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BME 501 > Section 3 - Genome Control and Gene Expression > Flashcards

Section 3 - Genome Control and Gene Expression Flashcards

1
Q

What is the central question of genome control?

A

How do I select particular DNA for gene expression?

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2
Q

What is the challenge with transmission of information (DNA -> RNA -> protein)?

A

Want it to be reliable, but don’t want to mess up DNA (wear)

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3
Q

What is the differences between different cells (in terms of gene expression)?

A

Different cells read different genes (different euchromatin) to get different protein products

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4
Q

True or false: the genome is organized cohesively

A

False: it has a disruptive organization

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5
Q

What is the organization of the genome?

A

Small bits of coding DNA are interspersed with large sections of noncoding DNA

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6
Q

True or false: proteins that work together are usually coded together

A

False: proteins coded together typically have dissimilar functions

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7
Q

What is the difference between mammallian genomes and bacterial genomes (based on gene expression)?

A

Similar bacterial proteins can all be transcribed under one promoter, while similar mammalian proteins are all over the genome

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8
Q

When can RNA be the final product (in terms of the central dogma)?

A

RNA can act as enzymes (gain catalytic activity by folding)

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9
Q

What is transcription?

A

DNA -> RNA

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10
Q

What step is DNA -> RNA?

A

Transcription

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11
Q

What is translation?

A

RNA -> protein

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12
Q

What step is RNA -> protein?

A

Translation

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13
Q

What does RNA formation rate depend on?

A

Cell regulation, promotors, etc.

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14
Q

What does the RNA formation rate (partially) dictate?

A

The amount of protein produced

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15
Q

What is the most common way to control protein production?

A

Through RNA

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16
Q

Why is RNA the most common way to control protein production?

A

It is transient and degradable

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17
Q

True or false: all RNA makes the same amount of protein

A

False: there are various controls that regulate the amount of protein

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18
Q

True or false: if there is higher production of a protein A (compared to another protein B), then protein A is more important

A

False: there could be other reasons (stability, toxicity, efficiency, etc.) for why A is produced more than B

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19
Q

What describes different levels of proteins in the cell?

A

The controls in place (tune processes to get result) at every stage

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20
Q

What is the first step in making a protein?

A

Transcription (DNA is transcribed into RNA)

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21
Q

What is RNA?

A

A linear polymer made of four different nucleotide subunits

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22
Q

What is the difference between DNA and RNA?

A

RNA has uracil (DNA has thymine), and RNA has ribose (DNA has deoxyribose)

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23
Q

What is the difference between ribose and deoxyribose?

A

Ribose has an OH group on the 2’ carbon, while deoxyribose has an H

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24
Q

What base is uracil most similar to?

A

Thymine

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25
Q

True or false: RNA is always single stranded

A

False: it can form interesting 3D structures by folding in on itself

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26
Q

How can RNA become more stable?

A

It can bind to itself to form 3D shapes, such as double helices

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27
Q

True or false: in RNA, the bases must be on the same side of the backbone

A

False: there is free rotation, so the bases can rotate freely

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28
Q

What is the first step of transcription?

A

To unwind and open DNA

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29
Q

How many strands act as a template for the RNA?

A

One of the two strands

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30
Q

True or false: all the template strands are one side of the DNA

A

False: they can be on either side

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31
Q

What determines which RNA base will bind to the complementary DNA base?

A

Binding kinetics

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32
Q

How stable are the bonds between RNA and DNA in transcription?

A

Fairly weak (RNA transcript is easily removed from DNA)

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33
Q

What does RNA polymerase do?

A

Transcribes DNA into RNA

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34
Q

What enzyme makes RNA from DNA?

A

RNA polymerase

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35
Q

True or false: RNA polymerase can also stabilize the unwound DNA

A

True: it can stabilize it while making the RNA transcript

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36
Q

What provides the energy for RNA transcription?

A

The breaking of the phosphate bonds from triphosphate nucleotides

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37
Q

What are the raw materials to create the RNA transcript?

A

Triphosphate nucleotides

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38
Q

What enzyme(s) is/are RNA polymerase analogous to?

A

Helicase (unzip and stabilize DNA) and DNA polymerase (make a nucleotide transcript)

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39
Q

How does RNA polymerase stabilize unwound DNA?

A

By having the different strands in different channels

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40
Q

Where are the nucleotides found during transcription?

A

In the ribonucleoside triphosphate uptake channel in RNA polymerase

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41
Q

What does the ribonucleoside triphosphate uptake channel do?

A

Place where the triphosphate nucleotides are found during transcription

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42
Q

What is meant by a “short loop of association” (in transcription)?

A

RNA and DNA are bound for a couple of base pairs before RNA dissociates from the DNA

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43
Q

True or false: multiple polymerases can act at one time

A

True: usually in bacterial cells, multiple polymerases can transcribe a gene at the same time

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44
Q

How come multiple polymerases can act on a gene at the same time?

A

RNA is almost immediately removed from the DNA

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45
Q

Looking at bacterial transcription, how can you tell what is the start / end of the gene?

A

By the lengths of the RNA transcript (shorter transcripts means closer to the start of the gene)

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46
Q

Why does DNA look “darker” in the regions with RNA transcripts?

A

The RNA polymerases are sitting on the DNA

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47
Q

What are some differences between RNA polymerase and DNA polymerase

A
  1. RNA polymerase works with RNA nucleotides
  2. RNA polymerase does not need a primer
  3. RNA polymerase makes a mistake every 10^4 nt (as opposed to 10^7)
  4. Dissimilar mechanisms
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48
Q

Why does RNA polymerase not need a primer?

