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BIOL 2321 - Cell Biology > Transcription Pt. 1 > Flashcards

Transcription Pt. 1 Flashcards

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1
Q

What does a gene contain?

A

a transcribed segment of DNA and related regulatory elements (whatever those are)

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2
Q

What is a transcription unit?

A

a transcribed segment of DNA

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3
Q

What will a eukaryotic DNA segment usually contain?

A

the information for a single polypeptide

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4
Q

What will a eukaryotic DNA segment less commonly contain?

A

the information for a functional RNA

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5
Q

What is the first step of gene expression in all cells?

A

transcription of the information in the DNA nucleotide sequence into an RNA nucleotide sequence

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6
Q

What information does the transcribed RNA nucleotide sequence contain? Is this information the same or different than the gene it was transcribed from?

A

the same information for the polypeptide assembly as the gene it was transcribed from

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7
Q

What is the purpose of transcribing an RNA nucleotide sequence that is complimentary to the gene?

A

The gene (original copy) can be safely stored as a part of the DNA molecule while its information can be sent off into the cytoplasm in the RNA

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8
Q

T or F: there are not very many types of RNA molecules

A

False

there are 7 types

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9
Q

What type of RNA code for proteins?

A

Messenger RNA (mRNA)

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10
Q

If an RNA does not code for proteins, what are they called? What do they do?

A

All other proteins are called ‘non-coding’ and they all have distinct functions

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11
Q

What are the components of DNA?

A

A nitrogenous base

A sugar (deoxyribose)

A phosphate

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12
Q

What are the 4 nitrogenous bases in DNA?

A

Adenine
Guanine
Cytosine
Thymine

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13
Q

Which of the DNA nitrogenous bases pair together?

A

A-T

C-G

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14
Q

How many strands of DNA will be transcribed into RNA?

A

only 1

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15
Q

Describe a template DNA strand

A

one of the 2 double helices acts as a template for synthesis of the RNA molecule

it is the strand that is transcribed into RNA

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16
Q

How is the nucleotide sequence of the RNA transcript determined?

A

By the complimentary base pairing between the RNA transcript and the DNA template

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17
Q

Describe the structure of RNA

A

a linear polymer composed of 4 different types of nucleotides linked by phosphodiester bonds

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18
Q

In what ways are DNA and RNA similar?

A

they are both linear polymers made of four different types of nucleotides linked by phosphodiester bonds

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19
Q

List the differences between DNA and RNA

A

number of strands
type of sugar
type of nucleotide bases
RNA can fold into complex 3D shapes

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20
Q

What is the key distinguishing feature of RNA from DNA?

A

the sugar in RNA backbone is a ribose (at C2, there is an OH)

the sugar in DNA backbone is deoxyribose (at C2, there is an H)

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21
Q

What is another important distinguisher between RNA and DNA but not the main distinguisher?

A

RNA has uracil instead of thymine

DNA has thymine

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22
Q

T or F: the definitive feature of RNA that makes it different from DNA is the presence of uracil instead of thymine

A

False

It is the presence of a ribose sugar (has OH) instead of a deoxyribose (has H)

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23
Q

If the pentose sugar has four hydroxyl groups, it is ___

A

RNA

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24
Q

If the pentose sugar has 3 hydroxyl groups, it is ___

A

DNA

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25
Q

In RNA what does adenine pair with?

A

uracil

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26
Q

Describe how mRNA is transcribed and translated in a prokaryotic cell

A

mRNA produced by transcription is immediately translated and there’s no additional processing

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27
Q

How do transcription and translation of mRNA occur in a prokaryotic cell?

A

in the same place at the same time

there is no additional processing between transcription and translation

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28
Q

How do transcription and translation occur in a eukaryotic cell?

A

Transcription occurs separately in the nucleus

pre-mRNA (the original RNA transcript) is processed before leaving the nucleus

mRNA leaves the nucleus and is translated in the cytoplasm

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29
Q

Where is mRNA transcribed in a eukaryotic cell?

A

in the nucleus

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30
Q

Does processing of the RNA transcript occur in prokaryotic cells? eukaryotic cells?

A

No processing in prokaryotic cells

Processing in the nucleus of eukaryotic cells

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31
Q

Where is mRNA translated?

A

in the cytoplasm

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32
Q

What are 6 major differences between prokaryotes and eukaryotes regarding transcription?

A
  1. the presence of histones
  2. compartmentalization of the genetic material
  3. spatial and temporal differences between transcription and translation
  4. whether mRNA is processed
  5. whether an exportin is required for transcript transportation
  6. the presence of operons
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33
Q

Do prokaryotes have histones?

