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biochem > Module 9 > Flashcards

Module 9 Flashcards

1
Q

What is the role of RNA pol II?

A
  • eukaryotic
  • expression of most genes
  • 12 subunits
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2
Q

What is the role of RNA pol I?

A

responsible for transcribing genes that encode rRNA molecules

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3
Q

What is the role of RNA pol III?

A

responsible for transcribing the genes that encode tRNAs, 1 rRNA, and other smaller RNA molecules

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4
Q

The transcriptional machinery finds a gene via. . .

A

promoter

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5
Q

Regulatory sequences determine. . .

A

WHEN and HOW MUCH the gene will be transcribed
- can be at both + or - sides

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6
Q

RNA pol II requires action of _____ which are required for the expression of. . .

A

general transcription factors (basal)
expression of ALL genes, e.g. TFIIA, B, C, . . .

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7
Q

Gene regulatory proteins are also called. . .

A

transcription factors - each trans. factor regulates the expression of a subset of genes

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8
Q

What is the coding strand in transcription?

A

the one that is NOT being transcribed

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9
Q

What is the function of TBP? (TATA binding protein)

A

the 1st protein that binds to the promoter and recognized TATA boxes in promoters that will be transcribed

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10
Q

What happens when TBP binds to TATA boxes?

A

it puts a huge dent in the DNA

  • dent might make it easier for other proteins to BIND and RECOGNIZE
  • dent might make it EASIER for DNA to be SEPARATED
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11
Q

What is the role of the transcription factor TFIIB?

A

binds to TBP and brings in RNA pol II

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12
Q

What is the role of the transcription factor TFIIH?

A

unwinds DNA at promoter (helicase activity)

phosphorylates Pol II at the CTD

recruits nucleotide-excision repair proteins

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13
Q

What kind of nucleotide is added to the 5’ end of RNA?

A

the 5’ cap is a 7-methylguanosine (modified nucleotide)

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14
Q

Outline the main features of the 5’-cap

A

retains all 3 of the phosphate groups

added to the 5’ end of both the end of RNA and 7-methylguanosine to form a 5’-5’ triphosphate bridge

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15
Q

What is the function of the 5’-cap?

A

protects the end of mRNA so it doesn’t get degraded by ENDONUCLEASES

allows it to be recognized by the translational machinery

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16
Q

Where does the 5’-cap occur?

A

occurs on the CTD of the RNA pol II

when the cap is produced, it is anchored to the CTD while the rest of the RNA is being transcribed

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17
Q

What is a spliceosome made of?

A

the subunits are made of both PROTEIN and DNA

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18
Q

What are the subunits of spliceosome called?

A

snRNPs

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19
Q

Before post-transcriptional modification, what is the RNA called?

A

the primary transcript

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20
Q

There are recognizable sequences within introns that guide splicing. What are they?

A

5’ end – GU
3’ end – AG
middle – usually has A

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21
Q

Where does splicing usually happen?

A

at the CTD of RNA pol II

can also happen DURING transcription

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22
Q

What is a polyA tail?

A

a large number of adenines that are added at the 3’ end

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23
Q

Define reading frame

A

a way of dividing the sequence of nucleotides in a nucleic acid molecule into a set of consecutive, non-overlapping triplets

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24
Q

What are the 2 vital components of tRNA?

A

anticodon

amino acid arm

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25
Q

Describe ‘wobble’ in translation (in 3rd base of a codon)

A

sometimes, one tRNA can be read by more than one codon

  • due to altered tRNA base

e.g. inosine can base-pair to any of U, A, or C

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26
Q

Describe the role of the aminoacyl-tRNA synthetases in translation

A
  • aminoacyl-tRNA synthetases make tRNAs that are attached to amino acids via ESTER linkages
  • the ester linkage forms between the carboxylic group of amino acid + 3’ OH of tRNA
27
Q

How is the transcriptional START codon AUG identified in prokaryotes? (translation)

A

the binding of the ribosome occurs are ANOTHER sequence called the Shine-Dalgarno sequence

28
Q

How is the transcriptional START codon AUG identified in eukaryotes? (translation)

A

the ribosome binds to the 5’cap and finds and AUG with some help from a sequence called the Kozak consensus sequence

29
Q

A site of ribosome

A

tRNA that is BOUND to 1 amino acid will bind here

30
Q

P site of ribosome

A

tRNA that is HOLDING the growing peptide binds here

31
Q

E site of ribosome

A

the tRNA that is LEAVING the ribosome will bind here

32
Q

Explain which chemical groups of the amino acids are interacting with other amino acids and with the tRNAs during translation.

A

the C-terminal of amino acid at P site interacts with the N-terminal of amino acid at A side

bound to tRNA via carboxyl group

33
Q

How does the peptide bond form between the two amino acids during translation?

