Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Human Genetics > DNA Basics > Flashcards

DNA Basics Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

DNA stands for

A

deoxyribonucleic acid

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

number of base pairs in nuclear genome

A

~3 billion

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

base pairs in mt genome

A

~16 kb (100s-1000s in cells)

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

nucleotide composition

A

sugar (deoxyribose), phosphate on 5’ of sugar, nitrogenous base on 1’ of sugar

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

nucleoside composition

A

sugar and nitrogenous base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

purines

A

A and G (double ring)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

pyrimidines

A

T and C (single ring)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

DNA backbone

A

phosphate (5’) - sugar (3’)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

G pairs with what? with how many bonds?

A

C, 3

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

A pairs with what? with how many bonds?

A

T, 2

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

what type of bond holds double helix together?

A

hydrogen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

which bases are more prevalent in gene rich areas?

A

GC

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

nucleosome

A

147 bp wrapped around 8 histones, plus some linker DNA to next nucleosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

solenoid

A

6-8 nucleosomes per turn. fifth histones bound to linker segments in middle

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

coding DNA amount

A

(produces protein) ~1.2% of genome. ~20,000 genes

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

does number of genes correspond to chromosome size?

A

no

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

what percent of nuclear genome is highly conserved?

A

~5%

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

five ways to get DNA duplication

A

unequal crossover (homologs or sister chromatids), transposons, ancestral cell fusion, genome duplication, translocation

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

retrotransposon

A

uses a reverse transcriptase

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

DNA transposon

A

migrates without copying. Just excised and reinserted elsewhere

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

LINES

A

autonomous transposons. Retrotransposons. 20% of genome. Usually integrate into gene poor areas

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

SINES

A

non autonomous retrotransposon. Alu is a SINE- 10% of genome, most abundant sequence

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

Satellite DNA

A

high copy number tandem repeats

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

mini-satellites

A

10-60 bp repeats, up to 20 kb

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

micro-satellites

A

1-4 bp repeats, up to 1 kb

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

nonprocessed pseudogene

A

contains introns, UTRs, etc. Matches full gene sequence. normally found near functional gene.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

processed pseudogene

A

only contains coding sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

is mt DNA more or less prone to error than nDNA?

A

more error prone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

characteristics of mtDNA

A

highly conserved, no introns, ~66% coding, circular, ds (except for triple stranded loop), 37 genes (mostly tRNAs and oxydative phosphorylation proteins)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

most proteins in the mitochondria are coded in?

A

the nucleus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

why do we call dna replication semi conservative?

A

two newly synthesized molecules contain one strand from the original, and one new

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

replication forks

A

replication complex binds to origin of replication (many per chromosome). Replication proceeds in both directions from origin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

what does DNA polymerase require? How does it get it?

A

a free 3’ OH on a ds molecule. RNA polymerase makes a small primer so DNA polymerase can start

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

how does cell replicate lagging strand?

A

Okazaki fragments. 100-1000 bases. Added as fork opens. Ligated together.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

what proteins are needed for DNA replication?

A

topoisomerase, ligase, helicase, DNA polymerase, primase, ss binding proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

is replication of mt DNA uni or bidirectional?

A

uni

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

what is replicative segregation in mitochondria?

A

during mitochondrial division, multiple copies of mtDNA replicate and sort randomly. During cell division, multiple mitochondria sort randomly.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

telomere composition/construction

A

repeats of TTAGGG. G-rich 3’ overhang folds back to create a T-loop.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

telomerase

A

TERC serves as an RNA template for telomeric repeats. TERT is reverse transcriptase that adds the bases. T-loop still created

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

how a ribonucleic acid differ from deoxyribonucleic acid?

A

RNA has an OH at 2’ of sugar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

how is U different from T?

A

T has CH3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

c-value paradox

A

gene number does not correspond to complexity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

what percent of human genome is highly conserved?

A

~10% (including mtDNA?)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

definition genotype

A

genetic constitution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

phenotype

A

chemical, physiological, and morphological characteristics as defined by genome and environment

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

three examples of ncRNAs

A

snoRNA, miRNA, snRNA, piRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

where does transcription start? what number?

A

Beginning of exon 1. Could be “negative whatever”

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

where does translation start? what number?

A

usually within exon 1, but not always. +1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

where is the poly A tail signal?

A

end of last exon, after 3’ UTR

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

histone modification

A

certain aa in histone tails can be acytylated or methylated. Alters charge of histones, and therefore configuration, and therefore openness of chromatin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

example of histone modification disease

A

Kabuki sydrome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

epigenetics

A

enduring changes in gene expression that do not involve sequence modifications

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

what DNA bases are methylated?

A

C’s preceding G’s

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

DNA methylation usually represses transcription. How?

A

Directly- some proteins can’t bind. Indirectly- contributes to tighter conformation of chromatin

55
Q

example of DNA methylation disease?

