymes are required for it
to be active?”. Make sure that the terms
apoenzyme, cofactor, coenzyme, and
substrate are mentioned and

Enzymes
o are biological catalysts that facilitate
chemical reactions in living organisms.
The activity of an enzyme is primarily
determined by its active site, where the
substrate binds and undergoes a chemical
reaction.
Several components of enzymes are crucial
for their activity:
Active Site:
o The active site is the region of an
enzyme where substrate molecules bind
and interact to catalyze a specific
chemical reaction.
o It consists of amino acid residues that
form temporary bonds with the
substrate, creating a unique chemical
environment for the reaction to occur
Apoenzyme:
o The protein component of an enzyme
without its cofactor or coenzyme is
known as the apoenzyme. The
apoenzyme alone may not be
catalytically active until it binds with its
required cofactor or coenzyme
Cofactor:
o Are inorganic ions or non-protein
organic molecules that assist enzymes
in their catalytic activity. They can be
metal ions like zinc or organic
compounds that bind to the enzyme
and participate in the reaction
Coenzyme:
o are organic molecules that work with
enzymes to facilitate catalysis. They
often act as carriers of specific
functional groups or electrons during
enzymatic reactions, aiding in the
conversion of substrates into products
Substrate:
o The substrate is the molecule upon
which an enzyme act. It binds to the
active site of the enzyme, initiating the
catalytic process by forming an
enzyme-substrate complex
QUESTION #11
Discuss nucleic acid
Nucleic Acids
o are made of biopolymers
o biopolymers is a kind of polymers that
are produced by derived living
organism
o are repeated sets of monomers that
create nucleotides, which form of
nucleic acids.
There are two types of Nucleic Acids:
 DNA- deoxyribonucleic acid, double
stranded and sugar ribose.
 RNA- ribonucleic acid, single stranded,
and sugar deoxyribosomal.
In DNA, there are four bases:
 Adenine
 Thymine
 Cytosine
  Guanine
QUESTION #12
Three important differences between the
structures of DNA and RNA. The differences
of DNA and RNA in terms of their functions.
3 important differences between the
structures of DNA and RNA are:
Sugar:
o DNA contains deoxyribose sugar, while
RNA contains ribose sugar. Ribose has
one more hydroxyl group than
deoxyribose
Base Pairing:
o DNA base pairs include adenine (A) with
thymine (T) and cytosine (C) with guanine
(G).
o RNA base pairs include A with uracil (U)
and C with G
Structure:
o DNA is a double-stranded helix, while
RNA is a single-stranded molecule
In terms of their functions, DNA is
responsible for storing and transferring
genetic information, while RNA directly
codes for amino acids and acts as a
messenger to deliver genetic information
necessary for protein synthesis
QUESTION #13
What is the differences between DNA
nucleotides and RN nucleotides?
DNA nucleotides
o contain a sugar called deoxyribose
o deoxyribose lacks one oxygen
o double-stranded
o forming a twisted ladder-like
structure called a double helix
RNA nucleotides
o contain a sugar called ribose.
o single-stranded.
Both DNA and RNA nucleotides have three
common bases:
 Adenine (A)
 Cytosine (C)
 Guanine (G).
However, DNA uses Thymine (T) as its fourth
base, while RNA uses Uracil (U) instead of
Thymine.
These differences in sugar
component, bases, and structure give DNA
and RNA distinct functions in the cell. DNA
serves as the genetic material, carrying and
storing the instructions for building and
maintaining an organism. RNA, on the other
hand, plays various roles, such as
transferring genetic information from DNA
to protein synthesis machinery, catalyzing
biochemical reactions, and regulating gene
expression.
The key differences between DNA and RNA
nucleotides lie in their sugar component,
bases, and structure, which contribute to
their unique functions in the cell.
QUESTION #14
Define what is meant by the term “Central
Dogma” and its importance in microbiology.
Central dogma
o is a flow of information in cells.
o theory that states genetic information
flows in only one direction from the
DNA, to RNA, to protein or RNA directly
to protein.
o once information had gone from DNA
into the protein, it could not get out of
the protein and go back into the genetic
code.
