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Genetics > Lecture 8 > Flashcards

Lecture 8 Flashcards

1
Q

Prokaryotes have how many polymerase? Eukaryotes?

A

1, 3

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2
Q

What is the relationship between consensus sequence and promotor stregnth

A

the closer to the Consensus Sequence, the stronger the promoter

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3
Q

Determines how well genes are transcribed

A

consensus sequence

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4
Q

In the initiation of bacterial transcription, the ____ binds and recognizes the -10 and -13 regions, which causes a….

A

sigma factor, closed complex

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5
Q

Formation of an open complex in bacterial transcription is made by…

A

RNA poly opening up 2 DNA strands

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6
Q

When RNA polymerase releases the sigma factor, what occurs

A

bacterial transcription

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7
Q

What eukaryotic RNA polymerase transcribes 3/4 rRNAs

A

poly 1

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8
Q

What eukaryotic RNA polymerase transcribes the majority of the RNA in eukaryotic cells

A

poly 1

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9
Q

What eukaryotic RNA polymerase transcribes ribosomal RNA (rRNA) …except 5S rRNA

A

poly 1

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10
Q

What eukaryotic RNA polymerase transcribes mRNA and snRNA and LINE-1 transposons

A

poly 2

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11
Q

What eukaryotic RNA polymerase transcribes the most genes

A

poly 2

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12
Q

Alu and LINE-1 have what feature?

A

internal promoters

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13
Q

What eukaryotic RNA polymerase transcribes tRNA and 5SrRNA and Alu transposons

A

poly 3

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14
Q

What eukaryotic rna polymerases are specialized

A

poly 1 and 3

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15
Q

Bacterial and eukaryotic RNA polymerases have what in common?

A

similar general structure

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16
Q

Euk. RNA poly 1 has what transcript?

A

45S transcript

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17
Q

In Euk. RNA poly 1, the processing of rRNA in eukaryotes is that….

A

45S transcript gets put in ultracentrifuge, cleavage occurs, and left with 3 rRNAs

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18
Q

In euk. RNA poly 3, when processing tRNA precursor into tRNA what occurs

A

base modification in tRNA, endonuclease cleaves and exonuclease cleaves

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19
Q

What is a special feature of euk RNA poly 3?

A

RNase P

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20
Q

is an “ribozyme” the catalytic activity resides in the RNA

A

RNase P (in rna poly 3)

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21
Q

Amino acids are brought to the ribosome by…

A

tRNA

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22
Q

Amino acids are brought to the ribosome by…

A

tRNA

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23
Q

What is commonly found at a eukaryotic RNA pol II promotor

A

TATA box

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24
Q

25 nucleotides upstream to initiation of transcription

A

TATA box

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25
Q

25 nucleotides upstream to initiation of transcription

A

TATA box

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26
Q

With RNA poly 2 in eukaryotes, TFIID binds to the…

A

TATA box

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27
Q

is a complex of proteins that includes the TATA binding protein (TBP)
and several TBP-associated factors (TAFs)

A

TFIID

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28
Q

Is TFIID found in bacteria?

A

No

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29
Q

TFIID recruit other proteins that….

A

tether to the RNA polymerase to the TATA box

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30
Q

Initiation of RNA poly 2 transcription needs help by….

A

TFIID

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31
Q

TFIID two roles with RNA poly 2 transcription

A

acts as a helicase to form open complex and phosphorylates CTD of RNA poly 2

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32
Q

releases the
RNA polymerase from the tether made up by
transcription factors and the tether falls apart

A

CTD phosphorylation

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33
Q

CTD phosphorylation causes a ___ and forms an ____

A

shape change and forms an open complex

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34
Q

The eukaryotic initiation of transcription is known as

A

basal transcription

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35
Q

Heat the DNA to break the hydrogen bonds
–> the two strands come apart (“denatured DNA”)
Then add mRNA and let it cool slowly

A

Hybridization of mRNA to DNA

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36
Q

In Hybridization of mRNA to DNA because DNA/RNA H bonds are stronger than DNA/DNA, you get an….