A

the amino group at A site attacks the carboxyl at P site, thus breaking the bond b/w tRNA & amino acid at P site

forms a peptide bond b/w the amino group and carboxyl group

34
Q

Describe the structure of a release factor

A

3 domains, similar to tRNA in shape

35
Q

What is the role of a release factor and how does it lead to the termination of translation?

A
  • release factor (protein) will bind to the A site at the STOP codon
  • can catalyze the hydroxylation of the carboxyl end to break it off the final tRNA
  • everything then dissociates to completion
36
Q

Does a tRNA bind to the STOP codon?

A

NO

37
Q

What is polycistronic mRNA?

A

an mRNA with multiple genes whose expression is also controlled by a single promoter & a single terminator

= operon

38
Q

All eukaryotes are _____

A

monocistronic

39
Q

Why are transcription and translation linked in prokaryotes?

A

Because there is no nucleus and it’s happening in the same place (doesn’t need to be transported into the cytoplasm)

40
Q

Why would some ribosomes be in the rER?

A
  • they may need to be modified (i.e. adding sugar molecule / lipid molecule)
  • later could be sent to different parts of the cell or outside the cell
41
Q

Where is the signal peptide found?

A

it is at the start of the protein sequence for those proteins that are modified, trafficked, and secreted

42
Q

What percentage of genes in the human genome are coding?

A

only about 1.5%

43
Q

What percentage of genes in the human genome are repetitive?

A

long repetitive sequences ~ 8%
centromeres, telomeres

44
Q

What percentage of genes in the human genome are introns?

A

26%

45
Q

Retrotransposons are sequences that. . .

A

descended from retroviruses

they can no longer make coat or go OUTSIDE the cell

they can only do the ‘transcription’ sequence

they ‘move’ using an RNA intermediate

46
Q

Almost 45% of our genome is made up of _____

A

mobile elements (transposons)

47
Q

What are the 2 types of retrotransposons?

A

SINEs
LINEs

48
Q

What is a transposon?

A

an active piece of DNA that can ‘move’ from place to place usually b/w genes or inside introns

DNA transposons move using a DNA intermediate

49
Q

Are retrotransposons actually moving?

A

No, they are not really ‘moving’ but rather they are making a new copy of themselves that inserts somewhere else in the genome

50
Q

What are some features of LINE elements?

A
  • 6.1 kb LONG
  • can encode REVERSE transcriptase so can move autonomously (RNA –> DNA)
51
Q

What are some features of SINE elements?

A
  • short, 350 bp
  • 1.5 million copies in human genome
  • do NOT encode reverse transcriptase and so CANNOT move autonomous
52
Q

How do SINE elements move without reverse transcriptase?

A

only way they can move is if there is a LINE element producing reverse transcriptase that can then act on the RNA of a SINE element

53
Q

How can mitochondrial diseases arise?

A

can be caused by mutations in the mitochondrial genome OR the mitochondrial genes in the nuclear genome

54
Q

What do mitochondrial diseases affect?

A

they affect energy, development, vision, and cause seizures

55
Q

Does mitochondria produce ALL of its proteins?

A

NO, some are also produced in the nucleus and IMPORTED into the mitochondria

RNA –> precursor protein –> imported protein

56
Q

Describe the human mitochondrial genome

A
  • circular chromosomes
  • dense gene-packing
  • no introns
  • less tRNAs (produces its own tRNAs)
  • ‘variant’ genetic code; 4 of the 64 codons encode a diff thing compared to the nuclear genome
57
Q

What are the really large fat bands on the gel?

A

rRNA

58
Q

The amount of signal is relative to . . .

A

the amount of STARTING DNA

  • tells us how highly expressed the gene is
59
Q

How can we make sure ONLY mRNA is replicated (and not rRNA, tRNA, etc.)

A
  • only mRNA has polyA-tails
  • we add an oligodT (series of T bases)
  • then we add an enzyme called reverse transcriptase (RNA –> cDNA)
  • then, we degrade away the mRNA (with alkali) so we’re left with a single strand of cDNA
  • we add a primer and use an enzyme (DNA pol I) to generate the 2nd strand
  • we end up with a double stranded cDNA
  • this will make a cDNA copy of every mRNA expressed in our sample
60
Q

The promoter is a _____ structure

A

double-stranded structure (on both strands)

61
Q

Operator is found in. . .

A

prokaryote

62
Q

Does the promoter include the operator? Or, in a eukaryote, the regulatory sequences?

A

promoter is a very loosely defined term, and can include promoter + operator or promoter + all regulatory sequences

63
Q

What is a Western blot used for?

A

to determine how much the gene is being expressed (how much mRNA is being translated into protein)

biochem (9 decks)

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