Its importance in biology:
o provides the basic framework for how
genetic information flows from a DNA
sequence to a protein product inside
cells
QUESTION #15
Basic processed of DNA replication,
transcription, translation:
1. DNA Replication:
o This process is like making a copy of a
book. DNA replication occurs before a
cell divides to ensure each new cell
receives a complete set of genetic
instructions.
o Imagine DNA as a double-stranded
ladder. Enzymes unwind the ladder,
separating the two strands.
o Special proteins called DNA
polymerases then add new
nucleotides (A, T, C, and G) to each
separated strand, following the
sequence of the original DNA. This
results in two identical DNA
molecules, each with one old strand
and one new strand.
2. Transcription:
o Transcription is like making a copy of
a specific chapter from a book. Here,
DNA is used as a template to make
RNA.
o RNA polymerase, a special enzyme,
binds to the DNA at a specific
starting point called the promoter
region.
o The DNA unwinds, and the RNA
polymerase starts reading the DNA
sequence, adding complementary RNA
nucleotides (A, U, C, and G) to form a
single-stranded RNA molecule. It only
copies the portion of DNA needed for a
particular gene.
o Once the RNA polymerase reaches
the end of the gene or a termination
signal, transcription stops, and the
newly formed RNA molecule is
released.
3. Translation:
o Translation is like assembling a protein
from instructions found in the copied
chapter (mRNA).
o mRNA (messenger RNA) carries the
genetic information from DNA to the
ribosomes, the cellular machinery for
protein synthesis.
o Ribosomes read the mRNA in sets of
three nucleotides called codons. Each
codon codes for a specific amino acid.
o Transfer RNA (tRNA) molecules carry
amino acids to the ribosome. The tRNA
anticodon matches the mRNA codon,
ensuring the correct amino acid is added
to the growing protein chain.
o As the ribosome moves along the
mRNA, it links the amino acids together
to form a protein chain.
o Translation stops when the ribosome
encounters a stop codon on the mRNA.
Then, the completed protein is released.
[ MICROBIAL PHYSIOLOGY AND GENETICS ]
Microbial physiology
o is the study of how microorganisms
function at the cellular and molecular
levels, exploring their metabolic,
genetic, and regulatory processes.
o Topics include metabolism, Enzyme,
Mutation, and gene
All organisms required a source of energy, a
source of carbon, and additional nutrients.
Source of energy
The terms "phototroph" and "chemotroph"
describe the sources of energy that an
organism uses.
Phototroph
o are organisms that obtain energy from
sunlight through the process of
photosynthesis
o converts light energy into a chemical
energy which is photosynthesis
Chemotrophs
o Use chemicals as a source of energy
Two categories:
 Chemolithotrophs
-are organisms that use inorganic
chemicals as a source of energy
 Chemoorganotrophs
-are organisms that use organic
chemicals as a source of energy
Source of Carbon
Two primary categories of organisms
classified based on their source of carbon.
 Autotrophs
-use carbon dioxide (CO2) as their sole
source of carbon
 Heterotrophs
-are organisms that use organic
compounds other than CO2 as their
carbon source
Enzymes
o are proteins that act as biological
catalysts, speeding up chemical
reactions in living organisms.
Apoenzyme
o refers to the protein part of an enzyme,
which alone does not have catalytic
activity.
Coenzyme
o refers to a non-protein molecule that
binds to the apoenzyme and is
necessary for the enzyme's catalytic
activity.
Holoenzyme
o When an apoenzyme combines with its
coenzyme
o is the functional, catalytically active
form of the enzyme
An enzyme can catalyze multiple types of
reactions, but only one at a time. Each
enzyme is specific, catalyzing only one type
of reaction in a single compound or a group
of structurally related compounds.
Two types of enzymes that differ in their
location and function within an organism.
 Endoenzymes
 Exoenzymes
Endoenzyme
o also known as an intracellular enzyme
o is an enzyme that functions within the
cell in which it was produced.
Exoenzyme
o extracellular enzyme
o is an enzyme that is secreted by a cell
and functions outside that cell
o are produced by both prokaryotic and
eukaryotic cells and have been shown to
be a crucial component of many
biological processes.
Biochemical pathway
o also called a metabolic pathway
o is a series of enzyme-mediated reactions
where the product of one reaction is
used as the substrate in the next.
Aerobic respiration
o is a biochemical process that occurs in
the presence of oxygen and involves the
breakdown of organic molecules (such
as glucose) to produce energy in the
form of ATP (adenosine triphosphate).
