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Lab exam Flashcards

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1
Q

Karyotype

A 
# and appearance of chromosomes in a eukaryotic cell
Also used for the complete set of chromosomes in a species, or an individual organism
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2
Q

Karyotypes can also be used to study ____.

A

Chromosomal abberations

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3
Q

P arm in the human chromosome is _____.

A

Short

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4
Q

Q arm in a human chromosome is _____.

A

Long

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5
Q

HeLA

A

A human tumor cell line named after Henrietta Lacks

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6
Q

Aneauploid

A

1 or more whole chromosomes of a normal set of chromosomes that are missing or are present in more than the usual number

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7
Q

Chromosome types:

A

Metacentric, Sub-metacentric, and acrocentric

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8
Q

Colchicine

A

A plane alkaloid that arrests cells in metaphase

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9
Q

Why is a HeLa cell arrested in metaphase?

A

Because it’s when the cell is most highly condensed, highly coiled and easiest to distinguish

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10
Q

Cells are ___ in order to get them to detach from the culture plate

A

Trypsinized

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11
Q

Why are HeLa cells exposed to a hypotonic solution?

A

It caused osmotic swelling which causes the membranes to rupture easily and spill out the chromosomes, so you can see the chromosomes spread

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12
Q

Eosin

A

Pink colour and stains nucleic acids (or the nucleus)

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13
Q

Haematoxylin

A

Purple colour and stains nucleic acids (or the nucleus)

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14
Q

GMO (Genetically modified organism)

A

Is an organism, plant, or animal that has been genetically manipulated

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15
Q

Disadvantages of GMO foods

A
  • Less sugar, protein, fibre, zinc
  • Exposure to possible toxins
  • Harm to environment
  • Antibiotic resistance
  • Spread of introduced genes to non-target plants
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16
Q

What are the 3 stages of a polymerase chain reaction?

A

Denature, Anneal primers, Extend

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17
Q

Purpose of gel electrophoresis

A

To separate, identify, and purify DNA fragments

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18
Q

2 types of gel electrophoresis

A

Agorase, Polyacrylamide

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19
Q

Why use agarose gel?

A

Lower resolution, greater range or separation

-Runs in horizontal configuration under constant strength electric field

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20
Q

Why use gel electrophoresis?

A
  • To determine if sample contains a specific segment of DNA
  • Compare DNA samples
  • Identify samples as a given species
  • Isolate and sequence DNA
  • Identify variances in DNA sequences
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21
Q

Which way does DNA flow in electrophoresis?

A

From negative to positive

-Because DNA is negatively charged

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22
Q

____ DNA fragments will migrate further down the length of the gel than ____ fragments

A

Smaller; Larger

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23
Q

Why put glycerol in well for gel electrophoresis?

A

Increases the density of sample which keeps DNA in the well

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24
Q

Why add bromophenol blue and xylene cyanol into wells for gel electrophoresis?

A

Dyes
-They track the migration of DNA sample in the gel
Xylene: -4000bp
Bromo: -300bp

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25
Q

What are factors that affect the rate of DNA migration in gel electrophoresis?

A
  • Agarose concentration
  • Applied voltage
  • Ionic strength of buffer
  • # of bp in sample
  • DNA confirmation
  • Size of gel
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26
Q

What is ethidium bromide?

A

Fluorescent dye used in gel electrophoresis

  • Absorbs UV light
  • Dangerous
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27
Q

Why is SYBR safe?

A

Same as ethidium bromide but not as toxic

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28
Q

Gene nomenclature

A

3 italicized lower case letters

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29
Q

Gene product nomenclature

A

First letter capitalized, no italics

Ex: LacZ

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30
Q

Operon

A

Structural genes under the control of 1 promoter

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31
Q

Lac promoter

A

RNA polymerase binds

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32
Q

Lac terminator

A

Gene that specifies end of transcription

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33
Q

LacZ

A

Encodes beta-galactosidase –> Causes lactose –> Galactose and glucose

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34
Q

LacY

A

Encodes lactose permease (Which transports lactose)

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35
Q

LacA

A

Encodes transacetylase

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36
Q

Competent cells are able to uptake exogenous ____.

A

DNA

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37
Q

E.Coli artificially induced to enter competency when treated with ____.

A

Metal cations- Ca 2+, Mg 2+

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38
Q

Non-coding regions of the genome contain ____.