A

No

Though other proteins do pack the genetic material a bit

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34
Q

Do eukaryotes have histones? explain the effect of this

A

Yes

histones package DNA tightly and affect gene expression depending on their modifications

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35
Q

How is the genetic material stored in prokaryotic cells vs. eukaryotic cells?

A

prokaryotic: no nucleus/no compartments for genetic material
eukaryotic: nucleus is compartmentalized into different regions

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36
Q

How do transcription and translation occur in prokaryotic cells?

A

together, at the same time and in the same place

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37
Q

Are exportins required to transport the mRNA in prokaryotic cells?

A

No because there is no nucleus or separate compartments

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38
Q

Why are nuclear exportins required for transcription?

A

RNA is transcribed and processed in the nucleus and mRNA is translated in the cytoplasm

So the mRNA needs to move out of the nucleus

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39
Q

What are the functional units of proteins in a prokaryotic cell that can be transcribed together called?

A

operons

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40
Q

Do operons exist in eukaryotic cells? why/why not?

A

No because a transcription unit will encode for one protein or a functional RNA

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41
Q

T or F: the template strand for a given gene is always different each time transcription occurs

A

False

It will always be the same template strand

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42
Q

T or F: different genes may have different template strands

A

true

What is the template strand for gene b is not the same template strand for gene a

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43
Q

What direction is the template strand copied?

A

3’ –> 5’

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44
Q

What direction is the RNA transcript synthesized?

A

5’ –> 3’

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45
Q

Explain why the template DNA strand and the RNA transcript are complementary and antiparallel

A

Complimentary because RNA will be synthesized with RNA nucleotides (AUGC) that are complementary to the DNA strand (ATGC)

Antiparallel because the template strand is copied from 3’-5’ and the RNA transcript is made 5’-3’

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46
Q

T or F: different genes are transcribed with the same efficiencies

A

False

based on the cell’s needs, different genes are transcribed with different efficiencies

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47
Q

On an electron micrograph, how can you tell where transcription began and where it ended?

A

beginning: where the transcripts are very short
end: where the transcripts are very long

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48
Q

In eukaryotic transcription, what creates the transcript?

A

RNA polymerase II

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49
Q

Describe RNA polymerase II

A

an enzyme complex that creates the RNA transcript in eukaryotic cells

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50
Q

What are the 3 main steps of transcription?

A

initiation
elongation
termination

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51
Q

Describe the initiation process of transcription

A

transcription is initiated by transcription factor proteins recruiting and helping RNA polymerase

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52
Q

Describe the elongation process of transcription

A

As the RNA polymerase moves downstream, nucleotides are added one at a time to the growing transcript

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53
Q

Describe the termination process of transcription

A

When a specific the poly-A signal is reached, transcription will stop

54
Q

What sequence triggers RNA polymerase to bind and start transcription?

A

the promoter sequence

55
Q

How is the promoter sequence referred to in relation to the coding region?

A

upstream because it’s at the 5’ (before the coding region)

56
Q

What sequence triggers RNA polymerase to fall off and end transcription?

A

the terminator sequence

57
Q

How is the terminator sequence referred to in relation to the coding region?

A

downstream because it’s at the 3’ end (after the coding region)

58
Q

What are the 3 RNA polymerase enzymes found in all eukaryotes?

A

RNA pol I

RNA pol II

RNA pol III

59
Q

What is the function of RNA pol I in eukaryotic cells?

A

transcribes most rRNA

60
Q

What is the function of RNA pol II in eukaryotic cells?

A

transcribes all protein-encoding genes

and snRNA and microRNA

61
Q

What is the function of RNA pol III in eukaryotic cells?

A

transcribes tRNA and other small RNAs

62
Q

What are the other two RNA polymerase enzymes found only in plants?

A

RNA pol IV

RNA pol V

63
Q

What is eukaryotic RNA pol II similar in structure to?

A

bacterial RNA polymerase

64
Q

Describe the function of RNA polymerases

A

they catalyze the formation of phosphodiester bonds that link nucleotides to form a linear chain

65
Q

What is the substrate of RNA polymerases?

A

a nucleoside triphosphate

could be G,U,T,A,C

ex. guanine triphosphate

66
Q

In what 2 ways are RNA polymerases similar to DNA polymerases?

A

they both catalyze the formation of phosphodiester bonds to link nucleotides

they both have nucleotide triphosphates as their substrate

67
Q

In what 4 ways are RNA polymerases different to DNA polymerases?

