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Dr. Kolomyjec Genetics > Genetics Test 3 > Flashcards

Genetics Test 3 Flashcards

1
Q

DNA A

A

Unwinding the helix, initiator protein, binds to ORI causing confirmation change, causes helix to destabilize and open up, exposes ssDNA

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2
Q

DNA helicase

A

Made of DNA B polypeptides, hexamer of subunits, subsequently recruits holoenzyme to bind replication fork and initiate replication, require energy supplies by hydrolysis of ATP-denatures hydrogen binds and stabilizes double helix

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3
Q

Single stranded binding proteins (SSBP)

A

Stabilize the open confirmation of helix, bind specifically to single strands of DNA,

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4
Q

DNA gyrase

A

Relieves coiled tension from unwinding of helix (member of the DNA topoisomerases) slide along ahead of helicase to relieve tension

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5
Q

Primase: RNA polymerase

A

Synthesizes RNA primer, provides 3’-OH required by DNA polymerase III for elongation, (aka build little short segments of RNA, capable of starting with nothing)

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6
Q

DNA polymerase I

A

Removes primer

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7
Q

RNA priming

A

Universal phenomena found in everything with DNA

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8
Q

Continuous DNA synthesis

A

Leading strand

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9
Q

Discontinuous DNA synthesis

A

Lagging strand

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10
Q

Okazaki fragments

A

The chunks of DNA that form from the lagging strand

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11
Q

DNA ligase

A

Catalyzes formation of phosphodiester bonds and seals nicks and joins Okazaki fragments

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12
Q

DNA clamp

A

Prevents core enzyme dissociation from template

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13
Q

Proofreading

A

DNA polymerase exonuclease can go back and correct mistakes (3’-5’)

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14
Q

Enzymes and proteins that are essential to DNA synthesis

A

DNA polymerase III, SSBPs, DNA gyrase, DNA helicase, RNA primers

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15
Q

Shared features of eukaryotic and Bacterial DNA replication

A

Double strand unwound at ORI, replication forks, bidirectional synthesis, requires four triphosphates, primer

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16
Q

Why is eukaryotic DNA replication more complicated

A

More DNA, linear chromosomes, DNA complexes with nucleotides

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17
Q

Do eukaryotic organisms have one ORI or many?

A

Many, speeds up the process

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18
Q

Autonomously replicating sequences (ARSs)

A

120 base pairs of consensus sequence (same sequence in all those places) in yeast

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19
Q

Prereplication complex (pre-RC)

A

Assembles at replication ORIs, early GI phase of cell cycle, for controlled timing of DNA replication

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20
Q

Does eukaryotic DNA replication have one polymerase or many?

A

Many

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21
Q

Polymerase switching

A

Occurs once the primer is in place

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22
Q

Telomeres

A

Inert chromosomal ends that protect intact eukaryotic chromosomes from improper fusion or degradation, long stretches of short repeating sequences preserve the integrity/stability of chromosomes

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23
Q

Telomerase

A

Eukaryotic enzyme, adds repeats of six nucleotide sequence to 3’ end to fill gaps

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24
Q

Ribonucleoprotein

A

RNA serves as template for synthesis of DNA complement (reverse transcriptase)

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25
Q

Telomerase activity and telomere length linked to….

A

Aging, cancer, other diseases

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26
Q

In most eukaryotic somatic cells telomerase is active or not active?

A

Not active

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27
Q

What cells maintain telomerase activity - immortalized

A

Stem cells and malignant cells

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28
Q

Homologous recombination

A

Genetic exchange at equivalent positions along two chromosomes with substantial sequence homology

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29
Q

Genetic recombination involves:

A

Endonuclease nicking, strand displacement and pairing with complement, ligation, branch migration, duplex separation

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30
Q

Gene conversion

A

Consequence of homologous recombination, characterized by nonreciprocal genetic exchange between two DNA molecules

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31
Q

Bacterial and viral chromosome components

A

Single nucleic acid
Largely devoid of associated proteins
Much smaller than eukaryotic

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32
Q

Bacterial chromosomes

A

Circular double stranded DNA compacted into nucleoid

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33
Q

Supercoiling

A

Closed circular molecules, more compact and sediment more rapidly

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34
Q

Topoisomerase

A

Enzymes that cut one or both DNA strands, wind or unwind helix before resealing ends

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35
Q

Polytene chromosomes

A

Represent paired homologs, NOT NORMAL, seen in interphase cells, found in tissues such as salivary, rectal, midgut, fruit flies

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36
Q

Polytene chromosomes definition

A

DNA of paired holologs undergoes many rounds of replication without strand separation or cytoplasmic division

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37
Q

Puff regions

A

Bulges where DNA has uncoiled that are visible manifestations of high level gene activity (transcription that produces RNA)

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38
Q

Lampbrush chromosomes

A

Large with extensive DNA looping, easily isolated from oocytes in diplotene stage or prophase I of meiosis (it’s like a giant puff)

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39
Q

Chromatin

A

At interphase, eukaryotic chromosomes uncoil and decondense into a form called chromatin which is dispersed throughout the nucleus during interphase

