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Test 3 Review Flashcards

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1
Q

What does Alpha DNA polymerase do?

A

synthesis of primers

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2
Q

What does Delta DNA polymerase do?

A

lagging strand DNA synthesis

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3
Q

What does Epsilon DNA polymerase do?

A

leading strand synthesis

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4
Q

What unwinds the DNA in bacteria (prokaryotes)?

A

gyrase

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5
Q

What unwindes the DNA in Eukaryotes?

A

topoisomerase

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6
Q

What is the primer made of in Eukaryotes?

A

DNA and RNA

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7
Q

How does Topoisomerase work?

A

it introduces negative supercoils and relieves strains in the double helix

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8
Q

Where can we find the A form of DNA?

A

In an RNA/DNA hybrid

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9
Q

What type of polymerase synthesis the leading strand of DNA?

A

epsilon

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10
Q

What type of polymerase synthesis the lagging strand of DNA?

A

Delta

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11
Q

Where does Delta primer conduct it synthesis?

A

Between the okasaki fragments on the lagging strand

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12
Q

In Eukaryotes DNA polymerase does not?

A

remove the primers.

Instead RPA is recruited replacing primer segment and the primer is degraded outside of the template

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13
Q

Where is DNA unwound in Eukaryotes?

A

at replication origins

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14
Q

Bidirectional DNA synthesis creates a?

A

Leading and lagging strand

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15
Q

What are the 4 things needed for Eukaryotic Replication?

A

dNTPs, templates, primers and DNA polymerase

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16
Q

Why are there so many origins of replication in Eukaryotes?

A

Because of the slowness of the replication

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17
Q

List the differences in Eukaryotic replication-

A

Rate of DNA synthesis is slower
Multiple origins of replication
Different DNA polymerases
Primer in eukaryotes is a short stretch of RNA followed by a short stretch of DNA
Primer is removed as an intact unit by RPA/endonucleases

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18
Q

Would synthesis in Eukaryotes still occur is there was no primer?

A

no

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19
Q

What makes Deoxyribose deoxyribose?

A

there is an OH at 3’ and not 2’

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20
Q

What is the difference between deoxyribose and dideoxynucleotide?

A

Dideoxynucleotide has no OH at group C3’ carbon

but other than that they have almost the same structure

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21
Q

What occurs is DNA polymerase picks up dideoxynucleotide instead of deoxyribose?

A

Chain termination occurs because DNA synthesis cannot continue (because there is no OH group at 3’

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22
Q

How can you tell if one is a dNTP or a ddNTP?

A

4 tubes are set up, and DNA is sequenced. ddATP^32 is used for a label.
As synthesis occurs, the DNA polymerase will pick up either dNTP or ddNTP.
If it picks up ddNTP then synthesis will not continue.
On second reaction, ddTTP is used as label and will yeild 3 different single stranded DNA and 4 different single stranded DNA

-Synthesis will stop at varying A’s because of the ddATP

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23
Q

On a gel electrophoresis, how can you tell which bend had ddNTP?

A

it will be the closest to the bottom (b/c its the shortest)

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24
Q

Give the 7 steps in didoxy sequencing

A
  1. Four separate reactions are prepared that each include:
    Single stranded DNA that needs sequencing (the template strand).
    5’ primer that will bond with the 3’ end of the template strand.
    DNA polymerase and all four regular nucleotides (A,T,G and C)
    One of the dideoxynucleotides in each reaction
  2. All 4 DNA synthesis reactions are allowed to proceed.
  3. Fragments of differing lengths will be produced for each reaction because of the dideoxynucleotides.
  4. The DNA in each of the four reactions is separated using gel electrophoresis.
  5. A radioactive tag attached to the dideoxynucleotides is used to visualize the DNA fragments.
  6. The film is read.The shortest fragment (bottom of the gel) is the 5’ end of the new DNA strand and is COMPLEMENTARY to the 3’ end of the template strand.
  7. The DNA strand that required the sequencing (template strand) is the complement to the sequence on the gel.
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25
Q

How do you read the full strand from the gel electrophoresis?