A

R loop

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37
Q

Where RNA binds to 1 DNA strand and single stranded DNA

A

R loop

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38
Q

A single “R Loop” was seen for…

A

most bacterial genes and some eukaryotic genes

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39
Q

An intro + mRNA equals…

A

mRNA bound to DNA with multiple R loops and intron loops

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40
Q

Discontinuous regions of DNA that are complementary to mRNA, spliced out

A

intron

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41
Q

Introns occur the most in what genes?

A

eukaryotic

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42
Q

Who discovered introns

A

Richard Roberts and Phil Sharp

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43
Q

introns occur in….

introns are spliced out when?

A

pre-mRNA

before mature mRNA leaves nucleus

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44
Q

Three different mechanisms for RNA splicing…

A
  1. Group I intron splicing
  2. Group II intron splicing
  3. Spliceosome
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45
Q

What can self-splice?

A

Group 1 and 2 intro splicing

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46
Q

discovered by Tom Cech (Nobel Prize)

A

self-splicing

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47
Q

Group 1 intron splicing contains a _____ with what that cleaves?

A

Guanoside, 3’ OH

48
Q

Group 2 intron splicing contains a _____ with what that cleaves? This forms?

A

sugar from an A nucleotide, 2’OH, covalent closed loop

49
Q

A lariat is an ____. Where is this found?

A

intron closed loop, group 2 intron splicing

50
Q

Splicing by a spliceosome involves…

Has the same structure as…

A

proteins, cannot self splice

Group 2 intron splicing

51
Q

Components of a spliceosome

A
  1. Bind to an intron sequence and precisely recognize
    the intron-exon boundaries
    – 2. Hold the pre-mRNA in the correct configuration
    – 3. Catalyze the chemical reactions that remove introns
    and covalently link exons
52
Q

intron RNA is defined
by particular sequences within the intron
and at the intro-exon boundaries in….

A

splicesome splicing

53
Q

What splicing requires less sequences

A

splicesome (self splicing need more sequences)

54
Q

The consensus sequences in spliceosome splicing includes

A

5’ donor site, 3’ acceptor site and an internal adenine

55
Q

a pre-mRNA with multiple
introns can be spliced in different ways

A

Alternative splicing

56
Q

This will generate mature mRNAs with different
combinations of exons

A

alternative splicing

57
Q

Different splicing choices occur in different cell types or
during different stages of development in….

A

alternative splicing

58
Q

The biological advantage of alternative splicing is
that….

A

two (or more) polypeptides can be derived from
a single gene (allows organism to carry fewer genes in its genome)

59
Q

The slower the life cycle of an organism, the…

A

more numerous and larger the introns

60
Q

Bakerʼs yeast contains about

A

6,300 genes

61
Q

Bacteria and yeast have how many introns

62
Q

Most mRNAs in ____ are spliced, what percent?

A

humans, 70%

63
Q

what contains different alternatively spliced versions that vary in function to meet the needs of the cell type in which they are found

A

alpha-tropomyosin

64
Q

Alternative splicing is or is not a random event, is it regulated?

65
Q

Alternative splicing involves what proteins? What is their role?

A

splicing factors, splice sites

66
Q

Some splicing factors inhibit the ability of a
spliceosome to recognize a splice site. Example?

A

Exon skipping by a splicing repressor

67
Q

A splicing repressor makes the what unrecognizable or masked

A

acceptor site

68
Q

Some splicing factors enhance the ability of
a spliceosome to recognize a splice site. Example?

A

splicing enhancer, promotes the recognition of poorly recognized junctions

69
Q

What process: Most mature mRNAs have a ____
covalently attached at their ___ end

A

Capping: 7-methyl guanosine, 5’

70
Q

Capping occurs when?

A

as the pre-mRNA is being
synthesized by RNA pol II (when transcript is 20-25 bases long)

71
Q

Capping contains what?

