Final Flashcards
(147 cards)
1
Q
What is an endocycle?
A
DNA replication without mitosis or cytokinesis
2
Q
What are polyploid cells?
A
When two winged flies (like Drosophila) continue to replicate their chromosomes within the nucleus.
3
Q
Why are polyploid cells advantageous?
A
Individual cells are able to grow to a very large size because they carry many copies of each gene �
This allows quick growth because no time is wasted going through mitosis or in preparation for mitosis.
�
4
Q
What is mycelium?
A
Filamentous growth
5
Q
Perithecium
A
A bag full of asci
6
Q
Ascus
A
product of one zygote that has undergone meiosis and mitosis, eight ascospores
�
7
Q
dihybrid cross of unlinked traits produces what in the F2 generation?
A
They produce all phenotypic traits in the F2 generation.
9:3:3:1 ratio of…
parental dominant : dom&rec : rec&dom : parental recessive�
8
Q
Dihybrid cross of 100% linked traits produces?
A
3:1 ratio of only parental phenotypes
9
Q
What are results of a dihybrid cross with PARTIALLY linked traits?
A
the 9:3:3:1 ratio would be skewed such that there would be a greater representation of the parental phenotypes and fewer of the recombinant phenotypes�
10
Q
How to calculate map units..
A
Crossover rate = M2/2 = map units
1 % crossover rate (e.g.1 crossover event in 100) = 1 map unit
�
11
Q
Why only half of the %M2?
A
Only half of the spores in an M2 pattern are the result of crossing over (two of the chromosomes are unaltered)
�
12
Q
What are SINE’s
A
highly repetitive sequences that don’t code for any genes
they are TRANSPOSABLE ELEMENTS that are capable of moving to different locations within a given genome.
13
Q
What is needed for PCR?
A
Template DNA
Primers
Deoxynucleotides (dATP, dCTP, dGTP, dTTP)
Magnesium ions (enzyme cofactor)
Buffer
Heat-stable DNA polymerase (Taq polymerase)�
14
Q
What is the purpose of InstaGene Chelator?
A
it binds intracellular Magnesium
15
Q
What are the steps of PCR?
A
Heat (94°C) to denature DNA strands (strands separate)
Cool (60°C) to anneal primers to template
Warm (72°C) to activate Taq polymerase, which extends primers and replicates DNA
Repeat multiple cycles
�
16
Q
p+q=1 is the equation for?
A
the frequency of the two alleles, p and q, in decimal form
17
Q
The Hardy-Weinberg equation is for?
A
The genotype frequencies
18
Q
What is the hardy weinberg equation and what does each letter stand for?
A
p2 + 2pq + q2 = 1
p^2 = the frequencies of the homozygous dominant genotypes�
2pq = the frequencies of the heterozygous genotypes
q^2 = the frequencies of the homozygous
recessive genotypes�
�
19
Q
What are the Hardy Weinberg frequencies?
A
p + q = 1, represents the f (frequency) of ALLELES in a population
p2 + 2pq + q2 = 1, represents the f of GENOTYPES in a population
�
�
20
Q
Describe the 5 criteria for Hardy Weinberg equilibrium populations?
A
1) Infinitely large population
2) No natural selection
3) No genetic drift/gene flow
4) No mutations
5) Random mating
21
Q
What pathway produces bright red pigment?
A
Drosopterin pathway
22
Q
What pathway produces brown pigments?
A
Ommochrome Pathway
23
Q
which two genes are on the same chromosome (2)?
A
Cinnabar and brown
24
Q
The functional Brown gene is involved in the production of what color pigment?
A
Red pigments
Brown mutants have brown eyes because the red pigment pathway is disrupted �
25
The functional Scarlet gene is involved in the production of what color pigment?
Brown pigments;
Scarlet mutants have bright red eyes because the brown pigment pathway is disrupted
�
26
What is epistasis and what is an example?
The action of one gene on another genes function.
Apterous overrides any other wing mutation.. LIke if Curly wing and apterous were two genes then fly would be wingless.
27
What is Quantitative continuous data?
Data that has measurable values which may fall anywhere within a finite or infinite range
e.g. Height, weight, velocities
�
28
What is Categorical nominal data?
Data that can be assigned a single label, but the information can’t be ordered or “measured”
Gender is an example. Individuals can be assigned to a category (male or female), but there is no order to that information, nor is their a measure of “how much” of a male or female an individual is
�
29
What are positive controls?
- Helps detect “false negatives”
An experimental set up that should produce a signal
�
30
What are negative controls?
