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BIOL 2030 > Section 2 - Module 7 > Flashcards

Section 2 - Module 7 Flashcards

1
Q

RNA molecules specific to Eukaryotes

A

MicroRNA (miRNA) and small interfering RNA (siRNA)

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2
Q

RNAi in transcription

A

condenses chromatin to suppress transcription, mRNA is not made

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3
Q

RNAi function

A

transcriptional gene silencing and post-transcriptional gene silencing

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4
Q

RNAi with mRNA

A

The mRNA is destroyed before it is translated into protein

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5
Q

RNAi in translation

A

Inhibit translation, protein is not made.

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6
Q

what are miRNA precursors

A

primary miRNA (pri-miRNA)

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7
Q

What encodes pri-miRNA

A

the genome. Relevant genomic regions are transcribed by RNA Pol II

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8
Q

What cleaves nucleus, Pri-miRNA into pre-miRNA

A

Drosha (RNAase III enzyme)

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9
Q

What structure is pre-miRNA

A

a stem-loop structure

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10
Q

What in the cytosol cleaves the pre-miRNA into 19-25 nucleotide miRNA:miRNA duplex with no stem loop

A

Dicer

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11
Q

Order or enzymes used in miRNA breakdown

A

Drosha, Exportin 5, Dicer

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12
Q

RISC

A

RNA-induced silencing complex

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13
Q

What type of protein dies RISC contain

A

Argonaute

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14
Q

how long is siRNA nucleotide duplex

A

21-23

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15
Q

how long is miRNA nucleotide duplex

A

19-25

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16
Q

how many targets does siRNA have?

A

one

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17
Q

how many targets does miRNA have?

A

multiple (could be over 100)

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18
Q

How do siRNAs degrade mRNA

A

cleavage

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19
Q

RITS (RNA-induced transcriptional silencing)

A

Effector complexes that are targeted to homologous sequences by base-pairing interactions involving the guide strand of the small RNA. Mediates gene silencing vis heterochromatin formation. RNAi mediated histone and DNA methylation.

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20
Q

How many histone proteins in a nucleosome

A

eight

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21
Q

What does a chromatosome consist of?

A

a nucleosome plus the H1 histone

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22
Q

T/F changes in chromatin structure affect the expression of eukaryotic genes?

A

True

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23
Q

Heterochromatin

A

Condensed inactive form of chromatin

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24
Q

Euchromatin

A

open and active form of chromatin. Since open, transcription factors access the DNA and initiate transcription

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25
Q

How does histone modifications occur at multiple locations?

A

Acetylation, methylation, and phosphorylation

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26
Q

What percent of human genes are thought to tbe regualted by RNAi?

A

30%

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27
Q

When is gene regulation arguably most important?

A

Embryo development

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28
Q

What type of gene is RNAi an important research tool?

A

‘knocking out’ (silencing) particular genes

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29
Q

Colinearity

A

the concept that nucleotide sequences in genes dictate amino acid sequences in proteins.

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30
Q

How are nucleotides related to amino acids

A

continuous sequences of nucleotides encode a continuous sequence of amino acids. the number of nucleotides in a gene is proportional to the number of amino acids in the protein.

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31
Q

is the colinear model accurate for prokaryotes?

A

yes

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32
Q

is the colinear model accurate for eukaryotes?

A

no

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33
Q

what is included in a gene?

A

exons, introns, the sequences at the beginning and end of the RNA that are not translated into a protein

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34
Q

Shine-Dalgarno sequence

A

ONLY in prokaryotes. A ribosomal binding site located upstream of the AUG start codon

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35
Q

Do prokaryotes have pre-mRNA?

A

No

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36
Q

Splicing mechanism of nuclear pre-mRNA intron

A

spliceosomal

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37
Q

Location of the nuclear pre-mRNA intron

A

protein-encoding genes in the nucleus of eukaryotes.

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38
Q

Operon

A

operates as a unit utilizing a single transcription start site for multiple genes

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39
Q

Prokaryotic protein-coding genes

A

usually found in a contiguous array in the DNA called an operon

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40
Q

Eukaryotic protein-coding genes

A

each gene is transcribed from its own start site to yield a pre-mRNA that is processed into a functional mRNA encoding a single protein

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41
Q

Prokaryotes DNA genes and introns

A

Prokaryotic DNA genes contain little to no noncoding gaps (introns) and the DNA is transcribed directly into linear mRNA, which then is translated into protein while the mRNA is still being produced.

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42
Q

Addition of 5’ cap post transcriptional modification in Eukaryotes

A

facilitates binding of ribosomes to 5’ end of mRNA, increases mRNA stability, enhances RNA splicing

43
Q

3’ cleavage and addition of poly(A) tail in post transcriptional modification in Eukaryotes

A

increases stability of mRNA, aids in export of mRNA from the nucleus, and facilitates binding pf ribosome to mRNA

44
Q

RNA splicing post transcriptional modification in Eukaryotes

A

Removes noncoding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced through alternative splicing

45
Q

What are the modification for eukaryotic posttranslational modifications?

A

1) capping of the 5’ end
2) polyadenylation of the 3’ end
3) splicing (Removal) of introns

46
Q

What type of nucleotide attached to the 5’-end of the pre-mRNA?

A

methylated (CH3) guanine (G)

47
Q

How does the methylated guanine (G) join to the pre-mRNA?

A

5’-5’ linkage involving 3 phosphate groups

48
Q

What nucleotides are added to the 3’-end of the pre-mRNA?

