Micro chap 8 and 9

Coding strand of DNA base pairs

ATG

base pairs on template strand start codon

TAC

base pairs on mRNA for start codon

AUG

AUG is the start codon which is the amino acid

Methionine

Where enzyme begins in transcription

promoter sequence

Where enzyme begins in replication

ori

DNA-binding proteins aka protein regulators

activator and repressors

DNA coding strand will have the base pairs that match

the RNA

“reversion” mutation in genetics

the gene will be restored to its wild type

genotype

genetic code

Phenotype

observable trait such as eye color

DtxR is a repressor that works when

the ligand Fe is attached, and an abundant supply of Fe present

LuxR is an activator that promotes transcription to produce light

when quorum sensing signals are abundant

Operon that is on

transcription is happening, RNA polymerase can reach the genes and mRNA is being produced

Operon off

RNA polymerase can not reach promoter, little to no transcription is happening

Vancomycin

antibiotic that can fight life threatening gram positive bacteria

kinase

adds a phosphate group to a molecule

Two component system

in an example of vancomycin, the protein sensor senses the antibiotic is near. Which then tells the response regulator to change transcription which can lead to antibiotic resistance

Positive feedback

there is reinforcement for something the cell is doing right, they will continue to do it

quorum sensing gram + bacteria

there is a two component system

two component system is gram + bacteria

Gram + bacteria makes a peptide that is sent out of the cell, when there is a multitude of peptides out there they can attach back to the cell protein sensors allowing the response regulator to respond to the situation (probably to start forming a biofilm)

quorum sensing gram - bacteria

Diffusible (Al) can leave the cell and come back when there is a multitude outside of the cell. Allowing the response regulator to change and a biofilm to be formed

Microbes can deal with environmental changes by

gene regulation, genetic changes

Genetic changes can be classified as

mutations or horizontal gene transfer (cell receives new DNA)

Bacteria can fix mistakes bc

DNA polymerases can proofread and there is mismatch repair

DNA polymerase proofreading

the DNA polymerase can move in the opposite direction and delete base pairs to fix them and correct the mistake

If DNA polymerase doesn’t catch the mistake there is mismatch repair

Can remove a SECTION of DNA and replace it

to become a parent strand the process goes

Parent strand —> daughter strand —> methylation

Basal rate

rate of everyday

Mutagen

an external factor that will increase mutation rate such as UV light, carcinogens, etc.

Thymine dimer

two adjacently covalently bonded thymine groups due to UV sunlight (bad and is a mutation)

DNA is held together by

Phosphodiester bonds

nonsense mutation

changes to a stop codon

missense mutation

codes for a different amino acid in the same spot where the initial one was

mismatch repair involves

methylation patterns in DNA

Base excision repair

DNA glycosylase fixing one singular DNA base

SOS repair

is when DNA has been severely damaged

difference between mismatch repair and base pair excision

mismatch repair is when the wrong bases were paired together such as (C and T) but a base pair excision is when a base has been damaged and needs to be replaced.

in base pair excision

DNA polymerase 1 is what fixes the new strand with the fresh base

transduction

DNA is inserted through a bacteriaphage

bacteria that is competent

they can take bacteria from their surroundings

single stranded recombination

only one strand of DNA is changed, meaning the modified strand and the unchanged strand make new DNA together making one new strand of DNA that is modified and one new strand of DNA that is with the unchanged strands.

Prophage

virus that infects a bacterium and inserts DNA into the chromosome

Base excision repair mech

DNA glycosylase binds to damaged base and cuts it out, removes base, adds new base, and keeps the phosphodiester bond

inversion

segment of DNA breaks off, inverts 180, and attaches back on. Classes example is with salmonella which can produce two different flagella in order to stay alive

Translation happens in 3 steps

1. initiation

2. elongation

3. termination

an operon vs an activator/repressor

an operon is a segment of DNA, an activator is a DNA binding protein that can activate or repress transcription

Anticodon

on tRNA that recognizes codon on mRNA

With DNA replication

the two new strands of DNA have both a modified strand and the old OG strand

Null mutation

the gene product in inactivated and completely useless

progeny

offspring

second generation progeny

the 4 strands of DNA in the flow chart

reversion

back to the wildtype through mutation

vertical gene transfer

DNA is passed though replication resulting in a daughter cell

horizontal gene transfer

bacteria can acquire DNA not from its parent

negative evolution

there is mutations, but the environment forces mutations to phase out and restore to its original form

bottleneck event

there is a small group of bacteria that survives and the rest are based off of that small population

pan-genome

all genes found in the same species of bacteria

the formation of mitochondria proves the

endosymbiotic theory

bacteria phage, plasmids, and transposons

mobile genetic elements

Transposons

pieces of dna that can move from location in genome to another, aka jumping genes, needs something to help them move

Transformation, conjugation, and transduction

ways of horizontal gene transfer

transformation

DNA taken up by cells from the environment such as plasmids

virulent

viruses ability to cause disease

avirulent

non-harmful, unable to cause disease

transformation

process of importing naked DNA into bacterial cells.

in order for transformation to happen

must be under competency (strict conditions)

reasons for transformation

use DNA as food source, take up similar DNA to fix mistakes (how the mice died)

review for gram + transformation/quorum sensing

competence factor is released as a peptide, then when there is an abundance the peptide attaches to a sensor kinase (which adds a phosphor group), which then turns on the transcription

Griffith experiment and quorum sensing

the dead virulent cells DNA was released, the live avirulent cells senses the DNA (CF) and then starts the transcription for capsules

regulation of transcription

sometimes it is constitutive, but other times it is due to genotoxic stress, carbon sources, starvation, or communication

Conjugation

donor cell has a sex pilus (grapling hook) and mating bridge (cell to cell contact)

recipient cells in conjugation

typically receives a plasmid

F+

donor cell for conjugation

F- cell

recipient cell, lacking genotype

the mating bridge

brings the cells closer and that is when DNA is transferred, recipient cell becomes donor cell

oriT

sequence found in DNA on conjugative plasmids. It is the site when the relaxase enzyme make a nick of the DNA strand to begin plasmid transfer between bacteria

Hfr

genotype from donor plasmid is integrated into the bacteria chromosome (rare)

difference between DNA replication and generalized recombination

replication is making a copy of DNA, generalized recombination is DNA is exchanged

bacteria phage

a virus that effects bacteria

generalized transduction

Phage accidentally adds random bacteria DNA. Why? packaging mistake

Specialized transduction

bacteria specifically adds other DNA nearby. why? wrong excision

Rec A

bacterial protein that facilitates recombination

Hfr recipient

will be F-

prophage

DNA has entered the chromosome after a phage injected it (transduction)

composite transduction

contain genes in addition to the insertion sequences on both sides