BI 438: Exam 3

nucleoid

Region within the cell containing the genome whihc consists of a single double-stranded circular piece of DNA encoding all essential genes required for bacterial growth

plasmid

small circular pieces of DNA which encode non-essential genes which can have benefits such as antibiotic resistance, tolerance of toxic materials, and virulence factors

origin of replication

place on the circular DNA chromosome where replication begins and continues bidirectionally

bacteria

What type of chromosome?

generally a single circular chromosome with one origin of replication

archaea

What type of chromosome?

All known genomes are a single circular chromosome with multiple origins of replication

DNA gyrase

protein in bacterial cells that coils the chromosome

NAPs

Nucleoid-associated proteins that provide scaffolding for supercoiled DNA

bacteria

What type of organism?

DNA is packaged with negative supercoiling by DNA gyrase

archaea

What type of organism?

DNA is packaged with negative supercoiling and histones; thermophiles use positive supercoiling

bacteria

What type of organism?

Uses ONLY nucleoid-associated proteins to help scaffold supercoiled DNA

archaea

What type of organism?

Uses both histones and nucleoid-associated proteins to organized supercoiled DNA

initiation

Step in transcription where RNA polymerase and regulatory factors associate with the promoter site to form an active RNA polymerase complex

promoter

Location where RNA polymerase attaches

sigma factor

protein that regulates transcription in bacteria by helping bind RNA polymerase to the correct promoter and activating it (many different types)

elongation

Step in transcription where DNA strands are separated and RNA is synthesized, only reads one strand of DNA

termination

step in transcription where RNA polymerase complex reaches the termination site and releases from the DNA template

hair pin loops

What forms in the transcribed RNA at a termination site that causes the RNA polymerase complex to disassociate

Pribnow box

-10 recognition site that are recognized by sigma factors in bacteria

-35

further away recognition site in bacteria that is recognised by sigma factors

TATA box

Repetativie sequence in archaea that attracts transcription factors

BRE site

B recognition site where transcrition factor 2B binds and recruits more transcrition factors

eukaryotic

Archaea promoters closely resemble (bacterial/eukaryotic) promoters.

RpoD

σ⁷⁰ is the most common and regulates “housekeeping” genes so it is always on

operon

a transcriptional unit comprised of multiple adjacent genes that are under the control of a single promoter, saves space in bacterial genome from having to have unnecessary promoters

constitutively expressed

characteristic of regulator genes and their promoter meaning they are always on

operator

binding site on the operon for regulatory proteins

repressor

regulatory protein that turns a gene off

activator

regulatory protein that turns a gene on

lac operon

negative inducible operon that control the expression of genes needed for lactose catabolism

active, absent

if low [lactose] than the repressor is (active/inactive) and the inducer is (present/absent)

inactive, present

if high [lactose] than the repressor is (active/inactive) and the inducer is (present/absent)

LacZ

Enzyme encoded by the lac operon for beta-galactosidase which cleave lactose into glucose and galactose

LacY

Enzyme encoded by the lac operon for glactoside permease which is embedded in the cell membrane and transports lactose into the cell

LacA

Enzyme encoded by the lac operon for transacetylase which acetylates glucosides, galactoside, and lactosides. Modifying sugers so they can get the most out of them

allolactase

inducer for the lac operon that inactivates the repressor when lactose is in high concentrations

CAP

catabolite activating protein that complexes with cAMP when glucose is low to promote lac operon function (activator)

cAMP

cyclic AMP complexes with CAP to promote the lac operon; more abundant when glucose is low so it will bind to CAP and activate the lac operon

diauxic growth

growth when two different sources are available for metabolism that is characterized by the organism first using the most efficient and effective energy source first (often glucose)

negative control

regulator protein is a repressor

positive control

regulator protein is an activator

inducible

expression is off until turned on

repressible

expression is on until turned off

pathogenicity factors

genes on plasmids that are associated with increased disease or pathogenesis, and R factors

R factor

resistance factors that can help with antibiotics

horizontal gene transfer

transfer between two individuals within the same generation

vertical gene transfer

transfer through replication to subsequent generations

expression

genetic information is used within a cell to produce the proteins needed for the cell to function (cell metabolizes and grows)

recombination

genetic information can be transferred horizontally between cells of the same generation (recombinant cell)

replication

genetic information can be transferred vertically to teh next generation of cells (offspring cells)

mutagenesis

mutations may alter genes making organisms aquire new traits

transformation

uptake of free DNA directly from their environment and incorporation into the gene by recombination (horizontal gene transfer)

conjugation

transfer of DNA from one bacterium to another via a sex pilus, incorporation in the genome is achieved by recombination

transduction

transfer of DNA via bacteriophages followed by recombination

inefficient

Incorporation of foreign DNA is often _________ and detreimental to the organism.

errors

Mutations can occur in prokaryotic genomes through _______ in DNA replication

chemical modifications

Mutations can be induced through spontaneous __________ ____________ causing spontaneous SNPs.

