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CMCB Fall > Gene Expression 10. 19.12 > Flashcards

Gene Expression 10. 19.12 Flashcards

1
Q

Learning Objectives

A
  1. Compare and contrast the differences between DNA and RNA stucture
  2. Explain why the 2’-hyroxyl group of RNA allows it, and not DNA, to readily fold
  3. List and describe the major classes of RNA, both coding and noncoding
  4. Explain how transcriptional initiation, elongation, and termination work and how RNA polymerase mediates each step
  5. Compare and contrast the differneces between bacterial and eukaryotic transcription
  6. Explaiin why supercoiling occurs during transcription and identify the enzymes that resolve supercoiling
  7. Describe the clinical relevance and basis of action of actinomycin D, alpha-amanitin, rifampin
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2
Q

Does transcription and translatino require more steps in eukaryotes or bacteria

A

Eukaryotes

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3
Q

what can occur with teh additional steps for eukaryotes?

A

provides euk with sites for regulatino but also create opprotunites for htings to go wrong and cause disease

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4
Q

what can an overexpression of oncogenes lead to?

A

Cancer

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5
Q

Why do physicians need to study bacteria? How much more bacteria are present on our body than human cells?

A

10x more bacterial cells

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6
Q

What is the target and mechanism of RIFAMPIN

A

To treat Tuberculosis

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7
Q

What is the target and mechanism of active agent in poisonous muchrooms

A

alpha amantin

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8
Q

What is the target and mechanism of the antibiotic Actinomycin D

A

used to ttreat some pediatric cancers

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9
Q

What are the ajor tyeps of RNA (6)

A
  1. mRNA
  2. rRNA
  3. tRNA
  4. miRNA
  5. siRNA
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10
Q

What is mRNA

A

messenger RNAs,

Code for proteins

For Eukaryotes, genes are transcribed as precursors, or pre-mRNAs

These precursors are modified iwth at CAP on their 5’ end and a poly(A)tail on their 3’ end

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11
Q

How are mRNAs modified in Euk?

A

the are modified with a CAp on their 5’end and a poly (A) tail on their 3’ end.

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12
Q

How are they processed further? (mRNA)

A

they must be furthe rocessed by splicing

mRNA is designated a coding RNA, whereas the following are designated noncoding RNAs

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13
Q

What are rRNAs

A

ribosomal RNAs, form the basic structure of the ribosome and catalyze protein synthesis

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14
Q

How many differenr rRNAs make up the ribosomes?

A

3-4 different rRNAs and several dozen robosomal proteins

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15
Q

What are transfer RNAS 9tRNA)

A

central to protein synthesis as ADAPTORS between mRNA and amino acids

they are adapotr moleucles in translation

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16
Q

what are miRNA

A

Micro RNA- regualte gene expression typically by blocking translation of selective mRNAs

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17
Q

how is miRNA transcribed?

A

like mRNA, transcribed as a precursor

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18
Q

What does miRNA regulate after processing?

A

miRNAs regulate either transcription or translation

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19
Q

what are siRNA

A

small interfering RNA- turn off gene expression by directing degradation of selective mNAs and the establishment of compact chromatin structures

siRNA destroys foreign RNA and may have improtnat therapeutic applications

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20
Q

What are other noncoding RNAs

A

function in diverse cell procesess, including telomere syntehsis, X-chromosome inactivation, and teh transport of proteins into the ER

many functions are unknown

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21
Q

What type of RNAs are disgnted as coding RNA?

A

mRNA

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22
Q

What process of protein synthesis is tRNAs invovled in (transcription or translation)

A

TRANSLATION

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23
Q

what are snRNAS

A

small nuclear RNAs,

Funciton in a variety of nucealr processes, including splicing of pre-mRNA

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24
Q

what are snoRNAs

A

small nucleolus RNAs, used to process and chemically modify rRNAs

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25
Q

What are siRNAs

A

small interfering RNAS

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26
Q

How do siRNAs regulate gene expression?

