Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Fall 2014 > Microbiology Exam 2 > Flashcards

Microbiology Exam 2 Flashcards

1
Q

DNA is always synthesized

A

-in 5’ to 3’ direction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Watson and Crick model

A
  • AT pairing has 2 hydrogen bonds
  • CG pairing has 3 hydrogen bonds
  • strands run antiparallel
  • 1 helical turn = 10 bp = 3.4 nm
  • major groove = 2.2 nm
  • minor groove = 1.2 nm
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

DNA replication

A
  • semi-conservative replication
  • copies information from one strand to a new, complementary strand
  • melt double-stranded DNA
  • polymerize new strand complementary to each melted single strand
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

topoisomerase

A
  • modulate supercoiling of the DNA
  • binds to DNA, breaking one or both strands and passes the DNA strands through the break before resealing it. The enzyme holds the cut ends of the DNA so they don’t rotate
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

topoisomerase type I

A
  • cuts one strand and passes the other strand through the break before resealing the cut
  • changes DNA one supercoil at a time
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

topoisomerase type II

A
  • cuts both strands and passes two other strands from somewhere else in the DNA or even another DNA through the break before resealing it
  • change DNA two supercoils at a time
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Primosome

A
  • DnaA and DnaB

- structure of proteins that initiate replication at the origin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

DNA helicase

A
  • DnaB
  • binds with DNA helicase loader (DnaC)
  • unwinds the helical DNA at replication forks
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Primase

A
  • DnaG
  • lays down the primers that are necessary for DNA polymerase activity
  • primers are composed of RNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

DNA polymerase III

A

-the polymerase that does the bulk of the DNA replication using its 5’ to 3’ polymerase activity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

DNA polymerase I

A
  • the polymerase that removes the RNA primers (after they have done their job of initiating DNA replication) using a 5’ to 3’ exonuclease activity.
  • then uses its 5’ to 3’ polymerase activity to fill in the resulting gaps
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

RNase H

A

-removes RNA strands of a DNA:RNA double helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

DNA ligase

A
  • seals nicks in DNA by linking up 3’ hydroxyl groups with adjacent 5’ phosphate groups
  • connects DNA to DNA but not DNA to RNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

SSB, single-strand DNA binding protein

A
  • binds single-stranded DNA at the replication fork and physically blocks potential hybridization
  • makes sure that the DNA is single-stranded when the polymerization machinery is ready to replicate it
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

DNA gyrase, a topoisomerase

A
  • puts swivel in DNA which allows strands to rotate and relieve strain of unwinding
  • adds negative supercoils
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

5’ > 3’ polymerase activity for DNA synthesis

A
  • DNA pol I

- DNA pol III

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

5’ > 3’ exonuclease activity for removal of RNA primer

A

-DNA pol I

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

3’> 5’ exonuclease activity for proofreading

A
  • DNA pol I

- DNA pol III

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

replication fork

A

-the structure where the two strands are separated and the new synthesis is occurring

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

leading strand

A

-synthesis is occurring in the 5’ to 3’ direction along the 5’-3’ strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

lagging strand

A
  • synthesis is occurring in the 5’ to 3’ direction along the 3’-5’ strand
  • polymerase III is released and needs to reassemble ahead at the next RNA primer
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Okazaki Fragments

A
  • initiation of DNA replication on the lagging strand is primed by a primase synthesizing an RNA primer
  • lowers mistakes using RNA primers
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

DNA replication

A
  • semiconservative replication
  • copies information from one strand to a new, complementary strand
  • melt double-stranded DNA
  • polymerize new strand complementary to each melted single strand
24
Q

Replication begins at oriC

A
  • DNA melts at oriC

- polymerization follows melting around the chromosome

25
Q

DNA helicase melts DNA

A
  • loader places helicase at each end of origin

- one helicase moves in each direction to copy genome

26
Q

Helicase recruits primase

A
  • primase begins replication
  • RNA primer forms 3’OH for DNA to attach
  • evolutionary remnant?
  • 1st cells thought to use RNA, not DNA
27
Q

Primer recruits clamp loader to each strand

A

-clamp binds DNA polymerase III to strand

28
Q

Polymerase proceeds 5’–>3’ on each strand

A
  • energy for polymerization comes from phosphate groups on added base
  • must add new base to 3’OH of a chain
  • new nucleic acid grow to extend 3’ end
29
Q

Clamp loader

A
  1. coordinates the position of Pol III on each strand
  2. since lagging strand is synthesized in opposite direction of the replication fork it is synthesized in a noncontinuous fashion
  3. new clamps have to be loaded on the DNA to facilitate the activity of Pol III that is synthesizing the lagging strand
  4. leading strand only needs the clamp loaded once to facilitate the activity of Pol III that is synthesizing the leading strand, since synthesis is continuous.
30
Q

RNase H removes primers

A
  • one primer for each leading strand
  • many primers on lagging strands
  • gaps filled in by DNA polymerase I
  • ligase seals nicks
31
Q

Both forks move to ter sites

A
  • movement is simultaneous
  • opposite directions until both meet again at terminus
  • replisomes are actually stationary
  • DNA is threaded through the rplisomes
32
Q

