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Lab Practical Flashcards

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Biology 101 flashcards
1
Q

the probability of two or more independent events occurring simultaneously = ___

A

the product of their individual probabilities

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2
Q

if two coins are tossed together, the chance that each will be heads is ___. the chance that both will be heads is ___. the chance for the first coin to fall heads and the second tails is ___. the total probability of obtaining a head on one and tails on the other is ___.

A

1/2
1/4
1/4
1/4+1/4=1/2

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3
Q

when Aa produces gametes, the probability is that ___ of the gametes will contain the A allele and ___ will contain a. when Aa x Aa, the probability is ___ that an A egg and A sperm come together to produce AA. probability is ___ for Aa and ___ for aa.

A

1/2
1/2
1/4
1/2
1/4

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4
Q

if four babies are born in a given hospital on the same day, what is the probability that all four will be boys?

A

1/2 x 1/2 x 1/2 x 1/2 = 1/16

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5
Q

what is the probability that three will be boys and one will be a girl?

A

1/16 + 1/16 + 1/16 + 1/16 = 1/4

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6
Q

what is the probability that two will be boys and two will be girls

A

6(1/16) = 3/8

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7
Q

what combination of boys and girls among the four babies is most likely to occur?

A

two boys and two girls

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8
Q

what is the probability that a fifth child will be a boy? girl?

A

1/32
1/32

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9
Q

the probability of either one or the other mutually exclusive events occurring = ___

A

the sum of their individual probabilities

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10
Q

the study of chromosome morphology, structure, pathology, function, and behavior

A

cytogenetics

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11
Q

an individuals collection of chromosomes

A

karyotype

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12
Q

karyotypes are used to look for ___

A

abnormal chromosome structure or number

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13
Q

technique for detecting and locating a specific DNA sequence on a chromosome

A

fluorescent in situ hybridization (FISH)

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14
Q

FISH relies on exposing chromosomes to a small DNA sequence called a ___ that has a ___ molecule attached to it

A

probe
fluorescent

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15
Q

what is the image of a chromosome set called

A

karyotype

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16
Q

T/F: FISH is a form of hybridization

A

true

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17
Q

T/F: karyotyping involves growing cells prior to their analysis

A

true

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18
Q

effectively inactivating ___ and preventing them from ___ is a key early step in the DNA purification process

A

endogenous nucleases (DNase enzymes)
digesting the genomic DNA

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19
Q

four things DNA purification methods must accomplish

A
  1. effectively disrupt cells or tissues
  2. denature proteins and nucleoprotein complexes
  3. inactivate endogenous nucleases
  4. purify nucleic acid target away from other nucleic acids and proteins
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20
Q

most purification methods disrupt cells using lysis buffer containing ___, ___, and ___

A

detergent, denaturants, and additional enzymes

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21
Q

disrupt the lipid bilayer of the cell membrane in DNA purification

A

detergents

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22
Q

release chromosomal DNA and denature proteins in DNA purification

A

denaturants

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23
Q

four overall steps of DNA purification

A
  1. collect cells
  2. break open (lyse) cells
  3. remove proteins
  4. condense the DNA
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24
Q

to break open the cells, ____ is used to dissolve the membranes in a solution called the ___

A

detergents
lysis buffer

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25
Q

to remove the proteins from DNA, ___ is added which breaks down proteins

A

protease

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26
Q

protease is an ___ that works best at ___ degrees. the protease denatures the proteins associated with ___ and helps digest any remaining ___

A

enzyme
50
DNA
cell or nuclear membrane proteins

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27
Q

___ and ___ are then used to bring the DNA out of the solution, or ___.

A

salt and cold alcohol
precipitate

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28
Q

match the outcomes with the laboratory steps
A- gently chew the insides of your mouth and then rinse vigorously with water
B- add protease, incubate at 50 degrees
C- mix in detergent solution
D- layer cold alcohol over cell extract
E- add salt
___ harvest the cells
___ dissolve cell membranes
___ precipitate the DNA
___ break down proteins
___ make DNA less soluble in water

A

A
C
D
B
E

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29
Q

which of the following differs between your DNA and that of bacteria living on your skin:
the specific information contained within the DNA
the location of DNA within the cell
the basic principles of how DNA is replicated
the role DNA plays in making proteins

A

A and B

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30
Q

what is a double stranded molecule of DNA called

A

chromosome

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31
Q

T/F: DNA is located inside the nucleus of all cells

A

false

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32
Q

in a nucleotide, what is attached to the 3’ carbon in deoxyribose?

A

a hydroxyl group (OH)

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33
Q

to which carbon in deoxyribose is the phosphate group attached?

A

5’

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34
Q

DNA polymerase always adds nucleotides onto the ___ end of the template strand

A

3’

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35
Q

there are ___ hydrogen bonds between A and T and ___ between G and C

A

two
three

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36
Q

which base pair (AT or GC) would be harder to separate

A

GC

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37
Q

in which direction does helicase move along the DNA

A

away from the origin of replication

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38
Q

what is the role of helicase

A

it separates the two strands of DNA by breaking the hydrogen bonds between bases

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39
Q

primase synthesizes ___

A

RNA

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40
Q

does the leading strand or the lagging strand have more RNA

A

lagging strand

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41
Q

which enzyme synthesizes RNA primers

A

primase

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42
Q

which enzyme seals nicks in DNA

A

ligase

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43
Q

which enzyme replaces RNA primers with DNA

A

DNA polymerase I

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44
Q

which enzyme extends RNA primers with DNA

A

DNA polymerase III

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45
Q

which enzyme separates DNA strands

A

helicase

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46
Q

in PCR, what are primers made of

A

single stranded DNA

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47
Q

in PCR, where should the primers bind

A

the ends of the region to be amplified

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48
Q

after every cycle of PCR, how does the amount of double stranded DNA change?

A

it doubles

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49
Q

why is DNA polymerase I not necessary for PCR

A

there are no RNA primers to remove

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50
Q

which statement about DNA is false?
DNA is present and essential for all living cells
DNA is located in the nucleus of eukaryotic cells
DNA is always copied perfectly during DNA replication
DNA can be circular or linear

A

DNA is always copied perfectly during DNA replication

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51
Q

what would be a consequence if a cell were unable to replicate its DNA

A

the cell would not be able to undergo cell division

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52
Q

one strand of DNA has the sequence 5’ AGC 3’. what is the complementary sequence?

A

5’ GCT 3’

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53
Q

what does it mean to say that DNA polymerase III proceeds 5’ to 3’

A

DNA polymerase III adds nucleotides to the 3’ end of a growing strand of DNA

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54
Q

what is the difference between the leading and lagging strands in DNA replication

A

after extension, the leading strand is continuous, and the lagging strand is composed of disconnected fragments

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55
Q

what is the order of enzymes used in DNA replication

A

helicase, primase, DNA polymerases, ligase

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56
Q

transcription is performed by ___ and translation is performed by ___

A

RNA polymerase
ribosomes

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57
Q

RNA polymerase binds to the ___ to start transcription

A

promoter

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58
Q

can an mRNA molecule be translated more than once

A

yes

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59
Q

the genes in an operon share a single ___

A

promoter

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60
Q

where can a repressor protein bind on DNA

A

operator

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61
Q

how does a repressor block transcription

A

physically blocks RNA polymerase from binding to the promoter

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62
Q

what is the relationship between a gene and an operon

A

an operon is a group of bacterial genes that share a promoter

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63
Q

what is a major difference between activator proteins and repressor proteins

A

activator proteins increase transcription when bound to DNA, but repressor proteins decrease transcription when bound to DNA

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64
Q

suppose you destroyed a bacterial cell’s ability to make cAMP. would this affect the cell’s ability to metabolize glucose and lactose, and if so, how?

A

yes. the cell could metabolize glucose normally, but could only use a small amount of lactose

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65
Q

what is the mechanism by which CAP (an activator protein) increases expression in the lac operon

A

CAP binds to its activator site, which helps RNA polymerase bind more tightly to a weak promoter

66
Q

what is a conditional mutation

A

the phenotype of the mutation is only observable under certain conditions

67
Q

the trp yeast strain has a conditional mutation that prevents it from growing in the absence of ___

A

tryptophan

68
Q

bakers yeast (S. cerevisiae) has a life cycle where the cells exist in either the ___ or ___ state

A

diploid or haploid

69
Q

in the haploid state of these cells, they in in one of two forms of ___ which will be attracted to each other where they will ___

A

mating types
fuse to form a diploid cell

70
Q

diploid cells can then undergo ___ where ___ progeny will reappear

A

meiosis
haploid

71
Q

yeast mating types are attracted to one another by releasing a ___ that the other can recognize through its expression of a specific ___

A

pheromone
cell surface receptor

72
Q

once the receptor and pheromone interact, the receptor activates ___ just under the cell membrane which then activate a series of ___ which ultimately activates a set of ___ which activates a specific set of ___

A

G proteins
kinases
transcription factors
genes

73
Q

one of the genes activated is called ___, whose gene product causes the cell to change so it can fuse with the other cell

A

FUS1

74
Q

to readily monitor the FUS1 gene, it has been fused with the reporter gene ___ which codes for enzyme ___

A

lacZ
beta galactosidase

75
Q

beta-galactosidase can be monitored through the use of the substrate ___, which is cleaved to release a ___ product which can be quantified with a spectrophotometer

A

ONPG
yellow

76
Q

the more enzyme (beta-galactosidase) produced, the ___ substrate converted to product

A

more

77
Q

most molecular analysis of DNA depends on ___

A

hybridization

78
Q

where does green fluorescent protein (GFP) come from

A

bioluminescent jellyfish

79
Q

one or more small circular pieces of DNA in bacteria

A

plasmids

80
Q

the pGLO plasmid encodes the gene for ___ and the gene for ___

A

GFP
ampicillin resistance

81
Q

the gene for GFP can be switched on in transformed cells by adding ___ to the cells’ nutrient medium

A

the sugar arabinose

82
Q

selection for cells that have been transformed with pGLO DNA is accomplished by growth on ___

A

antibiotic plates

83
Q

transformed cells will appear ___ on plates not containing arabinose, and ___ where arabinose is included in the medium

A

white
fluorescent green

84
Q

the goal of genetic transformation is to change ___

A

an organism’s phenotype

85
Q

scientists use a process called ___ to insert genes coding for new traits into a plasmid

A

genetic engineering

86
Q

three main steps of this transformation

A
  1. use a transformation solution of CaCl2
  2. heat shock
  3. provide cells with nutrients and a short incubation period to begin expressing their newly acquired genes
87
Q

four genes on the pGLO plasmid and what they code for

A
  1. BLA - codes for betalactamase (cleaves ampicillin)
  2. GFP - green fluorescent protein
  3. oriC - origin of replication
  4. araC - regulatory site, needs arabinose to initiation transcription of genes
88
Q

what do you expect to see on each plate?
1. +pGLO; LB/amp
2. +pGLO; LB/amp/ara
3. -pGLO; LB/amp
4. -pGLO; LB

A
  1. colonies
  2. colonies that glow
  3. negative control - no growth
  4. control - bacteria covering the whole plate
89
Q

what two factors must be present in the bacteria’s environment for you to see the green color?