A

Direct degradation of selective mRNAs and establish compact chromatin structures

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27
Q

Whatdo siRNAs do to foreign RNA?

A

Destroys foreign RNA and may have important therapeutic applciations

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28
Q

What do other noncoding RNAs do?

A

function in diverse cell processes
Telomere sntehsis
X-chroosome inactivation
Transport of proteins into the ER

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29
Q

Which Carbon on the ribose sugar does the base attach to

A

C #1

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30
Q

What are the two chemical differences between DNA and RNA?

A

RNA has a 2-OH group instead of the 2’-H atom of DNA

  1. RNA uses uracil (U) instead of thymine (T)
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31
Q

How does the 2’ OH atom of RNA alter teh properies of the polymer (in comparison to DNA)

A

3 ways

  1. 2’OH causes RNA duplexes to form A-form helices, not B-for helices as in DNA
  2. it allows RNA to fold
  3. it makes RNA significantly more susceptible to hydrolysis
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32
Q

How can RNA fold while it is single stranded?

A

B/c it is stabilized by its 2’OH gorups

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33
Q

What is the most common hsape an RNA can it fold into?

A

it can fold into complex shapes but the most common structural element in folded RNA is the DOULBE STRANDED A-FORM HELIX

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34
Q

Which helix form is DNA? RNA? (alpha or beta)

A

DNA- beta form

RNA-alpha form

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35
Q

Is the major or minor groove more accessible in RNA helix?

A

In alpha helix (RNA_< major group is narrow and shallower…the Minor groove (m) is now large and most accessible surface feature of A-form helix

minor groove is more accessbile in RNA

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36
Q

Which groove presents unique H-bonding patterns to permit site-specific recognition by proteins?

A

Major groove

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37
Q

Why is there limited recognition opportuniteis in teh minor groove of RNA

A

the H-bond pattern in this groove cannot be used by proteins to distriminate between A, C, G, and U

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38
Q

What kind of H bonding can DNA phosphodiester backbone participate in?

A

only H-bond acceptors

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39
Q

What kind of phosphodiester backbone does RNA have?

A

the 2’OH group of RNA contains both H-bond donors and acceptors

40
Q

Where do the H bonds for RNA come from?

A

There are 2 lone pairs of oxygen atom offer 2 H-bond acceptors

1 H atom provides 1 H-bond donor

41
Q

Ability to donate and accept H-bonds does what?

A

Ability to donate and accept H-bonds allows RNA to stabilize long range interactions adn thus fold to create active sites that catalyze reactions like peptide bone formation

42
Q

What does the base triple between one nucleotide form tRNA , anotehr from mRNA and a thrid from the ribosiome demonstarte?

A

the stabilizing role of 2’ OH groups

These 2’ OH interactions shown occur in all ribosomes and are essential for mRNA decoding

43
Q

What kind of interactions allow ssRNA to fold???

A

Non-Watson-Crick interactions and 2’OHs

44
Q

What kind of secondary structures does RNA fold into? Tertieary?

A

Helices, stem loops, and juncitons. These secondary structural elements then come togther to create a tertiary folded structure

45
Q

What is the most common structure in folded RNA?

What kind of pairs is this?

A

A-form helix

Only Watson-Crick bp fold into a classic A-form helix

46
Q

What do various combinations of non-Watson-Crick pairs create ?

A

distortions or bulges in teh helices and many other wondrous motifs thata re building blocks of the folded structure

base triples and even base quadruples

47
Q

What is a wobble pair?

A

Common no-Watson-Crick bp is a GU wobble pair

All possible cobinations ar foudn in these non-A-form RNA structures

48
Q

What stabilizes the non-Watson-Crick basepairs?

A

interactions with 2’ OH group

49
Q

What does gene expression begin with?

A

Trascription, which copies DNA into RNA

49
Q

What kind of RNA is made with transcription?

