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.

 May contain 10 – 40 million nucleotides.Bacterial DNA structure:  Consists of two chains of chemical units called nucleotides.  A nucleotides consists of a base (purine and pyrimidine)  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 division.  Duplicate and transfer itself to other species in process other than cell division.  Transcribe itself into a RNA to be translated into protein.  Mutate and change specific characteristics. .  Control the synthesis of proteins.

 Terminate the synthesis of the polypeptide.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 polypeptide.  Release the completed polypeptide.

Genetics codes .

Proteins work on the DNA replication process:  Unwinding proteins.  Each strand of the parent DNA serves as template for the formation of a complementary strand.  DNA polymerase .  Major errors in this process leading to prevent normal cell growth and development.  Helix-destabilizing proteins.DNA Replication:  The transmission of genetic material from parent to progeny requires an exact duplication of the original DNA strands.

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


Translation of the genetic code: Protein synthesis  mRNA is translated into polypeptides in a process that take place on the ribosome. .  Before protein synthesis begins.  Ribosomes are small structural components in the cell that are composed of rRNA and a variety of proteins.  The protein synthesis of the polypeptide takes place by the linear movement of ribosomes along the mRNA. each amino acids was brought to the ribosome by tRNA.


 Insertion sequence.mispairing. It is occur in case of:  Purine or pyrimidine bases temporarily exist in different electrochemical forms -------.Mutation The alterations in the base sequence of the hereditary material (DNA) Spontaneous mutations Occur in the absence of environment intervention.  Missmatch during replication Induced mutations Physical agents:  Ultraviolet light (UV)  X-rays  Gamma-rays Chemical agents .

Spontaneous mutation .

A A’ IS’ A’’ IS IS Movement of insertion sequence (IS) IS element replicates and inserts a copy within the A gene .

Mismatch during replication .

Mutagenic agent caused mutation .

 When it is shifted to the active site of the enzyme.Mechanism for ensuring the accuracy of DNA replication  Nucleotide selection  Proofreading by the exonulease enzyme. Incorrect nucleotide attached to the polynucleotide will be digested by the exonuclease enzyme. Nucleotide selection: The DNA polymerase operate nucleotides selection. Selection act in three different stages:  When nucleotide is first bound to the DNA polymerase enzyme. .  When it is attached to the 3’-end of the polynucleotide Proofreading: Exonuclease enzyme: Enzyme which has ability to cut the DNA from 3’ to 5’ end direction.



Open reading frame (ORF) How to read the codons sequences. DOGCANRUN DOG-CAN-RUN (Frame I) D-OGS-ANR-UN (Frame II) DO-GCA-NRU-N (Frame III) DOGCANRUN DOG-CAR-UN (Frameshift) .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.



. Coli expressed genes all the times.The effect of mutations on microorganism:  Auxotrophs Microorganism that will only grow when provided with a nutrient that is not produced by it self.  Conditional-lethal mutants : permissive condition. Prototrophs are the wild type microorganism.  Inhibitor-resistant mutants: able to resist the toxic effects of an antibiotic or other type of inhibitor. temperature-sensitive. restrictive condition.  Regulatory mutants: has mutation in the promoter or other regulatory sequence. EX: constitutive mutants of E.


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. whose site of action is the operator.  Promoter: A sequence of nucleotides lying outside the operator  Regulator gene: Its codes for the synthesis of the repressor protein.The Operon: protein synthesis control system An operon is a group of genes that are located adjacent to one another in the genome. .


Repressible operon .


. Transformation: Direct up take of the donor DNA by the recipient cell. Transduction: Donor DNA was carried in a phage coat and is transferred into the recipient by the mechanism used for phage infection. may be nature or forced. The recipient completes the structure of double stranded DNA.Mechanism of gene transfer in prokaryote Conjugation: Only one strand of DNA is transferred.

.Exogenote: The molecule of DNA introduced to the recipient cells Endogenote: The original DNA segment of the recipient cells.

Conjugation .


1000 bp  Contain genes need for transposition only  Encode enzyme for site-specific recombination.Transposable elements : Insertion sequences (IS)  Segment of DNA  Approx.  Has more complex enzyme/proteins Transposable proghages  Certain phage.  Called replicative recombination Transposons (Tn element)  10 fold of IS in length.  Has certain sequence in its termini. ex: Mu .

DNA viruses .

RNA viruses .


g. HIV) 7 Nicked dsDNA nicked dsDNA intact dsDNA mRNA Hepatitis B virus RNA . Baltimore Classification of Viruses Group Genome Replication Example 1 dsDNA dsDNA mRNA Herpes simplex virus 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 virus 6 ssRNA ssRNA dsDNA mRNA Retrovirus (e.

Positive Strand RNA Virus Genome .

Negative strand RNA Virus Genome .

Virus enzyme Segmen mRNA Protein RNA (-) Strand (+) Segmen RNA (+) Segmen RNA (-) Virus baru .

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