Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

M2M Unit I > DNA & RNA > Flashcards

DNA & RNA Flashcards

(80 cards)

Start Studying
1
Q

Dinucleotide sequence marking the 5’ end of intron

A

GU

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Dinucleotide sequence marking the 3; end of intron

A

AG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the spliceosome made of?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

U1 snRNA

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Relative solubility of DNA components

A

Nucleotide > Nucleosides > Base

Pyrimidines > Purines

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Deamination

A

Deamination of 5-methyl cytosine converts 5mC to thymine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Depurination

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Classes of RNA

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

B form DNA

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

DNA Methylation

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Alkylating agents

A

React with nucleophilic groups on purine/pyramidine bases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

RNA Polymerase I

A

Synthesizes pre-ribosomal RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

RNA Polymerase II

A

synthesizes mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

RNA Polymerase III

A

synthesizes tRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

TFIID

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

a-amanitin

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
RNA Polymerase II pre-initiation complex
RNA Polymerase II TFIID (TBP + TAFs) TFIIA, TFIIB, TFIIE, TFIIF, TFIIH
26
TFIIF
Part of RNA polymerase II preinitiation complex; phosphorylates RNA polymerase II, which activates it
27
TFIIH
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)
28
Xeroderma Pigmentosum
Autosomal recessive disorder of DNA repair, usually caused by mutation in one of the nucleotide excision repair pathways - often TFIIH
29
5' splice site consensus sequence
GU
30
3' splice site consensus sequence
AG
31
PolyA tail cleavage site consensus sequence
AAUAAA 10 to 30 nucleotides upstream from the cleavage site
32
U2 snRNA
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
33
DNA Polymerase III
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
DNA Polymerase I
Mostly involved in replacing RNA primer with DNA; has exonuclease activity in the 5-3' direction that removes the RNA primer
35
Hereditary non-polyposis colorectal cancer (HNPCC) / Lynch Syndrome
Caused by mutations in the machinery that performs mismatch DNA repair
36
Cockayne Syndrome (CS), Xeroderma Pigmentosum, and Trichiothiodystrophy
Caused by mutations in genes that mediate nucleotide excision repair (NER), often TFIIH
37
Deamination of C yields...
U; can result in permanent mutation of a CG base pair to a TA base pair
38
DNA Mismatch repair
Fixes errors in nucleotide incorporation made by DNA polymerase during DNA replication
39
MutS and MutL (proks) / MSH and LH (euks)
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
Nucleotide Excision Repair (NER)
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
Base excision repair (BER)
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
Homologous Recombination (HR)
Repairs double-stranded DNA breaks between homologous ends
43
Non-homologous end joining (NHEJ)
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
Lesion Bypass Repair
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
DNA control element
Regulatory sequences of DNA that act locally by binding transcription factors or other regulatory proteins to control expression of the gene
46
B-Thalassemia
Inherited anemia associated with a mutation in the B-globin promoter, reducing the amount of B-globin mRNA that is transcribed
47
Hemophilia B Leyden
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
Fragile X Syndrome
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
Sequence-specific DNA binding proteins
Trans-acting activators or repressors that bind directly to DNA control elements in their target genes to regulate transcription
50
Co-factors
Trans-acting activators or repressors that bind to sequence-specific DNA binding proteins to affect transcription
51
DNA Binding Domains - 4 categories
Helix-Turn-Helix Zinc Finger Basic Leucine Zipper Proteins (bZLP) Basic Helix-Loop-Helix motif (bHLH)
52
Androgen Insensitivity Syndrome
Caused by a mutation in the androgen receptor (a zinc finger DNA binding protein), making them less responsive to androgens
53
Waardenburg Syndrome Type II
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
Histone core complex
Octamer consisting of dimers of: H2A, H2B, H3, and H4
55
Histone H1
Bound to the linker DNA between histone octamers; functions to "slide" histones along DNA
56
Two classes of chromatin remodeling factors
ATP-dependent | Reversible modifiers
57
SWI/SNF family
ATP-dependent chromatin remodelers
58
Histone Acetyltransferaces (HATs)
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
Rubinstein-Taybi Syndrome
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
Reversible modification of chromatin
Activators recruit histone acetyl transferaces (HATs) = activator-directed hyperacetylation Repressors recruit histone de-acetyltransferaces (HDACs) = repressor-directed histone deacetylation
61
Tamoxifen
Tamoxifen antagonizes estrogen by binding to the estrogen receptor (ER) and preventing recruitment of HAT co-factors (activators)
62
NFKB pathway
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
How does aspirin work?
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
Id family of proteins
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
Ribosomal subunits (prok & euk)
Prok - 30S & 50S (70S total) | Euk - 40S & 60S (80S total)
66
Stop codons
UAA UAG UGA
67
Shine-Delgarno sequence
Prokaryotic ribosomal binding site; essentially corresponds with initiator AUG codon
68
Initiation Factor 4E (IF4E)
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
Elongation factors (prok & euk)
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
How many high energy bonds burned per AA?
4! 2 to charge aa-tRNA 1 to deliver aa-tRNA to A site 1 for translocation of ribosome
71
Initiation of Translation - Bacteria
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
Rapamycin
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
Interferon
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
Transferrin Receptor regulation
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
Ferritin Pathway
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
DNA Polymerase delta
Performs DNA synthesis on the lagging strand in eukaryotes; contains 3-5; exonuclease activity
77
DNA Polymerase alpha
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
DNA Polymerase epsilon
Performs DNA synthesis on the leading strand in eukaryotes; contains 3-5' exonuclease activity
79
Z-DNA
Left Handed Helix form
80
Release Factor (RF)
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)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions