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Exam 1 Flashcards

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1
Q

the fundamental properties of genetic material

A

must…
-contain complex information
-encode a phenotype
-replicate faithfully
-have the capacity to vary

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2
Q

Before the discovery of DNA people knew there was a source of heritable information and called it…

A

genetic information (will later be known as genes)

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3
Q

the word genetic means…

A

traits

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4
Q

genes reside where

A

chromosomes

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5
Q

chromosomes contain both __ and __

A

DNA and proteins

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6
Q

DNA contains nucleotides with …

A

bases which have pairing rules

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7
Q

Flow of genetic information

A

-DNA replication
-DNA to RNA
-RNA to proteins

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8
Q

nucleotides are the __ and contain three things which are…

A

building blocks
-phosphate (left), sugar (middle), base (right)

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9
Q

nucleotides have locations called primes: where are they…

A

-on the sugar
0 top
1top right
2 bottom right
3 bottom left
4 top left
5 outside by four

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10
Q

what prime if the phosphate and base on?

A

-phosphate: 5`
-base: 1’

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11
Q

what part of the nucleotide gives the DNA backbone a negative change

A

phosphate

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12
Q

the base of the nucleotide is either a …

A

purine or a pyrimidine

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13
Q

purine

A

nitrogenous base with a 6 member and 5 member ring (2 parts)
-has A and G
-each nucleotide is a monomer used to make a nucleotide

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14
Q

pyrimidine

A

nitrogenous base with only a six member ring (1 parts)
-has C, T, an U
-only have one phosphate
-called monophosphate
-make up nucleic acids

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15
Q

each DNA strand is a polymer meaning…

A

chain of repeating units

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16
Q

a polynucleotide strand (single strand of DNA or RNA) has…

A

polarity

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17
Q

polarity is referred to as…

A

5-> 3

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18
Q

each strand has a…

A

5 end and a 3 end

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19
Q

incoming nucleotides are always added on the __ end of the strand

A

3`

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20
Q

properties of double stranded DNA

A

-antiparallel (5 end of one strand is opposite the 3 end of the other strand)
-complementary (base pairs follow the rules)
-5 to 3 (each strand is directional (polar))
-negatively charger

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21
Q

DNA strands are held together by 2 natural forces

A

-hydrogen bonds (base to base )
-stacking forces (base rings stack on each other)

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22
Q

base pairing rules

A

-purine to pyrimidine
-A-T, C-G

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23
Q

the 3 forms of DNA

A

A, B, and Z

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24
Q

form of DNA: A

A

-less stable and more condensed
-right handed helix

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25
Q

form of DNA: B

A

-most stable with random nucleotides under physiological conditions
-right handed helix
-most common

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26
Q

form of DNA: Z

A

-zig-zag
-less stable
-left handed helix (counter clockwise)

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27
Q

difference between RNA and DNA

A

-ribose as -OH on 3` end of sugar wile deoxyribose only has H

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28
Q

topoisomerases

A

induces and removes supercoiling
-by nicking the DNA and turning is a certain way
-2 types

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29
Q

topoisomerases 1

A

-one strand of the DNA nicked

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30
Q

topoisomerases 2

A

-both strands of the DNA nicked

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31
Q

packaging DNA in chromosomes (bacteria)

A

-looping proteins

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32
Q

packaging DNA in chromosomes (bacteria)

A

-histones (proteins) with 2 strands of DNA wrapped around them

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33
Q

3 parts of the chromosome structure

A

-centromeres
-telomers
-arms

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34
Q

Chromosome structure: centromeres

A

-center of chromosome

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35
Q

Chromosome structure: Telomers

A

-ends of the arms

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36
Q

Chromosome structure: Arms

A

Arms (4)

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37
Q

All DNA is contained and regulated in …

A

chromosomes

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38
Q

Histone

A

-predominant protein in chromatin

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39
Q

Chromatin is…

A

DNA/ protein complex
-makes up chromosomes

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40
Q

The 3 levels of chromatin organization

A

-Euchromatin
-Heterochromatin
-Higher level DNA packaging into metaphase chromosome

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41
Q

level of chromatin (Euchromatin)

A

-1st level
-DNA wraps around histone octamers forming nucleosomes
-less condensed, expressed
-loose packaging

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42
Q

nucleosomes are also called…

A

beads on a string

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43
Q

level of chromatin (heterochromatin)

A

-multiple histones wrap into nucleosome arrays into their compact form
-condensed, few genes, not really expressed
-tight packaging

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44
Q

most basic level of chromatin is…

A

the nucleosome

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45
Q

chromatin

A

-a DNA/ protein complex that is able to be packaged into chromosomes

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46
Q

primary protein component of chromatin that compacts the DNA is called…

A

histones

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47
Q

the core unit of chromatin

A

nucleosome

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48
Q

unbound DNA in between nucleosomes is called __ DNA

A

linker

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49
Q

core nucleosomes

A

-2 of each
-all octameric
-H2A, H2B, H3, H4

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50
Q

additional histone (name and function)

A

-H1
-clamps onto the nucleosome

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51
Q

each core histone has a…

A

flexible tail that holds the DNA either tighter or looser

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52
Q

the charge of nucleosomes

A
  • positively charged so interacts with the negatively charged DNA backbone
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53
Q

replication is __ -> ___

A

DNA to DNA

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54
Q

4 fundamental properties of genetic information

A

-contain complex information
-replicate faithfully
-encode a phenotype
-have the capacity to vary

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55
Q

properties of DNA

A

-5 to 3polarity
-antiparallel strands
-complementary base pairs

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56
Q

the 3 proposed models of DNA replication

A

-conservative replication
-dispersive replication
-semiconservative replication

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57
Q

proposed model of DNA (conservative replication)

A

R1: P and N
R2: P:P +N, N: N+N

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58
Q

proposed model of DNA (dispersive replication)

A

R1:P makes hybrids (the DNA molecule has fragments of new and parent DNA)
R2: hybrids from the last 2 created

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59
Q

proposed model of DNA (semiconservative replication)

A

R1: DNA molecule has 1 strand of the parent and one of the new
R2: 2 completely new molecules and 2 with half new and half parent
-this makes the most sense

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60
Q

The Meselson and Stahl experiment

A

-wanted to test between the 3 models of DNA replication
-label the original DNA and follow it through the rounds of replication
-along the rounds the new DNA molecules will lift to the top of the test tube

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61
Q

DNA replication is always this type… (1 or 3 models of DNA replication)

A

semi conservative

62
Q

DNA replication uses many proteins that helps do what…

A

-ensures the accuracy in correct copying

63
Q

The first step of DNA replication involves…

A

the 2 strands of DNA helix being separated to expose the bases so that they can be used as a template for a new strand

64
Q

prokaryote replication is done on ___ DNA

A

circular

65
Q

requirements for DNA replication

A

-template
-substrate
-enzyme

65
Q

prokaryote replication (replication bubble)

A

-DNA is circular so the replication bubble selects a spot on the DNA
-in the bubble there are replication forks that grows across the original bubble
-in the bubble new DNA is made

66
Q

Initiator proteins

A

-Bind AT rich repeats at origin to make sure DNA replication starts correctly
-DNA is wrapped around these
-binds to origin of replication and causes a short stretch of DNA to unwind which causes replication

67
Q

Helicase

A

-unwinds DNA at the replication forks
-breaks H bonds

68
Q

SSBPs

A

-single stranded binding proteins
-binds to strands to keep them separated

69
Q

Gyrase

A

-topoisomerase 2
-relieves tension ahead of replication by breaking and rejoining DNA

70
Q

requirements for DNA replication

A

-template
-substrate to be assembled into a new polynucleotide strand
-enzymes and other proteins that assemble the substrates into molecules

71
Q

dNTP substrate has 3 phosphate groups

A

alpha (a), beta (b), and gamma(y)