A

VNTR

Variable number of random repeats

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39
Q

p < 0.05

A

Reject null hypothesis

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40
Q

p > 0.05

A

Fail to reject the null

assumption is correct

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41
Q

Epistasis

A

Genes that modify the expression of other genes

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42
Q

What is a meningioma?

A

Benign tumour that arise from meninges covering the brain and spinal cord

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43
Q

Somatic line mutation

A

A non-inheritable mutation occurring in a somatic cell

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44
Q

Germ line mutation

A

An embryonic cell lineage that forms that reproductive cells

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45
Q

Sporadic disease

A

Occurs in single and scattered cases

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46
Q

Familial disease

A

Transmitted through and expressed by members of a family

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47
Q

What is chromatin remodelling?

A

A process in which the structure of chromatin is altered by a protein complex
-Results in change in the transcriptional stage of genes

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48
Q

Define exome sequencing

A

Selective sequencing of the coding regions of the genome

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49
Q

Exons

A

Short, functionally important sequences of DNA

-Ones that are translated in proteins

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50
Q

Causes of meningiomas

A

NF2 mutations, Sporadic cases

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51
Q

How often are there germ line cases found in meningiomas?

A

Rarely

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52
Q

Positive control

A

Receives a treatment with a known response

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53
Q

Negative control

A

Groups where no phenomenon are expected

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54
Q

Define experimental control

A

A standard used for comparison that contains everything except the variable(s) you are testing

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55
Q

GM food lab: one control for the PCR

A

1 sample without DNA

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56
Q

Lac operon with glucose present

A

No cAMP production and no lac operon transcription

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57
Q

Define loss of heterozygosity

A

Loss of the wild type allele in a somatic cell

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58
Q

Define immunohistochemistry

A
  • Antibody that binds to protein or another molecule that reacts to produce a visual stain
  • Detects presence of protein
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59
Q

What does hemtoylin and eosin stain?

A

H-stains nucleus

E-counterstain, background is pink

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60
Q

Define clear cell histology

A

Cell whose cytoplasm is not stained by hematoxylin or eosin

-Indicates a neoplastic cell

61
Q

How do you enable E.Coli to take up exogenous DNA?

A
  • Treat with calcium chloride and heat
  • DMSO increases solubility of lipids in outer membrane
  • Ca 2+ creates positive charge on the membrane that will attract the negative DNA
62
Q

Why did recovery broth lack ampicillin?

A

Have to give bacteria time to transcribe gene for ampicillin resistance

63
Q

How would you differentiate between plasmids with gap in the correct (5’ to 3’) or incorrect orientation?

A

The gap and amp resistance gene are located on separate parts of the plasmid so the incorrect orientation of gfp wouldn’t affect resistance.
-These would still survive, but they wouldn’t fluoresce

64
Q

Steps cell apoptosis

A
  1. Nuclear DNA fragmented
  2. Internal cellular structures are disrupted
  3. Cell dissolved into small spherical structures: apoptotic bodies
65
Q

What happens when tumour-suppressor genes are mutated?

A

Cells are unable to respond to cell cycle checkpoints or do not undergo cell death
-Leads to accumulation or more mutations and development of cancer

66
Q

What is optimal primer length?

A

18-24bp

67
Q

What is optimal melting temp. for forward/reverse primers?

A

52-60 degree difference between the 2

68
Q

What is optimal G/C content for primers?

A

45-55%

69
Q

What is the optimal amplicon length of primers?

A

300-1000bp

70
Q

Query cover

A

How much of the primer sequence is covered by alignment to the database sequence

71
Q

E value

A

Probability of the sequence occurring the database

-Want it to be low

72
Q

Identity

A

The extent to which 2 sequences have the same residues at the same positions in an alignment

73
Q

Why boil with Chelex?

A

Boiling denatures proteins and Chelex protects sample from DNAases which cut DNA into small fragments making is unusable for PCR

74
Q

What does Chelex need to bind to DNAases?

A

Mg 2+ (Magnesium Chloride)

75
Q

dNTP’s

A

Deoxynucleotide Triphosphates

-Building blocks for DNA

76
Q

How do you choose annealing temp?

A

5 degrees lower than the Tm

77
Q

Describe initial denaturation in PCR

A

94 degrees for 3 minutes

-Heated to this temp in order to denature the double stranded DNA into single strands

78
Q

What temperature for Extension in PCR? Why?

