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Diagnostic Molecular Biology > Ch. 2 - RNA > Flashcards

Ch. 2 - RNA Flashcards

1
Q

RNA

A

Ribonucleic acid

Polymer of nucleotides similar to DNA
Has ribose instead of deoxyribose
Has Uracil instead of Thymine

SS instead of double helix
Can form loops
Can pair with complementary DNA or RNA ss to form double helix

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2
Q

Transcription

A

The copying of one strand of DNA into RNA

Occurs mostly in interphase

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3
Q

Gene expression

A

The process of transcribing and translating information stored by DNA into protein for utilization

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4
Q

mRNA

A

Messenger RNA

Carries information in DNA to the ribosomes where it is translated into protein

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5
Q

RNA polymerase

A

Catalyzes the transcription process

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6
Q

Pol I

A

RNA polymerase I
Synthesize non-coding RNA
Found in nucleolus
Produces 18S, 5.8S, and 28S rRNA

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7
Q

Pol II

A

RNA polymerase II
Synthesize mRNA
Found in nucleus
Produces mRNA, snRNA

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8
Q

Pol III

A

RNA polymerase III
Synthesize non-coding RNA
Found in nucleus
Produces tRNA, 5S rRNA

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9
Q

Nucleolus

A

Site of the nucleus where ribosomal RNA synthesis takes place

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10
Q

Reverse transcription

A

Replication of RNA by first making a DNA copy of the RNA genome

Used by retroviruses such as HIV and leukemia viruses

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11
Q

Promotor

A

A specific sequences of bases that signal the initiation of transcription

Greatly outnumber DNA initiation sites

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12
Q

Antisense strand

A

The strand of DNA that RNA polymerase uses as a template

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13
Q

Sense strand

A

The strand of DNA that is not used as a template for mRNA synthesis

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14
Q

Rho

A

Helicase enzyme that associates with RNA polymerase and inactivates the elongation complex at a cytosine-rich termination site in the DNA

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15
Q

Rho-independent termination

A

Occurs at GC-rich sites followed by AT-rich regions

GC are transcribed into RNA and fold into a short ds hairpin, which slows the elongation process

Elongation complex dissociates as it reaches AT-rich area

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16
Q

Polyadenylation signal

A

The site (PolyA site) on the DNA template termination of mRNA transcription is activated

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17
Q

rRNA

A

Ribosomal RNA
Largest component of cellular RNA
Important structural and functional part of ribosomes

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18
Q

3 RNA species in prokaryotes

A

16S - found in the ribosome small subunit

23S and 5S - found in the ribosome large subunit

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19
Q

Polycistronic

A

Coding for more than one protein on the same mRNA

Seen in some prokaryotes, not in eukaryotes

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20
Q

Monocistronic

A

Coding for one protein per mRNA

Seen in prokaryotes and eukaryotes

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21
Q

Constitutive transcription

A

Messages are transcribed constantly and are relatively abundant in the cell

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22
Q

Inducible or regulatory transcription

A

Messages are transcribed only at certain times during the cell cycle or under certain conditions

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23
Q

Polyadenylic acid

A

Nucleic acid comprised only of adenosine nucleotides

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24
Q

PolyA tail

A

Polyadenylic acid at the 3’ terminus of mRNA

Not coded in genomic DNA; added to RNA after synthesis of pre-mRNA

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25
Q

Genomic

A

Referring to the genome, as opposed to extra chromosomal plasmids

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26
Q

Polyadenylate polymerase

A

Enzyme that catalyzes the formation of polyadenylic acid at the 3’ terminus of mRNA

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27
Q

What are the two steps to mRNA processing?

A
  1. Polyadenylation - the addition of polyadenic acid to the 3’ terminus of mRNA
  2. Capping -
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28
Q

Cap

A

A structure that serves as a recognition signal for translation

A structure that blocks eukaryotic mRNA at the 5’ terminus

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29
Q

Open reading frame

A

Uninterrupted sequences that code for amino acids

Found in prokaryotic cells

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30
Q

Introns

A

Non-coding DNA sequences
Interrupt coding regions in eukaryotic cells
Aka intervening sequences

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31
Q

Exons

A

Protein-coding sequences in eukaryotic cells

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32
Q

hnRNA

A

Heteronuclear RNA
Newly transcribed mRNA
Much longer than mature mRNA due to introns