A

Lynch syndrome, many cancers

56
Q

promoters

A

usually upstream of 5’ UTR. Highly heterogenous, though some common motifs (TATA box) have been noted.

57
Q

enhancers and silencers

A

DNA sequence elements that can act at a distance from a gene to regulate transcription. Can be up or downstream

58
Q

TADs

A

topologically associated domains. discrete chromosome regions that interact with each other more often

59
Q

transcription initiation

A

requires promotor and transcription factors

60
Q

basal transcription aparatus

A

guides RNA polymerase to transcription start site. includes RNA polymerase and transcription factors

61
Q

transcription factors

A

sequence-specific DNA binding proteins that bind close to promoter

62
Q

does RNA polymerase need a primer?

A

No

63
Q

how is RNA pol released from DNA?

A

exonuclease begins removing bases in 5’-3’ direction until it catches up with RNA pol

64
Q

5’ capping

A

methylated nucleoside added to 5’ end by phosphodiester bond

65
Q

how is 3’ end of mRNA determined?

A

AAUAAA or variant in 3’ UTR signals cleavage about 15-30 bases downstream from itself. After cleavage, poly A tail added.

66
Q

start and end of introns

A

GT(U)….AG

67
Q

branch site

A

conserved intronic sequence. Has an invariable A. provides first nucleophilic attack for splicing mechanism. Also a binding site for elements of spliceosome?

68
Q

RNA editing

A

post translational (did I mean transcriptional?) base changes. ex, U to C, C to U, A to I

69
Q

microRNA

A

ss RNA, ~20 b. in cytoplasm. Guides RISC. Binds to 3’ UTR and down regulates (degradation if perfect match, repressing translation if imperfect match)

70
Q

nonsense mediated decay pathway

A

identifies premature stop codons. depends on proteins bound to splice areas, so does not work on intronless genes

71
Q

mtDNA transcription

A

bidirectional? Unlike replication? Large multigenic transcript

72
Q

structure of amino acid

A

amino group (+charge), carboxylic acid group (-charge), side chain.

73
Q

bonds between amino acids

A

peptide bonds. condensation reaction between carboxyl group and amino group

74
Q

does mitochondria need tRNA from nucleus?

A

No, makes all its own tRNA

75
Q

ribosome composition

A

~80 proteins and 4 RNA molecules

76
Q

ribosome binding sites

A

Positions itself until it finds AUG, then AUG tRNA binds P site, and tRNA for second codon binds A site. Bond created, second tRNA slides to P site, third tRNA enters A site

77
Q

translation termination

A

when termination codon encountered, protein release factor enters A site

78
Q

asymmetric exon

A

non divisible by 3

79
Q

four levels of protein organization

A

sequence, initial folding, overall three dimensional shape, interaction with other proteins

80
Q

protein folding stabilization

A

achieved by covalently and non-covalently bonded entities. Chaperones also help stabilize and fold.

81
Q

protein degradation process

A

ubiquitinated by ubiquitin ligase. Proteosomes then degrade protein.

82
Q

genomic imprinting

A

physiologic form of gene regulation that causes a subset of genes to be expressed from only 1 of the 2 parental chromosomes

83
Q

mechanism of genomic imprinting

A

differential methylation of imprinting control centers

84
Q

mechanism of x inactivation

A

Inactivation initiated at X inactivation center, Xic at Xq13. Xic encodes a long non coding RNA, XIST. XIST binds to inactive X and recruits proteins to organize chromatin into inactive state

85
Q

what genes escape X inactivation?

A

Two pseudoautosomal regions plus some others

86
Q

how does an X:autosome translocation affect x inactivation

A

chromosome with the Xic becomes inactivated. This can spread into the autosomal region. The x segment on the autosomal chromosome does not become inactivated

87
Q

skewing of x inactivation

A

when one X is abnormal, it is preferentially inactivated. When there is an X:autosome translocation, the normal X is preferentially inactivated.

88
Q

single strand repairs

A

base excision repair, single strand break repair, nucleotide excision repair, base mismatch repair, direct reversal of damage

89
Q

double strand repairs

A

homologous recombination mediated repair, nonhomologous end joining

90
Q

variant

A

any sequence change as compared to reference

91
Q

polymorphism

A

DNA variant that is prevelant at >1%

92
Q

copy number variants

A

200 bp - 2 Mb. recent discovery. common.

93
Q

SNP

A

1/300 nucleotides is polymorphic. numerically, most abundant type of genetic variant. usually biallelic

94
Q

origin of SNPs

A

ancestral chromosome segments (rather than recurrent mutation)

95
Q

tandem repeat polymorphisms source

A

relatively recent. 1) minisatellite diversity from mispairing in meiosis. 2) microsatellite diversity from polymerase slippage during replication

96
Q

what’s better for distinguishing between individuals- SNPs or tandem repeat polymorphisms?

