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Molecular Foundations of Medicine > RNA > Flashcards

RNA Flashcards

1
Q

transcription

A
  • RNA synthesized from the template DNA strand in a 5’ to 3’ direction.
  • The coding strand is complementary to the template strand and shows what the RNA will look like, aside from having thymadine instead of uradine
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2
Q

messenger RNA

A
  • longest chains of RNA

* nucleotides specify amino acids that are used to make proteins

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3
Q

ribosomal RNA

A

forms ribosomes (site of protein synthesis in cells)

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4
Q

transfer RNA

A
  • transfers amino acids to proteins

* important for translation

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5
Q

micro RNA (miRNA)

A
  • target mRNA molecules -> bind via base pairing -> remove poly-A tail -> mRNA degradation by endonucleases
  • block translation into protein
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6
Q

small interfering RNA (siRNA)

A
  • regulate gene expression

* cause degradation of mRNA

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7
Q

small nuclear RNA (snRNA)

A

splicing of pre-mRNA

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8
Q

RNA polymerase

A
  • synthesizes RNA from DNA template by binding to promoter region and opening double helix
  • does NOT require a primer
  • requires transcription factors (proteins)
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9
Q

types of RNA polymerase

A

Eukaryotes:
•RNA polymerase I -> most rRNA (5.8S, 18S, and 28S)
•RNA polymerase II -> mRNA
•RNA polymerase III -> rRNA (5S) and other RNAs
Prokaryotes have only 1 RNA polymerase that is a multisubunit complex

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10
Q

alpha amanitin

A
  • powerful inhibitor of RNA polymerase II
  • from death cap mushroom (amanita phalloides)
  • liver failure
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11
Q

Rifampin

A
  • inhibits bacterial RNA polymerase

* used for tuberculosis

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12
Q

actinomycin D

A

•used in chemotherapy to inhibit RNA polymerase -> blunts replication of cancer cells

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13
Q

promoters

A
  • DNA regions that are not transcribed
  • bind to RNA polymerase and transcription factors
  • binding to RNA polymerase opens double helix
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14
Q

common eukaryotic promoters

A
  • TATA box (TATAAA, binds esp TFIID)
  • CAAT box (CCAAT)
  • GC box (GGGCGG)
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15
Q

Enhancers

A
  • DNA sequences that increase rate of transcription
  • can be upstream or downstream from gene
  • bind to transcription factors called activators -> stabilize transcription factors/ RNA polymerase
  • b/c DNA coiling, can be geometrically close to gene while many nucleotides away
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16
Q

Silencers

A
  • DNA sequences that decrease rate of transcription
  • can be up- or downstream of gene
  • binds transcription factors called repressors -> prevent RNA polymerase binding
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17
Q

untranslated regions

A
  • 5’ end -> upstream coding sequence and recognized by ribosomes to initiate translation
  • 3’ end -> found after stop codon; importation for post-translational gene expression
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18
Q

significance of introns and exons

A
  • Eukaryotic DNA has introns and exons that are transcribed into RNA within the nucleus
  • before exiting nucleus the introns are cut out of the RNA
  • only the exon portions enter cytoplasm to be translated to protein
  • histone genes don’t have introns
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19
Q

heterogeneous nuclear RNA (hnRNA)

A

=pre-mRNA

•the initial transcript that is modified in nucleus to become mRNA

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20
Q

key modifications to mRNA before it leaves nucleus

A
  • 5’ capping
  • splicing out of introns
  • 3’ polyadenylation
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21
Q

5’ capping

A
  • addition of 7-methylguanosine to 5’ end soon after transcription begins
  • distinguishes mRNA from other RNA
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22
Q

RNA splicing

A
  • occurs during trancription
  • removal of introns
  • introns always have 2 nucleotides at either end: 5’ = GU and 3’ = AG
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23
Q

snRNPs

A

= small nuclear ribonucleaoproteins
•short RNA polymers with proteins
•RNAs have high content of uridine (U-RNA)
•5 U-RNAs: U1, U2, U4, U5, U6

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24
Q

spliceosome

A

= snRNPs + mRNA
•intron portion of mRNA forms loop called “lariat”
•lariat is released, then exons are joined

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25
Q

anti-SM (anti-smith)