A

a rna (GTP) nucleotide attached to the 5’ phosphate of rna in a phosphoate-to-phosphate linkage

72
Q

During capping what is released

A

pyrophosphate

73
Q

Capping is important why?

A

translation and stability of RNA

74
Q

In capping what is added to the gene? What is removed?

A

Methyl, 2/3 phosphates

75
Q

Most mature mRNAs have a string of adenine
nucleotides at their 3ʼ ends

A

polyA tail

76
Q

It is added enzymatically after the gene is completely
transcribed

A

polyA tail

77
Q

In tailing, what signal is transcribed? By what?

A

polyadenylation signal by endonuclease

78
Q

important in the
stability of mRNA and the
translation of the polypeptide

A

polyA tail

79
Q

Protein synthesis always begins with….

80
Q

Each amino acid is attached to….

81
Q

tRNA H bonds to what in mRNA in protein synthesis

A

3 bases (codon)

82
Q

There is no tRNA that can base pair in a….

A

stop codon

83
Q

The genetic code was determined by….

A

synthetic RNA

84
Q

contents of cells that have been broken open

85
Q

The genetic code was deciphered using….

A

Extracts
Degrade the DNA in the extracts by adding the DNase
Add synthetic RNA
Look to see the AA sequences of polypeptides that are made

86
Q

A method to synthesize RNA
also helped crack the Genetic Code. What was created?

A

short RNAs (3 nucleotides) that had a defined sequence

87
Q

Short RNAs with defined sequences that are linked together enzymatically to

A

copolymers

88
Q

Brings in AA to ribosome

89
Q

An anticodon H bonds with…

A

3 bases in mRNA (codon)

90
Q

Each AA has how many tRNAs

91
Q

AA have their own ____ that binds ATP

A

Aminoacyl-tRNA
synthetase

92
Q

When ATP attaches to an AA, what is released and then bound to the AA

A

pyrophosphate released and AMP bound

93
Q

What replaces the AMP bound to an AA

94
Q

When tRNA is attached to the AA, what is it called?

A

Charged tRNA

95
Q

How many aminoacyl-tRNA synthetase for every amino acid

96
Q

The macromolecular arena where translation (protein synthesis) takes place.

97
Q

A ribosome has how many pockets, what are they?

A

3: A, P, E

98
Q

Only occupied by tRNA with single AA attached

A

Aminoacyl site

99
Q

Occupied by tRNA with chain of AA (not Met)

A

Peptidyl site

100
Q

P site of ribosome in translation contains a…

A

AUG start codon

101
Q

E site of ribosome in translation contains a…

A

UAG stop codon

102
Q

In eukaryotes, transcription and translation occurs where?

A

transcription in nucleus, in cytoplasm

103
Q

In bacteria, transcription and translation occurs where?

A

occurs at the same place in cytoplasm

104
Q

A proteinʼs primary structure is its…

A

AA sequence

105
Q

What structure within the cell will the protein adapt

106
Q

The folding of a protein begins during…

A

translation

107
Q

The progression from the primary to the 3-D structure is dictated by…

A

the amino acid sequence within the polypeptide

108
Q

The primary structure of a protein folds to
form regular, repeating shapes known as

A

secondary structures

109
Q

alpha helix and beta sheet structures are stabilized by…

110
Q

Amino acids with non-polar R groups are…

A

hydrophobic

111
Q

Amino acids with polar or charged R groups are

A

hydrophilic

112
Q

The short regions of secondary structure in a protein
fold into a three-dimensional

A

tertiary structure

113
Q

final conformation of proteins that are composed of a single polypeptide

A

tertiary structure

114
Q

Proteins made up of two or more polypeptides have a

A

quaternary structure

115
Q

Forces/interactions responsible for polypeptide folding and the aggregation
of polypeptides into proteins:

A

Hydrophobic/hydrophilic
Ionic interactions
Hydrogen bonds
Van der Waals interactions

Genetics (11 decks)

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