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M2M Unit I > DNA & RNA > Flashcards

DNA & RNA Flashcards

1
Q

Dinucleotide sequence marking the 5’ end of intron

A

GU

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2
Q

Dinucleotide sequence marking the 3; end of intron

A

AG

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3
Q

What is the spliceosome made of?

A

Small nuclear ribonuclear proteins (snRPS) and snRNAs U1, U2, U4, U5, U6

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4
Q

U1 snRNA

A

Contains a sequence complementary to the mRNA sequence near the 5’ splice site of introns

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5
Q

Relative solubility of DNA components

A

Nucleotide > Nucleosides > Base

Pyrimidines > Purines

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6
Q

Gout

A

A defect in hypoxanthine-guanine phosphoribosyl transferase; leads to the accumulation of purines (uric acid) in tissues, often presenting as red/swollen, most commonly in the big toe

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7
Q

Lesch-Nyhan syndrome

A

A genetic defect in hypoxanthine-guanine phophoribosyl transferase (HGPRT); leads to the accumulation of purines (uric acid) in tissues; presents as severe gout, kidney problems, cognitive defects, and self-injuring behavior

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8
Q

Chargaff’s Rule

A

The ratio of purines (G + A) and pyrimidines (T + C) must be equal as a result of G-C and A-T base pairing; %G = %C and %A = %T

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9
Q

Tm

A

Temperature at which a given DNA strand is 50% denatured; affected by salt concentration, pH, DNA chain length, and GC content

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10
Q

Deamination

A

Deamination of 5-methyl cytosine converts 5mC to thymine

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11
Q

Depurination

A

Spontaneous hydrolysis of a purine base from it’s sugar-phosphate backbone, leaving the DNA backbone vulnerable to cleavage

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12
Q

Nucleoside analogue drugs

A

Inhibit DNA synthesis by mimicking normal nucleotide substrates in the DNApoly active site; ex: AZT inhibits HIV viral DNA synthesis by reverse transcriptase

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13
Q

Classes of RNA

A

Structural (rRNA, tRNA, snRNA, snoRNA)
Information-containing (mRNA)
Regulatory (miRNA, siRNA)

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14
Q

Puromycin

A

Antibiotic; inhibits bacterial translation by mimicking the 3’ tRNA acceptor region and interacting with the ribosome to cause premature peptide release

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15
Q

B form DNA

A

The most common form of DNA; two anti-parallel strands intertwined in a right-handed helix

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16
Q

DNA Methylation

A

Usually occurs on C within CpG dinucleotide sequences; performed by DNA methyltransferase; generally down regulates gene expression

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17
Q

Alkylating agents

A

React with nucleophilic groups on purine/pyramidine bases

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18
Q

RNA Polymerase I

A

Synthesizes pre-ribosomal RNA

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19
Q

RNA Polymerase II

A

synthesizes mRNA

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20
Q

RNA Polymerase III

A

synthesizes tRNA

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21
Q

TATA Box / Initiator sequence

A

DNA control element located 25-30 bp upstream from the transcription start site; bound by TATA-binding protein (TBP); this is the site at which general TFs bind

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22
Q

TFIID

A

Contains TATA-binding protein (TBP) as well as TBP-associated factors (TAFs)

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23
Q

a-amanitin

A

Death cap mushroom toxin; blocks the translocation of RNA polymerase II by interacting with its bridge helix

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24
Q

Rifampicin

A

Antibiotic; binds to RNA polymerase at the exit channel and sterically occludes the formation of mRNA chains > 2-3 nucleotides long

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25
Q

RNA Polymerase II pre-initiation complex

A

RNA Polymerase II
TFIID (TBP + TAFs)
TFIIA, TFIIB, TFIIE, TFIIF, TFIIH

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26
Q

TFIIF

A

Part of RNA polymerase II preinitiation complex; phosphorylates RNA polymerase II, which activates it

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27
Q

TFIIH

A

Part of RNA Polymerase II pre-initiation complex; CDK7 subunit phosphorylates Pol II CTD; has some helicase activity, and functions in nucleotide excision repair (NER)

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28
Q

Xeroderma Pigmentosum

A

Autosomal recessive disorder of DNA repair, usually caused by mutation in one of the nucleotide excision repair pathways - often TFIIH

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29
Q

5’ splice site consensus sequence

A

GU

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30
Q

3’ splice site consensus sequence

A

AG

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31
Q

PolyA tail cleavage site consensus sequence

A

AAUAAA 10 to 30 nucleotides upstream from the cleavage site

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32
Q

U2 snRNA

A

Base pairs with the intron at a position corresponding with the branch point A residue, causing a local distortion in the primary transcript that activates the branch point A