A

Because the RNA transcript is transient

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49
Q

True or false: RNA polymerase requires a primer to work

A

False: it does not need a primer

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50
Q

Why does RNA polymerase have a lower accuracy than DNA polymerase?

A

Because RNA is transient, so it can be easily degraded

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51
Q

Which has the higher accuracy: RNA polymerase or DNA polymerase?

A

DNA polymerase

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52
Q

What error correcting does RNA polymerase have?

A

It cannot move forward when the backbone is distorted

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53
Q

What error correcting does RNA polymerase not have?

A

It cannot remove bases (exonuclease) that are bound to the RNA like DNA polymerase can for DNA

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54
Q

What is mRNA and what does it do?

A

Messenger RNA codes for proteins

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55
Q

What is tRNA and what does it do?

A

Transfer RNA act as adaptors between amino acids and mRNA

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56
Q

What is rRNA and what does it do?

A

Ribosomal RNA catalyze protein synthesis in the ribosomes

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57
Q

What is snRNA and what does it do?

A

Small nuclear RNA aid in nuclear processes (splicing of pre-mRNA)

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58
Q

What is snoRNA and what does it do?

A

Small nucleolar RNA process and chemically modify rRNA

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59
Q

What is miRNA and what does it do?

A

Micro RNA regulate gene expression by blocking translation of mRNAs

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60
Q

What is siRNA and what does it do?

A

Small interfering RNA turn off gene expression by signaling degradation of mRNA

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61
Q

What is piRNA and what does it do?

A

Piwi-interacting RNA bind to piwi proteins to protect the germ line from transposable elements

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62
Q

What is lncRNA and what does it do?

A

Long noncoding RNA usually serve as scaffolds to regulate cell processes (X-chromosome inactivation)

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63
Q

How many RNA polymerases are in bacterial cells?

A

1

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64
Q

How many RNA polymerases are in eukaryotic cells?

A

3

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65
Q

What does RNA polymerase I do?

A

Transcribed 3 rRNA genes (5.8S, 18S, and 28S)

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66
Q

What does RNA polymerase II do?

A

All protein-encoding genes, plus other smaller RNAS (siRNA, miRNA, most snRNA, etc.)

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67
Q

What does RNA polymerase III do?

A

tRNA, 5S rRNA, and other small RNAs

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68
Q

What talking about transcription, which RNA polymerase is most likely being mentioned and why?

A

RNA polymerase II, since we usually talk about making proteins

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69
Q

What does the “S” value refer to in rRNAs?

A

The sediment value (how heavy it is after centrifugation)

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70
Q

What is a promoter?

A

The location where the gene starts and RNA polymerase needs to start transcribing DNA

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71
Q

What is needed to position RNA polymerase correctly at the promoter?

A

General transcription factors (GTFs)

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72
Q

What does GTF stand for?

A

General transcription factors

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73
Q

What do GTFs do?

A

Position RNA polymerase correctly, pull apart DNA strands, and release RNA polymerase from promoter

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74
Q

What is the promoter analogous to?

A

The origin of replication

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75
Q

True or false: an origin of replication is also a promoter

A

False: they both refer to different processes (DNA replication vs RNA transcription)

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76
Q

Where do GTFs bind on the DNA?

A

TATA box

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77
Q

What is a TATA box?

A

A region of DNA rich in A’s and T’s

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78
Q

What is the significance of the TATA box?

A

Weaker hydrogen bonding, thus easier to pull apart

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79
Q

What does binding of GTFs do to the DNA?

A

Distorts the backbone, allowing for other machinery to get into place

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80
Q

What is the combination of proteins and GTFs for transcription called?

A

Transcription initiation complex

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81
Q

Where is the TATA box located?

A

~25 nt upstream from the gene of interest

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82
Q

What is special about TF2H?

A

It is a growth factor that includes helicase

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83
Q

What transcription factor includes helicase?

A

TF2H

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84
Q

True or false: growth factors are relatively small proteins

A

False: they can be composed of many subunits

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85
Q

What is the significance of the tail region of RNA polymerase?

A

When phosphorylated, it switches sides and clamps the polymerase onto the DNA

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86
Q

What is the controller of RNA polymerase activity?

A

The C-terminal tail domain

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87
Q

When do the transcription factors fall off the DNA?

A

When the RNA polymerase tail is phosphorylated

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88
Q

What transcription factor stays on the DNA after the RNA polymerase tail is phosphorylated?

A

TF2D

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89
Q

Why does TF2D remain on the DNA, even after the RNA polymerase tail is phosphorylated?

A

It can reassemble the transcription initiation complex if needed

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90
Q

What makes using unpurified DNA more difficult to use?

A

More proteins are needed to transcribe DNA

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91
Q

What proteins are needed to transcribe unpurified DNA?

A

Transcription activators, mediators, and chromatin / histone remodeling complexes

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92
Q

Why are transcription activators needed to transcribe unpurified DNA?

A

Activator binds far away from the gene to help initiate transcription

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93
Q

Why are mediators needed to transcribe unpurified DNA?

A

Mediators couple the activators with transcription initiation complex

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94
Q

Why are chromatin / histone remodeling complexes needed to transcribe unpurified DNA?

A

Chromatin / histone remodeling complexes may be needed to help access the DNA

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95
Q

What is the structure of a mediator?

A

Fits like a glove for all the protein machinery

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96
Q

Why is meant by purified DNA?

A

Remove many parts of the transcription initiation complex

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97
Q

When would purified DNA be used?

A

When you are just trying to transcribe a gene

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98
Q

When would unpurified DNA be used?

A

When you are studying transcription specifically

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99
Q

What signals does a mediator respond to?

A

Whether more activators or inhibitors are signaling for the transcription of that gene

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100
Q

What does an activator bind to?

A

An enhancer region

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101
Q

What binds to an enhancer region?