A

RNA polymerase is:

  1. less accurate
  2. does not require a primer
  3. can unwind DNA themselves
  4. cannot dissociate from a transcript after initiation and before termination - the same enzyme has to complete the entire transcript
68
Q

Why is it acceptable that the RNA polymerase is less accurate?

A

the original DNA is stored safely so it is okay if there are some errors in the RNA transcript

69
Q

T or F: RNA polymerase, like DNA polymerase, can dissociate from a transcript at any point

A

False

the same RNA pol must complete the entire transcript

70
Q

T or F: RNA polymerases can unwind DNA by themselves

A

True

71
Q

What happens to the unwound DNA after the RNA polymerase has moved away?

A

it will rewind

72
Q

If the template strand for the RNA polymerase is

3’ - AGGGCTGA - 5’

what is the mRNA sequence? explain

A

5’ - UCCCGACU - 3’

the mRNA sequence will run antiparallel to the template strand (3’-5’) and thymine will be replaced by uracil

73
Q

If the (non-template) coding strand for the DNA polymerase is

5’ - AGGGCTGA - 3’

What is the mRNA sequence? explain

A

5’ - AGGGCUGA - 3’

the template strand will run antiparallel (3’-5’) to the non-template strand (5’-3’) and the mRNA sequence will run antiparallel to the template strand (5’-3’)

and thymine will be replaced by uracil

74
Q

What is the substrate for RNA polymerase? give examples

A

A nucleoside triphosphate

ex. ATP, CTP, GTP, UTP

75
Q

Why is RNA polymerase considered a ribozyme?

A

its function is catalytic (an enzyme)

76
Q

What is the energy source for the reaction catalyzed by RNA polymerase?

A

RNA polymerase has a nucleoside triphosphate substrate

two phosphate groups are hydrolyzed which creates the energy

77
Q

After two phosphate groups are hydrolyzed from the RNA polymerase substrate, what is incorporated into the growing RNA strand?

A

A nucleoside monophosphate

ex. AMP, CMP, GMP, UMP

whichever one was the triphosphate that was cleaved

78
Q

What happens to the 2 cleaved phosphates from the RNA pol substrate?

A

the pyrophosphates leave

79
Q

Describe transcription factors

A

proteins that encourage RNA polymerase to bind to the promoter region for initiation to begin

80
Q

What process is a main transcription regulation point?

A

When transcription factors encourage the RNA polymerase to bind to the promoter region of DNA

81
Q

How is transcription initiation a regulation point?

A

the efficiency of RNA pol can be increased or decreased by the presence of regulating transcription factors and their activity

82
Q

What are the two types of transcription factors?

A

general

specific

83
Q

Describe general transcription factors

A

proteins that encourage RNA polymerase to bind to almost all promoter regions

they are highly conserved

help form the initiation complex

84
Q

Describe specific transcription factors?

A

proteins that encourage RNA polymerase to bind to promoters in specific instances (ex. specific cell types or in certain stages of development, after certain environmental changes)

85
Q

What are the 3 general transcription factors looked at in this class?

A

TFIID
TFIIB
TFIIH

86
Q

Describe the TATA box

A

A highly conserved section of the promoter region (just before transcription starts) made up of mostly adenine and thymine bases

87
Q

Where is the TATA box located in relation to the start of transcription?

A

~25-30 base pairs upstream of the transcription start

88
Q

What does TFIID bind to?

A

the TATA box region of the promoter

89
Q

How does TFIID bind to the TATA box region?

A

through a TBP domain

TATA Binding Protein

90
Q

What is a TBP domain?

A

TATA Binding Protein domain

91
Q

What happens to the DNA when TBP binding occurs? What is the purpose of this?

A

when TBP binds to the DNA, it distorts the DNA so that other transcription factors can recognize the active promoter and bind to it

92
Q

What does the TBP binding to the TATA box trigger?

A

TFIIB to binds just upstream of the TATA box

93
Q

After TFIIB binds to the DNA, what happens?

A

Other transcription factors will bind (including TFIIH) and eventually RNA polymerase will bind

94
Q

Where do all the transcription factors and RNA polymerase bind?

A

To the TATA box on the promoter region of the template DNA strand

95
Q

What forms a complete transcription initiation complex?

A

RNA polymerase and the transcription factors (TFIID, TFIIB, TFIIH) bound to the TATA box on the promoter sequence of DNA

96
Q

What happens after the transcription initiation complex is formed?i

A

the 2 DNA strands must be separated

conformational changes in the initiation complex need to occur for RNA polymerase to leave the complex and enter the elongation phase

97
Q

Why do the DNA strands need to be separated?