A
  • antibodies against proteins in snRNPs

* seen in lupus

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26
Q

anti-RNP

A
  • antibodies against proteins in U1 RNA
  • strongly assoc with Mixed Connective Tissue Disease
  • also seen in lupus and scleroderma
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27
Q

alternative splicing

A
  • allows many proteins to be made from the same gene by using a different combination of exons for translation
  • allows eukaryotic cells to be more advanced and high functioning than prokaryotes
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28
Q

splicing errors

A
  • loss of exons, retention of introns/incorrect joining of introns
  • beta thalassemia - many mutations, but some involve splice sites
  • oncogenesis - many splice site errors described
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29
Q

3’ polyadenylation

A
  • triggered by polyadenylation signal (AAUAAA) which is followed by 10-30 nucleotides the CA
  • once CSF and CstF bind, transcription is terminated
  • then poly-A polymerase (PAP) binds and adds ~200 adenosines to the 3’ end (poly-a tail)
  • NO template
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30
Q

Cleavage and polyadenylation specificity factor (CSF)

A

RNA binding protein that binds to AAUAA (polyadenylation signal)

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31
Q

Cleavage stimulation factor (CstF)

A

RNA binding protein that binds to CA sequence

32
Q

poly-a polymerase (PAP)

A

the enzyme that binds after transcription has been terminated to add the poly A tails (~200 adenosine nucleotides) and removes part of the mRNA molecule

33
Q

Processing bodies (P-bodies)

A
  • organelles in cytoplasm
  • some mRNA with less extensive miRNA binding will be sequestered here so its not translated
  • mRNA often degraded, but some evidence shows it may be later translated
34
Q

translation

A
  • mRNA template -> protein
  • occurs in cytoplasm on ribosomes
  • tRNA brings amino acids to ribosome for protein assembly
35
Q

ribosomes

A
  • some free in cytoplasm, some part of rough ER
  • contain rRNA and proteins
  • large and small subunits
  • size measured in svedberg units
36
Q

svedberg units

A
  • used to measure sized of ribosomes

* measure of the rate of sedimenation by centrifucation

37
Q

prokaryotic ribosomes

A 
•70S ribosomes
•small units is 30S and large is 50S
•small subunit: 16S RNA + proteins
•large subunit: 5S RNA and 23S RNA + proteins
(LOW yield)
38
Q

protein synthesis inhibitor antibiotics

A
  • target ribosomes of the size found only in bacteria

* ie aminoglycosides

39
Q

Eukaryotic ribosomes

A 
•80S ribosomes
•small unit 40S and large unit 60S
•small subunit: 18S RNA + proteins
•large subunit: 5S RNA, 28 S RNA, 5.8S RNA + proteins
(LOW yield)
40
Q

tRNA

A
  • transfer amino acids to protein chains
  • synthesized by RNA polymerase III
  • many bases are chemically modified
  • cloverleaf shape (secondary structure) b/c base paring within molecule
  • 70-90 nucleotides in length (tiny)
41
Q

key portions of tRNA cloverleaf

A
  • anticodon loop
  • D loop (part of D arm)
  • T loop (part of T arm
  • 3’ end
42
Q

anticodon of tRNA

A
  • 3 nucleotides on tRNA
  • pairs with complementary mRNA
  • correct pairing -> correct protein synthesis
43
Q

D loop of tRNA

A
  • contains dihydrouridine

* recognized by aminoacyl-tRNA synthetase

44
Q

T loop of tRNA

A
  • contins T psi C sequence (TψC)
  • T = ribothymidine
  • psi = pseudouridine
  • C = cytidine
  • needed for tRNA ribosome binding
45
Q

3’ end of tRNA

A
  • always ends in CCA

* hydroxyl (OH) of A attaches to amino acid

46
Q

charging of tRNA

A
  • linking of amino acid to 3’ end of tRNA
  • catalyzed by Aminoacyl-tRNA synthetase
  • requires ATP
47
Q

aminoacyl-tRNA synthetase in eukaryotes

A

in general there is a unique enzyme for every amino acid

48
Q

hydrolytic editing

A
  • aminoacyl-tRNA synthetase can also proofread the amino acid
  • if incorrect it hydrolyzes it either from AMP or tRNA
49
Q

protein synthesis direction

A

new amino acids are added the c-terminus of previos amino acids in protein synthesis

50
Q

ribosome binding sites

A
  • one for mRNA
  • 3 for tRNA (they are codons in the mRNA)
  • A-site: amino acid binding (anticodon) (3’)
  • P-site: tRNA attached to growing protein chain
  • E-site: exit of tRNA (5’)
51
Q

initiation of translation

A
  • begins with tRNA for methionine binding to the P-site at AUG start codon
  • usually removed later by protease enzymes
  • uses GTP hydrolysis
  • in eukaryotes initiation factors are need to help assemble ribosomes and tRNA
52
Q

