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b11 Flashcards

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1
Q

what type of bond connects a base pair (ex A and T)

A

hydrogen bond

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2
Q

what do nucleosides consist of?

A

sugar + nitrogenous base

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3
Q

what do nucleotides consist of?

A

nucleoside + phosphate group (s)

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4
Q

what are the four nucleosides?

A

AdenoSINE, thrymidINE, guanoSINE, cytiDINE

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5
Q

true or false: purines and larger than pyrimidines

A

true, purines are double ringed and pyrimidines and single ringed

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6
Q

what are the purines and what are the pyrimidines

A

Purines: G and A
Pyrimidines: T, C, U (in RNA)

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7
Q

in a nucleotide, where is the phosphate group bonded to the sugar

A

5’ carbon of sugar

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8
Q

in a nucleotide, where is the nitrogenous base bonded to the sugar?

A

1’ carbon of sugar

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9
Q

nucleotides are joined together by:

A

3’ - 5’ phosphodiester linkages (3’ hydroxyl on carbon 3 joins to 5’ phosphate on carbon 5 of anther nucleotide)

  • 3’ end is a sugar of one nucleotide
  • 5’ is a phosphate of one nucleotide

thats why it is a SUGAR PHOSPHATE backbone!

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10
Q

how many hydrogen bonds are between nitrogenous bases

A

A and T: 2 hydrogen bonds
G and C: 3 hydrogen bonds

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11
Q

DNA to RNA

A

transcription

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12
Q

RNA to protein

A

translation

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13
Q

the complex of DNA and its tightly bound proteins

A

chromatin!

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14
Q

highly conserved means what

A

highly important

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15
Q

codes for the amino acid sequence of proteins

A

exons

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16
Q

spliced out during RNA processing

A

introns

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17
Q

changes in the nucleotide sequence of DNA can be caused by errors in what?

A

DNA replication OR DNA repair

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18
Q

change in the DNA sequence

A

mutation

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19
Q

switching one nucleotide for another

A

point mutation

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20
Q

who has a higher error rate? bacteria or humans

A

bacteria!
bacteria: 3 per 10^10 nucleotides copied
human: 1 per 10^10 nucleotides copied

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21
Q

addition of one or more nucleotide into a segment of DNA

A

insertions

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22
Q

removal of one or more nucleotide in a segment of DNA

A

deletions

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23
Q

addition of one or more copies of any piece of DNA into a segment

A

duplications

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24
Q

when a segment breaks off and reattaches within the same chromosome, but in reverse orientation

A

inversions

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25
Q

RNA that has catalytic activity

A

ribozymes

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26
Q

rearrangement between two chromosomes

A

interchromosomal rearrangements

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27
Q

rearrangement within 1 chromosome

A

intrachromosomal rearrangements

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28
Q

translocations where there is a swap of material without any net loss or gain to the genome

A

reciprocal translocation

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29
Q

translocations where there is a loss or gain or material

A

non-reciprocal translocation

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30
Q

defines the presence of two or more genes on the same chromosome of a given species

A

synteny

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31
Q

sequences that repeat over and over without interruption

A

Tandem repeats

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32
Q

what are the three types of tandem repeats

A

satellite DNA, minisatellite DNA, microsatellite DNA

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33
Q

5-500 bp in tandem repeats and repeats up to 100kb that can form very large clusters

A

satellite DNA

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34
Q

10-100bp with up to 3000 repeats

A

minisatellite DNA

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35
Q

1-5 bp in clusters of 10-40 bo scattered quite evenly throughout the genome

A

microsatellite DNA

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36
Q

present as a single copy per haploid set of chromosomes
Includes the genes for almost all proteins

A

non-repetitive DNA

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37
Q

are repetitive DNA sequences stable?

A

NO

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38
Q

repetitive sequences can be expanded or destroyed by

A

SLIPPAGE events causing misalignment

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39
Q

2 different forms of the same gene

A

alleles

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40
Q

DNA that moves from one place to another in the genome

A

Mobile DNA

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41
Q

what does it mean to say plants and animals have low gene density

A
  • we have lots of non-coding regions in our DNA
  • lots of unimportant stuff
  • lots of space due to HUGE genome
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42
Q

when does crossing over happen

A

prophase of meiosis I

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43
Q

similar genes with similar but distinct function

A

multigene families

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44
Q

one of two or more genes that are similar in sequence as a result of derivation from the same ancestral gene.

A

homolog

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44
Q

genes in two separate species that derive from the same ancestral gene in the last common ancestor of those two species.

A

ortholog

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44
Q

genes or proteins that are similar in sequence because they are the result of gene duplication event occurring in an ancestral organism.

