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BIOL 303 > CH8 Transcription, Translation, and Bioinformatics > Flashcards

CH8 Transcription, Translation, and Bioinformatics Flashcards

1
Q

what is an example of transcription factors

A

sigma factors

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2
Q

purpose of sigma factors in transcription

A

help RNA polymerase find the promoter on the DNA

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3
Q

the region that RNA polymerase binds to is called what?

A

a promoter

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4
Q

what are the three types of RNA in eukaryotes and what are their functions

A
  1. RNA polymerase I transcribes rRNA genes
  2. RNA polymerase II transcribes mRNA
  3. RNA polymerase III transcribes tRNA and 5S rRNA genes
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5
Q

what sequences do sigma genes bind to

A

the -30 and -10 shine dalgarno sequences

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6
Q

what is the house keeping sigma gene

A

sigma 70

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7
Q

what are the consensus sequences for sigma 70 promoters

A

-35: TTGACAT
-10: TATAAT

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8
Q

the three phases of transcription

A
  1. initiation
  2. elongation
  3. termination
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9
Q

characteristics of streptomyces bacteria

A
  • versatile in metabolism: suggests that they have high control over transcription making the slow growing
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10
Q

what happens to the sigma factor when RNA polymerase attaches to the promoter?

A

the sigma factor leaves

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11
Q

Two aspects to termination

A
  1. rho which is a hexomer that causes termination when it connects with RNA polymerase
  2. Hairpin loop: contact between hairpin, NusA protein and rna polymerase causes termination
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12
Q

what antibiotic inhibits RNA polymerase thus transcription

A

Rifampin

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13
Q

what is the purpose of actinomycin D as an antibiotic

A

-blocks transcription
-inhibits dna replication by inhibiting primer formation

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14
Q

purpose of small RNAs or regulatory rnas

A

Controls transcription, translation, or RNA stability

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15
Q

purpose of tmRNA

A

Frees ribosomes stuck on damaged mRNA

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16
Q

purpose of catalytic RNA
(ribosimes)

A

carries out enzymatic reactions

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17
Q

Least stable RNA (shortest half-life)

A

mRNA

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18
Q

Ecoli has a complex of four proteins that break down RNA. what are they called?

A

degradosomes

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19
Q

what is the start codon

A

AUG

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20
Q

how many stop codons?

A

three
1. UAA
2. UAG
3. UGA

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21
Q

Transfer RNA structure

22
Q

First transfer RNA to be vizualized

A

Alonien tRNA
using chromatography columns to purify the RNAse

23
Q

what is charging tRNA

A
  • it is used in translation as a form of energy to make proteins
  • the tRNA is charged when the amino acid attaches to hydrolized AMP (cleaved 2 phosphate groups off ATP)
24
Q

where are plasmids and DNA in nucleoid located in a cell?

A

plasmid at the poles and nucleoid in the middle
indicating that the two forms of DNA

25
are bacteria polycistronic or monocistronic?
polycistronic: If a stretch of replicating DNA contains more than one cistron, it is called polycistronic
26
are eucaryotic cells polycistronic or monocistronic?
monocistronic: If a stretch of replicating DNA contains a single cistron (or gene), it is called monocistronic
27
what are the three initiation factors involved in translation
1. initiation factor 1: 30s subunit binds to IF1 and mRNA 2. IF2: interacts with initiator tRNA 3. IF3: all initation factors fall off and GTP becomes hydrolized causing translation to occur
28
From DNA to protein video
https://www.youtube.com/watch?v=gG7uCskUOrA
29
What is the purpose of tmRNA?
has the properties of a tRNA and an mRNA. tmRNA uses these two functions to release ribosomes stalled during translation and target the nascent polypeptides for degradation.
30
what assistant protein is used to help proteins take their shape and what else happens to proteins to help them take the right shape
- GroEL chaperone (protein) after heat shock - phosphorylation - acetylation
31
what happens to proteins after heat shock?
their shape changes and chaperones are used to put them back together
32
what is the purpose of a proteasome
to degrade proteins
33
what are proteases
proteases are enzymes that break down protein Ex: ClpQ
34
what are ATPases
ATPases are a class of enzymes that catalyze the decomposition of ATP into ADP ex: ClpY
35
where is a protein degraded
on the active site of proteosomes
36
what does the stability of a protein depend on?
the N-terminal rule (half-life)
37
what are the three possible locations you can send a protein
- membrane - periplasm if its gram negative - outside the cell
38
what guides a protein to its destination
SRP (signal recognition particle)
39
the periplasmic proteins are secreted via what kind of system?
the Sec system protein transport video: https://www.youtube.com/watch?v=2aguTUg1sJk
40
where does SRP bind during protein secretion and what happens after it sends off the signal sequence?
FtsY receives then passes the signal sequence to the secYEG
41
when is translation completed?
when the ribosome reaches FtsY
42
what organism is responsible for strep throat?
Streptococcus pyogenes - HtrA is a cluster of secretory systems
43
what does the TAT system do
transfer a folded protein instead of an unfolded one
44
ABC transport system directs proteins from point A to point B what is point A and what is point B?
A: cytoplasm B: outside the cell
45
what are the two types of ABC transporters and what do they do?
1. influx: bring in macronutrients 2. efflux: pump out antibiotics. ABC transport video: https://www.youtube.com/watch?v=LwSKgrdomPM
46
what encodes proteins in eukaryotes
Exons
47
what is sequence homology
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history (common ancestor)
48
what is a paralog gene?
note: Homologous sequences are paralogous if they were separated by a gene duplication event note: if a gene in an organism is duplicated to occupy two different positions in the same genome, then the two copies are paralogous answer: -same genome different function
49
what is an ortholog gene
genes have the same function but are in different species note: Orthologs are defined as genes in different species that have evolved through speciation events only. Paralogs, on the other hand arise by duplication events
50
what is the CAZyme gene
in Japanese ppl so they can get the ability to degrade red algae.
51
how are genes transfer
horizontally - non-sexual movement of genetic information between genomes

BIOL 303 (26 decks)

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