Transcription

1. Initiation

Bind of the RNAP to the beginning of the gene, followed by opening the DNA helix and start of RNA synthesis

Transcription

Transcription (DNA to RNA) is carried out by RNA polymerase.

• RNA polymerase uses DNA as template.

• RNA precursors are ATP, GTP, CTP, and UTP.

• chain growth 5′ to 3′, just as in DNA replication

• only one strand transcribed
• no priming needed

Which statement is TRUE regarding protein synthesis?

The 23S rRNA catalyzes peptide bond formation in the growing polypeptide chain.

Transport to Periplasm via TAT system

used for folded proteins

• Signal sequence RRXFXK • TAT System
• Powered by Proton Motive Force (PMF)

Transport of synthesized protein to periplasm

Sec dependent

protein wraps around SecB--> goes over to SecA and SecYEG(embedded in membrane) -->protein is pushed through SecYEG with help from SecA and ATP and goes into periplasm -->LepB cleaves the signal sequence -->protein is folded in periplasm

SRP

Signal Recognition Particle

Transport to membrane: Protein is synthesized & localized

Protein is unfolded

polysome

clusters of ribosome bound to an mRNA

Translation

3. Termination

• Stop codon (UAA, UGA, UAG)
• release factor (either RF 1 or RF 2) enters A site, no tRNA for stop codons
• Peptidyltransferase is activated and releases the completed protein from tRNA in the P site
• Ribosome recycling factor (RRF) & EF-G undocks 50S from 30S
• IF3 removes uncharged tRNA & mRNA

Translation

2. Elongation

• EF-Tu-GTP binds tRNA, binds A site, GTP hydrolysis
• Peptidyltranferase makes peptide bond
• EF-G-GTP, hydrolysis of GTP, tRNA moves to P site

Translation

1. Initiation

Specific factors:

-E.coli- IF1, IF2 & IF3
-M. jannaschii- 6 IF proteins

An operon is a useful genetic element, because it

allows coordinated expression of multiple related genes in prokaryotes.

Transfer RNA (tRNA) molecules

function to transfer the correct amino acids to the ribosome during translation.

Shine–Dalgarno sequence

(5'-AGGAGGU-3')

Initiation is at any Shine– Dalgarno sequence; the mRNA can therefore be a polycistronic mRNA that codes for several polypeptides.

What is an operon and why is it beneficial to link expression of certain genes?

An operon is a cluster of genes that are under the control of a single promoter and are therefore cotranscribed as a single, polycistronic mRNA molecule. This arrangement allows related genes to be expressed in a coordinated fashion

structure of an ORF

Ribosomal binding site-Start codon-coding sequence-stop codon

Global regulatory systems include all of the following EXCEPT

transformation

anaerobic respiration

amino acid synthesis

heat shock response

amino acid synthesis

Attenuation is a type of regulation that can control

transcriptional activity exclusively

The function of a kinase is

phosphorylation

Which of the following do NOT bind to the promoter sequence during regulation?

activators

inducers

None of these bind directly to the promoter sequence

repressors

none of these

The lac operon is an example of ________ control in which the presence of an ________ is required for transcription to occu

negative / inducer

recombination-associated chi sites accumulate in the _____ strand

leading

Gene strand bias results in more genes in the _____ strand

leading

The Par system is necessary for

distribution of genetic material in replicating Caulobacter.

GcrA

Promotes growth of stalk, cell elongation and division

• GcrA levels rise and promotes elongation phase of chromosome replication, cell division & growth of the the stalk on immobile daughter cell
• GcrA levels fall, and high levels of CtrA reappear in the daughter cell

CtrA

Transcriptional regulator for flagellar synthesis; represses GcrA expression & DNA replication

• CtrA is activated by phosphorylation • CtrA~P activates genes need for flagella & represses synthesis of GcrA & • CtrA~P inhibits the initiation of DNA replication by binding the origin.
• CtrA gets degraded by a specific protease resulting in increasing DnaA levels
• Absence of CtrA allows for DNA replication to initiate • DnaA is then also degraded by a protease

Caulobacter crescentus

• Gram-negative
• α-proteobacteria
• Aquatic bacterium with differential life styles – Swarmer – Stalked/attached
• Good to study cell cycle in

The curved-rod shape typical of Caulobacter is due to the proteins ____ and ______

crescentin and MreB

• Can phenotype change without a change in genotype?

1. Phenotypic changes often occur without a genotypic change when an organism is placed in a different environment. This could be due either to changes in gene expression or abiotic (physical or chemical) factors that alter a gene product.

• Does the phenotype of an organisms change when the genotype changes?

1. Phenotypic changes do not always accompany genotypic changes. Genotypic changes that do not alter the phenotype could be due to point mutations that do not result in changes to the primary structure (amino acid sequence) of a protein (i.e., silent mutations)

Phenotype

• The observable characteristics of an organism based on its genetic composition.

• Genotype

1. The complete genetic makeup of an organism. Its precise determination would require genomic sequencing

Replication errors --> correction and repair

-Proofreading (make sure A & T together and C & G together)

-Thiamine dimer (detects damaged bases -->cuts nucleotides-->replaces nucleotides that were cut-->nucleotide linkage)

septation is directed by ____

FtsZ

OriC

origin of replication

After DNA helices has moved approx. _____ bases, another ___ primer is synthesized on each lagging strand

1,000

RNA

G & C have ___ hydrogen bonds

3

A & T have ___ hydrogen bonds

2

proofreading begins at time of _____ insertion

nucleotide

Tus protein

binds terminus and blocks progress of the replication fork

DNA ligase

ligA, ligB

seals nicks in DNA

DNA polymerase I

polA

excises RNA primer and fills in gaps

dnaQ

proofreading subunit

dnaE

polymerase subunit

strand elongation

Dimerization subunit (Tau)

dnaX

holds together the 2 core enzymes for the leading and lagging strands

holA-E

clamp loader

loads Poly III onto sliding clamp

processivity

an enzymes ability to catalyze consecutive reactions w/o releasing its substrate

dnaN

sliding clamp (beta clamp)

holds Poly III on DNA

involved in processivity; processivity factor for DNA polymerase

binds DNA polymerase III and prevents dislocation

exonuclease activity

3' to 5'

DNA polymerase III

main polymerizing enzyme; the main replication polymerase

subunit for proofreading (dnaQ)

dnaG

Primase

priming; primes new strands of DNA

RNA primer synthesis

rifampin resistant RNA polymerase

ssb

single-strand binding protein

cover and protect the unreplicated single strand

dnaB

helicase

unwinds double helix at replication fork

prepriming

DNA-dependent rNTPase

dnaC

helicase loader; loads helicase at origin

open the DNA helicase protein ring and place the ring around the single-stranded DNA at the origin. Loading of the DNA helicase leads to the release of the helicase loader

dnaA

origin binding protein; binds oriC

binds origin of replication to open double helix

initiation

dnaB loading

binding of dnaA leads to the strand separation at the 13-mer repeats

DNA gyrase

gyrAB gene

replaces supercoils ahead of replisome

one helical turn has ____ base pairs

10

Pyrimidines

1 ring

thymine and cytosine

Purines

2 rings

Adenine and Guanine

MinD

required for correct placement of division site