- Helps detect “false positives”
An experimental set up that should NOT produce a signal
�
31
What is a chi square analysis?
a test for significant difference between 2 data sets…observed vs expected �
32
What is the equation for chi square?
x^2 = sum of (O-E)^2/E
33
When p>0.05 then chi square value is_____ and we _______ the null hypothesis.
small; fail to reject
34
When p<0.05 then chi square value is_____ and we _______ the null hypothesis. (i.e. the null has a less than 5% chance of being correct)
large; reject
35
What does a large chi square indicate?
large difference between observed and expected= rejecting null
�
36
What does a small chi square indicate?
small difference between observed and expected= failing to reject null
�
37
What is the critical value?
The value that is the borderline between accepting or rejecting the null hypothesis.
38
What is the p-value?
The probability that your null hypothesis is actually correct.
39
What does a p-value of 0.05 indicate?
Chance of the observed effect is low (due to random chance) and it's good evidence that a significant change took place.
40
What is the null hypothesis?
Change is due to random error (lab error)
41
What is the NEGATIVE CONTROLS needed for PCR?
-Template (DNA you want to amplify for study)
-Sequence specific primers flanking the target sequence
-Nucleotides (dATP, dCTP, dGTP, dTTP)
�-Magnesium ions (enzyme cofactor)
�-Buffer, containing salt
�-Taq polymerase
42
What is CODIS?
Combined DNA Index System
43
What is a multiplex PCR?
PCR with multiple sets of primers in one reaction; amplifies multiple sequences simultaneously.
44
What are the 3 loci we used in DNA typing?
CSF1PO, TPOX, and THO1
45
What is a microvariant?
Noted as the number of whole repeats followed by the number of nucleotides of the partial repeat (e.g. 9.3)�
46
What is the product rule?
the chance of having a certain DNA type at multiple loci is the product of the probabilities for each locus.
47
Polyacrymalide (PAGE) vs. Agarose
Polyacrylamide gels are denser, holes in matrix of gel are smaller - better for sorting out smaller molecules (DNA or proteins)
Agarose gels are more open – good enough for sorting out larger molecules (DNA)
�
48
Why did THO1 locus have two bands for each allele?
Because when denatured the 2 strands of DNA are separated resulting in doublets
49
Genetically modified crops...
| What are the GMO-specific sequences?
Look at GMO primers;
A 203 bp fragment of the caulifower MV 35S PROMOTER
A 225 bp fragment of the NOS TERMINATOR used in most GMO plants
�
50
What are the plant-specific sequences?
Look at plant primers;
Amplify a 455 bp region of the photosystem II (PSII) chloroplast gene found in most plants
�
51
What are the 5 steps to genetically modify a crop?
1) Identify the protein of interest
2) Isolate the gene that codes for that protein
3) Engineer a gene so plant cells transcribe and translate the protein
4) Introduce the gene into a plant cell
5) Grow the crop with recombinant DNA
52
What is artificial selection?
The breeder chooses desirable traits in plant to be expressed in next generation.
53
What is polyploidy/aneuploidy?
An abnormal number of chromosomes; either one extra chromosome or one missing.
Occurs during cytokinesis
54
What is an example of aneuploidy?
Seedless fruits like bananas and watermelon.
| Odd numbered polyploidy results in sterile plants.
55
What is bacterial transformation?
Uptake and expression of foreign DNA usually by means of a plasmid in bacteria.
56
What is the meaning of competent?
When bacteria are able to be transformed
57
Describe the plasmid (pGLO) we used in the bacterial transformation?
It contained an ampicillin resistance gene (always expressed)
It contained an Ara promoter which was turned on in the presence of arabinose. Will ultimately control GFP expression
58
Describe the starting bacteria we use for transformation?
E. coli bacterial cells whose growth is inhibited by antibiotics and made competent.
Can't grow or glow.....
59
What DNA did we use for transformation?
Jellyfish DNA; the gene for GFP (green fluorescent protein)
60
What is the end result of our transformation?
Recombinant bacteria that CAN GROW in the presence of bacteria, AmpR) and CAN GLOW in UV light.
61
What is the name of the AmpR gene that makes all transformed bacteria resistant to ampicillin?
BLA gene (codes for beta lactamase enzyme)
62
Two methods of transformation are?
Electroporation - electrical shock makes cell membrane permeable to DNA
Calcium Chloride/Heat shock
63
The transformation procedure we used?
