Bacterial Genetics PDF

Bacterial Genetics  Introduction/Definition of Terms Genetics is the science study of heredity Heredity is the transfer of traits/ attributes of an organism to its descendants Phenotype is the totality of the specific traits/ attributes of an organism that is observable: STRUCTU...

Bacterial Genetics  Introduction/Definition of Terms Genetics is the science study of heredity Heredity is the transfer of traits/ attributes of an organism to its descendants Phenotype is the totality of the specific traits/ attributes of an organism that is observable: STRUCTURAL PHYSIOLOGIC  Introduction/Definition of Terms Genotype is the totality of genetic elements in an individual responsible for its specific phenotypic properties Genome is the totality of genetic information in an organism CHROMOSOMAL PLASMID DNA/RNA is the site where the genetic information in an organism reside  Introduction/Definition of Terms Chromosome coiled & super-coiled DNA, Haploid in bacteria Nil Recessive/ Dominant state Gene Unit of inheritance Part or Segment of the DNA/ RNA Performs a specific function: Segment of the DNA Coding for an amino acid, Segment of the DNA coding for a peptide, Segment of the DNA a polypeptide /Others Represented by sequence of nucleotide bases/ codon  Introduction/Definition of Terms Codon a set of 3 nucleotide bases coding for an amino acid Plasmids are small, circular pieces of DNA that are separate and replicate independently from the bacterial chromosome  DNA Structure Double stranded (double helix)-two chains Each Chain(Strand) consists of nucleotides Strands are anti-parallel = 5’ to 3’: 3’ to 5’ Complimentary base pairing – A-T – G-C  DNA Structure Phosphate-P (Red) Sugar-blue Bases-ATGC  DNA Structure Bacteria DNA is closed & circular DNA is coiled and super coiled to chromosome to make it fit into the cell E. coli 4 million base pairs 1 mm long over 1000 times larger that actual bacterial cell DNA takes up around 10% of cell volume  RNA Structure Same as DNA Exceptions – Single stranded – Uracil replaces Thymine  DNA Replication Bacteria reproduce by the process of binary fission – Chromosomal Replication – Cellular Divisions Chromosomal Replication is necessary Makes each of the daughter cells contain same genetic information as the mother cell The mother cell and descendants are identical  DNA Replication Chromosomal Replication starts with uncoiling of chromosome back into DNA by DNA helicase and gyrase Uncoiled DNA is unzipped to create the replication fork  DNA Replication Contd. DNA helicase-unzips the parental DNA strand that is used as a template – Leading stand synthesis is continuous (5’ to 3’) – Complimentary nucleotides are aligned to the DNA template – DNA polymerase joins aligned nucleotides to form growing DNA strand – Lagging strand synthesis is discontinuous (3’ to 5’) – RNA polymerase makes short RNA primer – DNA polymerase extends RNA primer by complimentary nucleotides alignment and linkage – DNA polymerase digests RNA primer and replaces it with DNA to form short DNA fragments called Okazaki fragments – DNA ligase seals Okazaki fragments DNA Replication  Plasmids Plasmids are small, circular pieces of DNA that exist and replicate separately from the bacterial chromosome Importance of Plasmid – Mutation (F-plasmid) – Resistance (R-plasmid) Resistance or R-plasmids carry genes that confer resistance to certain antibiotics – R-plasmid usually has two types of genes: R-determinant: resistance genes that code for enzymes that inactivate certain drugs RTF (Resistance Transfer Factor): genes for plasmid replication and conjugation.  Transposons aka – Transposable Genetic Elements – Jumping genes Definition – are pieces of DNA – Capable of moving from: one location on the chromosome another plasmid to chromosome or vice versa one plasmid to another Examples: Insertion sequence Episomes  INSERTION SEQUENCE Insertion sequences (IS) are jumping genes capable of attaching to other genetic elements of the cell from which they can move to another (transposition) IS contains usually only one gene that codes for transposase, the enzyme that catalyses transposition. The transposase gene is flanked by two DNA sequences called inverted repeats Inverted repeats have nucleotide arranged upside-down and backward to each other. Eg AATTCC TCATCA CCTTAA Transposase helps in binding & excision of inverted repeats Binding & excision of inverted repeats = MUTATION  EPISOME Episomes are fundamentally plasmids Are DNA segments Capable of independent existence and replication like plasmids Additionally, capable of integration into chromosomal DNA and excising from the chromosome Differs from IS in structure Like IS, can cause mutation  Mutations Inheritable changes in the genome of an organism The mutational changes can be: Harmful Lethal Helpful Silent  Types of Mutation 1. Point mutations aka base substitution occurs when a single nucleotide is replaced with a different nucleotide Results possibly in a mutant protein after transcription and translation. Types of point mutations: – Silent Mutation: causes no change in the activity of the protein. usually the result of a substitution occurring in the third location of the mRNA codon – Missence Mutation: a nucleotide substitution that changes a codon so that it codes for a different amino acid in the protein. usually results in a change of the activity of the protein change may be harmful or beneficial – Nonsense Mutation: same as a missense mutation except the resulting codon codes for a STOP signal result in premature termination of translation translated protein is shorter than usual and does not contain all the amino acids protein is most likely non-functional  Types of Mutation 2. Frameshift Mutations – caused by base insertion base deletion – An inserted or deleted nucleotide alters the triplet grouping of nucleotides into codons shifts the reading frame so that all nucleotides downstream from the mutation will be improperly grouped. – The result is a protein with extensive missense ending sooner or later in nonsense.  