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BIOL2520 > Unit 07: DNA to Protein > Flashcards

Unit 07: DNA to Protein Flashcards

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1
Q

transcription is a ______ process

A

amplification

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2
Q

what does it mean when i say that transcription is an amplification process?

A

multiple copies of RNA are made from one gene

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3
Q

is RNA or DNA longer?

A

DNA

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4
Q

what type of RNA are spliceosomes?

A

regulatory

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5
Q

T/F; each gene is transcribed at different rates

A

true!

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6
Q

describe how many genes make an mRNA and how many polypeptides that RNA makes in a eukaryote.

A

one gene makes one mRNA which encodes for one polypeptide

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7
Q

describe how many genes make an mRNA and how many polypeptides that RNA makes in a bacteria.

A

many adjacent genes make one mRNA which encodes for multiple polypeptides

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8
Q

what is the function of microRNAs (miRNAs)

A

regulators of eukaryotic gene expression

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9
Q

what is the monomer of RNA?

A

ribonucleoside triphosphate

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10
Q

RNA polymerase catalyzes ______

A

the formation of a phosphodiester bond

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11
Q

how long does it take for a medium length gene to be transcribed?

A

about 50 seconds

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12
Q

what is a promoter?

A

a sequence immediately upstream of a transcription start site that basically tells the cell RNA Polymerase that transcription is ab to start.

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13
Q

in bacteria, what is the subunit of RNA Polymerase that recognizes the promoter?

A

sigma factor

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14
Q

transcription in prokaryotes continues until _____

A

terminator sequence is found!

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15
Q

what is the polarity of the template strand of DNA?

A

3’ -> 5’

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16
Q

which RNAs does RNA Pol 1 encode for ?

A

most rRNA

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17
Q

which RNAs does RNA Pol 2 encode for ?

A

mRNA, miRNA

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18
Q

which RNAs does RNA Pol 3 encode for ?

A

tRNA

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19
Q

what initiates transcription in eukaryotes?

A

general transcription factors assembling at the promoter and positioning RNA Polymerase

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20
Q

how long can regulatory DNA sequences between genes get?

A

up to 100 000 nucleotides

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21
Q

which TF binds DNA at the TATAA box in eukaryotes?

A

TFIID

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22
Q

where is the TATAA box located relative to the transcription start site?

A

30 nucleotides upstream

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23
Q

which TF adds a phosphate group to the tail of RNA Pol to elongate transcription?

A

TFIIH

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24
Q

do general transcription factors stick around after RNA Pol starts moving?

A

no!

