Bacterial genetics
The bacterial genome is the total collection of genes carried by a
bacterium both on its chromosome and on its extra-chromosomal
genetic elements such as plasmids or bacteriophages(bacterial
viruses).
DNA and Chromosomes
Bacteria typically have a single circular chromosome (DNA).
The chromosome contains the genes which is segments of DNA.
Bacteria usually have one copy of their chromosome, therefore
called haploid.
DNA usually exists as a double-stranded structure.
Both strands coiled together to form the characteristic double-
helix.
Composed of 2 chains of polypeptides, each chain has a
backbone of deoxyribose sugar and phosphate residues
arrangedalternately.
The five nitrogenous bases in nucleic acids are adenine (A),
guanine (G), thymine (T), cytosine (C), and uracil (U).
Uracilis found in RNA but not in DNA.
Both A and G are purines (double –ring structures), whereas T, C,
and U are pyrimidines (single –ringed structures).
Adenine pairs with thymine (two hydrogen bonds), and guanine
pairs with cytosine (stronger: three hydrogen bonds).
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DNA STRUCTUR
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DNA strands have a directionality, and the different ends of
a single strand are called the "3' (three-prime) end" and
the "5' (five-prime) end.
The strands of the double helix are anti-parallel with one
being 5' to 3', and the opposite strand 3' to 5'.
Structure of RNA
Structurally similar to DNA except for two major differences:
a. Ribose sugar.
b. Uracil in place of thymine.
Three types of RNA:
a. Messenger RNA (mRNA).
b. Ribosomal RNA (r RNA).
c. Transfer RNA (t RNA).
Plasmids:
Small genetic elements that replicate independently of the
bacterial chromosomes (replicons).
Circular, double-stranded DNA molecules.
Some plasmids such as [Link] can integrate into the host
chromosome so called episomes.
Plasmids usually do not encode essential functions for bacteria
(e.g. unnecessary for the bacterial growth).
Plasmid carry additional genetic information which may provide
a selective advantage to the bacteria:
a) Confer high levels of antibiotic resistance.
b) Encode the production of bacteriocins or toxin.
c) Contain genes that may provide the bacteria unique
advantage in metabolizing some substrates.
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Transposons:
Are mobile genetic elements that are dependent replicons.
They can move from one position to another in the genome or
between different molecules of DNA.
The simplest transposons are called insertion sequences.
Complex transposons carry other genes (e.g. genes of antibiotic
resistance).
These transposons can jump in and out of genes.
Sometimes transposons insert into genes and inactivate them.
If this insertion and inactivation in gene that encodes an essential
protein, the cell will die.
DNA replication
Is the process of producing two identical replicas from one
original DNA molecule.
This biological process occurs in all living organisms and is the
basis for biological inheritance.
DNA is made up of two strands and each strand of the original
DNA molecule serves as a template for the production of the
complementary strand.
The process referred to as semi-conservative replication.
Semi-conservative replication would produce two copies that
each contained one of the original strands and one new strand.
Conservative replication would leave the two original template
DNA strands together in a double helix and would produce a copy
composed of two new strands containing all of the new DNA base
pairs.
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The double helix is unwind and each strand acts as a template for
the next strand. Bases are matched to synthesize the new partner
strands.
Replication process requires the presence of several proteins &
enzymes:
a. DNA polymerase (also known as DNA-dependent DNA
polymerase).
b. DNA helicase&DNA topoisomerase (both initiate the two
strands separation).
c. Primase (synthesizes of a short RNA primer).
d. DNA ligase (connects fragments of newly DNA).
The duplicated DNA chromosomes can be separated during cell
division.
Each daughter cell contains the same number of chromosomes
and the same genes.
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Depending on base pair guide, one strand can act as a template
for production of a new strand.
Steps of replication
At the origin of replication ‘’ replication fork”, Parental DNA is
unwind by helicase enzyme and stabilized by proteins.
One new DNA strand, called the leading strand, is synthesized
continuously by DNA polymerase toward the replication fork in 5 ’͢
3’ direction.
The lagging strand is synthesized ‘’discontinuously’’ in pieces
called Okazaki fragments.
RNA polymerase synthesizes a short RNA segment ‘’ RNA primer’’,
which is then extended by DNA polymerase away from the
replication fork.
DNA polymerase digests RNA primer and replaces it with DNA.
DNA ligase joins the newly made DNA fragments.
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DNA REPLICATION
RNA and protein synthesis
Genetic information in DNA is copied, or transcribed into a
complementary base sequence of RNA.
The cell then uses the information encoded in this RNA to
synthesize specific proteins through a process called translation.
