Microbio Exam 3

Must get an A

Main sources of bacterial genetic variation

Mutations, genetic rearrangements, and horizontal gene transfer

Mutation

Permanent, heritable change in DNA

Mutation vs DNA damage

DNA damage becomes a mutation only if it is not repaired before replication

Spontaneous vs induced mutation

Spontaneous occurs naturally during replication, induced is caused by mutagens

Mutagen

Physical or chemical agent that increases mutation rate

UV light

Physical mutagen that causes pyrimidine dimers

Bromouracil

Chemical mutagen that mimics thymine and can cause incorrect base pairing

Point mutation

Single base-pair change

Silent mutation

Point mutation that does not change the amino acid

Frameshift mutation

Insertion or deletion that shifts the reading frame, Usually severely disrupts protein function

Prototroph vs auxotroph

Prototroph is wild-type, auxotroph needs an added nutrient due to mutation

Histidine auxotroph

Mutant that cannot grow unless histidine is provided

Evolution in microbes

Evolution acts on populations, not individuals

Fitness

Ability to pass genes to the next generation

Fitness is relative

A trait may help in one environment but not another

Selective pressure

Environmental condition that favors certain genetic variants

Genetic rearrangement

Movement of DNA segments to new locations in the genome

Why genetic rearrangements matter

They can change when or how much genes are expressed

Recombination

Rearrangement or exchange of DNA molecules

General recombination

Exchange between homologous DNA sequences

Site-specific recombination

Recombination at specific recognition sequences

General vs site-specific recombination

General uses homologous DNA, site-specific uses specific DNA sites

Horizontal gene transfer

Gene movement between organisms rather than parent to offspring

Three types of horizontal gene transfer

Transformation, transduction, and conjugation

Transformation

Uptake of naked DNA from the environment by a competent cell

Competent cell

Cell able to take up external DNA

Naturally competent genera

Streptococcus, Acinetobacter, and Haemophilus

Griffith experiment

Showed transformation using Streptococcus pneumoniae

Artificially competent bacterium

Escherichia coli can be chemically treated to take up DNA

Transposon

DNA segment that can move within a genome

Insertion sequence

Simple transposon with inverted repeats and transposase

Composite transposon

Larger transposon that can carry genes such as antibiotic resistance genes

Plasmid

Extrachromosomal DNA that replicates independently

Conjugative plasmid

Plasmid that can transfer itself to another cell

Conjugation

DNA transfer requiring direct cell-to-cell contact

Pilus in conjugation

Brings donor and recipient cells together, but DNA does not travel through it

Davis U-tube experiment

Showed conjugation requires direct cell contact

Transduction

Transfer of bacterial DNA by bacteriophage

Generalized transduction

Random bacterial DNA is packaged into a phage during the lytic cycle

Specialized transduction

Specific genes near a prophage insertion site transfer after incorrect excision

Generalized vs specialized transduction

Generalized transfers random genes, specialized transfers nearby specific genes

Transformation vs transduction vs conjugation

Transformation uses naked DNA, transduction uses phage, conjugation requires cell contact

Central dogma

DNA is used to make RNA, and RNA is used to make protein

Bacterial replication

Usually one circular chromosome with one origin of replication

Eukaryotic replication

Linear chromosomes with many origins of replication

Archaeal replication

Prokaryotic location but more eukaryote-like replication machinery

DNA polymerase direction

Builds new DNA 5’ to 3’

Leading strand

Synthesized continuously toward the replication fork; New DNA is built 5’ to 3’

Lagging strand

Synthesized discontinuously as Okazaki fragments

RNA primase

Makes RNA primers for DNA replication

DNA ligase in replication

Seals gaps in the DNA backbone

Single-stranded binding proteins

Keep separated DNA strands from rejoining

Bacterial DNA polymerase III

Main enzyme for bacterial chromosome replication

Bacterial DNA polymerase I

Removes RNA primers and fills gaps with DNA

Eukaryotic DNA polymerases

Multiple specialized polymerases replicate and repair DNA

Replication location in prokaryotes

Cytoplasm/nucleoid region

Replication location in eukaryotes

Nucleus

Eukaryotic replication timing

Occurs during S phase

Promoter

DNA sequence where RNA polymerase begins transcription

Template strand

DNA strand used to make complementary RNA

Monocistronic mRNA

mRNA that codes for one protein

Polycistronic mRNA

mRNA that codes for multiple proteins

Prokaryotic mRNA

Often polycistronic and short-lived

Eukaryotic mRNA

Usually monocistronic and more stable

mRNA half-life comparison

Prokaryotic mRNA usually degrades faster than eukaryotic mRNA

Why eukaryotic mRNA lasts longer

5’ cap, poly-A tail, and RNA-binding proteins protect it

Transcription location in prokaryotes

Cytoplasm/nucleoid region

Transcription location in eukaryotes

Nucleus

Introns

Noncoding sequences removed from eukaryotic pre-mRNA

Spliceosome

Complex that removes introns and joins exons

Coupled transcription and translation

Prokaryotes can translate mRNA while it is still being transcribed

Bacteria vs eukaryotes transcription/translation

Bacteria couple them, eukaryotes separate them by the nucleus

Prokaryotic ribosome

70S ribosome

Eukaryotic ribosome

80S ribosome

Bacterial start amino acid

Formylmethionine, or fMet

Archaeal start amino acid

Methionine

Eukaryotic start amino acid

Methionine

Reverse transcriptase

Enzyme that makes DNA from an RNA template

Retrovirus

Virus that converts RNA into DNA using reverse transcriptase

Gene expression regulation

Control of when and how much a gene is transcribed

Most gene regulation in this module occurs

Transcription

Operon

Group of genes controlled together by one promoter/operator system

Repression

Gene expression is usually on until turned off

Induction

Gene expression is usually off until turned on

Positive regulation

Increases transcription level under certain conditions

Repressible operon example

trp operon

trp operon function

Controls genes needed to make tryptophan

trp operon default state

Usually on

trp operon signal

High tryptophan turns the operon off

Corepressor

Small molecule that activates a repressor

Tryptophan in trp operon

Corepressor that helps the repressor bind the operator

Inducible operon example

lac operon

lac operon function

Controls genes needed to use lactose

lac operon default state

Usually off

lac operon signal

Lactose turns the operon on

Allolactose

Inducer of the lac operon

Repressor

Protein that blocks transcription by binding the operator

Operator

DNA region where a repressor binds

trp vs lac operon

trp is repressible and usually on, lac is inducible and usually off

Catabolite repression

Glucose prevents full expression of genes for using other sugars