A

50 to 250 adenine (A) nucleotides, known as polyadenylation to generate a poly(A) tail

49
Q

How is the poly(A) tail added?

A

cleavage and polyadenylation

50
Q

T/F. Modification is necessary for efficient initiation of translation, transport of mRNA from nucleus, protects mRNA from degradation, and enhances RNA splicing

A

True

51
Q

What removes introns?

A

splicing

52
Q

When does splicing occur?

A

between the pre-mRNA to mRNA

53
Q

What are the three consensus sequences in the pre-mRNA?

A

5’ splice site, 3’ splice site, and branch point

54
Q

What uses consensus sequences to recognize and remove introns?

A

spliceosome

55
Q

In what forms are introns removed?

A

lariat

56
Q

How are exons spliced together?

A

two successive reactions (then go to translation)

57
Q

Where does splicing take place?

A

splicesome

58
Q

snRNAs

A

small nuclear RNAs

59
Q

What are the five snRNPs contained in the splicesome?

A

U1, U2, U4, U5, and U6

60
Q

snRNP

A

snRNA + protein = snRNP. And are central to the activity of the spliceosome

61
Q

T/F. The spliceosome assembles sequentially?

A

True

62
Q

Where do snRNAs of U1 and U2 base pair with the consensus sequence?

A

5’ splice site and the branch point site of the pre-mRNA

63
Q

What mediates coupling of events?

A

The ‘tail’ or C-terminal repeat domain (CTD) of the largest subunit of Pol II.

64
Q

Where are mRNA processing enzymes to during transcription?

A

CTD of Pol II

64
Q

When is CAP added?

A

CAP is added as soon as the 5’ end of the pre-mRNA emerges from the polymerase

64
Q

When are capping enzymes recruited to the C-terminal domain (CTD) of RNA polymerase II?

A

early stages of transcription

65
Q

How does the assembly of the spliceosome occur?

A

CO-transcriptionally while the RNA polymerase is still actively transcribing the template

65
Q

During transcription termination what is recruited to the CTD of pol II

A

Polyadenylation factors

66
Q

What end if RNA cleaved

A

Poly(a) 3’ cleavage site

67
Q

What does Rat1 degrading remaining RNA do?

A

terminates transcription

68
Q

Proteome

A

protein complement of the cell

69
Q

T/F. The proteome is more complex than the human genome?

A

True

70
Q

Why is the proteome more complicated than the genome?

A

Because a single gene can give rise to a number of different proteins

71
Q

What are the ways to process a single pre-mRNA to produce different mRNA molecules thereby translating to different proteins?

A

1) alternative splicing
2) alternative PolyA site

72
Q

Alternative splicing

A

pre-mRNA can be spliced different ways. Since each mRNA produces a different combination of exons. When translated produce isoforms of protein

73
Q

Alternative PolyA site

A

PolyA tail can be added at different 3’ cleavage sites

74
Q

Isoforms of proteins

A

different proteins

75
Q

Patterns of alternative splicing

A

exon skipped, intron retention, alternative 5’ or 3’ splice site, mutually exclusive exons

76
Q

What are 3’ cleavage sites used for?

A

Used to determine the length of the mRNA transcript

77
Q

Regulation of alterative processing

A

switch between the production of a functional or nonfunctional protein

78
Q

What is transformer (Tra)

A

Protein in Drosophila sex determination

79
Q

Male Tra protein phenotype

A

nonfunctional Tra protein

80
Q

Female Tra protein phenotype

A

functional Tra protein

81
Q

Male fly’s splice site

A

upstream 3’ slice site, results in premature stop codon of mRNA

82
Q

Where is the female fly’s slice site

A

downstream 3’ splice site, and the termination codon is spliced out with the intron

83
Q

T/F. Depending on RNA processing different forms of protein may be produced in different cell types

A

True

84
Q

RNA processing in Thyroid is associated with

A

calcitonin

85
Q

RNA processing in Brain cells is associated with

A

calcitonin-gene-regulated peptide (CGRP)

86
Q

point mutation

A

single nucleotide mutation

87
Q

Mutations can lead to exon_

A

skipping

88
Q

Mutations can lead to intron __

A

retention

89
Q

What results in gene loss of function?

A

Either nonfunctional proteins of altered stability of mRNA (mRNA is degraded and no protein is made)

90
Q

Does exon skipping or intron retention occur more frequently?

A

Exon skipping

91
Q

Cryptic splice site

A

a sequence not normally used for splicing

92
Q

Beta-globin is a component of __

A

hemoglobin

93
Q

What is beta thalassemia caused by?

A

mutations in the beta-globin which leads to incorrect splicing

94
Q

What is beta thalassemia?

A

One of the most common human genetic diseases, it is a disorder resulting from excessive destruction of red blood cells, which leads to anemia.

95
Q

What does RNA editing alter?

A

The coding information of the mRNA transcripts

96
Q

Methods of RNA editing?

A

1) Substitution editing (base conversion)
2) insertion editing

97
Q

Substitution editing

A

chemical alteration of individual nucleotide by specific enzymes.

98
Q

Insertion editing

A

guide RNA (gRNA) adds nucleotides to be pre-mRNA that were not encoded by the DNA

99
Q

What type of reactions splice together exons?

A

two transesterification reactions

100
Q

What is the goal of alternative processing

A

increases protein diversity

BIOL 2030 (7 decks)

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