A

Read starting at the bottom, and continue upwards on each bend.

*Slide 58 has diagram

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26
Q

What is the difference between the old method of sequencing and the new method?

A

In the old method they use P32 and in the new method they use flourescent

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27
Q

What are the two broad Categories of Recombination?

A

Homologous (general)

Site-specific

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28
Q

Homologous (or general) recombination is also called?

A

crossing over

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29
Q

Site-specific recombination requires?

A

special nucleotide sequences

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30
Q

Why did the Transgenic mouse die after birth?

A

The ribcage of the transgenic mouse did not allow for breath

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31
Q

Recombination?

A

Creates new DNA molecules by breaking and rejoining of DNA secquences

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32
Q

How does the Cre/loxP system work?

**

A

The recombinase Cre cuts DNA wherever it encounters a pair of sequences designated loxP. All the DNA between the two loxP sites is removed and the remaining DNA ligated together again.
As a result, the DNA between two loxP sites was lost

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33
Q

In normal DNA, the blocking DNA blocks the expression of?

A

COX2

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34
Q

A floxed mouse is?

A

Mouse that contains the blocking DNA

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35
Q

A cre mouse is?

A

a mouse that can have different areas where COX is expressed/

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36
Q

A transgenic mouse can be made that expresses Cre that is ONLY?

A

active in specific cell types or tissue.

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37
Q

floxed mouse has a “target” gene, the one whose function is?

A

to be studied, flanked by loxP sequences.

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38
Q

In the offspring of the Cre transgenic mouse and target gene floxed mouse what will we observe of Cre and floxed gene?

A

some will have both Cre and floxed target gene.

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39
Q

Because Cre is active only in specific cell types or tissue, the “target” gene under study will be removed?

A

will be removed by Cre-mediated recombination at two loxP sites (i.e. In a cell where Cre is expressed, the target gene of interest will be deleted). All other cells will lack Cre expression, so the target gene remains intact.

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40
Q

What is the result of the Cre/loxP system?

A

The result: a mouse with a particular gene is deleted in only certain cells.

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41
Q

If a single strand break occurs, how is it fixed?

A

Using biological information from intact DNA we can fix this single strand break

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42
Q

What how is a break which occurs on both strands fixed?

A

Genetic information is filled in from homologous chromosomes, and this is called homologous-recombinate mediated repair

If that is not available, non-homologous end-joining repair is used

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43
Q

Which DNA repair mechanism is almost error free?

A

Homologous-recombinate mediated repair

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44
Q

What DNA repair mechanism is very error prone, and last resort of cell to survive?

A

Non-homologous end-joining repair

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45
Q

What is a holliday junction?

A

A 4 way junction of the chromosome which combines two chromosomes

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46
Q

What are the ways to resolve a holliday junction

***

A

DNa cleavage occurs at both, resulting in no change to chromosome
Vertical transfer occurs at both junctions (Think crossover in only one place)
Vertical and horizontal transfer occurs (Think both sides of chromosome will be changed)

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47
Q

The picture below is two Holliday junctions in a pair of DNA molecules undergoing recombination. Breakage and rejoining of the strands indicated by the arrows ( ) and ( ) results in crossover.
SLIDE 90 on PP 6 has picture

A

2 and 3 result in crossover

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48
Q

Gene conversion can result?

A

can result in a one-way transfer of genetic information, resulting in an allele of a gene on one chromosome being changed to the allele on the homologous chromosome.

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49
Q

What does gene conversion result from?

A

mismatch repair or gap repair

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50
Q

Heteroduplex DNA is generated when a single strand from one duplex pairs with its complement in the other duplex. Repair systems recognize impaired bases in heteroduplex DNA, and then excise and replace one of the strands to restore complementarity. Such an event converts the strand of DNA representing one allele into the sequence of the other allele.

What type of repair does this represent?

A

Mismatch repair

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51
Q

During double strand DNA repair, one DNA duplex act as a donor of genetic information that directly replaces the corresponding sequences in the recipient duplex by a process of gap generation, strand exchange and gap filling.