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33
Q

DNA Polymerase III

A

The main polymerase involved in DNA replication; Pol III “holds on” to the DNA via a sliding clamp protein and has 3-5’ exonuclease activity that enables proofreading

34
Q

DNA Polymerase I

A

Mostly involved in replacing RNA primer with DNA; has exonuclease activity in the 5-3’ direction that removes the RNA primer

35
Q

Hereditary non-polyposis colorectal cancer (HNPCC) / Lynch Syndrome

A

Caused by mutations in the machinery that performs mismatch DNA repair

36
Q

Cockayne Syndrome (CS), Xeroderma Pigmentosum, and Trichiothiodystrophy

A

Caused by mutations in genes that mediate nucleotide excision repair (NER), often TFIIH

37
Q

Deamination of C yields…

A

U; can result in permanent mutation of a CG base pair to a TA base pair

38
Q

DNA Mismatch repair

A

Fixes errors in nucleotide incorporation made by DNA polymerase during DNA replication

39
Q

MutS and MutL (proks) / MSH and LH (euks)

A

Proteins that recognize mismatched DNA nucleotides as part of DNA mismatch repair pathway; these proteins recognize the error on the newly synthesized strand, which is unmethylated

40
Q

Nucleotide Excision Repair (NER)

A

Removes DNA lesions that distort the DNA structure and therefore block RNA or DNA polymerase (i.e. thymine dimers) - global and transcription-coupled pathways

41
Q

Base excision repair (BER)

A

Removes DNA lesions that do not cause distortions that block polymerase function, and therefore may be missed by NER; glycosylase enzymes hydrolyze the N-glycosidic bond to remove the damaged base, producing an AP site which is then removed by an AP-specific endonuclease

42
Q

Homologous Recombination (HR)

A

Repairs double-stranded DNA breaks between homologous ends

43
Q

Non-homologous end joining (NHEJ)

A

Repairs double-stranded DNA breaks; does not require sequence homology between the two broken ends - may lead to insertion or deletion of nucleotides at the break point

44
Q

Lesion Bypass Repair

A

Allows cells to continue replicating despite extensive DNA damage that cannot be repaired via other mechanisms; a DNA polymerase lacking 3-5; proofreading function is used to replicate past the lesion and is therefore highly mutagenic

45
Q

DNA control element

A

Regulatory sequences of DNA that act locally by binding transcription factors or other regulatory proteins to control expression of the gene

46
Q

B-Thalassemia

A

Inherited anemia associated with a mutation in the B-globin promoter, reducing the amount of B-globin mRNA that is transcribed

47
Q

Hemophilia B Leyden

A

X-linked disorder caused by an inherited mutation of the promoter of the Factor IX gene; affected males produce only 1% of the normal amount of Factor IX clotting protein until puberty, when trx increases to 60% of normal

48
Q

Fragile X Syndrome

A

Affected males have extra copies of a CGG trinucleotide repeat in the 5’ region of the Fragile X mental retardation 1 (FMR1) gene on the X chromosome, resulting in a failure to express the fragile X mental retardation protein (FMRP)

49
Q

Sequence-specific DNA binding proteins

A

Trans-acting activators or repressors that bind directly to DNA control elements in their target genes to regulate transcription

50
Q

Co-factors

A

Trans-acting activators or repressors that bind to sequence-specific DNA binding proteins to affect transcription

51
Q

DNA Binding Domains - 4 categories

A

Helix-Turn-Helix
Zinc Finger
Basic Leucine Zipper Proteins (bZLP)
Basic Helix-Loop-Helix motif (bHLH)

52
Q

Androgen Insensitivity Syndrome

A

Caused by a mutation in the androgen receptor (a zinc finger DNA binding protein), making them less responsive to androgens

53
Q

Waardenburg Syndrome Type II

A

Caused by a mutation in the MITF gene, which encodes a bHLH DNA binding protein that plays a role in the development of melanocytes

54
Q

Histone core complex

A

Octamer consisting of dimers of: H2A, H2B, H3, and H4

55
Q

Histone H1

A

Bound to the linker DNA between histone octamers; functions to “slide” histones along DNA

56
Q

Two classes of chromatin remodeling factors

A

ATP-dependent

Reversible modifiers

57
Q

SWI/SNF family

A

ATP-dependent chromatin remodelers

58
Q

Histone Acetyltransferaces (HATs)

A

Class of reversible chromatin modifiers; acetylate the N-termini of histones, neutralizing the positive charge on it’s N-terminal lysine AA and “freeing” the histone tails from electrostatic reactions with the DNA phosphate backbone

59
Q

Rubinstein-Taybi Syndrome

A

Results from mutations in one copy (haploinsufficiency) of the CREB binding protein (CBP) gene; CBP is a transcriptional co-activator for many TFs and is a histone acetyltransferase; presents as growth regardation, mental retardation, craniofacial dysmorphism