Termination sites

A
  • counterclockwise trap and clockwise trap

- coordinates dismantling of the replication fork and replisome

33
Q

Low-copy-number plasmids

A
  • one or two copies per cell

- segregate similarly to chromosome

34
Q

High-copy-number plasmids

A
  • up to 50 copies per cell
  • divid continuously
  • randomly segregate to daughter cells
35
Q

Plasmid genes

A
  • advantageous under special conditions
  • antibiotic-resistance
  • gene encoding resistance to toxic metals
  • genes encoding proteins to metabolize rare food sources
  • virulence genes to allow pathogenesis
  • genes to allow symbiosis
36
Q

Determining DNA base sequence

A
  • restriction enzymes cuts reveals location of specific DNA sequence
  • normally protect bacteria from viral DNA
  • PCR uses short oligonucleotides, primers that find complementary sites, that rapidly amplifies DNA segment
  • archaeal enzyme synthesizes DNA
  • Sanger metod determines sequence up to 1000 bases
37
Q

Whole-genome sequencing

A
  • break genome into thousands of pieces
  • determine sequence of many short pieces
  • computer determines sequence overlap to recreate entire genome sequence
38
Q

RNA polymerase

A
  • large molecular machine
  • 4 proteins in one complex: alpha, beta, beta prime, omega
  • binds DNA, reads sequences
  • polymerizes RNA
39
Q

Sigma factor

A
  • guides RNA polymerase to target DNA sequence
  • sigma70: guides RNA polymerase to most genes
  • sigma32: active when cell is stressed by heat; heat-shock response
  • Bs sigma32: active when cell is stressed by heat
40
Q

Transcription Initiation

A
  • sigma factor binds core RNA polymerase forming RNA pol holoenzyme
  • RNA pol binds promoter 10 & 35 bp upstream of TSS
  • polymerase unwinds DNA at promoter; open complex
  • sigma factor released
41
Q

Transcription elongation

A
  • core pol adds RNA to 3’ end
  • energy for addition comes from base (NTP)
  • mRNA has same sequence as non-template strand (U not T)
  • complementary to template strand
42
Q

Transcription termination:

Rho-dependent

A
  • pol slows at pause site (GC-rich sequence) forms stem loop

- rho protein (factor) chases RNA pol to knock it off

43
Q

Transcription termination:

Rho-independent

A
  • U residues downstream of pause site
  • stem loop binds to RNA pol to loosen interaction to DNA
  • series of A bases forming week AU interaction knocks off RNA pol
44
Q

snRNA

A
  • small nuclear RNA

- mRNA splicing in eukaryotes and archaea

45
Q

miRINA

A
  • micro RNA
  • interaction with mRNA and DNA to inhibit functionality
  • blocks translation and transcription in eukaryotes and prokaryotes
46
Q

tRNA

A
  • 61 codons to 20 amino acids and 3 codons signal stop
  • aminoacyl-tRNA transferase adds amino acid to tRNA
  • requires energy of ATP to AMP
  • anticodon loop interacts with codon
47
Q

Ribosome

A
  • protein polymerase
  • 2 subunits, 52 proteins, 3 rRNAs
  • 30S + 50S = 70S
48
Q

Translation initiation

A
  • 30S ribosome bound to IF3 (to prevent binding to 50S) attaches to start site, AUG, in the P site
  • IF3, blocks 50S and facilitates interaction to a sequence in RNA to initiate tranlation (with fMEt tRNA-IF2-GTP)
  • kicks off IF3 to bind 50S
  • IF1, IF2, and IF3 are removed
49
Q

Translation elongation

A
  • EF-Tu-GTP enters A site and amino acids bind via peptidyltransferase
  • EF-G-GTP shifts 50S forward one codon (translocation)
  • once 30S follows, EF-G-GTP is removed and A site is open
50
Q

Translation termination

A
  • stop codon reaches A site
  • protein release factor enters A site, releasing protein
  • RF3 removes protein release factor
  • RRF-GTP enters A site and unlocks the ribosome
  • IF3 rebinds to 30S to prevent 50S to bind
51
Q

Coupling of Transcription and Translation

A
  • ribosomes bind mRNA while mRNA is still being created

- advantage of not having a nucleus

52
Q

Protein modification

A
  • fMet removed from N-terminus
  • phsophoryl groups added
  • methyl groups added
  • adenylate (addition of adenosine)groups added
  • may be cleaved or degraded by proteases
  • may be refolded by chaperone
53
Q

Protein folding

A
  • many proteins fold spontaneously
  • -GroEL-GroES complex, barrel shaped, refolds denatured proteins that fit into center, using ATP
  • DnaK protein, Hsp70 is a heat shock protein
54
Q

Signal sequence

A

-on the N-terminal
-bound by signal recognition particle (SRP)
-targets ribosome to FtsY on membrane
FtsY guides to translocon that holds hydrophobic regions and spits them out into the membrane

55
Q

Type I secretion

A

-secretes protein out of baterium

56
Q

protein degradation

A
  • proteases cut proteins at specific amino acid sequences
  • proteasomes, barrel shaped, degrade proteins
  • eukaryotes add signal to proteins called ubiquitin tags for degradation

Fall 2014 (5 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions