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Exam 1 Flashcards

1
Q

Transformation

A

The uptake of naked DNA from the environment into bacterial cells

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2
Q

Purines

A

Adenine and guanine

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3
Q

Pyrimidines

A

Thymine and cytosine

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4
Q

Which bases are less likely to melt/break?

A

GC rich regions

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5
Q

Topoisomerase

A

Changes DNA supercoiling to maintain the proper number

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6
Q

Type 1 topoisomerase

A

Cleaves 1 strand of DNA, unwinds supercoils, ATP-independent

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7
Q

Type 2 topoisomerase

A

Cleave both strands of DNA, induces supercoils, ATP-dependent

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8
Q

DNA gyrase

A

Uncoils DNA for DNA replication

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9
Q

oriC

A

Origin of replication

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10
Q

A: DNA primase synthesizes RNA primers on the leading strand
B: DNA helicase and helicase loader associate with oriC
C: The sliding clamp is loaded on the leading strand
D: DnaA-ATP proteins bind with the oriC and separate the DNA
E: DNA poly III synthesizes the leading strand until the end. A sliding clamp is loaded on the lagging strand.

A

DBACE

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11
Q

Dam (DNA adenine methyltransferase) and SeqA

A

SeqA binds oriC after replication begins because the parent strain is methylated. After SeqA binds, Dam methylates the newly synthesized strand which weakens the bond between SeqA and oriC.

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12
Q

What triggers the start of bacterial replication?

A

DnaA accumulation during the growth phase

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13
Q

How does DnaA-ATP start replication

A

Binding to the 9-mer at oriC puts tension on the AT-rich 13-mer

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14
Q

DNA polymerase III

A

Performs replication and has a proofreading ability

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15
Q

DNA polymerase I

A

Removes RNA primers on lagging strand replaces them with DNA

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16
Q

mRNA

A

Encodes protein

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17
Q

rRNA

A

Synthesizes proteins as part of the ribosome

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18
Q

tRNA

A

Shuttes amino acids

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19
Q

sRNA

A

Controls transcription, translation, or RNA stability

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20
Q

tmRNA

A

Frees ribosomes that get stuck on damaged mRNA

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21
Q

Catalytic RNA

A

Carries out enzymatic reactions

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22
Q

RNA polymerase

A

DNA-dependent RNA polymerase that produces RNA that’s complementary to the template DNA.

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23
Q

Polycistronic vs Monocistronic

A

Encodes multiple genes under the control of one promoter, encodes one gene under the control of a promoter

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24
Q

Holoenzyme

A

Aka RNA polymerase, contains core enzyme and sigma factor

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25
Sigma factor
Subunit involved in promoter binding (decides which promoter the RNAP binds) that releases during elongation
26
Rho-dependent termination
Terminates transcription by binding Rho to an exposed C-rich region of RNA and forming a hexamer. The hexamer moves down the RNA to the polymerase, which triggers the release of the finished RNA from the polymerase.
27
Rho-independent termination
Terminates transcription with a GC-rich RNA region, forming a hairpin loop that binds NusA and halts RNAP. Melting of the polyU site releases the transcript.
28
Ribosome binding site
Binds 16s rRNA to correctly align the mRNA for translation
29
A site
Region of the ribosome that binds charged tRNAs
30
P site
Region of the ribosome that contains the growing protein attached to a tRNA
31
E site
Region of the ribosome that holds the uncharged exiting tRNA
32
Where does IF3 bind?
The 30s subunit to separate it from the 50s subunit
33
Where does IF1 bind?
IF1 blocks the A site
34
What does IF2 do?
Uses GTP to shuttle fMet-tRNA (contains the start codon) to the P site
35
What does EF-Tu-GTP do?
It brings the appropriate tRNA to the A site
36
Translocation
Moves the ribosome ahead by one codon or moves a protein from one compartment to another.
37
Transduction
Transfer of DNA through a bacteriophage
38
Generalized transduction
A phage can transfer any donor gene to a recipient cell
39
Specialized transduction
Phage can only transfer a short DNA sequence adjacent to a prophage to the recipient cell.
40
Conjugation
Transfer of DNA through pili from donor to recipient cell
41
Why methylate DNA after replication?
Methyl marks correct bases so mismatch repair can occur.
42
Chaperone
Provides a space for proteins to fold properly
43
Signal recognition protein
Receptor that recognizes peptide signal sequences, halts translation, and brings them to the appropriate protein.
44
A: fMet B: IF3 C: IF1 D: IF2 E: A site F: AUG
EFCBAD
45
A: Remodeling B: DnaK C: Trigger Factor D: ATP hydrolysis E: GroEL F: Recycling
CBDEAF
46
4 destinations of extracytoplasmic proteins
Plasma membrane, extracellular spaces, outer membrane, periplasm
47
What do ABC transporters move out of the cell?
Proteases, lipases, and antibiotics
48
Point mutation
A single nucleotide changes
49
Transition
Replacing a purine with a purine or vice versa
50
Transversion
Replacing a purine with a pyrimidine or vice versa
51
Insertion or deletion
Addition or removal of one or more nucleotides
52
Inversion
A fragment of DNA is flipped relative to the rest of the strand
53
Duplication
A copy of a fragment of DNA is produced next to the original
54
Transposition
A transposable element is moved from one DNA region to another
55
Reversion
Reverses a previous mutation
56
Silent mutation
The changed codon encodes the same amino acid as the original codon
57
Missense mutation
A point mutation that changes a single codon to a different amino acid
58
Nonsense mutation
Changes the amino acid to a premature stop codon
59
Methyl-directed mismatch repair
Fixes misincorporations of DNA nucleotides after synthesis by fixing the unmethylated strand to complement the methylated strand.
60
Nucleotide excision repair
It cuts out DNA damaged by UV which causes pyrimidine dimers. The correct bases are synthesized by DNA poly I
61
Base excision repair
Cleaves damaged bases off the sugar-phosphate backbone. A new, correct base takes its place
62
Homologous recombination
Fixes double-stranded blunt ends using two DNA molecules that "exchange" sequences
63
SOS repair
Introduces mutations to severely damaged DNA to keep the chromosome intact.
64
RecA
Binds ssDNA and mediates strand invasion and digests LexA to allow DNA repair genes to be transcribed.
65
Nonhomologous end joining
Repairs double-stranded DNA breaks by directly ligating the strands together
66
F factor
A plasmid transferred by F+ cells that has genes for pilus formation and DNA export
67
Hfr cell
Bacterial strain with the F factor integrated into the host chromosome.
68
Transposable elements
A segment of DNA that can move from one region of DNA to another
69
Transposase
Catalyzes the movement of transposable elements
70
Insertion sequence
A transposable element flanked by inverted repeats
71
Transposon
Transposable element + genes needed for transposition
72
A: SOS repressor B: Translession bypass replication C: Inhibits cell division D: Coprotease E: Nucleotide excision repair
CBEAD
73
A: The F factor is nicked at oriT, and one strand begins to transfer to the other cell B: Sex pilus forms and joins F+ cell to F- C: Transferred DNA circularizes and completes replication D: Sex pilus retracts, and a relaxosome forms E: DNA poly III synthesizes a replacement strand in the donor
BDAEC
74
Replicative transposition
Donor DNA retains a copy of the insertion sequence, recombination separates donor and target DNA, DNA polymerase fills in gaps, DNA ligase seals nicks, target sequence gets duplicated, requires a transposase
75
Nonreplicative transposition
Donor DNA loses insertion sequence, insertion sequence "jumps" into recipient DNA, hairpin structures form on insertion sequence, DNA polymerase fills in gaps, DNA ligase seals nicks, target sequence gets duplicated, requires a transposase
76
Is RNA single-stranded?
Not really because it folds
77
Actinomycin D mechanism
Intercalates between GC base pairs in DNA to block elongation. Affects replication, transcription, and translation. Affects humans as well
78
Tetracycline mechanism
Binds the A site of 30s and blocks tRNA from binding, no translation
79
How can proteins be degraded?
N-terminal rule (short vs long-lived based on N term aa), misfolding targets for degradation, ubiquitin tags

3200 (3 decks)

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