Module 5: Microbial Genetics

Genome

all genetic material of an organism; most genes are in chromosomes, some in plasmids, and some also in organelles

DNA packaging of eukaryotes

histone proteins allow DNA to fit into the cell

DNA packaging of prokaryotes

no histones, DNA binding proteins and polyamines, similar DNA packaging exists also in chloroplasts and mitochondria

Types of genes

structural genes, RNA machinery genes, and regulatory genes

Structural genes

code for proteins, produce some sort of structure

RNA machinery genes

used in protein production

Regulatory genes

control gene expression

DNA replication process

parental double strand DNA is unzipped, an RNA primer is made and attached to single stranded DNA, new bases are filled in using DNA polymerase, 2 daughter double stranded DNA result

Semi-conservative replication

daughter strand is half of the parental strand and half a new strand, reduces mistakes

Leading strand

made into one piece

Lagging strand

made into many smaller pieces that get fused together

Replication fork

where the helicase has unzipped the strand already

What does DNA replication always happen as?

DNA replication always happens in pairs, 2 helicases are put on one DNA strand and one unzips in one direction and the other helicase unzips in the other direction

Location of DNA replication

E: nucleus

P: cytoplasm

Origin of replication in DNA replication

E: many

P: one

Number of replication forks

E: many

P: two

Initiation of replication

E: protein complex

P: 2 proteins

Lagging strand size

E: 100-200 base pairs

P: 10x longer than eukaryotes

Speed(nucleotides/sec) of DNA replication

E: 100 nucleotides/sec

P: 2,000 nucleotides/sec

Central theme of biology

DNA→RNA→protein

Transcription

DNA→RNA

Translation

RNA→protein

RNA polymerase

enzyme that helps produce RNA

Other functions of RNAs

several RNAs regulate transcription and translation and gene function

Eukaryote vs Prokaryote: mRNA coding

eukaryotic mRNA code for 1 protein; prokaryotic mRNAs often code for more than 1 gene in series

Eukaryote vs Prokaryote: T&T location

Eukaryotic transcription occurs in nucleus, mRNA is exported to cytoplasm which is site of translation; prokaryotes have co-transcriptional translation in cytoplasm

Co-transcriptional translation

transcription and translation occur in the same place so they can occur at the same time

Eukaryote vs Prokaryote: introns

Eukaryotic genes contain introns which have to be cut out; prokaryotes have uninterrupted code for a protein

Gene expression

how to turn on and off genes; can be done by transcriptional controls, translational controls, or post-translational controls

Transcriptional controls

modulates mRNA production, will stop DNA from turning into RNA

Translational controls

modulates protein production, stops mRNA from turning into proteins

Post-translational controls

limits activity of an existing enzyme or protein

Why organisms go through sex

shuffles genetic deck which allows production of unique genetic combinations, useful genes can be “shared” through population

Useful traits for bacteria to share

antibiotic resistance, heavy metal resistance, virulence factors(toxin)

DNA recombination

one bacteria donates DNA to another which results in a bacteria strain different from donor and recipient strain, horizontal gene transfer and transposable elements

How bacteria change genomes

DNA recombination and mutation

Recombinant

organism containing genes from another organism

Horizontal gene transfer(HGT)

DNA transfer resulting in organisms acquiring new genes; not from parent; 3 types: transformation,

Plasmids

allow transfer of DNA between bacterial cells, about 30-50 genes, not needed for survival, often carry useful traits

Transformation

acceptance by bacterial cells of small DNA fragments from environment

Competent

cells able to accept genetic material through transformation

Fredrick Griffith

1920 discovered transformation from Streptococcus pneumoniae in mice

Different types of S. pneumoniae in Griffith experiment

Encapsulated: smooth(S) colony appearance, virulent

Non-encapsulated: no capsule=rough(R), non-virulent

Griffith’s experiment tests

S(capsule+)in mouse=mouse dies, R(capsule-)in mouse=mouse lives, heat-killed S in mouse=mouse lives, heat-killed S & live R in mouse= mouse dies

Griffith’s experiment explanation

The only way R strain to become pathogenic is to have picked up virulence genes(DNA) from dead S strain, virulence gene=capsule

Conjugation

genetic exchange, DNA is transferred(donor→recipient), pilus helps

F-factor transfer and high frequncy recombination

F-Factor transfer

fertility factor plasmid, allows production of pilus

entire plasmid is transferred, no other genes transferred

The point of F-Factor transfer

the bacteria with the F-factor plasmid have the ability to transfer them, after transfer both the donor and recipient have the plasmid

High Frequency Recombination(HFR) Transfer

donor must contain F-factor plasmid, its integrated into the chromosome and it is now able to transmit chromosomal genes

The point of HFR

once the F plasmid integrates into a bacterium, that bacterium is now able to pass any gene to another bacterium

Transduction

bacteriophage(virus) serves as a carrier of DNA from a donor to a recipient, occurs in many bacteria, donor and recipient have to be same species

Transposable Elements(TE)

transposons, “jumping genes” shift from one part of the genome to another, genes can be moved both internally and externally

Who first proposed transposons

Barbara McClintock

TE structure

insertion element(genes allowing TE activity) and any other gene

TE types

DNA transposons and retrotransposons

DNA transposons

DNA is cut and pasted in another location, TE is mobile

Retrotransposons

TE that replicates and inserts in a new location, TE duplicates

Mutations

random change to genomic nucleotide sequence, driving force of evolution

Wild type

organism exhibiting a natural, non-mutated characteristic; predominate trait in population

Mutant strain

organism with a mutation

Causes of mutations

spontaneous mutation and induced mutation

Spontaneous mutation

a random change in the DNA; error in replication

Induced mutation

result from exposure to mutagens, higher exposure to mutagen causes higher mutation rates

Impact of mutation

Lethal mutation(cell death), neutral mutation(no change), and beneficial mutation(increased survival and reproduction)

Gross mutations

large-scale change in chromosome structure

Point mutations

changes only one nucleotide; addition, deletion, or substitution of single bases

Back mutation

only way to repair a mutation, one mutation overwrites a previous mutation and original sequence is restored

Ames Test

uses his gene as a proxy to measure overall mutation rate due a chemical, chemicals capable of mutating bacterial DNA will do the same to human DNA