Microbiology 302: Exam 2

Front 1

translation

Back 1

protein synthesis

Front 2

transcription

Back 2

rna synthesis

Front 3

theta structure

Back 3

bidirection DNA replication; forms a intermediate structure similar to the greek letter theta

Front 4

supercoiling

Back 4

twisting double stranded DNA to pack DNA
*positive: overwound
*negative: underwound (twisted about its axis)

Front 5

ss DNA binding protein

Back 5

prevent annealing of DNA during replication

Front 6

semiconservative replication

Back 6

two resulting double helices consist of one newly made strand and one parental strand

Front 7

rna primer

Back 7

short RNA needed to start DNA replication (3' OH)

Front 8

replisome

Back 8

dynamic replication proteins; pulls the DNA template
*DNA pol 3
*primase
*ssDNA binding protiens
*helicase

Front 9

proofreading

Back 9

Pol 1 and Pol 3 contain exonuclease (recognizes incorrect hydrogen-bonding)

Front 10

primase

Back 10

enzyme that synthesizes a short RNA stretch to begin DNA synthesis

Front 11

origin of replication

Back 11

250 bases recognized by DnaA (opens double helix), DnaB (helicase); DnaC (helicase loader)

Front 12

leading strand

Back 12

growing from 5' PO4 2- to the 3' OH

Front 13

lagging strand

Back 13

discontinous replication; okazaki fragments

Front 14

helicase

Back 14

unwinds double helix at replication fork (DnaB)

Front 15

DNA polymerase III

Back 15

main polymerizing enzyme
*sliding clamp
*strand elongation
*prooofreading

Front 16

DNA ligase

Back 16

seals nicks in DNA (ligA, ligB)

Front 17

DNA polymerase I

Back 17

excises RNA primer and fills in gaps
*proofreading
(polA)

Front 18

DNA gyrase

Back 18

unwinds supercoils ahead of replisome (gyrAB)

Front 19

aminoacyl tRNA synthetase

Back 19

recognize both the cognate amino acid and the specific tRNA for that amino acid

Front 20

degenerate code

Back 20

no one-to-one correspondence between "words" and code

Front 21

elongation factors (EFs)

Back 21

aid in translation; help move the tRNA within the replisome

Front 22

heat shock proteins

Back 22

help refold proteins; chaperones are one example

Front 23

initiation complex

Back 23

30S subunit -> mRNA formylmethionine tRNA -> initiation proteins (GTP needed); 50S added last

Front 24

Shine Dalgarno

Back 24

sequence that directs the ribosome to the proper start site; interacts with 16SrRNA

Front 25

nonsense codons

Back 25

stop codons

Front 26

polycistronic mRNA

Back 26

produced by operons; encodes several polypeptides

Front 27

polysome

Back 27

translation by several ribosomes on a single mRNA

Front 28

primers

Back 28

oligonucleotide to which DNA polymerase can attach the first deoxyribonucleotide during replication

Front 29

promoter

Back 29

site on DNA to which rNA polymerase binds to commence transcription; contains pribnow box in prokaryotes and is recognized by the sigma factor

Front 30

rho-dependent terminator

Back 30

uses specific protein factor (E. Coli = Rho) bnds tightly to RNA and moves down the chain towards complex; at specific sequece RNA pol pauses and Rho causes release

Front 31

Rho-independent terminator

Back 31

governed by specific base sequences; often a GC-rich region, it forms a stem-loop structure that breaks off

Front 32

RNA polymerase core enzyme

Back 32

four different subunits making up RNA polymersase (does not include sigma factor)

Front 33

signal recognition particle

Back 33

15-20 residues at the beginning of the protein molecule indicate the need for membrane insertion by this particle

Front 34

Svedberg units

Back 34

refer to the sedimentation coeffiecients of ribosome subunits (30 and 50S) or intact

Front 35

tmRNA

Back 35

frees stalled ribosomes; attaches and presents a stop codon

Front 36

translocation

Back 36

movement along the ribosome by tRNA

Front 37

histones

Back 37

positively charged proteins that neutralize the negative charge of DNA; wind DNA

Front 38

histones

Back 38

positively charge proteins that neutralize the negative charge of DNA; wind the DNA into nucleosomes

Front 39

TBP

Back 39

TATA binding protein (18-27 nucleotides upstream of the transcriptional start site)

Front 40

INIT

Back 40

initiator element; TFB binds to both this and TATA

Front 41

activator protein

Back 41

positive control; helps RNA polymersase recognize the promoter and begin transcription (by bending DNA or directly acting upon)

Front 42

AHL

Back 42

chemical produced by cells for communication; used in quorem sensing

Front 43

alarmones

Back 43

triggers stringent response; (p)ppGpp synthesized by RelA
*inhibit tRNA and rRNA synthesis
*activate biosynthetic operons for amino acids
*inhibit DNA synthesis

Front 44

antisense RNA

Back 44

blocks transcription of mRNA by forming double stranded RNAs

Front 45

attenuation

Back 45

premature termination of mRNA synthesis (after initiation of transcription)
example-tryptophan

Front 46

autoinducer

Back 46

signal molecule; diffuses freely across the cell envelope in either direction, binds to specific activeator protein

Front 47

catabolite repression

Back 47

syntheses of unrelated, primarily catabolic enzymes are repressed when cells are grown in a medium that contain glucose ("glucose effects")

Front 48

CRP or CAP

Back 48

cyclic AMP receptor protein or catabolite activator protein; the catabolite repressible enzyme is expressed only if CRP protein binds to DNA in the promoter region

Front 49

DnaK

Back 49

part of heat shock response in E. Coli; prevents aggregation of newly synthesized proteins and stabilizes unfolded proteins

Front 50

heat shock response

Back 50

largely controlled by alternative sigma factors; refolds unfolded proteins by activating DnaK

Front 51

helix turn helix

Back 51

two segments of polypetide chain with an a-helix secondary structure connected by a short "turn"
*makes up many repressor proteins (lac,trp)

Front 52

zinc finger

Back 52

protein domain of DNA binding protein found often in eukaryotes; binds zinc ion "finger" = a helix that binds to DNA

Front 53

leucine zipper

Back 53

contain regions in which leucine residues are spaced every 7 amino acids

Front 54

inducers, corepressors

Back 54

substances that induce, repress enzyme activity on DNA

Front 55

leader

Back 55

encodes a short peptide that can fold up in attenuation (if folded one way, it allows synthesis, the other marks for destruction)

Front 56

operon

Back 56

one or more genes transcribed into a single RNA and under the control of a single regulatory site.

Front 57

regulon

Back 57

a series of operons controlled as a unit

Front 58

response regulator protein

Back 58

one of the member of a two component system; a protein that is phoshorylated by a sensor kinase and then acts as a regulaor often by binding to DNA

Front 59

sensor kinase protein

Back 59

one of the members of a two component system; a protein that phosphorylates itself in response to an external signal and then transfers teh phophoryl group to a response regulator protein

Front 60

riboswitches

Back 60

RNA doman, that binds a specific small molecule and alter its secondary structure; this in turn controls translation of mRNA

Front 61

stringent response

Back 61

global regulatory control that is activaged by amino acid starvation or energy deficiency

Front 62

RpoH

Back 62

alternative sigma factor is broken down by proteases at normal temperature (stimulated by binding of the chaperonin to RpoH); when Dnak is removed to fold proteins, the heat shock genes are transcribed