```
Suspend bacterial colonies in Ca++
Add pGLO plasmid DNA
Place tubes on ice
Heat shock at 42C and place on ice
Incubate with nutrient broth
Streak Plates
```
64
Why do we use CaCl2 as a transformation solution?
Because charged molecules are very hard to get across a membrane. Positive charge of Ca++ ions shields negative charge of DNA phosphates
65
What is the point of incubating on ice?
It slows the fluid cell membrane down.
66
What is the point of heat shock?
increases permeability by altering membrane potential
67
What is the point of nutrient broth incubation?
It allows time for beta-lactamase expression before exposure to antibiotic.
68
What does 50% crossover indicate?
That the genes are unlinked
69
What are the 5 steps to genetically modify E. coli?
1) Identify the protein of interest
2) Isolate the gene that codes for the protein
3) Modify the gene so that bacterial cells can transcribe and translate the protein
4) Introduce the gene into bacterial cells
5) Grow the bacteria with recombinant DNA
same thing for plant crops except in plant cells not bacterial.
70
What two processes are required for isolating proteins?
Concentration and Purification
71
Steps to isolate and purify a protein?
```
Phase 1:
-concentration bacterial cells
-lysis of cells
Phase 2:
-remove non-protein debris
Phase 3:
-Protein purification (column chromatography)
```
72
What is column chromatography?
separation of proteins based on different physical properties; the column matrix has hydrophobic beads-affinity for hydrophobic proteins
73
HIC columns
Hydrophobic interaction columns
74
In high salt is GFP hydrophobic or hydrophilic?
| Why is salt used?
hydrophobic
Salt is used because GFP changes shape as [salt] changes. and the process is reversible
becomes hydrophilic when [salt] decreases
75
What is elution buffer?
releases GFP from HIC column
76
What is equilibration buffer?
Medium salt buffer used to prime/equilibrate column for GFP binding
77
What is binding buffer?
Raises salt concentration that causes a conformation change in GFP.
78
What is Wash Buffer?
Wash away less hydrophobic proteins from column
79
What is morphological classification?
Traditional classification based on traits.
80
What is a cladogram?
A visual reconstruction/hypothesis of the evolutionary history of a group of organisms
81
What do branching points represent on a cladogram?
New features; divergence from ancestral from
| branch length is insignificant-only branching order matters
82
What is proteomics?
The study of protein diversity including structures, functions, protein-protein interactions, expression levels, and post-translation modifications.
83
What is phylogeny?
Studying evolutionary relationships over long periods of time.
84
What are sister taxa?
Groups that share an immediate common ancestor.
85
Proteomics-What is tris buffer used for?
Provide appropriate pH
86
Proteomics-What is reducing agent used for?
To break disulfide bonds so proteins can separate properly for PAGE
87
Proteomics-What is glycerol used for?
For density, makes samples sink into wells
88
Proteomics-What is Bromophenol blue used for?
visual tracking on gel
89
Proteomics-What is SDS used for?
detergent; helps dissolve proteins into solution by giving a negative charge. This negative charge allows proteins to migrate down the gel
90
SDS-PAGE allows us to determine sizes of proteins, what is size measured in and what is it's value?
kilodaltons (kD)
Dalton = mass of one hydrogen atom or
1.66e-24 grams
91
I band
only actin
92
A band
Entire myosin band including actin filaments
93
Z line
separates sarcomeres
94
H zone
only myosin
95
What actual distance traveled by any individual protein depends on what?
voltage/current/resistance
time current was applied
etc.
(no two gels will be the same but relative positions will be the same)
96
Can tell size of proteins in SDS-PAGE how?
compare to molecular weight standards.
97
When constructing a standard curve for protein migration, what must we take into account and how do we fix the problem?
That proteins don't separate in a linear fashion on a gel.
Plot the log of the molecular weight (kD) vs. distance travelled (mm) on semi-log paper for a linear line.
98
What does the best-fit line tell us?
the correlation between size and distance
99
What are southern blots used for?
Detecting DNA sequences that have been separated by electrophoresis.
100
What are northern blots used for?
Detecting specific RNA separated by electrophoresis
101
What are Western blots used for?
Detecting specific proteins separated by electrophoresis.
102
What does HRP stand for and what is it?
Horseradish peroxidase, an enzyme.
103
Why did we use two antibodies for western blot?
Amplification of signal
| Utility - can use HRP goat anti-mouse antibodies on numerous different mouse primary antibodies.