A

An activator protein

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102
Q

How large is the (unpurified) transcription initiation complex?

A

Over 100 proteins

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103
Q

What is the order of assembly of the transcription initiation complex?

A

Somewhat randomly

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104
Q

What happens after RNA is initially transcribed?

A

It is modified through covalent modifications and RNA splicing

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105
Q

What covalent modifications are done on RNA to process it?

A

A 5’ cap and a poly A tail

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106
Q

What is RNA splicing?

A

Removal of introns (and keeping exons) from the RNA transcript

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107
Q

What are introns?

A

Noncoding (intervening) regions of RNA that need to be removed

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108
Q

What are exons?

A

Coding (expressed) regions of RNA that remain in the transcript

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109
Q

What is the purpose of the covalent modifications of RNA?

A

Stabilization, and determine whether the entire transcript is intact or not

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110
Q

What is a primary RNA transcript?

A

Unprocessed RNA (no modifications)

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111
Q

True or false: prokaryotic RNA has a 5’ cap

A

False: it has 3 phosphate groups, but not a 5’ cap

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112
Q

True or false: prokaryotic RNA has a poly A tail

A

False: it has no covalent modifications to the 3’ end

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113
Q

True or false: after RNA modifications, the entire RNA transcript codes for a protein

A

False: there are also untranslated regions (noncoding) before and after the coding region

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114
Q

What is the structure of a 5’ cap?

A

A triphosphate bridge, with 7-methylguanosine

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115
Q

Besides starting RNA transcription, what does phosphorylation of the RNA polymerase tail do?

A

Recruit specific processing proteins

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116
Q

What happens to processing proteins once they are on the RNA polymerase tail?

A

They “hop” to the RNA to process it

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117
Q

What is the order of processing proteins on RNA?

A

Capping factors, then splicing proteins, then 3’ end processing proteins

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118
Q

What determines which processing proteins will bind to the RNA polymerase tail?

A

How it is phosphorylated (number and place)

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119
Q

True or false: RNA modification happens in real time

A

True: the modification proteins hop from the RNA polymerase tail to the RNA transcript to process it in real time

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120
Q

What are the 3 steps for RNA capping?

A
  1. A phosphatase removes a phosphate group from the 5’ end of mRNA
  2. A guanyl transferase adds GMP to the mRNA end
  3. A methyl transferase adds a methyl group
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121
Q

How does RNA splicing occur?

A

Through transesterifications, which breaks the phosphodiester bonds in two locations

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122
Q

What structures are formed during RNA splicing?

A

Intron lariats

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123
Q

What is a lariat?

A

A lasso-like structure that is made up of spliced introns

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124
Q

What is found in every intron?

A

An activated A

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125
Q

What does an activated A do?

A

Allows for the formation of the lariat

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126
Q

True or false: all exons and introns are the same size

A

False: they are all different sizes, which leads to a messy system

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127
Q

What are some reasons that introns may be useful?

A

Evolutionary, help modify genes, or help make cell specific proteins of similar genes

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128
Q

What is needed for specific splicing of RNA introns?

A

A specific RNA sequence needs to be recognized

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129
Q

Where are the specific RNA sequences for splicing found?

A

At the borders of the introns and exons, and around the activated A

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130
Q

What does the spliceosome do?

A

Induces splicing of RNA

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131
Q

What is the spliceosome?

A

A protein-nucleic acid complex that splices RNA

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132
Q

What forms the spliceosome?

A

snRNAs and 7 other proteins

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133
Q

What do the snRNAs do in the spliceosome?

A

Locate the specific regions of the RNA for splicing

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134
Q

What is the general process of splicing?

A
  1. Recognize sequences of RNA
  2. Pull together to form lariat
  3. Join ends together to remove lariat
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135
Q

How does an RNA recognize a particular sequence?

A

Through complementary binding (associations)

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136
Q

What associations are found in a functioning spliceosome?

A

Protein / protein, and snRNA to transcript RNA

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137
Q

True or false: exon sizes are somewhat uniform

A

True: within reason, exon sizes are fairly uniform

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138
Q

True or false: intron sizes are somewhat uniform

A

False: introns can have many different sizes

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139
Q

What does CstF stand for?

A

Cleavage stimulation factor

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140
Q

What does CPSF stand for?

A

Cleavage and polyadenylation specificity factor

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141
Q

What does CstF do?

A

Splices mRNA from RNA polymerase and helps end the reaction

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142
Q

What does CPSF do?

A

Helps other proteins bind (PAP and poly-A-binding proteins)

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143
Q

What does PAP stand for?

A

Poly-A polymerase

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144
Q

What does PAP do?

A

Adds ~200 adenines to the transcript

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145
Q

What enzyme adds the poly-A tail?

A

PAP (poly-A polymerase)

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146
Q

True or false: PAP needs a template to work

A

False: it just adds A’s

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147
Q

What do poly-A binding proteins do?

A

Bind to the poly-A tail to stabilize it (prevent looping) and keep it linear

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148
Q

What proteins bind to the poly-A tail to stabilize it?

A

Poly-A binding proteins

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149
Q

What are poly-A binding proteins analogous to?

A

Single strand DNA binding proteins

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150
Q

True or false: all RNA molecules leave the nucleus

A

False: many RNAs do not leave the nucleus and are degraded

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151
Q

What RNAs do not leave the nucleus?

A

Introns, improperly formed RNAs (no 5’ cap and poly A tail), RNAs that were unnecessarily transcribed (changed conditions), RNAs that stay in the nucleus (spliceosome) and RNAs that have an siRNA attached

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152
Q

What happens if an RNA does not meet the criteria to leave the nucleus?