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1) Transcription:
A strand of Messenger RNA (mRNA) is synthesized
using a piece of DNA as a template (G pairs with C and
A with U instead of T).
mRNA that convey genetic information from DNA to
the ribosome (site of protein synthesis).
A region of DNA that initiates transcription of a
particular gene termed as promoter.
RNA polymerase reads the DNA strand from 3-prime
(3') end to the 5-prime (5')end, while it synthesizes a
single strand of messenger RNA in the 5'-to-3'
direction.
RNA synthesis continues until RNA polymerase reaches
a site on the DNA called the terminator (the end of the
gene).
After that, RNA polymerase and the newly formed
single stranded mRNA are released from the DNA.
2) Translation:
It is a process of protein synthesis.
It is a following step after transferring the genetic
information into mRNA.
It is called translation because it involves decoding the
language of nucleic acid
The language of m RNA is in the form of codons,
group of three nucleotides such as AUG,GGC.
The sequence of the codons determines the sequence
of amino acids that will be in the synthesized protein
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There are 64 possible codons, 61 are sense codons
(code for amino acids) and 3 are nonsense codons
(stop codons).
In the ribosome, the transfer t RNA recognizes the
codons and transfers the required amino acids.
Each t RNA has an anticodon, a sequence of three
bases that is complementary to a codon.
The first t RNA binds to the start codon bringing with
it the amino acid methionine.
A t RNA carrying the second amino acid approaches.
The place on the ribosomes where the first
t RNA sits is called P site.
The first amino acid joins to the second by peptide
bond and the first t RNA is released.
The ribosomes moves along the mRNA in 5’ to 3’
direction until the second t RNA is in the P site and
the process continues.
When the ribosome reaches a stop codon, the
polypeptide, t RNA and the m RNA are released.
The released polypeptide forms a new protein.
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The regulation of bacterial gene expression:
Protein synthesis occurswhen a certain gene is expressed.
Because protein synthesis requires a great consumption of
energy, regulation of gene expression is vital to the cell’s energy
economy.
Repression and induction are two mechanisms which can control
protein synthesis( transcription and translation)
A. Repression:
Inhibition of gene expression and consequently decreased
protein synthesis.
Occurs as a result of overabundance of the reaction end-product.
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Repressors are regulatory proteins which can block the ability of
RNA polymerase to start transcription.
B. Induction:
It is a process that enhances gene transcription and protein
synthesis.
It is mediated by substances called inducers
Inducible enzymes are enzymes which are synthesized in the
presence of the inducers.
Mechanisms of Genetic Variations
A. Mutation
It is change in the genetic material (base sequence of DNA), which
in turn can change the product encoded by the gene.
There are three types of mutation;neutral (silent),
anddisadvantageous or lethal, beneficial mutation.
a) Neutral ( silent) mutation: meaning that they have no effect
on the cell
b) Beneficial mutation: which are benefit to the organism
(enable the organism to survive in an environment where
organisms without mutation would die).
c) Harmful mutation:which leads to the production of
nonfunctional enzymes that suppress their metabolic
reaction essential for bacterial growth and may be lethal.
d) Base substitution (point mutation): single base replaced
with different base.
e) Missense mutation: during translation and protein
synthesis, the incorrect base may cause the insertion of in-
correct amino acid in the protein.
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f) Nonsense mutation: nonsense (stop) codon occurs in the
middle of an mRNA molecule resulting in incomplete
protein synthesis.
g) Frame-shift mutation: in which one or a few nucleotide
pairs are inserted or deleted in the DNA results in
production of inactive proteins.
h) Spontaneous mutations: occurs in absence of mutagens.
Mutagens: are agents in the environment, such as certain chemicals
and radiation, that directly or indirectly causing mutations.
Mutations in the microbial world:
Some mutation can cause antibiotic resistance.
Certain mutation result in alteration of pathogenicity; for
example, mutations in gene encoding the outer membrane may
increase the pathogenicity.
Genetic transfer
It is exchange of DNA between cells, results production of new
strain of bacteria.
The transferred gene can be integrated into the recipient
chromosome, plasmid or bacteriophage.
Gene transfer occurs through three mechanisms:
a. Conjugation: the genetic material transferred through
direct cell to cell contact (sex pili).
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Conjugation
b. Transformation:
It is process where gens are transferred from
bacterium to another as a naked DNA in solution.
Species which are capable of taking up exogenous
DNA are called competent.
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b. Transduction: it is a mechanism in which bacterial DNA is
transferred from a donor cell to a recipient cell inside a
bacteriophage.
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