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40
Q

Histones

A

Positively charged proteins associated with chromosomal DNA in eukaryotes, five main types

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41
Q

Nucleosome

A

A length of DNA coiled around a core of histones (resembles beads on a string) are condensed several times to form intact chromatids

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42
Q

Superhelix

A

The structure the DNA forms when it makes a nucleosome

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43
Q

Histone tails

A

Not packed into the folded histone domains, allows for remodeling since we can stick things/remove things from the tails

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44
Q

Acetylation

A

Changes the charge if the histone, to make them spread out

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45
Q

Methylation

A

Makes the histones stick together

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46
Q

Phosphorylation

A

Adds phosphate groups

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47
Q

Euchromatin

A

Uncoiled and active, appears unsustained during telophase

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48
Q

Heterochromatin

A

Condensed areas are mostly inactive, appears stained during interphase

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49
Q

Chromosome banding techniques

A

Differential staining along longitudinal axis of mitotic chromosome (resemble polytene chromosome bands)

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50
Q

C-Banding

A

Only centromeres take up stain

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51
Q

G-banding

A

Differential staining along length of each chromosome

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52
Q

Nomenclature for human chromosome banding

A

Based on g banding, nomenclature applied to X chromosome

53
Q

Repetitive DNA sequences

A

Are repeated many times within eukaryotic chromosomes

54
Q

Satellite DNA

A

Highly repetitive and consists of short repeated sequences, found in heterochromatic centromeric regions of chromosomes

55
Q

Moderately repetitive DNA

A

Variable number tandem repeats (VNTRs), minisatelites

56
Q

Variable number tandem repeats (VNTRs)

A

Repeating DNA sequences 15-100 bp long, found within and between genes

57
Q

Micro satellites or STRs (short tandem repeats)

A

Tandemly repeated sequence, dispersed throughout genome

58
Q

Short interspersed elements (SINES) and long interspersed elements (LINES)

A

Transposable sequences that are mobile and can relocate within genome, dispersed not tandemly repeated

59
Q

Retrotransposons

A

Transposable elements generated via RNA intermediate (LINES)

60
Q

Pseudogenes

A

Large number of single-copy noncoding regions

61
Q

Unambiguous

A

Each triplet specifies only one amino acid

62
Q

Degenerate

A

A given amino acid can be specifies by more than one triplet code

63
Q

Start and stop signals

A

Triplets that initiate and terminate translation

64
Q

Commaless

A

Once translation begins the codons move in sets of three, no commas

65
Q

Nonoverlapping

A

Any single ribonucleotide within mRNA is part of one triplet

66
Q

Colinear

A

Sequence of codons in a GENE is colinear (genes sequence in DNA matches RNA matches the rest of the strands)

67
Q

Nearly universal

A

A single coding dictionary is used by viruses, prokaryotes, archaea, and eukaryotes

68
Q

mRNA (messenger)

A

Serves as intermediate in transferring genetic information from DNA to proteins (carries from DNA to ribosome)

69
Q

Triplet code

A

Provides 64 codons to specify 20 amino acids

70
Q

Reading frame

A

Contiguous sequence of nucleotides

71
Q

Frameshift mutation

A

Insertions or deletions shift reading frame and change codons downstream

72
Q

Nonoverlapping

A

Genetic code reads three nucleotides at a time in continuous linear manner (during translation genetic code is nonoverlapping)

73
Q

What is meant when it is said that the genetic code is degenerate?

A

Many amino acids specified by more than one codon (only tryptophan and methionine are encoded by a single codon)

74
Q

The wobble hypothesis

A

The initial two ribonucleotides of triplet codes are often more critical than the third

75
Q

Methionine (AUG) - initiator codon

A

Initial amine acid incorporated into all proteins

76
Q

Termination codons

A

UAG, UAA, UGA, do not code for any amino acid, translation terminates when these codons are encountered

77
Q

Nonsense mutations

A

Mutations that produce a stop codon internally in gene, translation is terminated and a partial polypeptide is produced

78
Q

Phage MS2

A

Bacteriophage that infects E. coli

79
Q

Mitochondrial DNA exemptions to universal genetic code:

A

Codon UGA encodes tryptophan in yeast and humans instead of termination, AUA encodes internal insertion of methionine instead of isoleucine

80
Q

Overlapping genes

A

Single mRNA has multiple initiation points and creates different reading frames

81
Q

ORF open reading frame (overlapping genes)

A

DNA sequence produces RNA with start and stop, series of triplet codons specify amino acids to make polypeptide

82
Q

Transcription

A

RNA synthesized on DNA template

83
Q

Promoters

A

Specific DNA sequences in 5’ region upstream of initial transcription point

84
Q

Consensus sequences

A

DNA sequences homologous in different genes of same organism

85
Q

Chain elongation

A

Ribosomes are added to RNA chain, elongation proceeds under direction of core enzyme

86
Q

Termination

A

Enzyme transverse entire gene until a termination nucleotide sequence is encountered