A

They encounter the nuclear exosome, which contains RNA exonucleases to cleave the RNA

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153
Q

What are nuclear pores?

A

Tightly regulated channels that control when enters and leaves the nucleus

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154
Q

What is more tightly regulated: plasma membrane or nuclear membrane?

A

The nuclear membrane

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155
Q

What does a complete RNA transcript have?

A

Multiple proteins to signal that it is properly made and can leave through the nuclear pores

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156
Q

What does the nuclear export receptor do?

A

Allows the nuclear pore to open and let the RNA transcript / attached proteins into the cytosol

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157
Q

What protein opens the nuclear pore for the completed RNA transcript?

A

The nuclear export receptor

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158
Q

When does the nuclear export receptor fall off the RNA transcript?

A

After the nuclear pore is open and the RNA transcript is in the cytosol

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159
Q

What does CBC stand for?

A

Cap-binding complex

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160
Q

What does the CBC do?

A

Helps protect the 5’ cap

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161
Q

What protein helps protect the 5’ cap?

A

The CBC

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162
Q

What does EJC stand for?

A

Exon junction complex

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163
Q

What does the EJC do?

A

Denotes where two exons have come together

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164
Q

What protein denotes where two exons have come together?

A

The EJC

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165
Q

What does SR proteins stand for?

A

Serine / arginine proteins

166
Q

What do SR proteins do?

A

Their function is not known currently

167
Q

What does hnRNP stand for?

A

Heterogeneous nucleus ribonuclear proteins

168
Q

What do hnRNPs do?

A

Help with binding to the ribosome

169
Q

What proteins help with binding to the ribosome?

A

hnRNPs

170
Q

Where do protein initiation factors bind to?

A

The 5’ cap (CBC)

171
Q

What is the structure of RNA ready for translation?

A

A loop (due to poly A tail)

172
Q

When does the CBC come off of the RNA?

A

When it forms a loop (signaling it is ready for translation)

173
Q

What happens if the RNA is not in a loop structure in the cytosol?

A

It gets degraded by enzymes

174
Q

What happens if the RNA is in a loop structure in the cytosol?

A

It is ready to be translated into a protein

175
Q

Why does an RNA not in a loop structure get degraded by enzymes?

A

Enzymes recognize the free poly-A tail, signaling the RNA for degradation

176
Q

True or false: rRNAs are final gene products

A

True: they do not encode for proteins, and they are themselves functional

177
Q

How many rRNAs are there?

A

4

178
Q

True or false: rRNA is chemically modified

A

True: it is chemically modified

179
Q

How is rRNA chemically modified?

A

Through methylation and isomerization of uridine (uracil + ribose)

180
Q

How many rRNAs make up the large subunit?

A

3 (5.8S, 5S, and 28S)

181
Q

How many rRNAs make up the small subunit?

A

1 (18S)

182
Q

Where is the nucleolus found?

A

Within the nucleus (not a physical barrier)

183
Q

What does the nucleolus do?

A

Contains the rRNA machinery (and perhaps other protein-nucleic acid complexes such as telomerase) (localization)

184
Q

What does the nucleolus contain?

A

rRNA genes, precursor rRNA, mature rRNA, rRNA processing enzymes, and ribosomal protein (localization)

185
Q

When do the large and small subunits of a ribosome combine?

A

When attached to mRNA

186
Q

How is mRNA decoded?

A

In sets of 3 (codon)

187
Q

How long is a codon?

A

3 nt

188
Q

What is the genetic code?

A

The rules to translate a codon into an amino acid

189
Q

True or false: there are no exceptions to the genetic code

A

False: there are some exceptions, such as in the mitochondria

190
Q

True or false: the genetic code is redundant

A

True: some amino acids have multiple codons that lead to the same amino acid

191
Q

What codon is the start codon?

A

AUG (Methionine)

192
Q

True or false: every protein starts with methionine

A

False: while it is the start codon, it is usually cleaved off

193
Q

Where is the redundancy (usually) in a codon sequence?

A

The third nucleotide

194
Q

What is a reading frame?

A

Where the RNA sequence is first read

195
Q

What is the significance of the reading frame?

A

Important to align amino acids, since it can drastically change the protein

196
Q

True or false: most frame shifts will not encode usuable proteins

A

True: frame shifts dramatically alter the amino acid sequence

197
Q

What is the adaptor between mRNA and the amino acids?

A

tRNA

198
Q

What is the structure of tRNA?

A

Cloverleaf shape, ~80 nt long

199
Q

What are the critical regions of tRNA?

A

Anticodon (links with codon), and amino acid binding site

200
Q

What is a wobble position?

A

The third site of the anticodon, which has weak hydrogen bonding

201
Q

What is the significance of the wobble position?

A

Helps explain redundancy (3rd position is less important than the first two)

202
Q

True or false: the wobble is the same between eukaryotes and prokaryotes

A

False: there are different wobbles between the two types of cells

203
Q

True or false: every codon is represented by a unique tRNA

A

False: due to wobble, not all tRNAs are needed

204
Q

True or false: tRNAs are processed similarly to mRNAs

A

True: they are both spliced and chemically modified

205
Q

What enzyme attaches amino acids to tRNAs?

A

Aminoacyl-tRNA synthetases

206
Q

What does aminoacyl-tRNA synthetase do?

A

Attaches an amino acid to a tRNA

207
Q

In most cells, how many aminoacyl-tRNA synthetases are there?

A

20 (one for each amino acid)

208
Q

How does an aminoacyl-tRNA synthetase get the correct amino acid?

A

By having a high binding affinity for only that amino acid (size / interactions)

209
Q

How does an aminoacyl-tRNA synthetase get the correct tRNA?