What type of repair does this represent?

A

Gap repair

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52
Q

The c Value is?

A

The total amount of DNA in the genome

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53
Q

What is the C-value paradox?

A

The range in C values does not correlate well with the complexity of the organism

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54
Q

What is the solution to the c-value paradox?

A

That the genome is filled with large tracts of modeling (normally repetitive DNA sequences)

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55
Q

Supercoiling occurs?

A

When two DNA double helices are twisted around each other

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56
Q

What is ‘relaxed’ DNA?

A

DNA that is not supercoiled (no twisting other than helical twisting)

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57
Q

Negative supercoils are?

A

Supercoils which involve right-handed twisting

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58
Q

What does negative supercoils compensate for?

A

underwinding of DNA

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59
Q

What will relaz supercoiled DNA?

A

a single nick by DNase will relax supercoiled DNA by free roation of the nicked strand about the other strand

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60
Q

What are the two methods of bacterial chromosome compaction?

A

Supercoiling

DNA binding to packaging proteins and DNA organized into a set of looped domains

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61
Q

folded chromosome=

A

nucleoid

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62
Q

Chromatin=

*****

A

DNA + specialized DNA binding proteins

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63
Q

What is the first level of chromosome condensation in Eukaryote?

A

formation of nucleosome

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64
Q

Very high concentration of lysine and arginine in histones because?

A

They are positively charged

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65
Q

How do you isolate the histones from the DNA I?

A

by adding a positively charged Na ion

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66
Q

What are the 5 types of Histones?

A

H1-4

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67
Q

Histones have an ________ mass to DNA.

A

equal

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68
Q

Nucleosome=

A

DNA(200 bp length) + 1H1 + 2 H2 + 2 H2B + 2 H3 + 2 H4

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69
Q

DNA will not be accessible for transcription if histones are?

A

tightly associated

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70
Q

In some cancer cells, there is an overexpression of HDAC (histone deacetylase). What could be the possible consequence of HDAC overexpression?

A. Increased acetylation of histones
B. Condensation of chromatin structure
C. Weak histone-DNA association
D. Activation of transcription

A

A. Increased acetylation of histones

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71
Q

The 2nd level of compaction (30-nm chromatin fibers) results in?

A

the string of nucleosome forms a right-handed coils

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72
Q

What are the steps of organization of chromosomes to metaphase chromosomes?

A
  1. Assembly of DNA and histones (Nucleosome formation)
  2. Nucleosome organization into 30 nm fiber
  3. 30-nm fiber forms radial loops that are attached to a protein scaffold
  4. Additional compaction by folding of the radial loops and protein scaffold
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73
Q

Scaffolds?

A

retain the shape of the original metaphase chromosomes even though the DNA strands have become elongated

74
Q

The structure of the metaphase chromosomes is determined by?

A

is determined by the scaffold and by the histones which are needed for to compact the radial loops.

75
Q

Telomeres are?

A

Repetitive DNA sequences at the ends of eukaryotic chromosomes

76
Q

What sequence do telomeres have thousands of repeats of in vertabrates?

A

TTAGGG

77
Q

What occurs if telomere is lost?

A

structral stability is lost

78
Q

What are telomeres thought of?

A

Telomeres are also thought to be the “clock” that regulates how many times an individual cell can divide

79
Q

Why are telomeres though to regulate how many times a cell can divide?

A

Telomeric sequences shorten each time the DNA replicates. Once the telomere shrinks to a certain level, the cell can no longer divide. Its metabolism slows down, it ages, and dies

80
Q

How does telomerase work?

A

Telomeric repeats are directly added to the 3’ ends of DNA by a reverse-transcriptase called telomerase.
Telomerase has within it a RNA homologous to the telomere repeat sequence.
The RNA acts as a template for the extension of telomere sequences.

81
Q

DNA that expresses telomerase will do what?

A

Never loose telomere when divided, essentially making them immortal

82
Q

What field is telomerase frequently used in?