It has 3 main phases / stages
 Glycolysis
- is the metabolic pathway that converts
glucose into pyruvate. Occurs in the
cytosol and is oxygen-independent.
 Krebs cycle
- pyruvic acid molecules produce during
glycolysis
 Electron transport chain
- During the electron transport chain, the
electrons carried by NADH and FADH₂,
which were produced in earlier stages of
cellular respiration (glycolysis and the
Krebs cycle), are transferred through a
series of protein complexes (including
NADH dehydrogenase, cytochrome bc1
 complex, and cytochrome c oxidase) in
the inner mitochondrial membrane. As
the electrons pass through these
complexes, energy is released and used
to pump protons (H⁺ ions) from the
mitochondrial matrix into the
intermembrane space, creating an
electrochemical gradient.
Oxidation-reduction reactions
o processes in which one substance loses
electrons, termed as oxidation, and
other gains electrons, referred to as
reduction, are crucial.
Photosynthesis
o is the process by which plants, algae,
and some bacteria convert light energy
into chemical energy stored in glucose.
This process involves two stages: the
light-dependent reactions and the
Calvin cycle.
1. Plasmid
o is a small, circular piece of DNA that
is different from the chromosomal
DNA, which is all the genetic
material found in an organism’s
chromosomes.
o it replicates independently of
chromosomal DNA.
o plasmids are mainly found in
bacteria, but they can also be found
in archaea and multicellular
organisms.
2. R-factor
o in the context of bacteria, an R-
factor is a group of genes present in
some bacteria that provide a basis
for resistance to antibiotics and can
be transferred from cell to cell by
conjugation.
3. Superbugs
o are strains of bacteria, viruses,
parasites, and fungi that are resistant
to most of the antibiotics and other
medications commonly used to treat
the infections they cause.
o can cause various infections such as
pneumonia, urinary tract infections,
and skin infections.
4. Mutation
o is a change in the DNA sequence of
an organism.
o can result from errors in DNA
replication during cell division,
exposure to mutagens, or a viral
infection.
o can have different effects on the
function, expression, or structure of
the gene product.
5. Mutant
o an organism that is different from
others of its type because of a
permanent change in its genes. This
change can be a result of a mutation.
6. Mutagen
o a chemical or physical agent capable
of inducing changes in DNA called
mutations.
 o Exposure to a mutagen can produce
DNA mutations that cause or
contribute to certain diseases.
Beneficial mutation
o is a type of mutation that has a positive
effect on an organism.
o are rare, but significant
o are key to the process of evolution, as
they help organisms adapt to changing
environments and increase their
chances of survival and reproduction.
Harmful mutations
o are changes in an organism's DNA that
negatively impact the function of a
gene or the health of the organism.
o When these mutations affect genes
coding for enzymes, they can lead to
the production of nonfunctional
enzymes and cause a variety of health
problems.
A nonfunctional enzyme is unable to
catalyze the chemical reaction that it would
normally catalyze if it were functional.
Silent mutation
o is a change in the DNA sequence that
doesn't affect the protein produced.
o are often neutral but can sometimes
influence how genes are expressed
Ways in which bacteria acquire genetic
1. Lysogenic Conversion: This occurs when a
bacteriophage (a type of virus that infects
bacteria) integrates its DNA into the
bacterial chromosome, a stage known as
'lysogeny'. The bacteriophage, ``now
referred to as a prophage, the
bacteriophage has the ability to bring new
genes to the bacterium, enabling it to
produce toxins and acquire other new traits.
Through this process, a harmless bacterium
can become a harmful pathogen
2. Transduction: This is another process that
involves bacteriophages. A bacteriophage
accidentally transfers bacterial DNA—rather
than its own viral DNA—into its capsid, a
protein shell, during transduction. This
bacteriophage transfers genes from one
bacterium to another by injecting the
bacterial DNA it unintentionally packaged
into the host bacterium.
3. Transformation: Through this process, a
bacterium absorbs DNA from its
surroundings. Usually, the DNA is derived
from deceased and divided bacteria. The
bacterium can acquire new characteristics if
it inserts this DNA into its own
chromosome.
4. Conjugation: Through a structure known
as a pilus, two bacteria are connected in this
process, and one of the bacteria gives the
other a copy of a plasmid, which is a tiny,
circular piece of DNA. Antibiotic resistance
is one of the traits that conjugation can
cause to spread quickly through a bacterial
population.