mutagens

Exposure to these can induce modifications to prokaryotic DNA

non-coding

Prokaryotes are more susepctible to DNA damage because their genomes do not have much __________ DNA.

more

Favorable mutations are (more/less) selected for in populations because of their hihg rate of repilcation

slippage

looping and hairpins in the template strand during replication of DNA that causes frameshifts

indels

Frameshifts caused by loops and hairpins of the template strand that results in mismatching and either insertions or deletions

positive selection

direct selection that detects mutant cells because they grow or appear different than un-mutated cells (gets mutants to grow)

negative selection

Indirect selection that detects mutant cells that cannot grow or perform a certain function (kills mutants b/c they can’t suvive the condition)

replica plating

Lab technique where imprints of colonies are made to transfer the same colonies to different plates to evaluate sensitivities

auxotrophs

organisms that have experienced a mutation that makes a nutrient acquisition process dysfunctional

Ames test

a simple test involving use of auxotrophs in the presence of test reagents to evaluate the strength of potential mutagens (see if they can mutate back to wild type)

Griffith’s Experiment

1928 experiment that:

• Demonstrated the concept of transformation of genetic material

• Set the foundation for studies leading to identifying the role of DNA in heredity

DNA release

First step of transformation when bacteria die or break apart and release their DNA fragments into the environment

DNA uptake

Second step of transformation when a living bacterium takes up free DNA from the environment

Integration

Third step of transformation where foreign DNA can integrate into the host’s genome by recombination

Gene expression

Fourth step of transformation where the cell expresses new genes from the acquired DNA

membrane instability

Salt treatment, electroporation, and heat shock are all ways to induce this for transformation

fertility plasmid

Plasmid that is necessary for the formation of a sex pilus for conjugation

episome

Plasmid that can integrate into the genome through recombination whihc menas chromosomal DNA is then in the plasmid to be transferred (F plamsid)

F+

Cells that contain the fertility plasmid

transfer gene region

Region on the plasmid that encode machinery associated with the F pilus formation to promote conjugation between cells

OriT

the origin for transfer for copying the plasmid during cell transfer

transposons

Regions on the F plasmid that cut themselves out of the genome and insert themselves randomly into the chromosome or elsewhere

Hfr cells

High frequency recombination cells where the F plasmid is fullt integrated into the genome

causes parts of the plasmid and chromosome to be transferred to the new cell during conjugation

prophage

genetic infection in a bacterial host where the phage genome is integrated into the host genome

lysogen

bacterial host of viral genome that is lying dormant

transduction

bacteriophage accidentally packages prior host genome and transfers these genes to the recipient which creates a recombinant cell (one lucky cell)

specialized transduction

process where omst of the bacteriophage DNA some of the prior host’s DNA are transferred to the recipient cell through transduction.

restriction modification systems

defense mechanisms in Bacteria and Archaea that destroy foreign DNA which enters the cell (2 main components)

restriction endonuclease

part of RM system that recognizes and cuts specific nucleotide sequences found within foreign DNA

methylase

a part of RM systems that typically attaches S-adenosylmethionine (SAM) to restriction site sequences to protect sites from being cut (MTase)

Type I

Type of RM system that is a single protein which encodes both methylation and endonuclease domains; recognition site is distant from the cleavage site

Type II

Type of RM system that consists of separate methylase and endonuclease enzymes; recognition site is at or close to the recognition site (often used in labs because it is the most simple system)

Type III

Type of RM system that is a single protein which encodes both methylation and endonuclease domains; recognition site is near by the cleavage site

molecular cloning

Using bacteria to copy foreign DNA of interst that can cut (nucleases) and paste (ligases) DNA from one source into another

DNA fingerprinting

Using restriction enzymes to cut at specific known places in the genome which can be used to identify species, clone new DNA, or look for genetic modifications

CRISPR Interference System

Adaptive (memory) immune system encoded within the genomes of most Bacteria and Archaea with two main components

CRISPR

Clustered regularly interspaces short palindromic repeats:

family of DNA sequences found in prokaryotes that are fragments remnants of previous phage infections (library in bacterial genomes that stores viral genes)

cas

CRISPR-associated Genes:

genes located near a CRISPR locus which encode the protein machinary for cleaving and destroying target DNA

spacer acquisition

First step in CRISPR system when Cas proteins recognize phage DNA and cleave it into pieces which are encorperated into the CRISPR locus

crRNA processing

Second step of CRISPR system with trascription of the CRISPR locus to produce RNAs that are processed by Cas to become crRNAs

destruction

thrid step of CRISPR sytem where phage injects its genome and crRNA recognizes and binds which recruits Cas9 the target and cut the DNA

polymerase chain reaction

lab technique used to amplify speqific DNA sequences exponentially from a target DNA sample (Taq and Pfu are from thermophiles)

small ribosomal subunit rRNA

Most common molecular clock gene being used in sequencing because it has the same function in all organisms and the averge mutation rate remains consistent amoung nearly all of life.

BLAST

tool used in classification that analyzes similarities of SSU rRNA with sequences of other organisms for the creation of phylogenetic trees