A

in order for RNA polymerase to be able to access the template strand

98
Q

Describe TFIIH

A

A large, multi-subunit protein complex that has 2 enzymatic activities:

helicase activity
kinase activity

99
Q

What are the two activities of TFIIH?

A

helicase activity

kinase activity

100
Q

Describe helicase activity - which transcription factor has this function?

A

TFIIH separates the DNA strands by cleaving the hydrogen bonds between nitrogenous bases using the energy from ATP hydrolysis

101
Q

What separates the DNA strands in transcription initiation?

A

TFIIH can unwind the DNA (helicase activity) by breaking the hydrogen bonds between nitrogenous bases and use the energy from the ATP hydrolysis

102
Q

What powers the process of unwinding the DNA in transcription iniation?

A

the energy released from ATP hydrolysis when TFIIH cleaves the hydrogen between the nitrogenous bases (helicase activity)

103
Q

Describe kinase activity - what transcription factor has this function?

A

TFIIH phosphorylates RNA polymerase to induce conformational changes and allow it to leave the complex

104
Q

How is RNA polymerase released from the transcription initiation complex?

A

the kinase activity of TFIIH phosphorylates the RNA polymerase which causes conformation changes

105
Q

What is RNA polymerase II phosphorylated on? How does this happen?

A

TFIIH phosphorylates RNA pol II on a C-terminal domain (CTD) by kinase activity

106
Q

Describe a C-terminal Domain (CTD)

A

a small tail trailing behind the enzyme that is very exposed

Where RNA Polymerase II is phosphorylated

107
Q

When does initiation end?

A

when the first 2 RNA triphosphates are brought in to form a phosphodiester linkage

108
Q

What remains when the RNA polymerase is released toward the coding region? why?

A

TFIID and TFIIB remain behind to initiate more transcription for the next incoming RNA polymerase

109
Q

Besides transcription factors, what are the other 4 protein types required for transcription initiation?

A

transcription activators

mediator protein

chromatin remodeling enzymes

histone modifying enzymes

110
Q

Describe transcription activators

A

proteins involved in transcription initiation that bind 100s - 1000s of base pairs away from the promoter at enhancer sites

111
Q

Where do transcription activators bind?

A

at enhancer sites (100s-1000s of base pairs away from the promoter)

112
Q

Describe the mediator protein

A

a large co-activator protein complex involved in transcription initiation

it allows transcription activators to bind to the general transcription factors at the promoter and RNA pol

113
Q

Describe chromatin remodeling enzymes

A

proteins that are involved in transcription initiation that increase access to the DNA in chromatin (DNA bends or curves)

114
Q

Describe histone modifying enzymes

A

proteins involved in transcription initiation that temporarily adjust histones so that the coiled DNA can be transcribed

115
Q

What phase begins after the initiation complex is cleared?

A

elongation

116
Q

How does elongation occur?

A

RNAPII move along the DNA template strand in the 3’-5’ to create a 5’-3’ RNA transcript

117
Q

Which direction does RNAPII move along the DNA template?

A

3’-5’

118
Q

What direction is an RNA transcript made?

A

5’-3’

119
Q

How is the DNA helix unwound in elongation?

A

by RNAPII helicase activity

120
Q

What forms temporarily in elongation?

A

an RNA-DNA hybrid

121
Q

What happens to the unwound DNA after the RNAPII passes?

A

it is rewound

122
Q

T or F: the new RNA strand is complementary to the DNA template

A

True

123
Q

when does elongation end?

A

when RNAPII reaches the termination signal

124
Q

What is the termination signal?

A

AAUUAAA sequence at the end of the coding region

125
Q

What binds to the end of the coding region when RNAPII reaches the terminal sequence?

A

a poly-adenlyation complex

126
Q

What does a poly-adenylation complex do?

A

cleave the RNA strand 10-35 nucleotides down so that RNA can leave

Add ~250 adenosine bases

127
Q

What 3 proteins are involved in eukaryotic termination?

A

cleavage factors

an endonuclease

A polyadenylate polymerase

128
Q

What are cleavage factors?

A

Proteins that are originally bound to the RNAPII CTD but transfer to the AAUAAA signal when it is transcribed

129
Q

What is the function of the endonuclease in termination?

A

it cuts in the middle of a nucleic acid polymer

130
Q

What is the function of polyadenylate polymerase in termination?

A

it adds ~250 adenine bases one at a time without a template

BIOL 2321 - Cell Biology (26 decks)

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