87
Q

Transcription in eukaryotes

A

Occurs within nucleus, mRNA must leave nucleus for translation

88
Q

Transcription factors

A

Scan/bind DNA, enhancers and silencers

89
Q

RNA polymerase 1 makes…

A

rRNA in the nucleolus

90
Q

RNA polymerase II makes

A

mRNA and snRNA in the nucleoplasm

91
Q

TATA box

A

Core promoter element, determines transcription start site

92
Q

Posttranscriptional modifications

A

Addition of 5’ cap, addition of 3’ tail, excision of introns

93
Q

Introns

A

Regions of initial RNA transcript not expresses in amino acid sequence of protein

94
Q

Exons

A

Sequence retained and expressed

95
Q

Splicing

A

Introns are removed, exons are joined together in mature mRNA, mature mRNA is smaller than initial RNA

96
Q

Self splicing RNAs

A

Self excision group I introns occurs in bacteria, lower eukaryotes, and higher in plants

97
Q

Spliceosome

A

Pre-mRNA introns spliced out by spliceosome, reaction involves formation of lariat structure

98
Q

Substitution editing

A

Identities of individual nucleotide bases are altered; prevalent in mitochondria and chloroplasts RNA derived in plants

99
Q

Insertion/deletion editing

A

Nucleotides are added/deleted from total number of bases, prevalent in mitochondrial and chloroplasts RNAs

100
Q

tRNAs transfer RNA

A

Adapt genetic information present as specific triplet codons in mRNA to corresponding amino acid

101
Q

Ribosomes

A

Have an essential role in expression of genetic information

102
Q

rDNA

A

rRNA genes, moderately repetitive DNA fraction present in clusters at various chromosomal sites

103
Q

Structure of tRNA

A

Cloverleaf

104
Q

Anticodon

A

tRNA has anticodon that complementarily base pairs with codon in mRNA

105
Q

Aminoacylation: tRNA charging

A

Before translation can proceed, tRNA molecules must be chemically linked to respective amino acids

106
Q

Three steps of translation of mRNA

A

Initiation, elongation, termination

107
Q

Initiation

A

Initiation complex = small robosomal subunit + initiation factors + mRNA at codon AUG

108
Q

Initiation factors

A

Small and large ribosomal subunits, mRNA molecule, GTP, charged initiator tRNA, Mg2+, imitation factors

109
Q

Elongation

A

Both ribosomal subunits assembled with mRNA, forms P and A site

110
Q

Termination

A

Signaled by stop codons in A site

111
Q

GTP dependent release factors

A

Stimulates hydrolysis of polypeptide from peptidyl tRNA - released from translation complex

112
Q

Polysomes or polyribosomes

A

mRNAs with several ribosomes translating at once, as mRNA passes through ribosome, it’s free to associate with another small subunit

113
Q

Where does transcription occur in eukaryotes?

A

Nucleus

114
Q

Where does translation occur in eukaryotes?

A

Cytoplasm

115
Q

Kozak sequence

A

Eukaryotic mRNAs contain luring (A or G) three bases upstream from AUG initiator codon, followed by a G
(A/NNAUGG

116
Q

Translation in eukaryotes requires…

A

More factors of initiation, elongation, and termination

117
Q

Are ribosomes in eukaryotes free floating?

A

Not all of them, usually associated with endoplasmic reticulum

118
Q

Alkaptonuria and phenylketonuria

A

Result from mutations that lead to metabolic blocks

119
Q

Phenylketonuria (PKU)

A

Phenylalanine hydroxylase is inactive in affected individuals, phenylalanine is not converted into tyrosine and enters cerebrospinal fluid, causing mental retardation

120
Q

One gene:one enzyme hypothesis

A

George Beadle showed genes are directly responsible for synthesis of enzymes (purposely exposed neurospora to bad things trying to force mutations, partner was Tatum)

121
Q

One gene: one polypeptide chain hypothesis

A

Nearly all enzymes are proteins - not all proteins are enzymes, proteins have subunit structure with two or more polypeptide chains

122
Q

Sickle cell anemia

A

Recessive genetic disease, affected individuals are homozygous for the gene, makes the blood cells pointy and easier to clog passages, heterozygotes are carried but largely unaffected

123
Q

Chemical differences between normal and sickle cell hemoglobin

A

HbS and HbA hemoglobin differ by single peptide fragment

124
Q

Colinearity

A

Order of nucleotides in gene correlates directly with order of amino acids in corresponding polypeptide

125
Q

Polypeptides

A

Precursors to proteins, amino acids assembled on and released from ribosomes as polypeptides

126
Q

Proteins

A

Polypeptides folded up into a functional three dimensional conformation

127
Q

Amino acids

A

Add to the diversity of proteins, carboxyl group on one side and amino acid on the other making it positive and negatively charged, and a r group which determines the overall reactivity of the amino acid and type of amino acid

128
Q

Peptide bond

A

Dehydration reaction facilitates bond between carboxyl group of one amino acid and amino acid group of another

Dr. Kolomyjec Genetics (7 decks)

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