104
How do we prevent antibodies from sticking to nitrocellulose?
coat nitrocellulose with a "non-reactive" protein like milk protein or bovine serum albumin to cover nitrocellulose
105
Western blow identifies protein by both their __________ and ________ ?
Molar Mass &
| Antibody Specificity
106
What is BLAST?
Basic Local Alignment Search Tool
| finds regions of local similarity between sequences.
107
What is the E value?
the number of hits one can expect to see by chance.
108
What is phylogeny?
Studying evolutionary relationships over long periods of time.
109
What are sister taxa?
Groups that share an immediate common ancestor.
110
Proteomics-What is tris buffer used for?
Provide appropriate pH
111
Proteomics-What is reducing agent used for?
To break disulfide bonds so proteins can separate properly for PAGE
112
Proteomics-What is glycerol used for?
For density, makes samples sink into wells
113
Proteomics-What is Bromophenol blue used for?
visual tracking on gel
114
Proteomics-What is SDS used for?
detergent; helps dissolve proteins into solution by giving a negative charge. This negative charge allows proteins to migrate down the gel
115
SDS-PAGE allows us to determine sizes of proteins, what is size measured in and what is it's value?
kilodaltons (kD)
Dalton = mass of one hydrogen atom or
1.66e-24 grams
116
What is phylogeny?
Studying evolutionary relationships over long periods of time.
117
What are sister taxa?
Groups that share an immediate common ancestor.
118
Proteomics-What is tris buffer used for?
Provide appropriate pH
119
Proteomics-What is reducing agent used for?
To break disulfide bonds so proteins can separate properly for PAGE
120
Proteomics-What is glycerol used for?
For density, makes samples sink into wells
121
Proteomics-What is Bromophenol blue used for?
visual tracking on gel
122
Proteomics-What is SDS used for?
detergent; helps dissolve proteins into solution by giving a negative charge. This negative charge allows proteins to migrate down the gel
123
SDS-PAGE allows us to determine sizes of proteins, what is size measured in and what is it's value?
kilodaltons (kD)
Dalton = mass of one hydrogen atom or
1.66e-24 grams
124
A band
Entire myosin band including actin filaments
125
Z line
separates sarcomeres
126
H zone
only myosin
127
What actual distance traveled by any individual protein depends on what?
voltage/current/resistance
time current was applied
etc.
(no two gels will be the same but relative positions will be the same)
128
Can tell size of proteins in SDS-PAGE how?
compare to molecular weight standards.
129
When constructing a standard curve for protein migration, what must we take into account and how do we fix the problem?
That proteins don't separate in a linear fashion on a gel.
Plot the log of the molecular weight (kD) vs. distance travelled (mm) on semi-log paper for a linear line.
130
What does the best-fit line tell us?
the correlation between size and distance
131
When constructing a standard curve for protein migration, what must we take into account and how do we fix the problem?
That proteins don't separate in a linear fashion on a gel.
Plot the log of the molecular weight (kD) vs. distance travelled (mm) on semi-log paper for a linear line.
132
What does the best-fit line tell us?
the correlation between size and distance
133
What are southern blots used for?
Detecting DNA sequences that have been separated by electrophoresis.
134
What are northern blots used for?
Detecting specific RNA separated by electrophoresis
135
What are Western blots used for?
Detecting specific proteins separated by electrophoresis.
136
What does HRP stand for and what is it?
Horseradish peroxidase, an enzyme.
137
Why did we use two antibodies for western blot?
Amplification of signal
| Utility - can use HRP goat anti-mouse antibodies on numerous different mouse primary antibodies.
138
How do we prevent antibodies from sticking to nitrocellulose?
coat nitrocellulose with a "non-reactive" protein like milk protein or bovine serum albumin to cover nitrocellulose
139
Western blow identifies protein by both their __________ and ________ ?
Molar Mass &
| Antibody Specificity
140
What is BLAST?
Basic Local Alignment Search Tool
| finds regions of local similarity between sequences.
141
What is the E value?
the number of hits one can expect to see by chance.
142
A mutation in cinnabar or scarlet produces?
bright red eyes
143
A mutation in white produces?
white eyes
144
A mutation in brown produces?
brown eyes
145
What does a p-value of 1 indicate?
that the null has been proved and there is no difference between the observed and expected
146
What are two good qualities used to select the best STR markers?
Low mutation rate
| Polymorphic (vary in size and length)
147
Explain how multiplexing works and how it increases the efficiency of DNA typing.
Allows the amplification of many sequences of DNA with the use of multiple primers. It increases efficiency by amplifying more DNA in a shorter period of time.