A

paralog

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45
Q

a DNA strand is synthesized in what direction

A

5’ to 3’

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45
Q

what adds new nucleotides to a growing DNA strand

A

DNA polymerases

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46
Q

what two sites does DNA polymerization have

A

polymerization site (to add nucleotides) and an editing site (when there is a mistake)

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47
Q

The ability of the two DNA strands to unwind and separate into two individual strands

A

Denaturation

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48
Q

complementary single stranded DNA molecules can re-associate

A

Renaturation or reannealing or hybridization

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49
Q

true or false:
double stranded DNA absorbs more UV light than single stranded DNA

A

false

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50
Q

The higher the ____content of DNA, the higher the Tm the melting temperature

A

G/C

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51
Q

where does DNA replication initiate

A

at sequences rich in A-T base pairs
why?
- because they have 2 hydrogen bonds and are easier to break apart than G-C which have 3 hydrogen bonds

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52
Q

1 replication bubble contains how many replication forks?

A

2 replication forks

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53
Q

points where a pair of replicating segments come together

A

replication forks

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54
Q

prokaryotic replication forks move in ________ direction(s)

A

opposite

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55
Q

enzyme that separates two strands of DNA in DNA replication, unwinds two strands of DNA

A

helicase

56
Q

what makes sure that single stranded DNA does not fold/reanneal on itself

A

SSBPs

57
Q

what does the RNA primer do in DNA replication

A

creates a 3’ OH in which DNA polymerase can build on

58
Q

what adds the RNA primer in DNA replicaiton

A

DNA primase a type of RNA polymerase

59
Q

produces a transient (short lasting) SINGLE STRAND break that allows rotation of DNA strands

A

topoisomerase I

60
Q

Produces a transient double strand break in the helix , reduces supercoiling, detangles DNA

A

topoisomerase II

61
Q

when does sliding clamp releases DNA polymerase from DNA

A

when a double stranded region is encountered

62
Q

covalently connected the okazaki fragments into a continuous strand

A

DNA ligase

63
Q

what direction does DNA polymerase move on the template strand

A

3’ –> 5’

64
Q

which DNA pol replaces RNA primers

A

DNA pol I

65
Q

describe the exonuclease activity of DNA pol III and DNA pol I

A

DNA pol III: 3’ to 5’ exonuclease activity to proofread
DNA pol I: 3’ to 5’ and 5’ to 3’ to proofread and remove RNA primers

65
Q

which polymerase extends RNA primers

A

DNA pol III

66
Q

in eukaryotes when does the nucleus/cell divide

A

M phase (mitosis)

67
Q

in eukaryotes when does DNA synthesis take place

A

S phase (lasts 40 mins to 8hours)

68
Q

eukaryotic cells replicate their DNA in small portions called

A

replicons

69
Q

initiation of DNA synthesis in a replicon needs

A

ORC (origin of replication complex)

70
Q

which enzyme is responsible for maintaining chromosome ends

A

telomerase

71
Q

what is something interesting about telomerase

A

it is a reverse transcriptase: is can make DNA from RNA template
also it contains its own RNA template

72
Q

what does telomerase do in terms of replicating the ends of eukaryotic chromosomes

A

telomerase extends the template strand (this is a source of repetitive DNA)
- one telomerase extends the template strand primase and DNA pol extend the LAGGING strand

73
Q

Distortions of the double helix is used for recognition of mismatched base pairing
Can distinguish which strand is newly synthesized and target that strand for correction (using other strand as the template)

A

strand directed mismatch repair (MMR)

74
Q

what does UV radiation cause in terms of DNA damage

A

pyrimidine dimers (when C or T pair together or C and C or T and T)

75
Q

what does ionizing radiation cause in terms of DNA damage

A

breaks in DNA backbone

76
Q

what does thermal energy do in terms of DNA damage

A

causes A/G to come off the sugar backbone

77
Q

what are the purines and pyrimidines

A

Purines: A, G (double ringed)
Pyrimidines: C, T (single ringed)

78
Q

removes purines (A, G) from DNA

A

depurination

79
Q

converts cytosine to uracil

A

Deamination

80
Q

removes bulky bad things/lesions (ex. Pyrimidine dimers, chemical alteration)

A

NER: nucleotide excision repair

81
Q

patients are unable to repair damage caused by exposure to UV light

A

Xeroderma pigmentosum (XP) result of defects in NER

82
Q

which enzymes would be most useful for detecting and/or repairing a depurination

A

AP endonuclease

83
Q

initiated by DNA glycosylase enzymes that recognize specific alternations (different versions of DNA glycosylase for different alternations)

A

Base excision repair (BER)

84
Q

is important for rescuing stalled/broken replication forks

A

Homologous recombination

85
Q

Highly active pathway in humans for rapid repair of double strand breaks in DNA

A

NHEJ, non homologous end joining

86
Q

the intermediate between DNA and protein- used as a template for protein synthesis by ribosomes in cytoplasm.