72
Q

a __ is necessary for the addition of a nucleotide at the __

A

NTP, 3`OH

73
Q
A
74
Q

dNTP is __ at the free 3` OH group

A

always

75
Q

Primase

A

-provides primer for the initiation of DNA synthesis
-acts on leading strands once and lagging strand many times

76
Q

DNA polymerase III

A

-also known as the workhorse polymerase
-responsible for bulk of DNA synthesis
-acts on both leading and lagging strand

77
Q

exonuclease function

A

removal of a nucleotide

78
Q

DNA polymerase I

A

-replaces primer with DNA
-acts on leading strand once and lagging strand many times
-can proofread and remove

79
Q

the leading strand replication

A

continuous (5->3)

80
Q

the lagging strand replication

A

discontinuous and causes fragments (3<-5)

81
Q

DNA primase

A

-synthesizes a short RNA primer to provide a 3`OH group for the attachment of DNA nucleotides
-an enzyme
-after synthesis the primer is removed

82
Q

DNA polymerase III

A

elongates a new nucleotide strand from the 3`OH group provided by the primer

83
Q

DNA polymerase I

A

removes RNA primers and replaces them with DNA which makes Okazaki fragments

84
Q

DNA ligase

A

-joins the Okazaki fragments by sealing the breaks in the new DNA
-uses a ligation reaction

85
Q

DNA proofreading is done backward in a ___ direction after ___

A

3->5
replication

86
Q

fidelity

A

low error rate

87
Q

steps of DNA replication in prokaryotes

A

1) initiation proteins find origin of replication and stretch DNA
2) helicase unwinds
3) SSBPs bind and stabilize to separate the strands
4)gyrase removes strain
5)primase adds primers for DNA pol III
6) DNA pol III replicates the strands
7) DNA pol I removes primers
8)ligase joins the spaces in the lagging strand
9)continues until termination

88
Q

Replication model theta (prokaryotic)

A

-circular DNA
-2 replication forks
-1 replication bubble
-occurs 1 time

89
Q

Replication model linear (eukaryotic)

A
  • 2 origins
    -2 replication forks
    -many replication bubbles
    -many replications
90
Q

in eukaryotic replication the entire genome is replicated only ___ for each ___

A

-once
-cell cycle

91
Q

eukaryotic replication is very fast due to…

A

-multiple origins
-controlling the timing
-firing (beginning synthesis) at each origin

92
Q

in eukaryotic replication the multiple ___ eventually ___ together forming 2 identical DNA molecules

A

-origins
-fuses

93
Q

(ER) the origins are first licensed by ORC (__) which means…

A

-origin recognition complex
-approved for replication

94
Q

(ER) after the origins are licensed ___ binds to the origin to start unwinding the DNA

A

-Helicase

95
Q

(ER) the same 3 tools are used to unwind the DNA as (PR)

A

-helicase
-SSBPs
-gyrase

96
Q

(ER) 4 main DNA polymerases

A

-alpha (a): primer
-delta (d): synthesizes lagging strand
-epsilon(E): synthesizes leading strand
-gamma (Y): mitochondrial DNA synthesis

97
Q

(ER) end replication problem

A

-1 molecule with 2 ends
-there us a 3` overhang of unpaired bases at the telomeres
-chromosomes get shorter with each division

98
Q

(ER) the fix for the end replication problem

A

-telomerase is an enzyme
-gives RNA template for copies of end of chromosome to be added

99
Q

telomerase is often considered a __

A

-reverse transcriptase because it used RNA to make DNA

100
Q

Mutation

A

-a inherited change in genetic information

101
Q

PCR

A

-technique for enzymatically replicating DNA
-allows DNA molecule to be amplified many times
-commonly used
-gives many copies form original

102
Q

who invented PCR

A

Kary Mullis

103
Q

PCR is used to know ___ from specific region

A

-specific

104
Q

PCR requirements

A

-template: the DNA of interest to amplify
-substrate
-enzyme: DNA polymerase
-primers: to target the change
-salts/ buffer (H2O, magnesium): to start reaction