N-formylmethionine (fMET)

A
  • initiation codon AUG -> N-formylmethionine (fMET) in bacteria
  • fMET in human bodies triggers chemotaxis of neutrophils (innate immunity)
53
Q

elongation of translation

A

•uses elongation factors -> hydrolyze GTP to GDP

  1. charged tRNA binds to A-site
  2. amino acid joined to peptide chain (catalyzed by ribozyme activity called peptidyl transferase)
  3. ribosome translocation -> protein moved to p-site, a-site now empty, and tRNA in E site, ready to exit
  4. tRNA leaves E site
54
Q

elongation factors in eukaryotes

A
  • EF1 and EF2

* EF2 is the target of bacterial toxins -> inhibit protein synthesis (ie diptheria toxin and eotoxin A)

55
Q

termination of translation

A
  • ends at mRNA stop codon (UAA, UAG, and UGA)
  • no tRNA anticodon for these codons -> no amino acid
  • stop codon encountered -> releasing factors bind to ribosome -> catalyze addition of water to protein chain (add OH group)
56
Q

posttranslational modification

A
  • create functional protein

* includes folding and addition of other molecules

57
Q

phosphorylation

A
  • posttranslational modofication

* amino acid residue phosphorylated by protein kinase enzymes

58
Q

glycosylation

A
  • posttranslational modification
  • formation of sugar-amino acid linkage
  • N-, O-, C-linked glycosylation (sugar + nitrogen, oxygen, carbon)
  • creates glycoproteins
59
Q

hydroxylation

A
  • posttranslational modification
  • addition of hydroxyl (OH) groups
  • important for collagen synthesis (hydroxilation of proline and lisine residues)
60
Q

methylation of protein

A
  • posttranslational modification

* addition of methyl (CH3) groups

61
Q

acetylation of protein

A
  • posttranslational modification

* addition of acetyl (CH3CO) group

62
Q

ubiquitination of protein

A
  • posttranslational modification
  • addition of ubiquitin (small protein)
  • tags proteins for destruction of proteasome
63
Q

chaperones

A
  • proteins that facilitate folding of other proteins

* classic example heat shock proteins

64
Q

heat shock proteins

A
  • aka stress proteins
  • chaperones that are constitutively expressed, but levels increased with heat, pH shift, and hypoxia
  • stabilized proteins/maintain structure
  • helps cells survive environmental stress
65
Q

mRNA start codon

A

AUG -> methionine in eukaryotes

school starts in AUGust

66
Q

mRNA stop codons

A

UGA -> u go away
UAG -> u are going
UAA -> u are away

67
Q

RNA stability

A
  • stability/decay affects gene expression
  • RNAs have varying half lives
  • 3’ UTR is important in RNA stability/instability
68
Q

Iron response elements (IRE)

A
  • if low [iron] iron response proteins (IRPs) bind to IREs and repress ferritin translation while promoting transferrin receptor translation
  • if high [iron] iron binds to IRPs and releases them from IREs -> ferritin translation occurs and transferrin receptor mRNA degraded
69
Q

nonsense mediated decay (NMD)

A

•surveillance pathway to reduce errors in gene expression by eliminating mRNA

70
Q

beta-thalassemia

A
  • autosomal recessive inheritance
  • anemia with reduced or absent synthesis of beta chains of hemoglobin
  • depends on nonsense mediated decay pathway
71
Q

Duchenne muscular distrophy (DMD)

A
  • mutation on dystrophin gene

* nonsense mutation that causes mRNA decay and loss of functional protein

72
Q

becker muscular dystrophy

A

•mutation on dystrophin gene, but does not involve a frameshift mutation

73
Q

diamond blackfan anemia

A
  • proapoptotic hematopoiesis, bone marrow failure, birth defects and predisposition to cancer
  • cause by mutations in ribosomal proteins
74
Q

treacher collins syndrome

A
  • autosomal dominal craniofacial disorder

* mutation in TCO1 (treacle) -> role in ribosome biogenesis

75
Q

small nucleolar RNAs (snoRNAs) mutations

A

mutations can cause prader-willi syndrome

76
Q

chronic lymphocytic leukemia (CLL)

A
  • most common leukemia in adults

* loss of part of chromosome 13 -> contains gene encoding miRNAs-15 and -16

Molecular Foundations of Medicine (21 decks)

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