MIC 102 Midterm 2

MIC 102 Midterm 2 Bragg

pyrimidine

nucleotide bases with one ring

purine

nucleotide bases with two rings

3' OH end (5' phosphate group of new nucleotide)

To which end of the growing strand are nucleotides added by DNAP?

oriC sequence

Where does replication begin?

DNA polymerase III

Polyermase that runs replication 5' to 3'

DNAa

\_______ binds to DNA at oriC sequence and "melts" DNA in order to open up and expose strands

oriC

region of DNA that is AT rich

SSBps

molecules that bind to DNA and hold it open after they have been "melted" by DNAa

AT bonds

nucleotide basepairs with 2 hydrogen bonds

CG

nucleotide basepairs with 3 hydrogen bonds

dnaC

loading factor for helicase DNAb

dnaB

helicase that recruits replisome proteins once loaded by dnaC

dnag

RNA polymerase that makes primers needed to start synthesis

dnaa

very important protein for controlling initiation; oriC has multiple binding sites that all need to be filled before cell can initiate
-need to time replication so there's enough ATP and also cell cycle growth

SeqA

protein that sequesters the origin: keeps replication from happening by blocking dnaA from binding to newly methlyated strands
-may also associate new origin to spot on cell mebrane

true

Newly synthesized strands are not methylated immediately and are hemi-methylated, which causes SeqA to have a high affinity and blocks dnaA binding site to initiate replication (T/F)

Elongation

DNAP 3 moves quickly on leading strand and adds bp to 3' end

RNAase H

removes RNA primer (made by DNAg) from lagging strand

DNA P1

fills in nucleotides on lagging strand between nucleotides proofreading as it goes

DNA ligase

fills in gaps between Okazaki fragments

replisome

protein machinery that controls replication made up of the proteins

DNA gyrase

as replisome moves forward, DNA ahead of it turns into positive super coils and this protein is needed to unwind and untangle the chromosome

ciproflaxin

broad spectrum antibiotic that targets DNA gryase

Tus, DnaB

\_______ protein binds to the ter sequence and causes termination by inhibiting \_____

exonuclease

DNA P 3 has \____ activity that allows it to proofread bases and remove mismatches

mismatch repair system, muts, mutl, muth, muth, Pol III

In the \_____, \_____ binds at mismatched sites and \_____ and \_____ are recruited. They move across the DNA until they hit a hemi-methylated GATC site. Then \____ cuts the new non-methylated strand and chews away until it hits the mismatch. \_____ comes and fills the nts back in.

Muk

\_____ proteins bind distant DNA sequences and pull them back together using ATP

rnap, 5, sigma

\____ enzyme has \_____ subunits and requires a \___ factor to initiate transcription

archaea

\____ rnap has up to 14 subunits and looks much more similar to eukaryotic rnap

sigma factor

bacterial transcription factor that enables binding of RNAP to gene promoters, each type has different favored sequence that gives specificity to RNAP

initiation, sigma factor, RNAP

in \____, \______ binds to \______ allowing it to recognize the promoter sequence

transcription

\____ will start and fail several times before RNAP can escape the promoter sequence and drop the sigma factor to begin elongation

NusA

helps RNAP get through hairpin loops (GC rich regions) which could stall transcription

polycistronic

bacterial mRNA is \_____, meaning multiple peptides can be encoded by the same transcript

termination

\__________ sequences cause the formation of hairpin loops which stall RNAP

rho dependent

in \________ termination, rho protein binds to the RNA and moves toward RNAP, catching up to it when it stalls and causing it to dissociate (ribosomes keep rho from binding if they are already present--\> control)

false

rRNA and tRNA are unstable while mRNA is stable (T/F)

rRNA

make up most of transcripts in cell, organized into operons cut by ribonucleases that self assemble into ribosomal subunits

tRNA

type of transcript that needs more modiciation, often add terminal CCA

DHU loop

part of tRNA recognized by aminoacyl-tRNA synthetase to add amino acid

anticodon loop

complementary to mRNA sequence, gives codon specificity

t-loop

helps bind tRNA to ribosome

variable loop

alters general shape and structure of tRNA

riframpin

binds to RNAP and prevents formation of phosphodiester bonds so elongation is not possible, broad spectrum antibiotic

amino-acyl tRNA synthetase

enzyme: add ATP and amino acid, then release AMP to bind amino acid and charge tRNA to "load" enzyme

wobble base

there are 20 aa t-rna synthetase enzymes that each have an anticodon for their specific amino acid with a \_____ for non specific pairing of the third base

70S, 50S, 30S, 80S, 60S, 40S

the prokaryotic ribosome is \_____, with a \_____ large subunit and \_____ small subunit in comparison to the eukaryotic ribosome which is \______ with a \_____ large unit and a \_____ small unit

initiation factors

IF1 and IF3, prevent 30S from binding to 50S and IF3 helps 16srRNA bind to SD sequence

shine delgarno sequence

RNA sequence that helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning ribosome with the start codon