A

tandem repeats- there are more alleles

97
Q

sources of genetic variation

A

errors of replication, errors of recombination during repair, meiosis, and mitosis, and DNA damage

98
Q

why are CpG sequences mutational hotspots?

A

If C is methylated then deaminated, it becomes T, which is not always recognized for repair

99
Q

DNA damage forms

A

deamination, depurination, ROS, aberrant DNA methylation, radiation

100
Q

mismatch repair (MMR)

A

checks newly synthesized DNA for mismatched base pairs or small indels

101
Q

microsatellite instability could indicated that what repair pathway isn’t functioning?

A

MMR (ex. Lynch syndrome)

102
Q

base excision repair

A

main repair mechanism for most common DNA damage. Glycosylases cleave sugar-base bond. Endonuclease cuts and removes sugar and phosphate. DNA polymerase and ligase fills and seals gap.

103
Q

nucleotide excision repair

A

recognizes distortion of helix, removes and resynthesizes 25-30 bases with pol and ligase

104
Q

homologous recombination as repair for ds breaks

A

Occurs in S phase, sister chromatid used as template. Break resected to leave overhangs, strand invasion, DNA synthesis

105
Q

nonhomologous end joining

A

ligase joins ds breaks without template

106
Q

missense mutation

A

new amino acid

107
Q

nonsense mutation

A

new stop codon

108
Q

synonymous mutation

A

same amino acid

109
Q

dynamic mutations

A

copy number of microsatellites expands substantially between generations

110
Q

transition substitution

A

purine to purine or pyrimidine to pyrimidine

111
Q

transversion substitution

A

purine to pyrimidine or vice versa

112
Q

trinucleotide repeats are found where in genome?

A

anywhere. intron, exon, UTR

113
Q

frameshift nomenclature

A

listing the first amino acid change and the number of amino acids before the stop codon

114
Q

allele nomenclature

A

”[ ]”, separated by “;”

115
Q

nomenclature for introns

A

number of the last nucleotide of the preceding exon, a plus sign and the position in the intron, like c.77+1G. number of the first nucleotide of the following exon, a minus sign and the position upstream in the intron, like c.78-1G

116
Q

conservative amino acid substitution

A

replacing with a similar aa

117
Q

requirements for sanger sequencing

A

DNA pol, primers, dNTPs, ddNTPs

118
Q

sanger sequence read length

A

up to 1000

119
Q

major limitation of sanger

A

medium to large size deletions can be missed in heterozygous individuals

120
Q

library preparation for NGS

A

fragment DNA, add adaptors, denature

121
Q

reversible terminator sequencing

A

add fluorescently labeled terminator nucleotides (no 3’ OH). Take pic after addition. Restore bonding ability. repeat process. Number of cycles determines read length

122
Q

pyrosequencing

A

enzyme reaction gives light when PP naturally released during nucleotide addition. Add different dNTPs sequentially. Flash of light for base addition. No light means no addition. Multiple of bases will have more light.

123
Q

mapping

A

The computational process of identifying the specific region of a reference genome from which an individual sequenced DNA template originated

124
Q

mappable reads

A

Very short DNA sequences that can be determined to

originate from a single location in the genome

125
Q

mappable yield

A

The number of bases generated by a DNA-sequencing

instrument that can be mapped to the reference genome

126
Q

average depth of coverage

A

The average number of times each base in the genome was sequenced, as a function of the distribution and number of sequence reads that map to the reference genome. Make sure to differentiate between raw and post-alignment coverage.

127
Q

benefits of NGS

A

fast, high throughput, better ability to detect indels, better ability to detect mosaicism

128
Q

main limitation of NGS

A

short read lengths (~100 bases).

129
Q

can NGS sequencing detect Robertsonian translocations?

A

No

130
Q

What mechanism leads to minisatellite diversity (-> tandem repeat polymorphism, “Variable Number Tandem Repeats, VNTRs)?

A

mispairing in meiosis

131
Q

What mechanism leads to microsatellite diversity (-> tandem repeat polymorphism, “Short Tandem Repeat Polymorphisms, STRPs)?

A

polymerase slippage during replication

132
Q

Nucleolus Organizer Region

A

the NORs are located on the short arms of the acrocentric chromosomes 13, 14, 15, 21 and 22, the genes RNR1, RNR2, RNR3, RNR4, and RNR5 respectively.[1] These regions code for 5.8S, 18S, and 28S ribosomal RNA.[1] The NORs are “sandwiched” between the repetitive, heterochromatic DNA sequences of the centromeres and telomeres.

133
Q

Nucleolus

A

largest structure in the nucleus of eukaryotic cells.[1] It is best known as the site of ribosome biogenesis

Human Genetics (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions