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Genetics > Genetics Test 2 > Flashcards

Genetics Test 2 Flashcards

1
Q

Where would you find denatured G:T dna and A:T dna in a centrifuge tube?

A

G:C-rich DNA—will be found at a lower position because the tighter hydrogen bonding of G:C base pairs makes this DNA more dense. (3 hydrogen bonds)

A:T-rich DNA—will be found at a higher position because its looser hydrogen bonding makes it less dense. (2 bonds)

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2
Q

What is Denaturation?

A

Loss of native configuration of a macromolecule, usually accompanied by loss of biological activity.
Denatured proteins often unfold their polypeptide chains and express changed properties of solubility.

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3
Q

What is Renaturation?

A

If the complementary single strands of DNA are cooled slowly, they find each other and re-form base-paired double helices

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4
Q

What does the rate of renaturation depend on

A

-Complexity of the sequence
-Concentrations of the renaturing DNA sequences (amount)

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5
Q

In a sample of genomic DNA from an organism, what DNA sequences are more concentrated? Why?

A

The repetitive DNA sequences are relatively more concentrated than the unique DNA sequences
Because they are present many times over; consequently, the repetitive sequences
re-form duplex molecules at a faster rate than the unique DNA sequences.

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6
Q

What is the degree of repetition called?

A

copy number

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7
Q

How many complex copies can be found in the prokaryotes genome?

A

1 copy

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8
Q

How many complex (unique) copies can be found in a eukaryote genome? # and %

A

1-10 copies (30-85%)

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9
Q

How many moderately repetitive copies can be found in a eukaryotic genome?

A

10-10^5
5-80%

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10
Q

How many highly repetitive copies can be found in a eukaryotic genome

A

> 10^5
50%

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11
Q

What do the moderately repetitive copies in a genome do?

A

-ribosomal proteins
-help in the cytoskeleton as actin or myosin
-transposable elements (make up 44% of the genome)

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12
Q

What do the highly repetitive copies in a genome do?

A

-are usually the functioning regions such as on centromeres and telomeres
-used for protection of DNA (non-coding)
-used for structurization and recombination

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13
Q

What are transposable elements?

A

LINES

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13
Q

What are LINES

A

They are non long terminal repeats which help with protection of the sequencing

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14
Q

What does LINES stand for?

A

-Stands for long interspersed nuclear elements

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15
Q

How many base pairs are in LINES?
How much of the genome do they make up?

A

-6-10 kb (6000-10,000 base pairs)
-20%

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16
Q

What are the subdivision of LINES

A

L1
L2
L3

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17
Q

What does L1 do?

A

-L1 is only active in mammals
-they have an internal promoter that is
recognized by RNA polymerase II
-they have two open reading frames: ORF1 and ORF2

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18
Q

What is the size of L1

A

-6 kb in size (6000 base pairs)

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19
Q

How many L1 can be found in the human genome

A

3000 and 5000 complete L1 elements

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20
Q

What is ORF1 and ORF2

A

-ORF1 encodes a nucleic acid-binding protein
-ORF2, which encodes a protein with endonuclease and reverse transcriptase activities

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21
Q

What happens in L1 transposition?

A

L1 transposition involves the transcription of a complete L1 element into RNA
and the reverse transcription of this RNA into DNA

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22
Q

Where does L1 transposition occur

A

Both processes take place in the nucleus

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23
Q

What happens before the L1 RNA is reverse transcribed

A

it journeys to the cytoplasm where it is translated into polypeptides that remain associated with it when it returns to the nucleus

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24
Q

What does the polypeptide encoded by ORF2 possess?

A

possesses an endonuclease function that catalyzes cleavage of one strand of the DNA
duplex at a prospective insertion site in a chromosome

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25
Q

What does the exposed 3′ end of the cleaved DNA strand serve as during transposition?

A

Serves as a primer for DNA synthesis using the L1 RNA as a template and the reverse transcriptase activity provided by the ORF2 polypeptide

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26
Q

How many copies of L2 and L3 do humans have?

A

L2= 315,000 copies
L3=37,000 copies
Both are inactive

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27
Q

What does SINES stand for?

A

short interspersed nuclear elements

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28
Q

How much of the genome do SINES make up?

A

13%
Second most abundant behind LINES

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29
Q

What do all retroposons have?

A

they have a sequence of A:T base pairs at one end

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30
Q

What do SINES do?

A

-transpose through a process that involves reverse transcription of an RNA that has been transcribed by RNA polymerase III from an internal promoter.
-do not code for anything; but good at moving things

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31
Q

What do SINES use as their reverse transcriptase?

A

the reverse transcriptase needed for
the synthesis of DNA from the SINE RNA is furnished by a LINE-type element

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32
Q

True or False.
SINES rely on the LINES to multiply and insert within the genome.

A

True

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33
Q

What is the only transpositionally active element found in SINES

A

Alu elements

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34
Q

What are Cut and Paste transposons?

A

-3% of genome
-not active

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35
Q

What are the 4 basic types of transposable elements found in the human genome?

A

LINEs,
SINEs,
retroviruslike elements
cut-and-paste transposons

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36
Q

True or False.
L1 LINE and the Alu SINE are the only transpositionally active transposons.

A

True

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37
Q

What do transposons have the ability to do?

A

the ability to change position in the genome—that is, they are mobile.

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38
Q

What percentage of the human genome is transposable?

A

44%

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39
Q

The coding region of a retroviruslike elements contain a small number of genes.
What are these three genes?
What do they code for?

A

gag=encodes a structural
protein of the virus capsule (glycoprotein)

pol= encodes a reverse transcriptase/
integrase protein (polymerase)

env=encodes a protein component of the virus envelope

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40
Q

What does LTR stand for?

A

long terminal repeats

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41
Q

What do LTRs do?

A

They are required for integration of the viral genome into the DNA of the host cell.

The initiation site for transcription of the viral genome.

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42
Q

What do you want in a centromere?

A

-Attachment and separation
-A-T rich (easily breakable)
-high copy number

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43
Q

At what stage do sister chromatids of the duplicated chromosome move to the opposite poles of a cell?

A

anaphase

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44
Q

The movement of sister chromatids to opposite poles depends on what?

A

This movement depends on the
attachment of spindle microtubules to the kinetochores

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45
Q

What are kinetochores

A

Complex protein structures associated with the centromeres of each of the sister chromatids

46
Q

What is a key step in the transition from metaphase to anaphase?

A

The production of two functional centromeres

47
Q

How many copies of alpha satellite sequences do humans have? (repeats)

A

5000 to 15,000 copies of a 171 base-pair-long sequence called the alpha satellite sequence (repeats)

48
Q

How big is an alpha satellite region in humans?

A

40 nm or 110 nucleotides long

49
Q

What is heterochromatin?

A

Chromatin staining darkly even during interphase, often containing repetitive DNA with few genes.

50
Q

What is euchromatin?

A

Genetic material that is not stained so intensely by certain dyes during interphase and that comprises many different kinds of genes

51
Q

What is CENP-A

A

A protein variant of histone H3

52
Q

What are the ends of chromosomes called?

A

telomeres

53
Q

What does CENP-A do?

A

-binds to the centromeres of eukaryotes
-even to the small centromeres of yeast
-helps with kinetochore formation
-helps with left hand assembly of DNA

54
Q

What are the 3 important functions of telomeres?

A

-They prevent dioxyribonucleases from degrading the ends of linear DNA molecules
-They prevent fusion of the ends with other DNA molecules
-They facilitate the replication of these ends without the loss of material

55
Q

Where would you find the sequence.
What is it?
5′ TTAGGG 3′

A

-The telomeres of eukaryotic chromosomes
-A short nucleotide sequence present as a tandem repeat
-Most frequently observed

56
Q

In a normal human cell, how many tandem repreats are found on a telomere?