A

mRNA

87
Q

provide structural support in the ribosome and catalyzes the chemical reaction in which amino acids are covalently linked to each other

A

rRNA

88
Q

required for translation of mRNA information into polypeptide sequence i.e. convert the language of nucleotides to the language of amino acids

A

tRNA

89
Q

true or false: mRNA are long lived

A

false: mRNA have shorter half lives

90
Q

direction of transcription is determined by what in DNA

A

orientation of promoters sequence in the DNA at the beginning of each gene

91
Q

what are the three stages of transcription?

A
  1. initiation
  2. elongation
  3. termination
92
Q

RNA polymerase binds to the promoter sequence

A

initiation: STEP 1 of transcription

93
Q

DNA strand temporarily unwinds allowing synthesis of complementary RNA
Ribonucleotides are linked together by phosphodiester bonds (5’ to 3’ like DNA synthesis!)

A

elongation: STEP 2 of transcription

94
Q

WHICH Strand?

5’ to 3’ sequence of the gene; it matches the 5’ to 3’ sequence of the RNA

A

sense, coding or nontemplate strand of DNA

95
Q

3’ to 5’ sequence of the gene used to make the RNA

A

template, antisense, noncoding strand

96
Q

increases the RNA polymerases affinity for promoter sequences

A

sigma factor

96
Q

RNA polymerase (5 subunits) + sigma factor is called the

A

RNA polymerase holoenzyme

97
Q

one promoter and multiple genes

A

polycistronic mRNA (prokaryotic)

98
Q

one promoter and one gene

A

monocistronic mRNA (eukaryotic)

99
Q

what synthesizes all eukaryotic mRNA precursors (pre-mRNA)

A

RNA polymerase II

100
Q

recognizes TATA box and other DNA sequences near the transcription start point

A

TFIID

101
Q

unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase C-termal domain (CTD); releases RNA polymerase from the promoter

A

TFIIH

102
Q

site of assembly of preinitiation complex (PIC) that contains general transcription factors and RNA polymerase

A

TATA box

103
Q

are RNA sequences that do not encode protein but play important regulatory roles

A

Untranslated regions (5’ UTR or 3’UTR)

104
Q

expressed sequences

A

exons

105
Q

intervening sequences

A

introns

106
Q

what removes introns from pre-mRNA

A

RNA splicing

107
Q

splicing of introns as lariats are carried out why what

A

5 snRNA (small nuclear RNA) and 100s of proteins

108
Q

what are the sequences required for intron removal?

A

5’ splice site, branch point, 3’ slice site

109
Q

sites of RNA biosynthesis

A

nucleoli

110
Q

5S rRNA is made by which RNA pol and where

A

RNA pol III, not in the nucleolus

111
Q

change in ___________ cell DNA can be passed to offspring

A

germline

112
Q

________ cells make up the tissues of the body

A

somatic

113
Q

name three things supercoiling does

A
  1. increases stability
  2. makes DNA more compact
  3. allows unwinding of sections
114
Q

which protein enzymes regulate/relive supercoiling

A

topoisomerases

115
Q

helix is overwound

A

positive supercoils

116
Q

helix is underwound

A

negative supercoils

117
Q

any of a group of basic proteins found in chromatin.

A

histones

118
Q

eukaryotic DNA associates with histones and other proteins to form

A

chromatin

119
Q

histones packages DNA into repeating units called

A

nucleosomes

120
Q

repeating subunit of DNA + histones

A

nucleosomes

121
Q

histones are _______ charged

A

positively

122
Q

where does the negative charge of DNA come from

A

phosphate

123
Q

Regulates how tightly these nucleosomes pack together, without this nucleosomes would look like beads on a string

A

histone H1

124
Q

DNA that is less compacted and functionally active (accessible for protein binding and transcription) genes here can be expressed

A

euchromatin

125
Q

DNA that is highly compacted and has little to no functional activity

A

heterochromatin

126
Q

what connects one nucleosome to another

A

histone H1 (linker histone) binds linkner DNA

127
Q

phenomenon in which a gene is either expressed or not expressed in the offspring depending on which parent it is inherited from.

A

genomic imprinting

128
Q

covalent modifications (ex. methylation) of DNA and histones

A

epigenetic

129
Q

does epigenetics influence heterochromatin or euchromatin

A

heterochromatin

130
Q

causes compaction/repression

A

methylation

131
Q

leads to more open structure, more transcription

A

acetylation

132
Q

DNA methyltransferase can add the methyl group to DNA at sites where

A

a C is followed by a G

133
Q

some (very few) methylation patterns are passed from parents to offspring what is this called

A

genomic imprinting

134
Q

can histone tail modifications be passed on to daughter cells during cell division

A

yes

135
Q

can DNA methylation patters be passed on to daughter cells during cell division?

A

yes

136
Q

what are examples of ribozymes

A

spliceosomes and ribosomes

137
Q

how many possible reading frames for every nucleotide sequence

A

3

138
Q

splicing is carried out by what

A

5 snRNA (small nuclear RNA) molecules and 100s of proteins

Psychology (21 decks)

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