Microbial Genetics

• Nucleic Acids:

  • Heredity material found in cells
  • Large molecules that are acidic in nature
  • Associated with the nuclear material of cells
• Deoxyribonucleic Acid (DNA):

  • Responsible for all cellular activity
  • Directs the production of proteins
  • Double stranded and helical
  • Maintained by weak hydrogen bonds
  • Very stable and can survive high temperatures, salt concentrations, and acid environments
• Ribonucleic Acid (RNA):

  • Consists of a long chain of nucleotide units
  • Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate
  • Usually single-stranded
  • Three types of RNA: mRNA messenger, tRNA transfer, rRNA ribosomal
• mRNA messenger RNA:

  • Complementary to one strand of DNA
  • Functions to carry genetic material from the chromosome to the ribosome
  • Involved in Transcription
• tRNA transfer RNA:

  • Responsible for transferring information from mRNA to rRNA
  • Involved in Translation
• rRNA ribosomal RNA:

  • Associated with the ribosome
  • Accepts information from tRNA and correlates it to synthesize proteins
  • Involved in Protein Synthesis
• Base Types:

  • Purines contain 2 nitrogenous rings (Adenine and Guanine)
  • Pyrimidines contain 1 nitrogenous ring (Cytosine and Thymine in DNA, Uracil in RNA)
  • Rules for Base Pairings: Adenine pairs with Thymine in DNA (A-T), Guanine pairs with Cytosine (G-C)
• Central Dogma Theory:

  • DNA -> RNA -> protein pathway
  • Major processes: replication, transcription, and translation
• Reverse Transcriptase:

  • Process of copying RNA information into DNA using reverse transcriptase enzyme
  • Adds another pathway to the central dogma of molecular biology
• DNA Replication in Bacteria:

  • Bacteria contain 1 chromosome and may have plasmids
  • Replication is semi-conservative with both strands duplicated
  • Enzymes transport nucleotides to complement the template
• RNA Synthesis in Bacteria:

  • Transcription involves RNA polymerase assembling nucleotides
  • RNA polymerase binds to DNA at a promoter site and travels along the DNA template
• Protein Synthesis in Bacteria:

  • Carried out in the cytoplasm
  • Involves DNA duplication by mRNA (Transcription) and transfer of information to rRNA by tRNA (Translation)
  • Takes place in three stages: Initiation, Elongation, Termination
• Codon:

  • Group of three nucleotides in DNA that code for amino acids in a protein molecule
  • AUG begins protein synthesis, UAA, UAG, UGA are termination codons
• Plasmids:

  • Small, circular, double-stranded DNA molecules distinct from chromosomal DNA
  • Exist naturally in bacterial cells and some eukaryotes
  • Can provide genetic advantages like antibiotic resistance
  • Can be transferred through conjugation
• Resistance Plasmids:

  • Contain genes that help bacterial cells defend against environmental factors like antibiotics
  • Can transfer themselves through conjugation, leading to antibiotic resistance
• Virulence Plasmids:

  • Turn bacteria into pathogens causing disease
  • Easily spread and replicated among affected individuals
  • Example: Escherichia coli (E. coli) with virulence plasmids
• E. coli has several virulence plasmids
• Certain strains of E. coli can cause severe diarrhea and vomiting
• Salmonella enterica contains virulence plasmids
• Degradative plasmids:

  • Help the host bacterium digest compounds not commonly found in nature
  • Contain genes for special enzymes that break down specific compounds
  • Are conjugative
• Col plasmids contain genes that make bacteriocins (colicins) which kill other bacteria and defend the host bacterium
• Bacteriocins are found in many types of bacteria, including E. coli
• Transposons are able to direct synthesis of copies of themselves and become incorporated into the chromosome
• Transposons are small pieces of DNA found in chromosomes and plasmids
• Transposons are called "jumping genes" because of their ability to move from one location to another in a cell's genome
• DNA transposons move using a cut-and-paste mechanism
• Retrotransposons move in a copy-and-paste fashion by duplicating the element into a new genomic location via an RNA intermediate
• Mutation:

  • One base pair is exchanged for another in the DNA molecule
  • One or more base pairs are inserted in the DNA molecule
  • One or more base pairs are deleted in the DNA molecule
  • There is a rearrangement of sections in the DNA molecule
  • There is an exchange of DNA region with another DNA molecule (Recombination)
  • Some mutations are harmful, some beneficial, some neutral
• Chemical and physical agents that cause mutations:

  • UV light is absorbed by pyrimidines (cytosine and thymine)
  • UV causes adjacent thymines in the same strand to react and bond with each other
  • Thymine dimers are replication errors in transcription and can lead to cellular death
  • Nitrous acid alters the chemical structures of adenine, cytosine, and guanine, introducing mutations during DNA replication
• Transfer of Genetic Material in Bacteria:

  • Transformation is the process of taking up naked DNA in a stably inherited form
  • Conjugation is a mating process involving bacteria and requires physical contact between the two bacteria
  • Transduction involves the exchange of DNA between bacteria using bacterial viruses as an intermediate
• Basic conjugation involves two strains of bacteria: F+ and F-

  • F+ cells contain the Fertility factor (F factor) which confers the ability to conjugate
  • Genetic transfer in conjugation is from an F+ cell to an F- cell, transferring the F factor itself
• Generalized transduction:

  • During bacteriophage replication, a fragment of host DNA gets packaged into a viral capsid
  • The resulting phage can infect another cell but cannot replicate
  • The infected cell may have an extra piece of bacterial DNA that can undergo recombination with the host chromosome
• Central Dogma Theory: DNA guides the synthesis of mRNA which in turn directs the order in which amino acids are assembled into proteins. DNA directs its own replication by giving rise to two complete, identical DNA molecules.
• Reverse Transcriptase: retroviruses use the enzyme "reverse transcriptase" to transcribe DNA from a RNA template. The viral DNA then integrates into the

  nucleus of the host cell. Then it is transcribed, and further translated into

  proteins. This biological process adds another pathway to the central dogma of molecular biology
• During replication, enzymes known as polymerases transport nucleotides from the cytoplasm that are complimentary to the template and fit them into place, resulting in two strands, one parental and one new one.
• Steps of DNA Replication:

  • DNA unwound with enzyme (replication fork)
  • Complementary bases added to template (parent strand) using enzyme
  • Replication fork moves down strand
  • Newly replicated DNA rewinds
  • Process called Semiconservative Replication
• DNA Replication:

  • Copied in 5’ to 3’ direction Polymerase can only add nucleotides to 3’ end

  • Replication of DNA begins a specific site on the DNA template termed the origin and proceeds in both directions from the origin until nuclear division and cytokinesis take place.
• Initiation: Start codon = formylmethionine (f-met) (AUG)

  Elongation: By a complex that begins with f-met, amino acids attach to form a chain (amino acids joined repeatedly to form proteins)

  Termination
• When a bacterium divides, all of the plasmids contained within the cell are copied such that each daughter cell receives a copy of each plasmid.
• Fertility F-plasmids

  • also known as F-plasmids, contain transfer genes that allow genes to

  be transferred from one bacteria to another through conjugation.

  • These make up the broad category of conjugative plasmids. F-plasmids

  are episomes, which are plasmids that can be inserted into chromosomal DNA.

  • Bacteria that have the F-plasmid are known as F positive bacteria without it are F negative When an F+ bacterium conjugates with an F – bacterium, two F+ bacterium result.

  • There can only be one F-plasmid in each bacterium.