105
Q

(PCR) guidelines for primer design

A

-length: 17-20 bases, ideal 50% GC
-melting temp: 55-65*C
-polarity: 5->3

106
Q

Temperature of bases

A

GC: 4C
AT: 2C

107
Q

(PCR) Taq DNA polymerase

A

-thermophile (can handle very hot conditions)
-special enzyme
-discovered in a bacteria in a hot spring

108
Q

(PCR) 5 to 3 is always on ___

A

top

109
Q

(PCR) sense strand

A

-also known as positive strand
-top

110
Q

(PCR) anti-sense strand

A

-also known as negative strand
-bottom

111
Q

(PCR) Electrophoresis

A

-technique to confirm presence and size of PCR products
-utilizes the physical and chemical properties of the products to separate them when in an agarose gel

112
Q

(PCR) in agarose gel the DNA products get “shifted” so the large fragments are at the ___ and the smaller fragments are at the ___

A

-top
-bottom

113
Q

(PCR) dideoxy sequencing

A

-technique to determine the nucleotide sequence of your target DNA product
-can use gel but takes a long time
-or can use automated computer (much faster and can use larger genomes)

114
Q

dideoxy sequencing

A

-technique to determine nucleotide sequence of target DNA product
-uses special substrate during DNA synthesis

115
Q

DNA polymerase can only extend on an __ not a __

A

-OH
-H

116
Q

the dideoxy sequencing mechanist (chain termination)

A

-stopping the building chain of nucleotides

117
Q

The reference genome

A

-a genome for a species or population that represents as an example of a species set of genes

118
Q

Read assembly

A

-reads are lines of bases (raw data) from DNA
-reads are aligned into contigs (assembled reads)
-used to see alignments

119
Q

metagenomics

A

-the study of genetic material recovered directly from environmental samples

120
Q

Transcription

A

DNA to RNA

121
Q

prokaryotes storage of genetic info

A

-operon
-polycistronic
-simple
-genetic info on one chromosome
-no histones

122
Q

eukaryotes storage of genetic info

A

-simple gene
-monocistronic
-big range of gene sizes
-genetic info on multiple chromosomes
-has histones

123
Q

operon

A

-multiple genes that can be transcribed at once
-all into the same RNA
-more than 1 gene

124
Q

polycistronic

A

-multiple genes together

125
Q

gen organization differs between __ and __

A

-prokaryotes
-eukaryotes

126
Q

promoter

A

start

127
Q

terminator

A

end

128
Q

introns

A

removed

129
Q

exons

A

exposed

130
Q
A
131
Q

DNA is stable because it has a __ bond in the sugar

A

H

132
Q

RNA is unstable because it has a __ bond in the sugar

A

hydroxyl (OH)

133
Q

is RNA a double or single strand?

A

single strand

134
Q

RNA folds to form ___ structures

A

secondary

135
Q

the 3 main types of RNA are all…

A

generated through transcription

136
Q

transcription unit

A

a stretch of DNA that encodes an RNA molecule and the sequences that are necessary for its transcription

137
Q

coding region

A

is the actual area that is being transcript

138
Q

RNA is synthesized on the ___ strand

A

antisense

139
Q

coding vs noncoding strand

A

-coding strand= sense (top strand)= non template (being transcribed)
-non-coding strand= antisense (bottom strand)=template (not transcribed)

140
Q

which strand is the template for RNA

A

antisense strand

141
Q

protein needed in transcription

A

-sigma and DNA polymerase

142
Q

sigma protein

A

-initiation factor

143
Q

transcription steps

A

-bubble moves along DNA reading info to make RNA
-breaks H bonds
-copies 1 strand of the DNA

144
Q

RNA has __ instead of T

A

-U (uracil)

145
Q

exons are removed by…

A

splicing

146
Q

-35 and -10 regions are ___ back from start site

A

bases

147
Q

consensus sequence

A

-comparison of common features among a set of sequences
-short stretches of common nucleotides

148
Q

the -35 and -10 determine the __

A

+1 start site

149
Q

when RNA hits the terminator it ___ on itself

A

folds up

genetics (20 decks)

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