IF3

helps 16s rRNA bind to SD sequence

IF2GTP

loads initiator tRNA (fmet) onto start codon AUG and kicks out IF3, subsequent hydrolysis of GTP adds on large subunit (50S) and kicks off other IF factors

codon

3 nucleotides that specify amino acid

AUG, UAA, UAG, UGA

translation begins at the start codon \____ and ends at the stop codons \____, \_____ or \_____

A site

charged tRNA's ARRIVE here (aminoacyl)

P site

has tRNA with growing PEPTIDE chain (peptide)

E site

uncharged tRNAs EXIT (empty)

Ef-Tu

elongation factor that uses the hydrolysis of GTP to load A site with charged tRNA (used up ones with GDP recycled (rephosphorylated) and used again)

23S rRNA

ribozyme that catalyzes peptide bond formation between amino acids in A and P site, chain added onto A site

EF-G

elongation factor that uses hydrolysis of GTP to enter A site and push tRNAs through to the next site, can also be recycled

P

When Ef-G enters the A site, the uncharged tRNA will enter the E site and exit while the growing peptide chain moves into the \____ site

protein termination, stop codon, stalls, hydrolyze, dissociate, IF1, IF3

\________ occurs when the ribosome finds a \____, which enters the A site and the ribosome \______. This releases factors that \______ the tRNA peptide bond, release the peptide and cause the ribosome to \_______. \______ and \________ bind to the small subunit to prevent reassociation and the cycle starts over

chaperones

proteins made to properly fold other proteins including trigger factor, DNAk, GroEL/GroEs

first cell membrane

amphiphatic lipids self assemble--\> self organizing micelle--\> vesicle--\> protocell--\> divide

acyl carrier proteins

involved in phospholipid synthesis, prevent hydrophobic fatty acids from accumulating in cytoplasm while they're being made

exporting proteins

process where signal sequence is cleaved during transport

SRPs

bind signal sequences with protein ffh and rna ffs in order to carry hydrophilic peptides to secretion machinery to become part of membrane

sec system

system used to transport periplasmic and outer membrane as well as secreted proteins, needs ATP/PMF

secA

part of sec system, binds to signal sequence

secB

chaperone protein in sec system that prevents folding before protein has passed through channel

LepB

signal peptidase that cleaves peptide during transport in sec system

Skp

chaperone that holds peptide in periplasm

Bam complex and Sur A

transports peptide into outer membrane and folds with beta barrel assembly complex

degP

degrades misfolded mistakes in sec system

Type III secretion

secretion system that is not sec dependent, commonly found on plasmids and very useful for virulence (shigella, salmonella, e.coli etc)
-proteins inserted into cell

Type IV secretion

secretion system that is also not sec-dependent and evolved from bacteriophage injection mechanisms, can target prokaryotic and eukaryotic cells and found in 1/4 of bacterial species

NAG, NAM, UDP, attached, PBPs

in cell wall synthesis, \_____ and \______ are made in cytoplasm bound to \_____ and pentapeptide. These enter the UDP cycle and are \________ via a peptide crossbridge (becoming a disaccharide) and moved across the membrane where \______ polymerize it into peptidoglycan.

gram negative

in \______ cell wall synthesis liporoteins connect cell wall to outer membrane

gram positive

in \_______ cell wall synthesis some species lose murein at the outside surface of the cell wall and it must constantly be replaced

PBP

penicillin binding protein

transglycolase

adds NAM-NAG into peptidoglycan polymer

transpeptidase

adds peptide crosslinks, inhibited by penicillin and beta lactam antibiotics

LPS

assembled in inner membrane and flipped by MsbA, transport pathway exports through serious of proteins (LptB, F, G, C, A, D, E) through cell wall to outer membrane

FlgM

inhibits production of flagellin

FlgM inhibitor

secreted by basal body once assembled to translate flagellin for filament

capsules

attached to cell envelope, can be made by exporting pre-formed polymers or by secreting polymers and ploymerizing during transport or outside cell

auxotrophs

lose ability to synthesize a building block or other growth factor

temperature sensitive

mutants that lose functions at particular temperatures

conditional lethal

unable to grow in a particular environment in any media

point mutation

change in a base pair

frameshift

mutation where nucleotides are deleted or inserted causing whole reading frame to shift

replication

formation of supplemental copy of DNA

deletion

loss of segment of DNA

translocation (insertion)

movement of fragment of DNA from one location to another

inversion

reversal of the order of segment of DNA

physical, chemical

Spontaneous mutations are rare (proofreading etc) and other factors like \_____ agents (ionizing radiation) or \______ agents are more likely to cause mutation.

enrichment

grow mutants in a medium without component you want to find in auxotrophs

screening

take colonies from master plate and restreak onto medium without component; colonies that can't grow on new medium are auxotrops

mobile elements

pieces of DNA that can move themselves around a chromosome or between chromosomes
-each element has transposase gene and inverted repeats and can place themselves in side of a gene

insertion sequence elements

minimal state transposon, has inverted repears

non composite transposons

minimal state transposon plus drug resistance genes