A

RNA is either coding RNA (mRNA) or noncoding RNA

mRNA is translated into protein by the ribosome whereas noncoding RNAs are end products like tRNA or rRNA

50
Q

How are eukaryotic RNA different from bacteria mRNA

A

Euk messages are transcribed as a precursor mRNA (pre-mRNA)

50
Q

What modifications must be done to the pre-mRNA in order to produce the mature mRNA

A

pre-mRNA must be modified by 5’ capping, splicing and 3’-polyadenylation

51
Q

What is RNA transcription catalyzed by?

A

template driven polymerase with nucleotide triphospahte NTP substartes

51
Q

How does RNA Transcription contrast with DNA replication (5 ways):

A
  1. It produces ss product instead of ds one
  2. It doesn’t require a primer
  3. It uses NTP (ribonucleotide substrate) not dNTPs (deoxynucleotide substrates);
  4. it uses U bases instead of thyine ones
  5. It has lower fidelity! DNA polymerases have editing sites and as a result they are highly accurate, making about 1 mistake/10 million nucleotides

RNA Polymerase in contrast, do not have editing sites and as a result are not asaccurate, making 1 mistake/10,000 nucleotides

52
Q

what three steps do RNA polymerases carry out?

A

Initiation, Elongation, Termination

52
Q

Describe how difficult initiation of transcription might be?

A

Starts by lcoating correct start site

This is challengin in bacteria (E. coli), b/c there could be over 4.6 millino potential start sites

IT is more difficult in humans wher ethere could be 3.2 billion potential start sites

Ds DNA must be melted to expose the template strand for copying –> transcription bubbl

53
Q

What is a transcription bubble?

A

it is a transietn stie made by melting of the strands, to expose template strand for copying

54
Q

What occurs during Elongation step?

A

Stepwise and iterative process that catalyzes teh addition of one nucleotide at a time until the termination signal occurs

At end of each elongation step a 3’ hydroxyl group is exposed on the growing RNA polymer

55
Q

What happens at the end of each elongation step?

A

3’ OH group is exposed on the growing RNA polymer

Only when the base of the incoming NTP forms a Watson base pair (WC bp formation is requried) with teh base of the template strand located in the active site is this 3’OH group activated to attack the alph phosphate group (phaopste closest t sugar moetiy) of this incoming NTP

This reaction releases pyrophosphate (PPi) to drive reaction forward

56
Q

What is termination? What is the product?

A

process of stpping transcripton at the correct site. The resultant product is a single stranded RNA, which often folds

57
Q

Why is Polymerase Orientation important during transcription?

A

Oritentation of Poly defines which starnd is the template

58
Q

What provides the directions for intiiation and termination >

A

DNA sequence offers a road map of sorts (promotoer and termiantion sites.

59
Q

What is the signifiance of sites at -10 and -35 (assymmettry_

A

critical to define directino in which polymerase binds to template

60
Q

How do proteins recognize these different sequences that direct initiation and terminatino?

A

Proteins dock into teh acessible major groove of the B-form DNA helix

reads out sequence by forming complementary interactions iwth accessible functinoal groups at the adges of the bases

61
Q

What does the red shaded region lead to (pg 14)

A

a sequence that will form a stem loop structure that signals termination.

62
Q

What is the sigma factor? Function? (bacterial RNA pol)

A

A subunit of the RNA polymerase holoenzyme, that recognizes the asymmetric promotor sequence located just upstream of the start nucleotide

63
Q

What composes the holocoplex? (bac RNA pol)

A

DNA promotor, sigma factor, and RNA Polymerase

64
Q

What ocurs with the assembly of the holocomplex? (Bac RNA Pol)

A

ATP independent helix unwinding to expose bottom template strand for transcription

65
Q

How many nucletotides are transcribed (RNA pol bac) before sigma factor interaction with the promotor weaken

A

about 10

sigma factor interactions with the promotor weaken

66
Q

How does the RNA Pol (bacteria) transition form intiiation mode to elongation mode?