A

72 degrees

-Allows synthesis of new DNA

79
Q

Temperatures for PCR

A
  • Initial denaturation: 94 (3 mins)
    • Denature: 94 (1 min)
    • Anneal: 54 (1 min)
    • Extension: 72 (1 min)
  • Hold at 12 degrees
80
Q

Optimal primer: There are G/Cs within the last ___ bases of the ___ end, but not more than ___ of either G or C.

A

4
3’
3

81
Q

Mitosis

A

The process of nuclear division of either a diploid (2n) or haploid (n) eukaryotic cell whereby 2 daughter nuclei are produced that are genetically identical to the parent nucleus
-Cell division usually follows nuclear division

82
Q

What happens in the 1st phase (G1, Gap 1) of the cell cycle?

A

Cell growth and prep for DNA replication

83
Q

What are included in interphase?

A

G1, S, G2

84
Q

What occurs in S phase?

A

DNA replication and chromatid duplication

85
Q

What takes place in the G2 phase?

A

More cell growth

86
Q

When is a single centrosome duplicated?

A

Early in interphase

87
Q

Prophase

A
  • Chromosome becomes visible
  • Nucleolus disappears
  • Spindles form
  • Nuclear envelope disappears
88
Q

Metaphase

A

Chromosomes arrange on the place and attach to spindle

89
Q

Anaphase

A

Sister chromatids separate and move to opposite poles

90
Q

Telophase

A

Chromosome sets assemble at opposite poles

  • Nuclear envelope reforms around each set
  • Cytokinesis follows usually
91
Q

Cytokinesis

A

The cytoplasm divides, the cell contents are separated into 2 separate cells

92
Q

S phase of telophase

A

Migration of the daughter chromosome s to the 2 poles is complete

93
Q

How is the chromosome in G1 different from G2?

A

G1: Single and unreplicated
G2: Present as 2 chromatids

94
Q

Meiosis

A

Process producing 4 haploid daughter cells from 1 diploid (2n) cell.
-2 successive divisions: Meiosis I and Meiosis II

95
Q

What happens prior to meiosis?

A

All chromosomes are duplicated prior to this

96
Q

Meiosis I: Prophase I

A
  • Chromosomes become visible
  • Crossing over occurs
  • Nucleolus disappears
  • Meiotic spindle forms
  • Nuclear envelope disappears
97
Q

When does crossing over of homologous chromosome s occur?

A

Prophase I

98
Q

Meiosis I: Metaphase I

A

Pairs of chromosome become arranged on the metaphase plate and attach to fully formed spindle

99
Q

Meiosis I: Anaphase I

A

Sister chromatids separate and migrate towards opposite poles

100
Q

Meiosis I: Telophase I

A

Homologous chromosome pairs reach the poles of the cells

  • Nuclear envelope forms
  • Cytokinesis follows to produce 2 daughter cells
101
Q

What does DNA replication occur?

A

S phase

102
Q

When do sister chromatids separate?

A

Anaphase II

103
Q

Meiosis II: Prophase II

A

Nuclear envelope breaks down and the spindle forms

104
Q

Meiosis II: Metaphase II

A

Chromosomes becomes arranged on the plate and attach to spindle

105
Q

Meiosis II: Anaphase II

A

The 2 chromosomes in each bivalent separate and migrate towards opposite poles

106
Q

What is the stage of meiosis during which the pairs of chromosomes become arranged on a plane equidistant from the poles?

A

Metaphase I

107
Q

What is the key difference between Anaphase I in meiosis and Anaphase in mitosis?

A

Sister chromatids remain joined during anaphase I in meiosis, whereas in anaphase of mitosis they separate

108
Q

In what stage of meiosis do the centromeres separate, and the 2 chromatids of each chromosome move to opposite poles on the spindle?

A

Anaphase II

109
Q

When is synapsis of homologous chromosomes?

A

Prophase I

110
Q

Synapsis

A

Pairing of homologous chromosomes

111
Q

When does the independent assortment of unlinked genes occur?

A

Metaphase I

112
Q

When does the reduction of chromosome number in cell from 2n to n?

A

Telophase I

113
Q

What 2 events in meiosis lead directly to genetic diversity?

