[PSM] Microbial Genetics

OriC

Starting point of replication in E. coli

Helicase (DnaB)

Enzyme that breaks hydrogen bonds to open or unwind DNA double helix

Primase (DnaG)

Enzyme that synthesizes RNA primers

RNA Primer

Provides 3' OH for DNA polymerase to start

DNA polymerase III

Extends DNA strand in 5' → 3' direction

DNA polymerase I

Has 5' → 3' exonuclease activity

DNA polymerase I

Removes RNA primers after replication

DNA ligase

Seals gaps between Okazaki fragments

Phosphodiester bonds

What kind of bonds are created by DNA ligase for Okazaki fragments?

TATAAT

Pribnow box sequence

-10

What is the location of the Pribnow box?

Pribnow box

Site recognized by sigma factor for transcription?

RNA polymerase

Enzyme that synthesizes RNA from DNA template

Sigma factor

Part of RNA polymerase holoenzyme that recognizes promoter for transcription

Intrinsic terminator

Type of transcription terminator with hairpin loop

Intrinsic terminator

Can end transcription without need for Rho factor

Shine-Dalgarno sequence

Ribosome binding site on mRNA for translation

N-formylmethionine

Amino acid coded for by AUG for prokaryotes?

30S, 50S

Small and large subunits of 70S ribosome?

Release factor

Factor that recognizes stop codon for translation and releases peptide chain

Borrelia burgdorferi

Bacteria known for having linear chromosomes

Col plasmids

Plasmids that code for bacteriocins

Insertion sequence

Simplest form of transposon

Riboswitches

In prokaryote operons, these regulate gene expression by directly binding metabolites

Paul Berg

First recombinant DNA using frog DNA and bacterial plasmids was created in 1972 by?

Pathogenicity islands

Gene clusters in pathogenic bacteria that confer virulence

Tetracycline

Antibiotic that can block tRNA binding

Chloramphenicol

Antibiotic that inhibits peptidyl transferase

Streptomycin

Antibiotic that causes misreading of mRNA

Joshua Lederberg

Discovered conjugation in bacteria

Frederick Griffith

Showed transformation in Streptococcus pneumoniae

Avery, MacLeod, McCarthy

Identified DNA as the transforming principle

Hershey and Chase

Proved DNA is genetic material using phages

Meselson and Stahl

Showed semiconservative DNA replication

RNA

What molecule does Rho protein bind to?

rRNA

What kind of RNA makes up the catalytic site of the ribosome?

SOS response

Mechanism in bacteria that triggers error-prone repair in response to DNA damage and is regulated by RecA and LexA

RecA, LexA

What regulates SOS response in bacteria?

Shine-Dalgarno sequence

This sequence aligns the mRNA on the ribosome by binding to the 16S rRNA.

Allolactose

In the lac operon, what molecule acts as the inducer by binding to the repressor?

Episome

What is the term for a plasmid that can integrate into the bacterial chromosome?

RecA

What is the name of the protein that binds to LexA to initiate the SOS response in bacteria?

Nucleosome

Repeating structural unit within eukaryotic chromatin

Nucleosome → 30-nm Fiber → Radial loop domain → Chromatin (300 nm diameter) → Chromatid (700 nm diameter)

Explain levels of chromatin packaging for eukaryotes

Solenoid, Zigzag

2 models of 30-nm fiber arrangement

G-banding

Banding in metaphase chromosome due to differential staining along length of each chromosome (A-T rich regions).

C-banding

Banding in metaphase chromosome wherein only cemtromeres are stained

Constitutive

Classification of Gene Product: Continuously produced regardless of chemical makeup

Inducible

Classification of Gene Product: The presence of a specific molecule promotes gene expression

Repressible

Classification of Gene Product: The presence of a specific molecule inhibits gene expression

Repressors, Activators

2 Types of Regulatory Proteins

Inducer, Corepressor

2 Types of Effector Molecules

Effector Molecules

Molecules that increase or decrease transcription

Regulatory Proteins

Molecules that promote or inhibit gene expression

Francois Jacob, Jacques Monod

Who were the discoverers of the lactose operon?

Inducible system, Negative regulation

The lac operon is a [___] system and follows a [___] regulation

Operator

Site in an operon where a repressor can bind to block transcription

Isopropylthiogalactoside (IPTG)

What is the sulfur analog of lactose that serves as an inducer that can bind to lac repressor?

Catabolite-activating protein (CAP)

A protein that activate expression of lac operon or inhibit its expression if glucose is present

Cyclic Adenosine Monophosphate

Secondary signal that binds with CAP in lac operon

Repressible system, Negative regulation

The lac operon is a [___] system and follows a [___] regulation

Induction-repression, Attenuation

2 regulatory mechanisms for the Trp Operon

Attenuation

Type of Trp operon regulation that forms stem-loop structure and controls termination of transcription of trp leader

Virulent phage

Viruses that can kill cells

Lysogenic phage

Viruses that can coexist with bacterial cell

Prophage

Viral DNA that can integrate into the bacterial chromosome

Temperate phage

Viruses that might or might not kill host cells

F+

State of the F plasmid: Contains F factor that acts as a donor cell

Hfr

State of the F plasmid: F factor is integrated into the bacterial genome

F’

State of the F plasmid: F factor exists as an extrachromosomal element but contains some sections of the chromosomal DNA

F-

State of the F plasmid: Contains no F factor that acts as a recipient cell

R-determinants

Component of the R plasmid that confer resistance to antibiotics

RTF segment

Component of the R plasmid that encodes genetic information essential to transferring plasmid between bacteria

Colicins

Toxin proteins encoded by the ColE1 plasmid that can kill or inhibit the growth of other bacteria

Prototrophs

Bacteria that can grow in minimal media

Auxotrophs

Bacteria that are unable to grow in minimal media due to mutation

Conjugation

Gene Transfer: Genetic information from one bacterium is transferred to and recombined with another bacterium

Bernard Davis

Did an experiment using a U-shaped tube and proved that genetic exchange requires cell-cell contact

Joshua Lederberg and Edward Tatum

Discovered bacterial conjugation through experimentation with auxotrophs and prototrophs

Merozygote

Partially diploid cell that results from the transfer of F’ to F- cell

Transformation

Gene transfer method wherein small pieces of extracellular DNA are taken up by living bacterial cells

Cotransformation

Single transfer event of several genes simultaneously

Salmonella

What bacteria did Joshua Lederberg and Norton Zinder work with to discover phage transduction in bacteria?

Cotransduction

Two linked genes on a bacterial chromosome are simultaneously transduced