A

Through binding with its anticodon

210
Q

How does the editing site of aminoacyl-tRNA synthetase work?

A

Only closely related amino acids can go into the editing site, where it is hydrolyzed

211
Q

What directions are proteins made in?

A

From N-terminal to C-terminal

212
Q

Where does the energy come from to form a peptide bond?

A

The high energy linkage between the tRNA and the amino acid

213
Q

What does the ribosome do?

A

Site for protein synthesis

214
Q

What is the ribosome composed of?

A

~50 proteins and 4 rRNAs

215
Q

What does the large subunit of a ribosome do?

A

Catalyzes the peptide bond

216
Q

What does the small subunit of a ribosome do?

A

Framework to hold mRNA and site for tRNA binding

217
Q

How many sites are on a ribosome?

A

4 (1 for mRNA, 3 for tRNA)

218
Q

What are the three sites on a ribosome that tRNA binds to?

A

E (exit), P (peptidyl), and A (aminoacyl)

219
Q

Which sites hold the tRNA tight?

A

A and P sites

220
Q

What are the 4 steps of protein synthesis?

A
  1. tRNA binding
  2. Peptide bond formation
  3. Large subunit translocation
  4. Small subunit translocation
221
Q

What happens during tRNA binding?

A

The correct tRNA enters the A site (proper codon-anticodon binding)

222
Q

What happens during peptide bond formation?

A

The carboxyl group is released in the P site, and attached to the amino group in the A site

223
Q

What enzyme is active during peptide bond formation?

A

Peptidyl transferase

224
Q

What does peptidyl transferase do?

A

Creates a new peptide bond during protein synthesis

225
Q

What happens during large subunit translocation?

A

The large subunit shifts relative to tRNA and mRNA (P -> E, A -> P)

226
Q

What happens during small subunit translocation?

A

The small subunit shifts three nucleotides

227
Q

What happens at the A site of the ribosome?

A

A new amino acid is added to the growing chain (tRNA enters)

228
Q

What site does a new tRNA (amino acid) enter and get added to the growing chain?

A

A site

229
Q

What happens at the P site of the ribosome?

A

Holds the growing amino acid chain

230
Q

What site holds the growing amino acid chain?

A

P site

231
Q

What happens at the E site of the ribosome?

A

The tRNA leaves the ribosome

232
Q

What site does the tRNA leave?

A

E site

233
Q

Where is peptidyl transferase found?

A

Part of the ribosome

234
Q

Why is a tRNA always found in either the P or the A site?

A

Holds everything (mRNA, subunits of ribosome) together

235
Q

True or false: during protein synthesis, there is always a tRNA in either the P or the A site

A

True: this ensures that the ribosome is together

236
Q

What do elongation factors do?

A

Drive protein synthesis in the forward direction (kinetics), provide energy, and partially provide a proofreading mechanism

237
Q

What reactions do elongation factors help in?

A
  1. Binding of correct tRNA to the mRNA

2. Preventing large subunit from going backwards on mRNA

238
Q

What is a ribozyme?

A

An enzyme that functions due to RNA

239
Q

What is an example of a ribozyme?

A

The ribosome

240
Q

Why would enzymes require RNA to function?

A

To locate other nucleic acids through that RNA

241
Q

What does rRNA do in the ribosome?

A

Positions tRNA / mRNA, and forms peptide bonds

242
Q

What is peptidyl transferase composed of?

A

Solely rRNA

243
Q

What tRNA is needed to start translation?

A

Initiator tRNA

244
Q

What does initiator tRNA bind to?

A

Start codon (AUG)

245
Q

True or false: initiator tRNA binds to only the small subunit

A

True: it is the only tRNA that can do this (bind without the large subunit)

246
Q

What does the small subunit do once it is bound to an initiator tRNA?

A

Finds an mRNA (with initiation factors) and scans for the first AUG

247
Q

When does the large subunit bind to the small subunit?

A

Once the first AUG is found on the mRNA

248
Q

True or false: the initiation factors fall off of the mRNA once protein synthesis begins

A

False: they can stay on the mRNA so it can be translated again

249
Q

What is the control of protein synthesis?

A

When the initiation factors fall off of the mRNA, it cannot code for more proteins

250
Q

What codons cause translation to end?

A

UAA, UAG, or UGA

251
Q

True or false: there are tRNAs associated with the stop codons

A

False: there is a release factor instead

252
Q

What does the release factor do?

A

Binds to stop codon, causing the end of translation

253
Q

What does peptidyl transferase do when a release factor is present?

A

Adds a water to the end of the protein to break the chain

254
Q

What step of translation does the ribosome fall apart?

A

Large subunit translocation

255
Q

Why does the ribosome fall apart during large subunit translocation (at the end of translation)?

A

No tRNAs are bound in the A or P sites to hold everything together when the large subunit moves

256
Q

What is release factor made out of?

A

Protein

257
Q

What is the structure of a release factor?

A

Similar to tRNA

258
Q

What are polysomes (or polyribosomes)?

A

Combinations of ribosomes, proteins, and mRNA

259
Q

What is the purpose of a polyribosome?

A

Allows for multiple proteins (from the same mRNA) to be formed at once

260
Q

Where does most of the free energy of the cell go towards?

A

Protein synthesis

261
Q

What bonds (and how many) are split to make a peptide bond?

A

4 high-energy phosphate bonds (two to put amino acid on tRNA, two to move ribosome and form peptide bond)

262
Q

True or false: protein synthesis is energetically costly

A

True: a lot of energy is needed to create a protein

263
Q

What happens if an mRNA is not spliced properly?

A

It will likely reach an aberrant stop codon (found in intron)

264
Q

True or false: EJCs can only tell the boundary between two exons

A

False: they can also be used to determine if the mRNA is spliced properly

265
Q

If an mRNA is not spliced properly, what can you say about the stop codons and the EJCs?