A

the GFP gene and UV light

90
Q

what advantage would there be for an organism to be able to turn on or off particular genes in response to certain conditions

A

certain genes (like the fluorescence gene) could make organisms more susceptible to predators

91
Q

transformation efficiency is equal to ___

A

total number of cells growing on the agar plate / amount of DNA spread on the agar plate (in ug)

92
Q

what is bioinformatics

A

the science of using computational methods to decipher the biological meaning from information contained in an organismal system

93
Q

regions that look like a gene but are nonfunctional

A

pseudogenes

94
Q

beta globin has ___ pseudogenes on chromosome ___

A

2
11

95
Q

a mutations for which codon leads to sickle cell disease

A

codon 6, resulting in glutamic acid being replaced with valine

96
Q

how many mutations have been identified for beta thalassemia

A

over 500

97
Q

five genes found within the beta globin region of chromosome 11

A

epsilon, G-gamma, A-gamma, delta, and beta

98
Q

how are the five genes similar

A

they all function to carry oxygen in the blood

99
Q

how are the five genes different

A

timing of expression

100
Q

epsilon is normally expressed in the ___; A-gamma and G-gamma are normally expressed during ___; beta and delta are normally expressed in ___

A

embryonic sac
fetal development
adulthood

101
Q

beta and delta produce hemoglobin with a ___ affinity for oxygen than the other three genes

A

lower

102
Q

is intron or exon size more free to evolve. why?

A

intron; mutations in introns cause no harm, therefore more mutations can occur.

103
Q

process where a molecule absorbs light at one wavelength and then gives off light at another wavelength

A

fluorescence

104
Q

GFP is fluorescent because it contains a ___ portion that fluoresces

A

chromophore

105
Q

three steps of producing a pure protein

A
  1. get the cells to make or “express” the protein
  2. break open the cells to let the protein out
  3. purify the protein from the other cell contents
106
Q

what did we use to make GFP

A

E. coli that we transformed with the pGLO plasmid

107
Q

to break open the E. coli cell wall, the enzyme ___ was used and then the cell membrane was broken with ___

A

lysozyme
repeated cycles of freezing and thawing

108
Q

two steps of purifying GFP from other cell contents

A
  1. discard any material that is not water soluble
  2. separate GFP from water-soluble material with chromatography
109
Q

a term that describes a huge and diverse set of methods for separating molecules based on their different properties

A

chromatography

110
Q

three simple steps of chromatography

A
  1. binding
  2. wash
  3. elution
111
Q

in the binding step of chromatography, a mixture of molecules is exposed to a ___, the molecule of interest binds to solid via ___, the others do not

A

solid material
non-covalent interaction

112
Q

in the wash step of chromatography, the solid is rinsed with ___ which allows the molecules of interest to ___ while the unwanted molecules ___

A

wash buffer
remain bound to the solid
wash away

113
Q

in the elution step of chromatography, the solid is rinsed with ___ which allows the molecule of interest to ___. the resulting solution ideally contains ___

A

elution buffer
release from the solid
only the molecule of interest

114
Q

the GFP we used has significantly more ___ amino acids on its surface that most proteins

A

hydrophobic

115
Q

because GFP is so hydrophobic, it will bind to a solid that has a ___ surface more tightly than other proteins would

A

hydrophobic

116
Q

in solutions with a high salt concentration, the hydrophobic effect is ___; in solutions with a low salt concentration, the hydrophobic effect is ___

A

strengthened
weakened

117
Q

the solid material used for purification (called ___) was packed into a tube called the ___

A

resin
chromatography column

118
Q

what salt concentration is used in the binding step

A

high

119
Q

what salt concentration is used in the wash step

A

medium

120
Q

what salt concentration is used in the elution step

A

low

121
Q

what is a protein

A

a macromolecule that is made up of amino acids held together by peptide bonds

122
Q

list three examples of proteins found in your body

A

collagen, enzymes, hemoglobin

123
Q

explain the relationship between genes and proteins

A

genes are transcribed into mRNA, which is translated into proteins

124
Q

describe cloning

A

a process of copying or duplicating DNA

125
Q

describe how bacterial cloned cells on your LB/amp plate differ from cells on your LB/amp/ara plate

A

bacterial cloned cells on the LB/amp plate will only be resistant to ampicillin, but will not glow under the US light because the plate lacks arabinose. the cells on the LB/amp/ara plate will be resistant to ampicillin and glow under UV light

