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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

A
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
Q

are bacteria polycistronic or monocistronic?

A

polycistronic: If a stretch of replicating DNA contains more than one cistron, it is called polycistronic

26
Q

are eucaryotic cells polycistronic or monocistronic?

A

monocistronic: If a stretch of replicating DNA contains a single cistron (or gene), it is called monocistronic

27
Q

what are the three initiation factors involved in translation

A
  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
Q

From DNA to protein video

A

https://www.youtube.com/watch?v=gG7uCskUOrA

29
Q

What is the purpose of tmRNA?

A

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
Q

what assistant protein is used to help proteins take their shape and what else happens to proteins to help them take the right shape

A
  • GroEL chaperone (protein) after heat shock
  • phosphorylation
  • acetylation
31
Q

what happens to proteins after heat shock?

A

their shape changes and chaperones are used to put them back together

32
Q

what is the purpose of a proteasome

A

to degrade proteins

33
Q

what are proteases

A

proteases are enzymes that break down protein
Ex: ClpQ

34
Q

what are ATPases

A

ATPases are a class of enzymes that catalyze the decomposition of ATP into ADP
ex: ClpY

35
Q

where is a protein degraded

A

on the active site of proteosomes

36
Q

what does the stability of a protein depend on?

A

the N-terminal rule
(half-life)

37
Q

what are the three possible locations you can send a protein

A
  • membrane
  • periplasm if its gram negative
  • outside the cell
38
Q

what guides a protein to its destination

A

SRP (signal recognition particle)

39
Q

the periplasmic proteins are secreted via what kind of system?

A

the Sec system
protein transport video: https://www.youtube.com/watch?v=2aguTUg1sJk

40
Q

where does SRP bind during protein secretion and what happens after it sends off the signal sequence?

A

FtsY receives then passes the signal sequence to the secYEG

41
Q

when is translation completed?

A

when the ribosome reaches FtsY

42
Q

what organism is responsible for strep throat?

A

Streptococcus pyogenes
- HtrA is a cluster of secretory systems

43
Q

what does the TAT system do

A

transfer a folded protein instead of an unfolded one

44
Q

ABC transport system directs proteins from point A to point B
what is point A and what is point B?

A

A: cytoplasm
B: outside the cell

45
Q

what are the two types of ABC transporters and what do they do?

A
  1. influx: bring in macronutrients
  2. efflux: pump out antibiotics.
    ABC transport video:
    https://www.youtube.com/watch?v=LwSKgrdomPM
46
Q

what encodes proteins in eukaryotes

A

Exons

47
Q

what is sequence homology

A

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
Q

what is a paralog gene?

A

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
Q

what is an ortholog gene

A

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
Q

what is the CAZyme gene

A

in Japanese ppl so they can get the ability to degrade red algae.

51
Q

how are genes transfer

A

horizontally
- non-sexual movement of genetic information between genomes

BIOL 303 (26 decks)

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