A

Conformation change in teh polymerase allows it to wrap itself aroudn the incoming ds DNA, making this enzye more processive (favoring continuing Tx rather thtan falling off the template, which would prematurely terminate transcription)

67
Q

What happens to sigma and RNA poly (bac) during elongation?

A

polymerase is highly processive and the sigma factor dissociates

68
Q

What are the two mechanisms for termination of RNA Pol (bact)

A

. stem-loop structure, which leads to release

  1. other option employs the p (Rho) protein, which is a helicase that dissociates the RNA transcript form teh DNA tempalte
69
Q

What does termination involve?

A

release of transcribed ss RNA product and release of ds DNA

70
Q

What is supercoiling?

A

coiling of DNA that causes HELICAL TENSION

71
Q

In order to create the transcription bubble…

A

DNA must rotate to alleviate the srai caused by unwinding

72
Q

What are positive supercoils and negative supercoils

A

Positive supercoils precede and negative supercoils follow the action of RNA polymerases

73
Q

Positive superocils

A

upstream of RNA polymerase

+ superhelical tension ahead of polymearse makes DNA helix more difficult to open p (unwind to create a bubble) but helps unwrap DNA helix from teh nucleosome

74
Q

What removes superhlical tension in euk?

A

Topoisomerases

75
Q

What do bacterail cells do with suprcoils?

A

bacteria have specialized ATPase called DNA gyrase that uses energy of ATP hyrdolysis to pump supercoils into DNA

DNA gyrase will either increse or decrease helical tensino so that bacterial chromosome maintains a constant negaative supercoil

76
Q

What does negative supercoil do? (bactera)

A

makes it easer to unwind DNA , thereby adiing bacterial transcription

77
Q

How many RNA polymerases do baceteria have?

A

one

78
Q

How many RNA polymearses do eukaryotes have?

A

three main RNA polymerases

79
Q

What are the three RNA Polymerases

A

RNA Pol I- transcibe rRNAs along with a few otehr small RNAs

RNA Poly II- transcribes all the coding RNAs (the mones that become mRNAS as well as some nonconding RNAs)

RNA Poly III- transribe rRNAs along with a few other small RNAs

80
Q

What does poisonous mushroom amanita phalloides preferentially inhibit?

A

RNA Pol II

shutting down all protein production

81
Q

What genes do RNA Polymerase I transcribe?

A

5.8S, 18S, 28S rRNA genes,

insensitive to Amantin

82
Q

RNA Poly II transcribes?

A

all protein-coding genes, plus snoRNAs genes, miRNA genes, siRNA genes, and moost snRNA genes

Stronngly inhibited by amantin

83
Q

RNA pol II transribes?

A

tRNA genes, 5S rRNA genes, some snRNA genes and genes for other small RNAs

Only inhibited at high concentrations

84
Q

what does “S” value mean?

A

refer to reate of sedimentation in an ultracentrifgue. The larger the S value, the larger the rRNA

85
Q

Which polymerases are used to make Eukaryotic Ribosome Biogenesis? (eRB)

A

RNA Pol I, II, and III

86
Q

What does Pol I in eRB

A

Pol I transcribes the pre-rRNA that embeds 3 or f the four rRNAs of the ribosome

87
Q

RNA pol II transribes?

A

tRNA genes, 5S rRNA genes, some snRNA genes and genes for other small RNAs

Only inhibited at high concentrations

88
Q

what does “S” value mean?

A

refer to reate of sedimentation in an ultracentrifgue. The larger the S value, the larger the rRNA

89
Q

Which polymerases are used to make Eukaryotic Ribosome Biogenesis? (eRB)

A

RNA Pol I, II, and III

90
Q

What does Pol I in eRB

A

Pol I transcribes the pre-rRNA that embeds 3 or f the four rRNAs of the ribosome

91
Q

What is the purpose

A

j

CMCB Fall (17 decks)

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