A

There is at least one ECJ downstream of a stop codon (which shouldn’t normally happen)

266
Q

How does a ribosome know if an mRNA is not spliced properly?

A

If there is an ECJ downstream of a stop codon (which shouldn’t normally happen)

267
Q

What do UPFs do?

A

Trigger mRNA for degradation if it isn’t spliced properly

268
Q

True or false: proteins are functional right after translation

A

False: they need to be chemically modified to be useful

269
Q

What does nascent polypeptide mean?

A

Unfolded protein

270
Q

How can a protein be chemically modified?

A

Phosphorylation, co-factors, etc.

271
Q

What do molecular chaperones do?

A

Help fold proteins by stabilizing intermediate structures

272
Q

What proteins help with protein folding?

A

Molecular chaperone proteins

273
Q

What are some examples of molecular chaperone proteins?

A

Heat shock proteins

274
Q

True or false: molecular chaperone proteins can only hook onto the polypeptide chain

A

False: they can also hook onto necessary chemical modifications

275
Q

Without molecular chaperone proteins, what dictates protein folding?

A

Thermodynamics

276
Q

True or false: the polypeptide starts folding after being released from the ribosome

A

False: it starts folding in real time (while it is being produced)

277
Q

What are “on-folding” and “off-folding” pathways?

A

Pathways that determine the proper and improper ways a protein can fold

278
Q

What do molecular chaperone proteins do (in terms of the folding pathways)?

A

Move a protein from an “off-folding” pathway to an “on-folding” pathway

279
Q

What happens if protein misfolding is irrecorverable?

A

The chaperone proteins take the polypeptide to the proteasome for degradation

280
Q

Besides the flow of information, what does the steps of the central dogma suggest?

A

Each step can be controlled from DNA -> RNA -> protein

281
Q

True or false: cells have different genomes since they have different functions

A

False: cells all have the same genome

282
Q

How can cells have the same genome but different functions?

A

They can selectively control which genes are expressed, and thus which proteins are expressed

283
Q

How is gene expression a spatial problem?

A

Need to locate the proper genes on the chromosome

284
Q

How is gene expression a temporal problem?

A

Need to respond to external stimuli through gene expression

285
Q

What were the (general) experiments to show that cells contained the whole genome, and not different pieces?

A

Information from a differentiated cell could be used to produce a new organism

286
Q

What were some species used in the experiments to show that cells contained the whole genome?

A

Frogs, carrots, and cows

287
Q

True or false: mRNA expression for the same gene in different cells is the same

A

False: there are subtle differences

288
Q

True or false: a subtle change in mRNA expression leads to a subtle change in protein expression

A

False: since protein synthesis is highly controlled, there can be a large difference in protein expression based on a subtle difference in mRNA expression

289
Q

What are the 6 steps to control gene expression?

A
  1. Transcriptional control
  2. RNA processing control
  3. RNA transport and localization control
  4. Translation control
  5. mRNA degradation control
  6. Protein activity control
290
Q

True or false: external cues can drive gene expression

A

True: these stimuli can change gene expression

291
Q

True or false: cells respond to the same stimuli the same way

A

False: based on the signaling determinants, there can be different responses to the same stimuli

292
Q

Why is it common to use one cell type in a lab?

A

Cells have varying responses, so it is easiest to study one cell response in depth

293
Q

What are gene regulatory proteins?

A

Proteins that interact directly with DNA to turn genes on or off

294
Q

What are some examples of gene regulatory proteins?

A

Lambda repressor and lac repressor

295
Q

Where do gene regulatory proteins usually bind?

A

The major groove on DNA

296
Q

Why do gene regulatory proteins bind to the major groove on DNA?

A

Can read the sequence based on the noncovalent interactions

297
Q

What interactions can be read from the major groove?

A
  1. H atom
  2. H-bond acceptor
  3. H-bond donor
  4. Methyl group
298
Q

How come gene regulatory proteins do not bind to the minor groove?

A

There is no specificity in the binding chemistry (an A-T looks the same as a T-A)

299
Q

What is the importance of the major groove?

A

Can use the structures found in the major groove to read the DNA sequence

300
Q

What is the difference between the major groove and the minor groove?

A

Can see more of the chemical substance in the major groove

301
Q

What leads to the specificity of the major groove in reading the DNA sequence?

A

The specific pattern of interactions is unique for each base pair

302
Q

What is used to read the DNA sequence (structurally)?

A

The major groove

303
Q

What are the recognition sites for gene regulatory proteins?

A

Short DNA sequences

304
Q

True or false: each recognition site is recognized by a specific protein

A

True: this increases the specificity of gene expression

305
Q

How many different recognition sites are there?

A

Over 1000

306
Q

True or false: there are strong interactions between the DNA and gene regulatory proteins

A

False: it is a weak, reversible interaction

307
Q

How many interactions are there between gene regulatory proteins and DNA?

A

Around 20

308
Q

What are the mechanisms that gene regulatory proteins can bind to DNA?

A

Helix-turn-helix, zinc finger, beta sheets, and leucine zippers

309
Q

What is the helix-turn-helix motif?

A

Two alpha helices with a bend inbetween them

310
Q

How does the helix-turn-helix motif bind to DNA?

A

One helix is the DNA recognition helix, and the other one binds to the backbone to stabilize it

311
Q

True or false: the helix-turn-helix motif binds as symmetric dimers

A

True: two monomers are needed to bind to either side of the DNA

312
Q

What is the consequence of needed a symmetric dimer for the helix-turn-helix motif?

A

The DNA recognition site must be palindromic

313
Q

How far apart are the alpha helices in the helix-turn-helix motif?