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33
Q

Splicing

A

The removal of introns (intervening sequences) from hnRNA

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34
Q

Alternative splicing

A

Modifies products of genes by alternate insertion of different exons

I.e. Production of calcitonin in the thyroid or calcitonin gene-related peptide in the brain depends on the exons included in the mature mRNA in these tissues

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35
Q

snRNA

A

Small nuclear RNA

Splicing in eukaryotes

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36
Q

tRNA

A

Transfer RNA
Short, ss polynucleotides
Adaptor molecules

Usually have 8 or more modified nucleotides after synthesis

Most have a guanylic residue 5’ and the sequence CCA 3’

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37
Q

Ribosomes

A

Complex of RNA and proteins that catalyze the formation of peptide bonds

Protein synthesis occurs here

Read mRNA using tRNA

38
Q

What was the first demonstration that RNA could act as an enzyme?

A

Self-splicing

39
Q

Structure of tRNA

A

Cruciform of 4-5 ds stems and 3-4 ss loops

Due to intrastrand hybridization

40
Q

Prokaryotic RNA polymerase initiation site

A

Basal transcription complex comprised of large and small RNA polymerase subunits and additional sigma factors assemble at initiation site

41
Q

Eukaryotic RNA polymerase initiation site

A

Transcription complex requires RNA polymerase and up to 20 additional factors for accurate initiation

42
Q

Alpha phosphate

A

The phosphate closest to the ribose sugar

The first ribonucleoside triphosphate retains all phosphate groups, subsequent ones only retaining the alpha phosphate

43
Q

How are the various types of rRNA named?

A

S for their sedimentation coefficient in density gradient centrifugation

44
Q

Eukaryotic rRNA synthesis

A

Copied from DNA as a single 45S precursor RNA (pre-rRNA)

Then processed into 18S of the ribosome small subunit and 5.8S and 28S of the large subunit

5S is found in the large ribosome and is synthesized separately

45
Q

mRNA synthesis in prokaryotes

A

mRNA is synthesized and simultaneously translated into protein

46
Q

Abnormalities in splicing are responsible for several diseases, such as _________.

A

Beta-thalassemias (from mutations in splice recognition sequences of the beta-globulin genes) and certain autoimmune conditions (from production of antibodies to RNA protein complexes)

47
Q

miRNA

A

Micro RNA

Regulatory RNAs derived from endogenous RNA hairpin structures

Discovered in the work Caenothabiditis elegans

Control gene expression by pairing with partially complementary sequences in mRNAs and inhibit translation

48
Q

Hairpin structure

A

RNA folded into ds states through intrastrand H bonds

49
Q

siRNA

A

Small interfering RNA

Functional unit of RNA interference

50
Q

RNAi

A

RNA interference

A defense in eukaryotic cells against viral invasion

51
Q

RNA-dependent RNA polymerases

A

Require an RNA template

Carried by viruses such as the hepatitis C virus and Dengue virus

52
Q

Bacterial RNA polymerase subunits

A

Five subunits

Two α and one each of β, β’, and σ

53
Q

Eukaryotic RNA polymerase subunits

A

Three multisubunit, nuclear DNA-dependent RNA polymerases, Pol I, Pol II, and Pol III

54
Q

Core enzyme (prokaryotic RNA polymerase)

A

Two α and one each of β, β’

Synthesize RNA

55
Q

σ cofactor (prokaryotic RNA polymerase)

A

Aids in accurate initiation of RNA synthesis

56
Q

PolyA polymerase

A

Template-independent RNA polymerase
Adds adenine nucleotides to the 3’ end of mRNA
Resulting polyA tail is important for mRNA stability and translation into protein

57
Q

Ribonucleases

A

Degrade RNA

Several types of ribonucleases, generally classified as endoribonucleases and exoribonucleases

58
Q

RNase H

A

Endonuclease

Digests the RNA strand in a DNA/RNA hybrid

59
Q

RNase I

A

Endonuclease

Cleaves ss RNA

60
Q

RNase III

A

Endonuclease

Digests ds RNA

61
Q

RNase P

A

Endonuclease

Removes precursor nucleotides from tRNA molecules

62
Q

RNase A, RNase T1, RNase T2

A

Endonucleases
Cleave ss RNA at specific residues
Used in combination in some lab procedures investigating gene expression and transcript structure

63
Q

Exoribonuclease

A

Enzymes that digest ss RNA from 3’ to 5’ end

PNPase (polynucleotide phosphorylase) 
RNase PH
RNase II
RNase R
RNase D
RNase T
64
Q

RNase D

A

Like endoribonuclease RNase P, 3’-to-5’ processing of pre-tRNAs

65
Q

RNases

A

Ubiquitous (found everywhere), stable enzymes that degrade all types of RNA

Important in labs where RNA work is performed, as they are very resistant to inactivation

66
Q

RNA helicases

A

Enzymes that catalyze the unwinding of ds RNA
Remove proteins from RNA-protein complexes

Some work only on RNA
Some work on RNA:DNA heteroduplexes and DNA substrates

67
Q

What are the two types of factors responsible for regulation of RNA synthesis?

