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 nucleotides.  May contain 10 – 40 million nucleotides. A binds to T G binds to C .  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.

upstream exon intron exon downstream Initiation codon termination codon 5’ 3’ 3’ 5’ .


Circular shape of microbial DNA .


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

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

Genetics codes .

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

 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). DNA Protein DNA mRNA rRNA tRNA .


. each amino acids was brought to the ribosome by tRNA.  Before protein synthesis begins.  The protein synthesis of the polypeptide takes place by the linear movement of ribosomes along the mRNA.Translation of the genetic code: Protein synthesis  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 proteins.


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.  Insertion sequence.mispairing.  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 .

Nucleotide selection: The DNA polymerase operate nucleotides selection.  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.  When it is shifted to the active site of the enzyme. . Incorrect nucleotide attached to the polynucleotide will be digested by the exonuclease enzyme.Mechanism for ensuring the accuracy of DNA replication  Nucleotide selection  Proofreading by the exonulease enzyme. Selection act in three different stages:  When nucleotide is first bound to the DNA polymerase enzyme.



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



 Regulatory mutants: has mutation in the promoter or other regulatory sequence. EX: constitutive mutants of E. . restrictive condition. temperature-sensitive. Prototrophs are the wild type microorganism.  Conditional-lethal mutants : permissive condition.The effect of mutations on microorganism:  Auxotrophs Microorganism that will only grow when provided with a nutrient that is not produced by it self.  Inhibitor-resistant mutants: able to resist the toxic effects of an antibiotic or other type of inhibitor. 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. whose site of action is the operator. 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 operator  Regulator gene: Its codes for the synthesis of the repressor protein.


Repressible operon .


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

.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.  Has more complex enzyme/proteins Transposable proghages  Certain phage.Transposable elements : Insertion sequences (IS)  Segment of DNA  Approx. ex: Mu .  Called replicative recombination Transposons (Tn element)  10 fold of IS in length.  Has certain sequence in its termini.

DNA viruses .

RNA viruses .


g. 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. HIV) 7 Nicked dsDNA nicked dsDNA intact dsDNA mRNA Hepatitis B virus RNA .

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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