60
Q

Reversible modification of chromatin

A

Activators recruit histone acetyl transferaces (HATs) = activator-directed hyperacetylation
Repressors recruit histone de-acetyltransferaces (HDACs) = repressor-directed histone deacetylation

61
Q

Tamoxifen

A

Tamoxifen antagonizes estrogen by binding to the estrogen receptor (ER) and preventing recruitment of HAT co-factors (activators)

62
Q

NFKB pathway

A

NFKB protein is usually held in the cytoplasm by binding to its inhibitor (IKB); phosphorylation of IKB targets it for degradation, releasing NFKB to move into the nucleus where it turns on its target genes, including genes involved in inflammation

63
Q

How does aspirin work?

A

In part by inhibiting the phosphorylation of IKB, keeping it bound to NFKB and preventing translocation of NFKB from the cytoplasm to the nucleus

64
Q

Id family of proteins

A

Inhibitors of DNA-binding proteins (Id) heterodimerize with bHLH transcription factors to inhibit DNA binding - they contain the HLH-dimerization domain but lack the basic DNA-binding domain

65
Q

Ribosomal subunits (prok & euk)

A

Prok - 30S & 50S (70S total)

Euk - 40S & 60S (80S total)

66
Q

Stop codons

A

UAA
UAG
UGA

67
Q

Shine-Delgarno sequence

A

Prokaryotic ribosomal binding site; essentially corresponds with initiator AUG codon

68
Q

Initiation Factor 4E (IF4E)

A

Binds the 7-methyl guanosine cap on the 5’ unit of the mRNA; facilitates scanning of the ribosome down the primary transcript to the start AUG codon

69
Q

Elongation factors (prok & euk)

A

Ef-Tu (in bacteria) & EF1A in eukaryotes; deliver charged aa-tRNA to the A site of the ribosome, burning GTP when it dissociates from a correctly matched codon/anti-codon pair

70
Q

How many high energy bonds burned per AA?

A

4!
2 to charge aa-tRNA
1 to deliver aa-tRNA to A site
1 for translocation of ribosome

71
Q

Initiation of Translation - Bacteria

A

IF1 and IF 3 bind the small subunit, which binds the mRNA at the AUG start codon via base pairing between the Shine-Delgarno sequence and the 3’ rRNA
IF2 (bound to GTP) delivers initiation Met-tRNA to the P site to pair with the AUG codon
GTP hydrolysis on IF2 release all IFs and signals binding of the large subunit

72
Q

Rapamycin

A

An immunosuppressant drug; Inhibits mTOR (mammalian target of Rapamycin), which is a kinase that phosphorylates 4E-BP; inhibition of mTOR leads to dephosphorylation of 4E-BP, which is the state in which it binds eIF4E, silencing translation

73
Q

Interferon

A

Produced in response to cellular infection, interferon signals other cells by activating a kinase that phosphorylates eIF2; phosphorylation of eIF2 inhibits it from facilitating the binding of initiation Met-tRNA to the ribosome thereby shutting down translation

74
Q

Transferrin Receptor regulation

A

Brings iron into the cell; under conditions of low iron, IRE-BP is not bound to iron; it is free to bind the IRE element in the 3’ UTR of the transferrin receptor mRNA, protecting it from degradation and increasing translation of transferrin receptor

Under conditions of high iron, Iron is bound to IRE-BP, IRE-BP cannot bind the IRE element, and the mRNA is degraded

75
Q

Ferritin Pathway

A

Binds excess levels of iron; mRNA has IRE element in it’s 5’ UTR

Under conditions of high iron, IRE-BP is not bound by iron; it binds the IRE and prevents ribosomes from accessing the AUG start codon, silencing translation

Under conditions of high iron, the IRE-BP is bound by iron; it cannot bind the IRE and ferritin is translated to bind excess iron

76
Q

DNA Polymerase delta

A

Performs DNA synthesis on the lagging strand in eukaryotes; contains 3-5; exonuclease activity

77
Q

DNA Polymerase alpha

A

Functions in the synthesis of the first ~20 DNA nucleotides immediately following the RNA primers; also synthesizes the first basepairs of each Okazaki fragment

78
Q

DNA Polymerase epsilon

A

Performs DNA synthesis on the leading strand in eukaryotes; contains 3-5’ exonuclease activity

79
Q

Z-DNA

A

Left Handed Helix form

80
Q

Release Factor (RF)

A

Enters the A site (bound to GTP) in conjunction with a stop codon; hydrolysis of GTP induces release of the ribosomal subunits

M2M Unit I (5 decks)

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