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Neuroscience > Structure, Function and Replication of DNA > Flashcards

Structure, Function and Replication of DNA Flashcards

1
Q

3´–OH terminus

A

End of a polynucleotide that terminates with an -OH.

Attached to 3´-carbon of the sugar

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2
Q

5´–P terminus

A

End of polynucleotide that terminates w/ a mono-, di- or

triphosphate attached to 5´-carbon of the sugar

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3
Q

β-N-glycosidic bond

A

Linkage between base and sugar of a nucleotide.

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4
Q

adenine

A

Purine base found in DNA and RNA.

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5
Q

A-form DNA

A

Not common in cellular DNA, only found in dehydrating conditions

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6
Q

antiparallel

A

Refers to opposite directional arrangement of 2 polynucleotide strands in double helix (5’ to 3’ & 3’ to 5’)

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7
Q

Base pairing

A

Attachment of one polynucleotide to another, or one part of one to another part of the same polynucleotide, by base pairs.

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8
Q

B-form DNA

A

Commonest structural conformation of the DNA double helix in living cells

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9
Q

Complementary

A

Refers to two nucleotides or nucleotide sequences that are able to base-pair with one another.

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10
Q

Cytosine

A

One of the pyrimidine bases found in DNA and RNA

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11
Q

Deoxyribonucleic acid (DNA)

A

One of two forms of nucleic acid in living cells;

genetic material for all cellular life & many viruses

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12
Q

Guanine

A

Purine nucleotide found in DNA and RNA.

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13
Q

Hydrogen bond

A

Weak electrostatic attraction between an electronegative atom (e.g. Oxygen/nitrogen) and a hydrogen atom attached to a second electronegative atom

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14
Q

Major groove

A

Larger of two grooves that spiral around the surface of the Bform of DNA.

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15
Q

Minor groove

A

Smaller of two grooves that spiral around the surface of the Bform of DNA

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16
Q

Monomer

A

One of the structural units that are joined together to form a polymer

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17
Q

Nucleoside

A

Purine/pyrimidine base attached to 5-C sugar

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18
Q

Nucleotide

A

Purine/pyrimidine base attached to 5-C sugar, to which a mono-, di-, or triphosphate is also attached. The monomeric unit of DNA and RNA.

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19
Q

Pentose

A

Sugar comprising five carbon atoms.

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20
Q

Phosphodiester bond

A

Chemical link between adjacent nucleotides in a

polynucleotide.

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21
Q

Polymer

A

Compound made up of a long chain of identical or similar units.

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22
Q

Polynucleotide

A

Single-stranded DNA or RNA molecule.

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23
Q

Purine/pyramidine

A

One of two types of nitrogenous base found in nucleotides.

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24
Q

Thymine

A

One of the pyrimidine bases found in DNA

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25
Q

Z-form DNA

A

Conformation of DNA in which the 2 polynucleotides are wound into a left-handed helix. Found naturally w/ B-DNA but only in certain regions. Unclear function.

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26
Q

Complex multigene family

A

Type of multigene family where genes have

similar nucleotide sequences, but are different enough to code for proteins w/ distinctive properties

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27
Q

Discontinuous gene

A

Gene split into exons and introns

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28
Q

Exon

A

Coding region within a discontinuous gene

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29
Q

Intergenic DNA

A

Region of genome not containing genes

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30
Q

Intron

A

Non-protein coding region within a discontinuous gene

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31
Q

Kilobase pair (kb)

A

1000 base pairs

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32
Q

Megabase pair (Mb)

A

1000kb or 1,000,000 bp

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33
Q

Molecular clock

A

Device based on inferred mutation rate enabling measure of rate at which gene sequence changes

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34
Q

Multigene family

A

Group of genes, clustered or dispersed, w/ related nucleotide sequences

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35
Q

Pseudogene

A

Inactivated and non-functional copy of a gene

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36
Q

Simple multigene family

A

Multigene family in which all genes are the same

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37
Q

Tandem array

A

Set of identical or very similar genes arranged one after the other in a group

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38
Q

Buoyant density

A

Density possessed by a molecule/particle when suspended in an aqueous salt or sugar solution

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39
Q

Conservative replication

A

Hypothetical mode of DNA replication in which one
daughter double helix is made up of the two parental polynucleotides and the other is
made up of two newly synthesized polynucleotides

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40
Q

Dispersive replication

A

Hypothetical mode of DNA replication in which both polynucleotides of each daughter double helix are made up partly of parental DNA and partly of newly synthesized DNA.