A

3.4 nm

314
Q

Why are the alpha helices in the helix-turn-helix motif 3.4 nm apart?

A

This is the size of one turn of DNA

315
Q

What is a zinc finger?

A

A motif that uses zinc to hold an alpha helix and beta sheet for DNA binding

316
Q

True or false: one protein corresponds to one zinc finger

A

False: one protein can have many zinc fingers for recognition

317
Q

What tradeoffs must be considered when considering how many zinc fingers are in a protein?

A

Specificity vs. ease of regulation

318
Q

In a zinc finger, what does the zinc atom bind to?

A

Four specific amino acids in the protein

319
Q

What determines the sequence a zinc finger will recognize?

A

The amino acid structures of the zinc finger

320
Q

How do beta sheets work in DNA recognition?

A

Two beta sheets can bind together to form a DNA recognition site (similar to helix-turn-helix)

321
Q

What do all the mechanisms of DNA recognition have in common?

A

They use protruding amino acids

322
Q

What are protruding amino acids?

A

Amino acids that stick out of the protein

323
Q

What do protruding amino acids do?

A

Recognize the DNA sequence through noncovalent interactions

324
Q

True or false: a protruding amino acid has a single contact with the DNA base pair

A

False: it can have either a single contact or multiple contacts

325
Q

What is a leucine zipper?

A

Two alpha helices that dimerize due to protruding hydrophobic amino acids (such as leucine)

326
Q

True or false: the leucine zipper binds as symmetric dimers

A

False: they can bind as either homodimers or heterodimers

327
Q

What is the consequence of leucine zippers being either homodimers or heterodimers?

A

They can recognize either a symmetric sequence or an asymmetric sequence

328
Q

True or false: it is easy to predict the binding between gene regulatory proteins and DNA

A

False: there are complicated interactions that are hard to predict

329
Q

What does the tryptophan repressor do?

A

Regulates the production of tryptophan in bacteria

330
Q

What does the operator do?

A

Binding site of repressors to regulate gene expression

331
Q

What is the operator?

A

A DNA segment that is the binding site for a regulator

332
Q

Where is the operator found?

A

Within the promoter (or far away, depending on the site)

333
Q

When is the tryptophan operon active?

A

When there is no repressor (and thus no tryptophan in the cell) bound to the operator

334
Q

When is the tryptophan operon inactive?

A

Where the repressor (bound to tryptophan) is bound to the operator

335
Q

Why is the tryptophan repressor used in labs?

A

It is extensively studied and easy to control

336
Q

What happens when a repressor is bound to the operator?

A

RNA polymerase cannot bind to the promoter, and thus cannot transcribe the gene

337
Q

What is a positive regulator (in terms of gene expression)?

A

A protein that increases the likelihood for transcript formation when bound

338
Q

How do positive regulators work (in terms of gene expression)?

A

Aid in RNA polymerase binding, or activating a bound polymerase

339
Q

What are the possible combinations of regulatory protein actions?

A
  1. Repressors are activated by addition of a ligand
  2. Repressors are activated by removal of a ligand
  3. Activators are activated by addition of a ligand
  4. Activators are activated by removal of a ligand
340
Q

If a gene is controlled by a repressor activated by addition of a ligand, when is the gene transcribed?

A

When there is no ligand present, so the repressor is not bound to the operator

341
Q

If a gene is controlled by a repressor activated by removal of a ligand, when is the gene transcribed?

A

When there is ligand present, so the repressor is not bound to the operator

342
Q

If a gene is controlled by an activator activated by addition of a ligand, when is the gene transcribed?

A

When there is ligand present, so the activator is bound to the operator

343
Q

If a gene is controlled by an activator activated by removal of a ligand, when is the gene transcribed?

A

Where there is no ligand present, so the activator is bound to the operator

344
Q

What is unique about the lambda repressor?

A

It can activate certain genes when bound, and can inhibit other genes when bound (can do both functions)

345
Q

What determines whether the lambda repressor will activate or inhibit a gene when activated?

A

The position of the operator relative to the promoter

346
Q

What controls the lac operon?

A

Levels of glucose and lactose

347
Q

True or false: controls only function at one site

A

False: they can be coupled to multiple sites

348
Q

What is an example of an operon that have controls coupled at multiple sites?

A

The lac operon

349
Q

When is the lac operon gene transcribed?

A

When there is low amount of glucose, and high amount of lactose

350
Q

What regulators mediate the lac operon?

A

A lac repressor, and a glucose activator

351
Q

When is the lac repressor active?

A

When there is lactose present

352
Q

When is the glucose activator active?

A

Where there is glucose absent

353
Q

Why is the lac operon used in labs?

A

It is well understood and easy to control

354
Q

In a lab, how can the lac operon be used and controlled?

A

By having specific media, a gene of interest can be activated or inhibited

355
Q

True or false: operators only work at very short distances

A

False: they can also work at very long distances

356
Q

How can operators regulate genes when they are very far away?

A

Through DNA looping (loop back to the gene of interest)

357
Q

What is an enhancer?

A

A DNA sequence where an activator or a repressor can bind to regulate gene expression

358
Q

What does an enhancer do?

A

Allow for binding of activators or repressors to regulate gene expression

359
Q

How does a regulatory protein ensure it binds to two enhancer sites?

A

When bound to one site, it has a large affinity for the other site as well

360
Q

How does DNA looping work?

A

A protein binds to two regions in the DNA, which causes it to loop

361
Q

In terms of general transcription factors, how do eukaryotic cells differ from prokaryotic cells?

A

Eukaryotic cells need 5 general transcription factors, while prokaryotic cells need 1 transcription factor

362
Q

In terms of genome arrangement, how do eukaryotic cells differ from prokaryotic cells?