126
Q

what is the function of the centrifuge in GFP purification

A

pellets the bacteria to separate it from the growth media

127
Q

what is the function of lysozyme in GFP purification

A

digests the bacterial cell wall before freezing

128
Q

what is the function of freezing in GFP purification

A

causes the digested bacterial cell wall and membrane to burst

129
Q

why does the bacterial cell membrane burst when the cells are frozen

A

cytoplasm expands when its frozen

130
Q

what was the purpose of rupturing or lysing the bacteria

A

GFP had to be released in order to purify it

131
Q

briefly describe hydrophobic interaction chromatography and identify its purpose in this lab

A

chromatography is a method of separating proteins. hydrophobic chromatography does this by using the hydrophobic properties of the desired protein to accomplish the goal of purifying it. GFP has hydrophobic properties, so this method was used in this lab.

132
Q

functions to prepare the column for binding to GFP

A

equilibration buffer

133
Q

a high salt buffer that allows GFP to bind to the column

A

binding buffer

134
Q

a medium salt concentration buffer used to wash away other proteins while still allowing GFP to stay bound to the column

A

wash buffer

135
Q

a low salt buffer that allows GFP to come loose from the column and be collected

A

TE (elution) buffer

136
Q

process in which DNA is cut with enzymes that recognize specific sequences and then the fragments are separated on a gel to reveal a specific pattern for an individual

A

DNA profiling / DNA fingerprinting

137
Q

enzymes produced by bacteria to cut the DNA of viruses that attack them that are used in DNA profiling

A

restriction enzymes

138
Q

different restriction enzymes recognize ___ to cut

A

different specific sequences

139
Q

Restriction enzymes cut DNA in specific locations resulting in a unique combination of ___ for each organism

A

fragment sizes

140
Q

three steps of DNA profiling

A
  1. digest DNA samples with restriction enzymes
  2. use electrophoresis gel chamber to separate the DNA fragments by size
  3. use a staining process to stain and visualize the DNA fragments in the gel
141
Q

to cut DNA with restriction enzymes:
isolated DNA samples are added in a ___ to a microcentrifuge tube. ___ is then added and the sample is centrifuged then incubated in a water bath

A

restriction enzyme buffer
restriction enzyme mixture

142
Q

loading dye that contains ___ is added to each sample which helps ___ the samples in the gel and also contains ___ which helps each sample to ___ in the well.

A

bromophenol
glycerol

143
Q

a solution of DNA fragments of known size used to compare unknown DNA to estimate fragment size

A

DNA ladder

144
Q

do large or small molecules go further in the gel matrix in electrophoresis

A

small

145
Q

DNA fingerprinting is often based on ___ analysis

A

RFLP

146
Q

How many grams of agarose would you add to 200ml of buffer to give you a final concentration of 2%?

A

4G

147
Q

what is needed for PCR

A

template DNA, DNA polymerase (Taq polymerase), primers, dNTPs, buffer

148
Q

three steps of PCR

A
  1. denaturation
  2. priming (annealing)
  3. extension
149
Q

what happens in the denaturation step and at what temperature does this step occur

A

hydrogen bonds are broken between nitrogenous bases to separate DNA into two single strands
95C

150
Q

what happens in the annealing step and at what temperature does this step occur

A

primers attach to their complementary sites on the separated DNA strands
60C

151
Q

what happens in the extension step and at what temperature does this step occur

A

Taq polymerase begins synthesizing new strands starting at the primers
72C

152
Q

p = ___

A

the frequency of the dominant allele

153
Q

q = ___

A

the frequency of the recessive allele

154
Q

p^2 = ___

A

the frequency of the homozygous dominant genotype

155
Q

2pq = ___

A

the frequency of the heterozygous genotype

156
Q

q^2 = ___

A

the frequency of the homozygous recessive genotype

157
Q

p + q = ___

A

1

158
Q

what is the hardy Weinberg equation

A

p^2 + 2pq + q^2 = 1

159
Q

chi squared = ___

A

(observed - expected)^2 divided by expected

160
Q

degrees of freedom = ___

A

number of groups minus one

Genetics (24 decks)

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