A

Crossing over and independent assortment

114
Q

Distinguish between homologous and non-homologous chromosomes

A

Homologous: Contain alleles for the same type of genes

Non-homologous: Contain alleles for different types of genes

115
Q

Distinguish between chromatids and chromosomes

A

Chromatid is a single strand

Chromosomes consist of 2 sister chromatids

116
Q

Wild type

A

Most abundant phenotype among individuals of a particular species

117
Q

Mutant

A

A phenotype resulting from a mutation

-Anything other than the wild type

118
Q

Map unit

A

An arbitrary unit of measure used to describe relative distances between linked genes

119
Q

When calculating the map distance from the centromere why do you divide by 2?

A

Each crossover produces 2 spores like the parents and 2 new spores as a result of the crossover.
So only 2 are the result of crossing over.

120
Q

Name the 3 types of chromosomes found in the HeLa cells based on the location of the centromere

A

Metacentric (P=Q)

Submetacentric (P

121
Q

Klinefelter Syndrome

A

XXY
XXXY
XXXXY

122
Q

Turner syndrome

A

X

123
Q

Female with trisomy X

A

XXX

124
Q

Trisomy 21, Trisomy 18, Trisomy 13 (Downs, Edwards, Patau)

A

XX or XY

125
Q

Submetacentric

A

P

126
Q

3 phases of PCR

A

Denaturation
Annealing of primers
Polymerization

127
Q

At what temperatures do proteins usually start to denature?

A

Temperatures above 43 degrees

128
Q

Why can taq polymerase withstand high temps?

A

Because it comes from bacteria that live in hot springs and hydrothermal vents

129
Q

From which organism does Taq originally come from?

A

Thermus aquaticus

130
Q

What is the potential use of PCR products?

A

Detect mutations
Recombine
Paternity tests
Solve a crime

131
Q

What happens to PCR when you forget to add DNA?

A

No bands appear

132
Q

Which were the positive controls for the soy PCR lab?

A

Plant chloroplast, Soy lectin

Both are plant and soy specific

133
Q

What happens to PCR if you only add 1 primer?

A

Instead of a geometric amplification, you get a linear one

-Much less product

134
Q

What is the function of the buffer in gel electrophoresis?

A

Prevents the anode and cathode from becoming alkaline and acidic
-Also contains ions to help transport the current

135
Q

The rate of linear DNA migration is inversely proportional to _____?

A

The log of its molecular weight

*Does not include circular DNA

136
Q

Function of transacetylase

A

Covalently modifies lactose and lactose analogues

137
Q

How is lac operon regulated?

A

Negative control mechanism: Lac repressor protein binds to the lac operator site and prevents RNA polymerase from transcribing
Catabolic repression: cAMP binds to CAP. This complex binds to lac site and increases rate of transcription. Glucose decreases cAMP production.

138
Q

Functions of beta-galactosidase

A
  1. Catalyzes the breakdown of lactose into glucose and galactose
  2. Catalyzes conversion of lactose into allolactose
139
Q

Ampicillin

A

Derivative of penicillin and inhibits bacterial growth by interfering with the synthesis of cell walls

140
Q

What is a DNAase?

A

Enzymes that occur naturally in all body tissues

-Cut DNA into small fragments rendering it unsuitable for PCR

141
Q

What cause cranial and spinal meningiomas?

A
  • Associated with a tumour suppressing syndrome

- Mutations in SWI/SNF chromatin-remodelling complex subunits which regulates gene transcription and apoptosis

142
Q

Are individuals with familial spinal meningiomas associated with NF2 mutations?

A

No, they are not associated with these mutations

143
Q

What does the loss of heterozygosity and SMARCE1 in tumours suggest?

A

That it functions as a tumour suppressor to induce apoptosis

144
Q

What did the researchers use to screen the genome for mutation?

A

The researchers used exome sequencing for this

145
Q

Describe how the loss of function mutations in SMARE1 predispose individuals to a specific disease phenotype
ie: spinal meningiomas

A

CNS tumours are rarely found in coffin-iris syndrome

  • No one with spinal meningiomas has neurodevelopment problems
  • So loss of function mutations in SMARE1 likely specific to familial spinal meningiomas
146
Q

How does SMARE1 induce apoptosis?

A

Stimulates the expression of tumour suppressor genes

-Loss of activity leads to the cell not being triggered to undergo apoptosis

147
Q

Trisomy 13

A

Patau syndrome

148
Q

Trisomy 18

A

Edwards syndrome

149
Q

Trisomy 21

A

Downs syndrome

Biology 230 (1 decks)

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