dr. Tri Wibawa, PhD

Department of Microbiology
Gadjah Mada University School of Medicine
Two types of organism:
 Eukaryotes; cells contain membrane-bound
compartments, including a nucleus and organelles.
Eukaryotes include: animals, plants, fungi, and
 Prokaryotes: Lack internal compartments extensively.
Divided into two groups: bacteria and archaea.

The entire genetic complement of a living organism.

A DNA segment containing biological information and
hence coding for an RNA and / or polypeptide molecule.
Eukaryotes genomes;
 Divided into two or more linear DNA molecules.
 Each contained in a different chromosome.
 Possess smaller, usually circular, mitochondrial
 Third genome located in the chloroplast (in plant and
other photosynthetic organism)
 10 Mb – 100,000 Mb in length.
 Higher eukaryotes need larger genome to
accommodate the extra genes.
 Correlation between genome size and complexity (???)
--- C-value paradox.
 Space is saved in the gnomes of less complex
organism because the genes are more closely packed
Prokaryotes genomes:
 Whole prokaryotes genomes are smaller than
 Most – if not all -- are contained in a single DNA
 The molecule is circular.
 Have second circular or linear genome, called
 Have fewer genes
 More compact genome organization, more gene but
less space.
 There is NO INTRONS (some exception is in
 Infrequency of repetitive sequences.
Bacterial DNA structure:
 Consists of two chains of chemical units called
 May contain 10 – 40 million nucleotides.
 A nucleotides consists of a base (purine and
 Purine : adenine (A) and guanine (G)
 Pyrimidine: Thymine (T) and cytosine (C)
 DNA contains a specific sequence of purine and
pyrimidine base.

A binds to T
G binds to C
upstream exon intron exon downstream

Initiation codon termination codon

5’ 3’

3’ 5’
Circular shape of microbial DNA
DNA performs specific functions in the bacterial
cell includes the ability to:

 Duplicate itself for transfer to the progeny during cell
 Transcribe itself into a RNA to be translated into
 Control the synthesis of proteins.
 Mutate and change specific characteristics.
 Duplicate and transfer itself to other species in
process other than cell division.
DNA and Genetics Code:

The sequence of codons on the mRNA contain
the necessary information to :
 Initiate polypeptide synthesis.
 Designate the sequence of amino acids in the
 Terminate the synthesis of the polypeptide.
 Release the completed polypeptide.
Genetics codes
DNA Replication:

 The transmission of genetic material from parent to
progeny requires an exact duplication of the original
DNA strands.
 Major errors in this process leading to prevent normal
cell growth and development.
 Each strand of the parent DNA serves as template
for the formation of a complementary strand.

Proteins work on the DNA replication

 Unwinding proteins.
 Helix-destabilizing proteins.
 DNA polymerase
DNA transcription:

 The process in which one strand of DNA serves as a
template for the synthesis a single-stranded
messenger RNA (mRNA).
 It is the information on the RNA that can be
translated into usable information by the cell.

DNA Protein


Translation of the genetic code: Protein

 mRNA is translated into polypeptides in a process
that take place on the ribosome.
 Ribosomes are small structural components in the
cell that are composed of rRNA and a variety of
 Before protein synthesis begins, each amino acids
was brought to the ribosome by tRNA.
 The protein synthesis of the polypeptide takes place
by the linear movement of ribosomes along the
The alterations in the base sequence of the hereditary
material (DNA)

Spontaneous mutations
Occur in the absence of environment intervention.
It is occur in case of:
 Purine or pyrimidine bases temporarily exist in different
electrochemical forms -------- mispairing.
 Insertion sequence.
 Missmatch during replication

Induced mutations
Physical agents:
 Ultraviolet light (UV)
 X-rays
 Gamma-rays
Chemical agents
Spontaneous mutation
A A’ IS’ A’’


Movement of insertion sequence (IS)
IS element replicates and inserts a copy within the A gene
Mismatch during replication
Mutagenic agent caused mutation
Mechanism for ensuring the accuracy of DNA
 Nucleotide selection
 Proofreading by the exonulease enzyme.

Nucleotide selection:
The DNA polymerase operate nucleotides selection.
Selection act in three different stages:
 When nucleotide is first bound to the DNA polymerase
 When it is shifted to the active site of the enzyme.
 When it is attached to the 3’-end of the polynucleotide

Exonuclease enzyme: Enzyme which has ability to cut the
DNA from 3’ to 5’ end direction.
Incorrect nucleotide attached to the polynucleotide will be
digested by the exonuclease enzyme.
How mutations affect the genetics code ?
 Silent mutation (has no effect)
 Missense mutation (change to a different amino acids)
 Nonsense mutation (change to a stop codon)
 Frameshift mutation.

Open reading frame (ORF)
How to read the codons sequences.


DOG-CAR-UN (Frameshift)
The effect of mutations on microorganism:

 Auxotrophs
Microorganism that will only grow when provided with a
nutrient that is not produced by it self. Prototrophs are the
wild type microorganism.

 Conditional-lethal mutants : permissive condition,
restrictive condition, temperature-sensitive.

 Inhibitor-resistant mutants: able to resist the toxic effects
of an antibiotic or other type of inhibitor.

 Regulatory mutants: has mutation in the promoter or other
regulatory sequence. EX: constitutive mutants of E. Coli
expressed genes all the times.
The Operon: protein synthesis control system

An operon is a group of genes that are located
adjacent to one another in the genome.

The operon unit consist of:
 Structural gene: gene coding for enzymes involved in the
formation of specific molecule
 Operator: A sequence of nucleotides adjacent to the
structural gene.
 Promoter: A sequence of nucleotides lying outside the
 Regulator gene: Its codes for the synthesis of the
repressor protein, whose site of action is the operator.
Repressible operon
Mechanism of gene transfer in prokaryote

Only one strand of DNA is transferred. The recipient
completes the structure of double stranded DNA.

Donor DNA was carried in a phage coat and is
transferred into the recipient by the mechanism used
for phage infection.

Direct up take of the donor DNA by the recipient cell,
may be nature or forced.
The molecule of DNA introduced to the recipient cells

The original DNA segment of the recipient cells.
Transposable elements :
Insertion sequences (IS)
 Segment of DNA
 Approx. 1000 bp
 Contain genes need for transposition only
 Encode enzyme for site-specific recombination.
 Has certain sequence in its termini.
 Called replicative recombination

Transposons (Tn element)
 10 fold of IS in length.
 Has more complex enzyme/proteins

Transposable proghages
 Certain phage, ex: Mu
DNA viruses
RNA viruses
Baltimore Classification of Viruses
Group Genome Replication Example
1 dsDNA dsDNA mRNA Herpes simplex

2 ssDNA ssDNA dsDNA mRNA Parvovirus

3 dsRNA dsRNA mRNA Reovirus

4 +ve ssRNA dsRNA +ve ssRNA [Acts as mRNA] Enterovirus

5 -ve ssRNA dsRNA -ve ssRNA mRNA Influenza A

6 ssRNA ssRNA dsDNA mRNA Retrovirus
(e.g. HIV)

7 Nicked dsDNA nicked dsDNA intact dsDNA mRNA Hepatitis B
Positive Strand RNA Virus Genome
Negative strand RNA Virus Genome
Virus enzyme

Segmen mRNA Protein
RNA (-) Strand (+)

RNA (+)

RNA (-)

Virus baru

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