A

anti-aging

83
Q

Telomerase is expressed in?

A

Expressed by 80-90% of cancer cells

84
Q

What does colchicine do?

A

freezes cells in metaphase

85
Q

Describe the steps in creating a human karyotype

A

Harvested cells are first cultured
The cells are then treated with colchicine which arrests the cells in metaphase, and then treated and stained to observe the chromosomes
Chromosomes can be photographed or visualized using a computer, and then analysed
Chromosomes are identified by size, position of the centromere, and banding and staining regions

86
Q

How are the chromosomes matched with each other?

A

by comparing bends and size on chromosome

87
Q

A karyotype refers to?

A

the number and type of chromosomes present in an individual

88
Q

What is a karyogram?

A

A display or photomicrograph of an individual’s somatic-cell metaphase chromosomes that are arranged in a standard sequence (usually based on size and structure)

89
Q

Three copies on chromosome 21 indicates?

A

Down syndrome

90
Q

A karyotype that only contains one x chromosome is indicative of?

A

Turner’s syndrome

91
Q

A karyotype containing two x chromosomes and a y chromosome is indicative of?

A

klienfelters syndrome

92
Q

What are the steps in chromosome FISH?

A

Cell is fixed onto microscope slide
DNA is denatured and incubated in solution containing probe. Probe is labeled with florescent dye.
Probe binds with complementary base pair.
Pink dot of probe will appear under microscope

93
Q

What does chromosome FISH stand for?

A

fluorescence in situ hybridization

94
Q

Chromosomal painting is?

A

an application of FISH using a large collection of different DNA fragments from a specific chromosome

95
Q

If there is no elastin locus on chromosome 7 on a FISH what is this indicative of?

A

William’s syndrome

96
Q

Chromosome painting uses?

A

chromosome specific DNA sequences attached to fluorescent dyes, the labeled DNA sequences attach to their targets painting them with distinctive colors
: allows the visualization of individual chromosomes

97
Q

What were the two models of chromosome nucleus between cell division?

A

Chromosome territory model

Spaghetti model

98
Q

Chromosome territory model is?

A

Chromosome territory model : the DNA of each chromosome occupies a defined volume of the nucleus and only overlaps with its immediate neighbors

99
Q

The spaghetti model is?

A

the DNA fiber of multiple chromosomes meanders through the nucleus in a largely random fashion, and the chromosomes are therefore intermingled and entangled with each other

100
Q

How do we know which model is correct? Could you propose an experiment which would prove/disprove the models?

A

Making chromosome specific probes in which each chromosome specific probes labeled with different colors

101
Q

What group has the largest chromosomes?

A

A group

102
Q

What group has the smallest chromosomes?

**

A

G group

103
Q

How can chromosomes be sorted?

A

by size and by location of the centromere

104
Q

What are the three categories of centromere sorting?

A

Metacentric
Submetacentric
Acrocentric

105
Q

A metacentric chromosome looked like?

****

A

the centromere lies near the center of the chromosome

106
Q

A submetacentric chromosomes look like?

****

A

centromere that is off-center, so that one chromosome arm is longer than the other.

107
Q

A acrocentric chromosome looks like?

****

A

Centromere resides very near one end

108
Q

Nomenclature:

Above the centromere is called?

A

the short arm and labeled with p

109
Q

Nomenclature:

Below the centromere is called?

A

the long arm and is labeled with q

110
Q

Nomenclature:

What is the top of the short arm called?

A

pter

or p-terminus

111
Q

Nomenclature:

What is the bottom of the long arm called?

A

qter

or q-terminus

112
Q

Nomenclature:

Can q be split into subsections?

A

Yes

113
Q

Nomenclature:

The layout for nomenclature is?

A

Chromosomes #->arm->#section of arm->Bend#

114
Q

Using more elongated (non-metaphase chromosomes) such as late prophase chromosome will create?

A

create sub-bends which also need to be labelled.

115
Q

46,XX,del(5)(p14pter)

What does this tell us?