A

Prokaryotic cells have genes arranged in operons, while eukaryotic cells do not (regulate each gene individually)

363
Q

What is the significance of eukaryotic cells not having operons?

A

Each gene needs to be regulated individually (as opposed to a group of genes regulated together)

364
Q

In terms of regulatory proteins, how do eukaryotic cells differ from prokaryotic cells?

A

Eukaryotic cells have 100s of regulatory proteins, while prokaryotic cells are controlled by a few

365
Q

In terms of DNA storage, how do eukaryotic cells differ from prokaryotic cells?

A

Eukaryotic cells have DNA arranged into chromatin, while prokaryotic cells do not

366
Q

What is the significance of eukaryotic cells packaging their DNA into chromatin (in terms of gene expression)?

A

Allows for more opportunities to control gene expression

367
Q

What are promoters?

A

DNA sequences where general transcription factors bind

368
Q

What are regulatory sequences?

A

DNA sequences where regulatory proteins bind

369
Q

What does a mediator do?

A

Mediates the interactions between the regulatory proteins and the polymerase

370
Q

What is the structure of a mediator?

A

Shaped to associate nicely with the regulators (activators and repressors)

371
Q

Besides enhancing the transcription of a gene, what do enhancers do?

A

Modulate the chromatin sequence to allow for transcription

372
Q

How is DNA (in terms of its gene sequences) wrapped into the histones?

A

The TATA box is within the wrapping, and the regulatory domains are outside of the wrapping

373
Q

What is the significance of the TATA box being wrapped within the histones?

A

Not accessible for gene transcription when wrapped

374
Q

What is the significance of the regulatory domains being wrapped outside of the histones?

A

Accessible for regulatory proteins to come and regulate the wrapping of DNA (and allow for subsequent transcription)

375
Q

What are the possible results of a regulator binding to DNA wrapped around a histone?

A

Remodeling, removal, replacement, or modification

376
Q

What is synergy?

A

Multiple activators have a more than additive effect on gene transcription

377
Q

True or false: gene expression is an additive process

A

False: it is a synergistic process

378
Q

How is gene expression a synergistic process?

A

While the activators themselves may lead to 1 UT (unit of transcription), together they may lead to 100 UT, not 2 UT

379
Q

Which regulatory proteins are most important to gene expression?

A

The regulatory proteins close to the gene / promoter

380
Q

How do regulatory proteins far away from the gene affect the mediator (in terms of gene expression)?

A

May help synergistically, but are most likely not required for transcription to occur

381
Q

What are the possible mechanisms of gene repression?

A

Competitive DNA binding, direct interactions with the general transcription factors, masking the activation site, and recruitment of chromatin remodeling complexes

382
Q

How does competitive DNA binding work in repression?

A

Overlapping sequences lead to a repressor binding, and not an activator

383
Q

How does direct interactions with the general transcription factors work in repression?

A

Repressor binds to the transcription factor, preventing the looping of DNA that would allow the activator to bind

384
Q

How does masking the activation site work in repression?

A

Repressor binds to the activator, preventing the activator from binding to the mediator

385
Q

How does recruitment of a chromatin remodeling complex work in repression?

A

The chromatin remodeling complex can wrap up DNA so it is inaccessible by the translation machinery

386
Q

What is an insulator?

A

A DNA sequence that blocks an enhancer from working on the wrong gene

387
Q

What is the purpose of a barrier sequence?

A

Prevents interaction with heterochromatin

388
Q

What is the purpose of insulators?

A

Make sure that enhancers far from the gene of interest work on that gene, and not other, closer genes

389
Q

What is post transcriptional control?

A

mRNA can be modulated after it is transcribed

390
Q

What is a riboswitch?

A

A small RNA segment that binds to metabolites

391
Q

What does a riboswitch do?

A

Turns an RNA polymerase on or off based on its change in shape

392
Q

How does a riboswitch change shape?

A

Upon binding to a ligand (ex: guanine)

393
Q

What is alternative splicing?

A

Having different exons to encode different proteins

394
Q

What is the consequence of alternative splicing?

A

Can have the same gene coding for different proteins

395
Q

What regulates alternative splicing?

A

Activators and repressors

396
Q

True or false: alternative splicing involves the removal of introns and exons

A

False: it is only concerned with removing certain exons (not introns)

397
Q

What are the (eventual) products of alternative splicing?

A

Cell specific proteins (different “versions”)

398
Q

True or false: alternative splicing can change the properties of the protein

A

True: through altering the coding mRNA, the protein can be different

399
Q

How can alternative splicing alter the properties of a protein?

A

By changing the amino acid chain, and consequently the noncovalent interactions, in the protein

400
Q

If a protein is going to be membrane bound, what types of amino acids will it need?

A

Hydrophobic

401
Q

If a protein is going to be secreted, what types of amino acids will it need?

A

Hydrophilic

402
Q

What is RNA editing?

A

Transcribed RNA can be edited by adding various nucleotides

403
Q

How does RNA editing occur?

A

Through guide RNAs

404
Q

How do guide RNAs work in RNA editing?

A

Guide RNAs find specific sequences, rip apart the mRNA, and add nucleotides

405
Q

What increases the stability of mRNA?

A

The 5’ cap and the poly-A tail

406
Q

What enzyme degrades the poly-A tail?

A

Deadenylase

407
Q

What does deadenylase do?

A

Break down the poly-A tail to degrade mRNA

408
Q

What does RNAi stand for?

A

RNA interference

409
Q

What is RNAi?

A

Using small RNA strands to bind to mRNA and prevent translation

410
Q

What RNAs are used in RNAi?

A

siRNA

BME 501 (5 decks)

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