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41
Q

DNA topoisomerase

A

Enzyme that adds.takes turns from the double helix by breakage & reunion of one or both polynucleotides

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42
Q

Plectonemic

A

Helix whose strands can only be separated by unwinding

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43
Q

Semiconservative replication

A

Mode of DNA replication in which each daughter

double helix is made up of one polynucleotide from the parent and one newly synthesized polynucleotide

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44
Q

Type I topoisomerase

A

Topoisomerase that makes a single-stranded break in a double-stranded DNA molecule

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45
Q

Type II topoisomerase

A

Topoisomerase that makes a double-stranded break in a double-stranded DNA molecule.

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46
Q

3´→5´ exonuclease

A

Enzyme that sequentially removes nucleotides in 3´→5´direction from end of a nucleic acid molecule

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47
Q

5´→3´ exonuclease

A

Enzyme that sequentially removes nucleotides in 5´→3´direction from the end of a nucleic acid molecule

48
Q

DNA polymerase III

A

Main prokaryotic DNA replicating enzyme

49
Q

DNA polymerase α

A

Enzyme that primes DNA replication in eukaryotes

50
Q

DNA polymerase δ

A

Main eukaryotic DNA replicating enzyme

51
Q

DNA-dependent DNA polymerase

A

Enzyme that makes a DNA copy of a DNA

template.

52
Q

Leading strand

A

Strand of double helix which is copied in a continuous fashion during genome replication.

53
Q

Primase

A

RNA polymerase enzyme that synthesizes RNA primers during bacterial DNA replication.

54
Q

Replication fork

A

Region of a double-stranded DNA molecule that is being opened up for DNA replication to occur

55
Q

Single-strand binding protein (SSB)

A

One of the proteins that attach to single-stranded
DNA in region of replication fork, preventing base pairs forming between the two parent strands before they have been copied.

56
Q

Adenine full name

A

2’ -deoxyadenosine 5’ -triphosphate dATP

57
Q

Guanine full name

A

2´-deoxyguanosine 5´-triphosphate dGTP

58
Q

Cytosine full name

A

2’ -deoxycytidine 5’ -triphosphate dCTP

59
Q

Thymine full name

A

2’ - deoxythymidine 5’ -triphosphate dTTP

60
Q

Example of structural proteins

A

Collagen

Keratin

61
Q

Motor proteins

A

Myosin, dynenin

62
Q

Catalytic proteins

A

Hexokinase

DNA polymerase

63
Q

Transport proteins

A

Hemoglobin

Serum albumin

64
Q

Storage proteins

A

Ovalbumin

Ferritin

65
Q

Protective proteins

A

Immunoglobulins

Thrombin

66
Q

Regulatory proteins

A

Insulin
Somatostatin
Somatotrophin

67
Q

Primer for DNA synthesis in prokaryotes

A
  • Made of RNA by primase enzyme
  • Is 4-15 nucleotides in length
  • DNA pol III makes strand once primer is made
68
Q

Primer for DNA synthesis in eukaryotes

A
  • Made of RNA by primase but first extended by DNA pol alpha
  • DNA pol alpha adds about 20 nucleotides
  • DNA pol delta then makes the rest of the strand
69
Q

DNA ligase

A

Enzyme that synthesizes phosphodiester bonds in DNA replication, repair & recombination processes.

70
Q

DNA polymerase I

A

Bacterial enzyme which completes synthesis of okazaki fragments during genome replication of the lagging strand

71
Q

Lagging strand

A

Strand of the double helix which is copied in a discontinuous fashion during genome replication

72
Q

FEN1

A

The ‘flap endonuclease’ involved in replication of the lagging strand in eukaryotes

73
Q

Telomerase

A

Enzyme that maintains ends of eukaryote chromosomes by synthesizing telomeric repeats

74
Q

What are the 5 types of histones associated with DNA?

A 
H1
H2A
H2B
H3
H4
75
Q

Gamma-complex

A

Multisubunit bacterial protein that attaches and detaches DNA
pol. III during copying of the lagging strand

76
Q

Helicase

A

Enzyme that breaks base pairs in double-stranded DNA.

77
Q

Origin of replication

A

Site on DNA where replication initiates

78
Q

Prepriming complex

A

Protein compex including the DnaB helicase which triggers construction of a replication fork on bacterial DNA.

79
Q

Primosome

A

Protein complex including DnaB helicase and primase involved initiation of DNA replication in bacteria.

80
Q

Proliferating cell nuclear antigen (PCNA)

A

Accessory protein involved in DNA replication in eukaryotes, whose function is to hold DNA polymerase delta tightly to DNA.

81
Q

Terminator sequence

A

One of several sequences on a bacterial genome involved in termination of genome replication.

82
Q

Tus

A

Protein that binds to a bacterial terminator sequence and mediates termination of genome replication.

83
Q

30nm chromatin fibre

A

Relatively unpacked form of chromatin made of a possibly helical array of nucleosomes in a fibre approximately 30nm in diameter, beads on a string.

84
Q

Beads-on-a-string

A

Unpacked form of chromatin consisting of nucleosome beads on a string of DNA

85
Q

Centromere

A

Constricted region of chromosome that is the position at which the pair of chromatids are held together.

86
Q

Chromatid

A

Arm of chromosome

87
Q

Chromatin

A

Complex of DNA and histone proteins found in chromosomes

88
Q

Chromatosome

A

Subcomponent of chromatin made up of a nucleosome core octamer with associated DNA and a linker histone.

89
Q

Constitutive heterochromatin

A

Chromatin that is permanently in a compact organisation

90
Q

Core octamer

A

Central component of a nucleosome, made up of two subunits each of histones H2A, H2B, H3 and H4, around which DNA is wound.

91
Q

Euchromatin

A

Regions of a eukaryotic chromosome that are sparse and likely to contain active genes.

92
Q

Facultative heterochromatin

A

Chromatin that has a dense, compact organization in some cells,, thought to contain genes that are inactive in some cells or at some periods of the cell cycle.

93
Q

Heterochromatin

A

Chromatin that is relatively condensed and is thought to contain DNA that is not being transcribed.

94
Q

Histone

A

Basic protein found in nucleosomes

95
Q

Interphase

A

Period between cell divisions

96
Q

Karyogram

A

Entire chromosome complement of a cell, with each chromosome described in terms of its appearance at metaphase.

97
Q

Linker DNA

A

DNA that links nucleosomes: ‘string’ in ‘beads-on-a-string’ model for chromatin structure

98
Q

Linker histone

A

Histone (like H1) that is located outside of the nucleosome core octamer

99
Q

Metaphase chromosome

A

Chromosome during metaphase, when chromatin takes on most condensed structure and features (like banding pattern) can be visualized

100
Q

Nuclear matrix

A

Proteinaceous scaffold-like network that permeates the cell

101
Q

Nuclease protection experiment

A

Technique that uses nuclease digestion to determine the positions of proteins on DNA or RNA molecules

102
Q

Nucleosome

A

Complex of histones and DNA that is the basic structural unit in chromatin

103
Q

Telomere

A

End of a eukaryotic chromosome

104
Q

Joining okazaki fragments in prokaryotes

A

DNA pol III stops at RNA primer of fragment and is replaced by DNA pol I. DNA ligase joins fragments with phosphodiester bond.

105
Q

Joining okazaki fragments in eukaryotes

A

DNA pol delta stops at RNA primer. Helicase and DNA pol delta lift up primer as flap. FEN1 cuts it off. Ligase joins fragments.

106
Q

DnaA

A

Protein involved in genome replication. DNA winds around it, base pair at origin of replication break as a result

107
Q

DnaB

A

Helicase, whose addition to origin of replication forms prepriming complex

108
Q

Primosome

A

Formed when two primase enzymes are added to prepriming complex

109
Q

Enhancer

A

Sequence of DNA containing regulatory information

110
Q

What accessory factor recruits RNA pol II to the promoter?

A

TTIID

111
Q

TATA

A

Promoter sequence in RNA polymerase II initiation complex

112
Q

TBP

A

Binding protein in RNA polymerase II initiation complex.
Interacts with minor groove of DNA.
Attracts TFIIA and TFIIB.
Similar sequence to sigma factor in prokaryotes.

113
Q

TAFs

A

TBP-associated factors.

Interact with TBP and DNA

114
Q

TFIIA

A

Helps TFIID bind

115
Q

TFIIB

A

Sets distance from TATA element to start site

116
Q

What makes up TFIID

A

TATA
TBP
TAFs

Neuroscience (22 decks)

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