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25
which factors help RNA Pol move down the DNA in DNA Transcription?
elongation factors
26
the removal of _____ release RNA Pol from the DNA in transcription?
phosphates
27
is there mRNA processing after transcription in bacteria?
no!
28
______ and ______ occur simultaneously in bacteria
transcription and translation
29
where do processing enzymes "ride" on when talking about mRNA?
the phosphorylated tail of RNA polymerase II
30
what IS the 5' cap?
a guanine nucleotide with an extra methyl group
31
on what end of the mRNA does polyadenylation occur?
3'
32
what is the function of mRNA modifications?
- make mRNA more stable - facilitate export from nucleus - mark RNA as being mRNA - indicate to ribosomes that mRNA message is complete
33
how long can introns be?
can get more than 100 000 nucleotides long
34
what are spliceosomes?
large assemblies of RNA and proteins that carry out RNA splicing
35
what is the function of snRNPs?
indicate where there is an intron, then forms the intron into a loop to allow the ribozyme to splice out intron
36
what is true of alternative splicing?
- transcripts are spliced in different ways for diff proteins - many proteins can be made from same gene - increases coding potential of genome
37
RNA transport from nucleus to cytoplasm is regulated by _____
nuclear pore complex
38
what constitutes an export ready mRNA?
- correctly processed - poly-A-binding proteins - cap binding proteins - exon junction complexes
39
what is the mRNA lifespan in bacteria?
3 mins
40
what is the mRNA lifespan in eukaryotes?
can be less than 30 minutes up to longer than 10 hours
41
what does a longer mRNA lifespan indicate?
protein made in larger amounts
42
what controls mRNA lifespan?
the 3' UTR
43
what happens to mRNA after translation?
degrades and nucleotides are then reused!
44
what is a reading frame?
the sequence of codons depending on where the decoding process begins in mRNA
45
what are the stop codons?
UAA, UGA, UAG
46
how many tRNA genes do humans have? how many anticodons do we have?
500 genes, 48 diff anticodons
47
what is the function of aminoacyl-tRNA synthetase?
covalently coupes a^2 to tRNA via the hydrolysis of ATP
48
how many a^2 tRNA synthetases are there?
one for each a^2, so 20
49
describe the fractions of components that makeup ribosome
1/3 small ribosomal proteins and 2/3 rRNA
50
what is the function of the large ribosomal subunit?
catalyzing formation of peptide bonds
51
what is the function of the small ribosomal subunit?
matching tRNAs to mRNA codons
52
what is the speed of translation in bacteria?
20 a^2/sec
53
what is the speed of translation in eukaryotes?
6 a^2/sec
54
what subunit of the ribosome translocates first?
large subunit
55
describe the process of translation elongation.
1. charged tRNA enters a-site 2. polypeptide chain in p-site forms polypeptide bond with the a^2 in a site, allowing the chain to shift over to the tRNA in the a-site 3. large subunit translocates, shifting tRNA in a-site to p-site and tRNA in p-site to e-site 4. tRNA in e-site leaves ribosome and new tRNA comes into a-site
56
what are the 3D structures that form the core of the ribosome?
rRNA
57
what forms the catalytic site for peptide bond formation?
23S rRNA in large subunit
58
if rRNA is the structural core of a ribosome, what is the function of the small ribosomal proteins structurally?
fill the gaps between rRNA on surface of ribosome, providing support for the RNA core.
59
describe translation initiation in eukaryotes.
1. initiator tRNA binds to p-site on small ribosomal subunit 2. the complex binds the 5' end of the mRNA, identified by the 5' cap 3. ribosome scans mRNA from 5' to 3' to find start codon 4. translation initiation factors dissociate to allow for binding of large ribosomal subunit
60
describe translation initiation in bacteria.
1. ribosomes bind to ribosome binding sequences (6 nucleotides long) upstream of AUG
61
in what organisms is mRNA polycistronic (can make several diff proteins from one mRNA sequence)
bacteria!
62
what do polycistronic mRNAs require to be able to produce so many proteins from one molecule?
separate ribosome-binding sequences for each protein coding sequence
63
what is the N-terminus end of the polypeptide?
the start!
64
what is the effect of release factors binding to stop codons?
alters the activity of peptidyl transferase to add water instead of polypeptide chain, releasing it from the C-terminus end
65
what is a polysome?
cytosolic assemblies of many ribosomes along a single RNA molecule, allowing for the synthesis of many copies of a polypeptide at once.
66
how far apart are ribosomes on a polysome?
about 80 nucleotides
67
how do polysomes in bacteria?
ribosomes acc attach to the free end of mRNA while it is being synthesized
68
what is proteolysis?
breakdown of proteins into their constituent a^2
69
what is the function of proteases? what type of proteins do they breakdown?
they hydrolyze peptide bonds. degrade short lived proteins as well as remove damaged/misfolded proteins
70
what is a proteasome? where can they be found?
large protein machines that breakdown proteins in the eukaryotic cytosol and nucleus
71
describe the structure of a proteasome
- cylinder formed from proteases, with their active sites facing the inside - the ends of the cylinder are plugged by large protein complexes that bind the proteins destined for degradation, as well as unfolding the protein and threading it into the chamber
72
what is ubiquitin?
a small protein that tags other proteins for degradation via covalent linkages
73
what type of proteins typically have a^2 sequences that promote ubiquitylation?
short lived proteins
74
describe the relationship between damaged proteins and a^2 sequences promoting ubiquitylation
when a protein gets damaged, a^2 sequences promoting ubiquitylation that are typically buried get exposed
75
what are thought to be fossils from the earlier molecular world where RNA contained the genetic info and catalyzed chemical rxns?
ribozymes
76
what is autocatalysis? how can it be observed in RNA?
when a molecule can catalyze a reaction to replicate itself. can be seen by using RNA as a template to make another complimentary RNA strand.
77
did RNA evolve before DNA and proteins?
yes!
78
what is easier to make, ribose or deoxyribose? why?
ribose! bc to make deoxyribose, cell has to first make ribose and then remove an oxygen
79
ribose is made from what subunits?
formaldehyde
80
why did cells evolve to using DNA instead of RNA?
- deoxyribose more stable than ribose - DNA can grow larger than RNA without breaking - thymine more stable than uracil - deamination easier to detect in DNA therefore more easily repaired
81

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