Prokaryote Biology Exam 3

DnaA

- activates INITIATION of replication

- needs to be in its active form (DnaA-ATP)

- binds to the origin of replication (oriC)

regulation of levels of DnaA

-cell mass

-growth rate

-cellular health

gene

region of DNA encoding a particular polypeptide chain or functional RNA

operon

a collection of genes that are transcribed into a single RNA

promoter

the site on DNA where RNA polymerase binds and begins transcription

--> non coding DNA sequence UPSTREAM of structural gene (coding sequence) required for transcriptional initiation

cistron

functional unit of RNA containing information from a single gene

polycistronic

RNA produced from an operon containing information from more than one gene

open reading frames (ORF)

DNA sequence predicted to encode a protein, can be translated, and has start/stop codons

codon

sequence of 3 bases in mRNA that code for a specific amino acid

start codon

special codon that signals the start of translation (AUG)

stop codon

do not encode an amino acid and trigger that end of translation (UAG, UAA, UGA)

DnaB

-helicase enzyme

-requires ATP (energy)

Primase

-RNA polymerase

-synthesizes RNA primer

%GC and Tm

-Tm (midpoint temperature) is proportional to the %GC content in a thermal denaturation graph

-the absorbance at 260 nm increases going from double strands to single strands (*melting)

-sigmoidal shape graph

oriC

origin of replication (during initiation for DNA replication)

purine

adenine and guanine (A,G)

pyrimidine

Thymine, cytosine, and uracil (RNA) (T,C,U)

DNA ligase

-seals nick in DNA that have adjacent 5'-P and 3'OH (makes the last phosphodiester bond during the nick repair

-requires energy

-most ligases use ATP

Regulon

a group of genes/operons that are coordinately regulated

ter sequences

termination sequences that trap/block replication forks

Tus

(terminus utilization substance)

-binds to ter sequences

-blocks DnaB (helicase)

sigma factor

- transcription initiation

-ONLY in bacteria

-binds to RNA polymerase and recognizes the promotor

-key to initiation

-when bound to RNA polymerase = holoenzyme

TBP

"TATA binding proteins"

- recognizes TATA box sequence

TFB

"Transcription factor B"

-recognizes BRE (B recognition element) sequence

Two types of termination signals during transcription

Rho-dependent and Rho-independent

Rho-dependent

-relies on protein called Rho

-strong pause site at 3' end of the gene

-sequence specific

Rho-independent

-requires a GC rich region of RNA

-and 4-8 consecutive U residues

-sequence specific

peptidyl transferase

-in ribosome

-makes the peptide bonds between the amino acids to make a polypeptide

Shine Dalgarno sequence

-TRANSLATION initiation

-purine rich (A and G)

-Ribosomal binding site (RBS)

-in bacteria and archaea

fMet

-start codon in bacteria

-formylmethionine

Chaperons/chaperonins

assist in protein folding

(DnaK, DnaJ, GroES, GroEL --> helper proteins/heat shock proteins)

RecA

-protein that mediates recombination

-found in all three domains

-recognizes single stranded DNA

Transformation

the process of importing free DNA into cells (ex: griffith experiment)

Conjugation

"bacterial sex"

-requires cell to cell contact

-requires pilus (sex pilus)

-F plasmid (plasmid encoded mechanism)

F plasmid

-fertility plasmid

-components: Tra region, oriT, IS3, IS2, oriV

oriT

origin of transfer during conjugation

IS

insertion sequences

phage

a virus that infects prokaryotes (bacteriophage)

lytic

a viral life cycle in which the virus lyses the cell releasing progeny

virulent phage

phage that lyses (kills) host cell after infection (nontemperate phage)

lysogeny

a viral life cycle in which the viral genome integrates into and replicates with the host genome (can become lytic)

temperate phage

phage capable of lysogeny

prophage

a phage genome integrated into the host genome

lysogen

a prokaryotic cell that harbors a prophage

phage conversion

alteration of a host cell by lysogenization

Examples:

-lysogens become immune to further infect by the same type of phage

-corynebacterium diphtheriae

transducing phage particle

-during generalized transduction

-does not degrade host DNA or lyse cell

-allows transfer of any gene

-low frequency and low efficiency

restriction endonucleases

allows enzymatic cleavage (restriction) of alien DNA

DNA methylase

protective methylation (modification) of host DNA

CRISPR

"clustered regularly interspaced short palindromic repeats"

- and adaptive system

-consist of repeats and spacers that do not encode proteins

-a primitive microbial immune system

three stages of CRISPR

1. spacer acquisition

2. crRNA processing

3. effector stage

translocasome complex

transfers ssDNA into cell

-used by naturally competent gram positive bacteria

anticodon

hydrogen bonds with the mRNA codon specifying an amino acid (reading the codon)

3' (acceptor) end

binds the amino acid

charged tRNA

-each tRNA must be charged with the proper amino acid before it encounters the ribosome

-charged by using aminoacyl-tRNA synthetases (20 of these for each amino acid)

sense strand

coding strand (5' to 3")

antisense strand

template strand (3' to 5')

replisome

forms during initiation stage of DNA replication

-forms before DnaB unwinds DNA

Catenane

???

"catenane resolution"

-during termination stage of DNA replication

rolling circle replication

unidirectional plasmid replication

phosphodiester bond

nucleotide

nucleoside

deoxyribose

ribose

okazaki fragments

-in elongation stage of DNA replication (replication fork)

-present in the lagging/discontinuous strand (5' to 3')

integrase

Merodiploid

RepA

Inverted repeats

mRNA

-encodes protein

-thousands of types

-1500 nt

- 3 to 5 min

rRNA

-synthesizes protein

-three types

-5S = 120 nt; 16S = 1500 nt

-hours

tRNA

-shuttles amino acids

-27 types (set) --> 86 genes

-80 nt

-hours

sRNA

-controls transcription and translation

-20 to 30 types

-less than 100 nt

-variable half life

tmRNA

-free ribosomes on damaged mRNA

-about one type per species

-300 to 400 nt

-3 to 5 min

catalytic RNA

-enzymatic reactions

-size varies

-3 to 5 min half life