A

-500 to 3000 TTAGGG repeats and gradually shorten with age.

57
Q

True or False.
Telomeres of germ-line cells and cancer cells shorten with age.

A

False.
Telomeres of germ-line cells and cancer cells do not shorten with age.

58
Q

How do most telomeres terminate?

A

With a G-rich single-stranded region in the DNA strand with the 3′ end (a so-called 3′ overhang)

59
Q

What is a t-loop?

A

The single strand at the 3′ terminus invades an upstream telomeric repeat (TTAGGG in mammals) and pairs with the complementary strand, displacing the
equivalent strand

60
Q

What does shelterin do in the t-loop process that effects DNA

A

The DNA in these t-loops is protected from degradation and/or modification by DNA repair processes

61
Q

What is Shelterin?

A

telomere-specific protein complex

62
Q

What are the 6 different proteins found in Shelterin?

A

-TRF1
-TRF2
-POT1
-TIN2
-TPP1
-RAP1

63
Q

What is common to all methods involving probe binding to complementary sequences?

A

The use of hybridization probes that are linked to fluorescent dyes or antibodies
tagged with fluorescent compounds

64
Q

What does colchicine do?

A

It is known that colchicine binds to microtubules and prevents the formation of functional spindle fibers. As a result, daughter chromosomes do not undergo their normal anaphase separation.

65
Q

What is the function of Autoradiography?

A

Autoradiography is a method for detecting and localizing radioactive isotopes in cytological preparations or macromolecules by exposure to a photographic emulsion that is sensitive to low-energy radiation

66
Q

Where is Thymidine found?

A

Thymidine is incorporated almost exclusively into DNA;

67
Q

What is the single origin of replication in e. coli chromosomes?

A

oriC (245 bp)

68
Q

What conserved component of e. coli causes the replication bubble

A

One 13-bp sequence is present as three tandem repeats. These three repeats are rich in A:T base pairs, facilitating the formation of a localized region of strand separation referred to as the replication bubble.

69
Q

What is another conserved component of e. coli that causes the binding of proteins in order to create the replication bubble

A

9-bp sequence that is repeated four times and is interspersed with other non random sequences

70
Q

How many proteins bind due to the 9-bp sequence in e. coli?

A

4

71
Q

What is cooperative binding

A

-a few bind, causing more to bind because of it
-causes stabalization

72
Q

What proteins are the key to unwinding the origin of replication, noting the order of assembly?

A

The DnaA protein appears to be largely responsible for the localized strand separation at oriC during the initiation process.

73
Q

In what direction can DNA polymerase add nucleotides onto a strand of DNA

A

They can only add nucleotides onto the 3′ end of a DNA strand—that is, they
synthesize DNA only in the 5′ to 3′ direction

74
Q

What does DNA ligase do

A

an important enzyme that seals single-strand breaks in DNA double helices

75
Q

True or False.
The replication of prokaryotes is unidirectional

A

false.
The replication of e.coli is bidirectional

76
Q

What is satellite DNA? What is it made up of?

A

It is repetitive DNA sequences.
It a DNA made up from G-C rich or A-T rich sequences.

77
Q

Where is moderately repetitive DNA found? What can they do?

A

They are found in the arms of a chromosome; some in tandem arrays while others occupy dispersed sites.
They are mobile; they move in the genome

78
Q

What is a key step in the transition from metaphase and anaphase?

A

The production of two functional centromeres

79
Q

What happens if a chromosome or chromosome fragment lacks a centromere?

A

It dies during cell division

80
Q

What does flanking mean?

A

refers to the nucleotide sequences adjacent to a specific DNA sequence of interest. Flanking sequences can be found on either side of the target sequence and are typically used as reference points or landmarks

81
Q

What is heterochromatin Protein 1 (HP1) and what does it do?