A

Cis and trans (transcription) factors

68
Q

Cis factors

A

DNA sequences that mark places on the DNA involved in initiation and control of RNA synthesis

69
Q

Trans (transcription) factors

A

Proteins that bind to cis sequences and direct assembly of transcription complexes at the proper gene

70
Q

Operon

A

A series of structural genes transcribed together on one mRNA and separated into individual proteins

71
Q

What are the three structural genes of the lac operon, their product and its function?

A

LacZ - β-galactosidase - hydrolyzes lactose into glucose and galactose
LacY - lactose permease - transports lactose into the cell
LacA - thiogalactoside transacetylase - transacetylates galactosides

72
Q

LacI gene (i not 1)

A

Encodes a protein repressor and the protein’s operator (binding site in the DNA) just 5’ to the start of the operon

Responsible for the regulated expression of the operon

73
Q

Promotor

A

Part of the lac operon where RNA polymerase binds to the DNA to start transcription

Precedes the operator and structural genes

74
Q

Operator

A

The cis regulatory element of the lac operon where the protein repressor binds to

Precedes the structural genes

75
Q

Repressor protein (lac operon)

A

Binds to the operator sequence in the absence of lactose and prevents transcription of the operon

Lactose, when present, binds to the repressor protein and changes its conformation which lowers its affinity to bind to the operator sequence, resulting in the expression of the operon

76
Q

Modes of regulation in prokaryotes

A
  1. Induction (lac operon)
  2. Repression (arg operon)
  3. Activation (mal operon)
77
Q

Induction/Enzyme induction

A

As found in the lac operon
Mode of regulation in prokaryotes
An inducer (i.e. lactose) binds to the repressor protein, changing its conformation and lowering its affinity to bind to the operator sequence, resulting transcription

78
Q

Repression/Enzyme repression

A

As found in the arg operon
Mode of regulation in prokaryotes
A corepressor must bind to a repressor in order to turn off transcription

79
Q

Activation

A

As found in the map operon
Mode of regulation in prokaryotes
An activator binds to RNA polymerase to turn on transcription

80
Q

Attenuation

A

Mechanism of regulation found in bacteria (prokaryotes)

Formation of stems and loops in the RNA by intrastrand H bonding of complementary bases, allow or prevent transcription

81
Q

Enhancers

A

Distal regulatory elements that stimulate expression of distant genes

82
Q

Silencers

A

Distal regulatory elements that dampen expression of distant genes

83
Q

Epigenetic regulation

A

Gene regulation in ways other than by cis elements and transcription factors

Histone modification
DNA methylation
Gene silencing

84
Q

Chromatin

A

NuclearDNA that is compacted onto nucleosomes

85
Q

Nucleosome

A

~ 150 bp of DNA wrapped around a complex of 8 histone proteins, two each of H2A, H2B, H3, H4

86
Q

Histones

A

Structural proteins
Can regulate access of transcription factors and RNA polymerase to the DNA helix

Modification of histones affects the activity of chromatin-associated proteins and transcription factors that increase or decrease gene expression

Protein interactions allows chromatin to move between transcriptionally active and silent states

87
Q

Enhanceosome

A

Architectural and regulatory proteins assembled on an enhancer element

88
Q

DNA methylation

A

Type of epigenetic regulation of gene expression in prokaryotes and eukaryotes

Methylation occurs on CpG islands
Main mechanism of genomic imprinting

89
Q

CpG islands

A

CG-rich sequences

Found around the first exons, promotor regions, and sometimes toward the 3’ ends of genes

90
Q

Genomic imprinting

A

Gamete-specific silencing of genes

Maintains the balanced expression of genes in growth and embryonic development by selective methylation of homologous genes

91
Q

RISC

A

RNA induced silencing complex

Uses associated siRNA to bind and degrade mRNA with sequences exactly complementary to the siRNA, therefore allowing translation of specific genes to be inhibited

Diagnostic Molecular Biology (22 decks)

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