A

Female with deletion of the short arm of chromosome 5 from p14 to terminus

116
Q

47, XY, +21

What does this tell us?

A

Male with an extra chromosome on 21

Down syndrome

117
Q

46, XY, del(7)(q11.23q21.2)

What does this tell us?

A

A male with a deletion on chromosome 7 on the long arm from 11.23-21.2

118
Q

46, XX, inv(2)(p13p24)

What does this tell us?

A

Woman with an inversion on chromosome 2 that extends the short arm 13 & 24

119
Q

What are the consequences of X activation?

A

(i) dosage compensation for X-linked genes between female and male.
(ii) a normal female as mosaic for X-linked genes.

120
Q

What are female sex cells referred to as?

A

Mosaic due to X inactivation

121
Q

Calico female cats will always be?

A

heterozygous

122
Q

How are there male calico cats?

A

If male cats have two copies of X chromosome and one y we will still have male calico cats.

123
Q

What is a barr body?

A

The inactive X chromosome forms a compact body within the nucleus

124
Q

Where is the barr body generally located?

A

on the periphery of the nucleus

125
Q

Number bar body=

A

number x chromosome-1

N-1
For example the number of bar bodies in someone with XXX chromosomes would be two

126
Q

X and Y chromosomes pair and crossover where?

A

in the pseudoautosomal region

127
Q

SRY gene is?

A

sex reversal on y

128
Q

SRY gene is also?

A

TDF (testis determining factor)

129
Q

The conclusion of sex linked gene crossovers is?

A

Portion of Y that causes male-ness must lie just next to pseudoautosomal region

130
Q

What are the gonads and reproductive ducts like before Sry expression?

A

In early embryos unspecialized gonads and two sets of reproductive ducts

131
Q

An embryo gonad develops as ______ if it has the Sry gene and an _______ if it does not.

A

An embryo gonad develops as a testis if it has the Sry gene and an ovary if it does not

132
Q

What are the 3 viable trisomies?

A

13, 18, and 21

133
Q

____ percent of all recognized pregnancies in human beings terminate in spontaneous abortion

A

15 percent of all recognized pregnancies in human beings terminate in spontaneous abortion

134
Q

About 50% of all spontaneous abortions the fetus?

A

has a major chromosomal abnormality

135
Q

What does monosomy refer to?

A

refers to an otherwise diploid organism that has a missing copy of an individual chromosome.

136
Q

Why are monosomy spontaneous abortions so low in number?

A

monosomy is not found among aborted fetuses in table 8.2 because the abortions take place so early in the development that the pregnancy goes unrecognized by the mother.

137
Q

Which trisomies are viable?

A

13, 18 and 21

138
Q

What are 95% of Down syndrom cases caused by?

A

non-disjunction

139
Q

47,XY,+21 or 47,XX,+21

What does this represent?

A

Down syndrome in a man or woman

140
Q

47,XY,+18 or 47,XX,+18

What does this represent?

A

Trisomy 18 in a male or female

Also known as Edward’s Syndrome

141
Q

What is the survival rate of infants with trisomy 18?

A

50% die within the first several weeks and only about 5% survive until adulthood

142
Q

47,XX,+13 or 47,XY,+13

What does this represent?

A

Trisomy 13 or Patau syndrome

143
Q

What is the survival rate of Trisomy 13?

A

95% of infants die within the first year of life

144
Q

What is prob of down syndrome in children in mother has down syndrome?

A

50%

145
Q

What are the examples of Sex Chromosome Aneuploidy?

A

Kleinfelter’s XXY
Turner’s X
Jacob’s XYY
Triple X syndrome XXX

146
Q

What are some symptoms of Klienfelter’s?

A

Men, usually sterile and tend to have long arms and legs

Shy, quiet, and have high incidence of speech delay and dyslexia

147
Q

What are some symptoms of Turner’s?

A

female characteristics are present but undeveloped.

low hairline, abnormal eye features and bone development

148
Q

What are the symptoms of Jacob’s syndrome?