A

A protein associated with centromeric heterochromatin and may be involved with the packaging of DNA of the centromeric heterochromatin

82
Q

What does “Pericentric Heterochromatin” mean?

A

It is the heterochromatin which is flanking the centromere (beside the centromere)

83
Q

What does the Pericentric Heterchromatin consist of?

A

mainly of repetitive, nongenic DNA;does contain some genes

84
Q

What are the three functions of telomeres

A
  1. Prevent DNase from degrading the ends of linear DNA molecules
    2.Prevent fusion of the ends of other DNA molecules
    3.They facilitate the replication of ends (without the loss of material) rep. ends
85
Q

How long is the average “overhang” in humans

A

50-500 bases

86
Q

What do telomeres usually terminate with? (sequence)

A

a G-rich single stranded region in the DNA strand with the 3’ end (3’ overhang)

87
Q

What is the point of the t-loop

A

To help stop degradation of the strand and/or modification of DNA repair processes by shelterin

88
Q

What is the job of DNA ligase?

A

It seals single stranded breaks in DNA double helices

89
Q

What is DNA ligase used for in ALL organisms?

A
  1. DNA replication
  2. DNA repair
  3. Recombination between DNA molecules
90
Q

What converts the phage lambda chromosome from its hydrogen bonded form to its covalently bonded form?

A

DNA Ligase

91
Q

What is the first thing that occurs when a lambda chromosome is injected into a host cell?

A

It forms a covalently closed circular molecule

92
Q

How is e. coli DNA coiled?

A

it is negatively supercoiled

93
Q

What is needed for DNA replication to occur in e.coli?

A

DNA gyrase activity

94
Q

What is considered the “replicase” in e.coli?

A

DNA Polymerase III

95
Q

The initiation of the okazaki fragments on the lagging strand is carried out by what?

A

primosome

96
Q

What is a Primosome

A

a protein complex containing DNA primase and DNA helicase (works by ATP)

97
Q

What does a primosome do?

A

It unwinds the DNA and DNA primase synthesises the RNA primers needed for the attachment of okazaki fragments

98
Q

How are the RNA primers extended in e.coli?

A

They are covalently extended with the addition of deoxyribonucleotides by DNA pol III

99
Q

what is apart of the replisome of DNA polymerase III in e.coli

A
  1. DNA polymerase III holoenzyme
  2. 2 Catalytic cores (one does the leading and one does the lagging strand)
  3. The primosome unwinds the DNA + synthesis of RNA primers
100
Q

How is a change in the conformation of PCNA achieved?

A

Rf-C induces a change in the conformation of PCNA that allows it to encircle DNA, providing the essential sliding clamp

101
Q
A
102
Q

At what stage are histones created

A

during s phase

103
Q

what occurs in g1 and g2 of mitosis

A

protein synthesis

104
Q

What does NAP-1 do

A

it transports histones from their site of synthesis into the cytoplasm to the nucleus

105
Q

What does CAF-1 do

A

it carries them to the sites of replication by binding to PCNA clamps that tether DNA polymerase delta to the DNA template

106
Q

What are NAP-1 and CAF-1 apart of

A

the disassembly and assembly of nucleosomes during chromosome replication in eukaryotes

107
Q

What do NAP-1 and CAF-1 stand for?

A

-Nucleosome assembly protein 1
-chromatin assembly factor 1

108
Q

What is used to slow down the process of telomere shortening?

A

telomerase

109
Q

What does telomerase do?

A

-it recognizes the g rich overhang and extends it 5’-3’ one repeat at a time
-it extends the 3’ end of the template strand

110
Q

where does translation occur?

A

ribosomes

111
Q

what is an intron?

A

non coding sequences

112
Q

what do introns do?

A

they separate the expressed sequences or exons of the genes

113
Q

In strand selection, there is a template strand and a non-template strand, what is the m-RNA (sense strand) the same as (minus an adjustment)

A

the non-template strand; however, the T’s are switched to U’s

Genetics (9 decks)

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