Causes of mutation in bacteria 1. Errors made during replication, repair, or recombination – Corrected by proof reading – Even with proof reading, error abound  Causes of mutation in bacteria 2. Exposures chemical agents (mutagens) – Nitrous Acid: Nitrous Acid affects DNA complementation. The acid randomly modifies the base pairing adenine pairs with cytosine instead of thymine. – A Base Analog: A base analog is a compound sufficiently similar to one of the four DNA bases but have different pairing properties. Examples: 5-bromouracil is the analog of thymine but sometimes pairs with guanine 2-aminopurine is the analog of adenine but sometimes pairs with cytosine. The incorporation of a base analog leads to a base pair substitution  Causes of mutation in bacteria 3. Exposures to physical agents (Mutagen) – UV Light: Exposure to direct UV light induces covalent linking between adjacent thymine nucleotides on a DNA strand forming a thymine dimer. These dimers cause the strand to buckle, disrupting normal base pairing. This prevents proper replication and transcription. Bacteria have enzymes to fix the damage created by UV light. An enzyme cuts the DNA at two point and removes the damaged portion. DNA polymerase synthesizes a new DNA segment using the healthly strand as a template. DNA ligase joins the new fragment to the old strand.  Causes of mutation in bacteria 4. Genetic transfer in bacteria – Genetic transfer in bacteria involves the mechanism by which DNA fragments are moved from a donor cell to a recipient cell – Once donor DNA is inside the recipient, crossing over can occur (Recombination) – The result is a recombinant cell that has a genome different from either the donor or the recipient. Mechanisms of genetic transfer in Bacteria – Transformation – Transduction – Conjugation They are biological phenomenon associated with genetic element transfer in a bacterial population  Transformation The process by which a bacterium takes up naked DNA fragment from the environment Sources of DNA in the environment: bacterial cell death, bacterial cell lyses,  Transformation Up taken DNA segment can align with homogenous section of recipient cell DNA Aligned DNA can be incorporated/ integrated with recipient cell DNA (recombination) Recombinant cell is a TRANSFORMED cell TRANSFORMED cell is a MUTANT cell  Transformation Any up taken DNA that is not integrated into the recipient DNA will be degraded. Recombinant cell /Transformed cell / Mutant cell has a different genetic makeup compared to Donor & Recipient. All of the descendants of the recombinant cell will be identical to parent cell. Recombination gives room to genetic diversity in bacterial population. Transformation  Transduction BEFORE DESCRIBING TRANSDUCTION: 1. What is a BACTERIOPHAGE? 2. How can you classify BACTERIOPHAGES? 3. Describe the lytic cycle of a BACTERIOPHAGE 4. Describe the lysogenic cycle of a BACTERIOPHAGE 5. Enumerate the differences between the LYTic & lysogenic cycles of BACTERIOPHAGEs LYTic & lysogenic cycles of BACTERIOPHAGEs  Transduction Involves the transfer of DNA from one bacterium to another through a bacteriophage (phage) – A phage is a virus that infects bacteria. – Examples of Phage infecting E. coli 1. T4 phage -replicate by the lytic cycle - Cell death 2. Lambda phage -replicate by the lysogenic cycle -latent infection in the host until it breaks out in a lytic cycle  Types of Transduction: 1. Generalized uses lytic cycle any part of bacterial DNA can be transferred by transduction 2. Specialized uses lysogenic cycle Specific part of bacterial DNA can be transferred by transduction Transduction  Conjugation Transfer of genetic element between bacterial cells through conjugation bridge Conjugation bridge is fromed through sex pilus (Cf: Common pilus) Conjugation bridge = Cytoplasmic bridge Cytoplasmic bridge is temporary, dissolves after conjugation Donor & Recipient cell are of opposite polarity (+ & -) + Cell is the donor - Cell is the recipient and becomes + Donated genetic element is a plasmid/ episome  Conjugation Not all bacteria can undergo conjugation Presence of a special plasmid called the F plasmid is important for conjugation Bacteria that have a F plasmid are referred to as F+ or male. Those that do not have F plasmid are F- or female. conjugation event occurs when the male cell extends his sex pili and attaches to the female. a temporary cytoplasmic bridge is formed through which the F plasmid is transferred from the male to the female. When transfer is complete, the result is two male cells.  Conjugation The F plasmid can behave as an episome. When the F+ plasmid is integrated with the bacterial chromosome, the cell is called an Hfr cell (high frequency of recombination cell). The F plasmid always insert at the same spot for a bacterial species. The Hfr cell still behaves as a F+ cell, transferring F genes to a F-cell, but now it can take some of the bacterial chromosome with it. Conjugation Conjugation in Motion