A

boys are taller than their brother’s. Likely to be hyperactive

149
Q

What are symptoms of Triple-X syndrome?

A

girls are tall and thin and often shy.

High incidence of dyslexia

150
Q

What is translocation?

A

A chromosomal aberration resulting from the interchange of parts between non-homologous chromosomes

151
Q

What are the two types of translocation?

A

Nonreciprocal translocation

Reciprocal translocation

152
Q

What is nonreciprocal translocation?

A

one way transfer of genetic material

153
Q

What is reciprocal translocation?

A

Two way exchange of genetic information

154
Q

What is Robertsonian translocation?

A

Centromeres from two non-homologous chromosomes fuse and chromosomal material from the short arm is lost

155
Q

3% of Down syndrome cases what kind of translocation between what chromosomes?
*****

A

Robertsonian translocation between chromosomes 21 and 14

156
Q

Families that have a high translocation down syndrome have?

A

high risk of spontaneous abortion due to chromosomal abnormalities

157
Q

Non-affected children of Robertsonian translocation have what percent of carrying the translocation?

A

50% chance of carrying the translocation

158
Q

Robertsonian translocation occurs in what type of chromosome?

A

acrocentric

159
Q

If a parent is a carrier then offspring will be?

A

If parent is carrier than 50% viable and 50% non viable

160
Q

Out of the viable offspring carrying Robertsonian what are the chances of normal/carrier/down syndrome?

If out of all possible offspring what are the chances?

A

1/3 viable offspring would be normal
1/3 carrier
1/3 down syndrome

If not asked about viablity then it is 1/6

161
Q

What is heterochromitin?

A

DNA is tightly wrapped around histone and highly condensed low gene expression

162
Q

What is Euchromatin?

A

Loose wrapping around histone. High gene expression

163
Q

Positive-effect variegation?

A

Mosaic phenotype due to variation in the level of expression of gene in different cell lineages owing to its position in the genome.
PEV usually results from a chromosome aberration that moves a wild type gene from a position in euchromatin to a new position in or near heterochromatin.

164
Q

What does the c-myc gene control?

A

cell growth and division

165
Q

What occurs when the c-myc gene becomes translocated

A

the translocation doesnt function properly and is actively expressed and leads to cancer

166
Q

What are the 3 different RNA polymerases in Eukaryotes?

*****

A

RNA pol I = rRNA genes (except 5S)
RNA pol II = mRNAs (structural genes)
RNA pol III = tRNAs and 5S rRNA

167
Q

What determines where transcription starts?

A

TATA box

168
Q

What do general transcription factors do?

A

Bind to the core promoter and then they recruit RNA polymerase II

169
Q

What do core promoters do?

A

Form the binding sites for general transcription factors

-Necessary for the assembly of a transciptopm apparatus and recruitment of RNA polymerase II core promoter

170
Q

What are some examples of specific transcription factors?

A

SRY and P53

171
Q

What do specific transcription factors do?

A

Bind to the regulatory elements and recruit general transcription factors
-These recruited transcription factors will bind to the core promoter

172
Q

cis-acting elements are?

A

DNA sequenses that exert their effect only on nearby genes

173
Q

What are some examples of cis-acting elements?

A

TATA box, enhancers and silencers

174
Q

What are trans-acting elements?

A

Regulatory proteins that bind to such DNA sequences (cis-acting elements)
e.g. transcription factors

175
Q

What binds to the TATA box first?

Step 1

A

TFID which is a complex of protiens that include the TATA-binding protein and several other TBP associated factors

176
Q

What binds to TFID?

Step 2

A

TFIIB

177
Q

What does TFIIB do?

Step 3

A

Acts as a bridge to bind RNA polymerase II and TFIIF

178
Q

What do TFIIE and TFIIH bind to?

Step 4

A

RNA polymerase to form a preinitiation sequence

179
Q

What is the general transcription factor that has helicase activity?

A

TFIIH

180
Q

How do you prove the hypothesis that irradiation will cause p53 expression that will lead to gene x epression?

A

By using a gel shift assay

Genetics (4 decks)

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