Unit 4 (chap 18, 19, 20, 25, 26) Flashcards
1
Q
A nucleotide in a DNA strand was depurinated. What type of DNA repair mechanism could be used to repair this nucleotide?
A
direct repair
2
Q
Consider the following original DNA strand and mutant DNA strand. Which of the following would best characterize the mutation in the polypeptide strand?
Original: 5’-TTTCCCGGGAAA- 3’
Mutant: 5’-TTTGGGAAA- 3’
- in-frame mutation
- frameshift mutation
- nonsense mutation
- missense mutation
A
in frame mutation
3
Q
Classify each definition or example as a somatic mutation, gametic (germline) mutation, or both.
-The mutation arises in the gametes of the individual and is transmitted to the progeny
- Mutations can be caused by an alteration in the DNA sequence
-The mutation affects only the individual in which the mutation occurs and is not passed on to the progeny
- A particular tobacco leaf becomes discolored due to a mutation halfway through the life of the plant
-A man receives a pelvic X-ray. Nine months later, his child is born with a chromosomal abnormality.
A
Somatic mutation:
A particular tobacco leaf becomes discolored due to a mutation halfway through the life of the plant
The mutation affects only the individual in which the mutation occurs and is not passed on to the progeny
Germline Mutation:
A man receives a pelvic X-ray. Nine months later, his child is born with a chromosomal abnormality.
The mutation arises in the gametes of the individual and is transmitted to the progeny
Both:
Mutations can be caused by an alteration in the DNA sequence
4
Q
Which of the following can be mutagenic? Select all that apply.
transposons
ionizing radiation
base analogs
UV radiation
intercalating agents
A
transposons
ionizing radiation
base analogs
UV radiation
intercalating agents
(all of them)
5
Q
Categorize the following base substitutions as transition mutations or transversion mutations:
C to a T
G to a T
T to an A
T to a C
C to an A
A to a G
G to an A
G to a C
A
Transition Mutation:
A to a G
C to a T
T to a C
G to an A
Transversion Mutation:
T to an A
C to an A
G to a C
G to a T
6
Q
Which type of DNA mutation results in a change in the reading frame of an mRNA?
deletion of a single nucleotide
deletion of a single codon
substitution of one codon for another
substitution of one nucleotide with another
A
Deletion of a single nucleotide
7
Q
A DNA non‑template sequence reads: 5’ A T G A A G C G C T C A G T A 3’
If a thymine was substituted for nucleotide 6, this would be called a _______ and would result in a ________.
If a guanine was substituted for nucleotide 11, this would be called a _______ and would result in a __________.
If a guanine was substituted for nucleotide 15, this would be called a _______ and would result in a _______.
A
If a thymine was substituted for nucleotide 6, this would be called a transversion and would result in a missense mutation.
If a guanine was substituted for nucleotide 11, this would be called a transversion and would result in a nonsense mutation.
If a guanine was substituted for nucleotide 15, this would be called a transition and would result in a silent mutation
8
Q
Strand slippage can cause: (select all that apply)
deletions
insertions
trinucleotide repeats
frameshift mutation
base substitutions
A
deletions
insertions
trinucleotide repeats
frameshift mutation
9
Q
Define mutation
A
an inherited change in the DNA sequence of genetic information
10
Q
what is the difference between a germline mutation and a somatic mutation
A
somatic mutations arise in somatic tissues, that do not produce gametes.
germ-line mutations arise in cells that produce gametes and they are passed on to future generations
11
Q
what is the difference between a gene mutation and a chromosome mutation
A
a chromosome mutation is a large-scale alteration that affects chromosome structure or the number of chromosomes
a gene mutation are relatively small DNA lesions that affect a single gene
12
Q
what is a base substitution
A
an alteration of a single nucleotide in the DNA. It can be a transition or a transversion
13
Q
what is the difference between a transition and a transversion
A
transitions are when a purine is replaced by a different purine or a pyrimidine is replaced by a different pyrimidine.
transversions are when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine.
Transitions are more likely to happen than transversions
14
Q
what are insertions and deletions, and what type of mutations do these cause
A
insertions and deletions are collectively called indels
insertions and deletions are the addition or removal of one or more nucleotide pairs.
these can cause frameshift mutations: changes in the reading frame of the gene. Frameshift mutations usually alter all amino acids encoded by the nucleotides following the mutation.
15
Q
what are in-frame insertions and deletions and how do they arise
A
insertions or deletions consisting of any multiple of 3 nucleotides leaves the reading frame intact.
16
Q
what are expanding nucleotide repeats
A
mutations where the number of copies of a set of nucleotides increases.
The number of copies of the repeat often correlates with the severity or age of onset of the disease.
17
Q
How can strand slippage cause the expansion of nucleotide repeats
A
strand slippage is the misalignment of the sequences or stalling of replication.
If a DNA molecule has 8 copies of a CAG repeat, the two strands separate and replicate. In the course of replication, a hairpin forms on the newly synthesized strand, causing part of the template to be replicated twice and increasing the number of repeats on the newly synthesized strand, causing part of the template to be replicated twice and increasing the number of repeats on the newly synthesized strand. The 2 new strands of the new DNA molecule separate. The strand with the extra CAG copies serves as a template for replication. The resulting DNA molecule contains five additional copies of the CAG repeats.
18
Q
how can expanding nucleotide repeats correspond to anticipation
A
Number of copies of the repeat also correlates with its instability: when more repeats are present, the probability of expansion is more to even more repeats increases.
diseases caused by expanding nucleotide repeats gets more severe with each generation (attenuation)
18
Q
what are the three effects base substitutions can have on the amino acid sequence
A
Missense mutation: the new codon encodes a different amino acid; there is a change in amino acid sequence
Nonsense mutation: The new codon is a stop codon; there is a premature termination of translation
Silent mutation: The new codon encodes the same amino acid; there is no change in amino acid sequence
19
Q
what is the difference between a forward mutation and a reverse mutation
A
a forward mutation alters the wild-type phenotype to a mutant
a reverse mutation changes a mutant phenotype back into the wild type.
20
Q
what is a neutral mutation
A
a missense mutation that alters the amino acid sequence of a protein but does not significantly alter its function.
21
Q
What is a loss of function mutation
A
these are mutations that cause partial or complete loss of normal protein function. This mutation alters the structure of the protein that the protein no longer works anymore.
22
Q
what is a gain of function mutation
A
this mutation causes the cell to produce a protein or gene product whose function is not normally present. Gain of function mutations are frequently dominant in their expression because a single copy of the mutation leads to the presence of a new gene product.
23
Q
what is a conditional mutation
A
conditional mutations are expressed only under certain conditions
24
what are lethal mutations
mutations that cause premature death.
25
Define Suppressor mutation
It is a genetic change that hides or suppresses the effect of another mutation. A suppressor mutation occurs at a site distinct from the site of the original mutation; thus an individual with a suppressor mutation is a double mutant, possessing both the original mutation and the suppressor mutation
this mutation can either be intragenic or intergenic
26
What is the difference between intragenic and intergenic suppressor mutations and how may each one occur
An intragenic mutation takes place in the same gene that contains the mutation being suppressed. This may work by the suppressor changing a second nucleotide in the same codon altered by the original mutation, producing a codon that specifies the same amino acid that was specified by the original, nonmutated codon. They can also work by suppressing frameshift mutation. Lastly, it may work by making compensatory changes in the protein.
An intergenic mutation occurs in a gene other than the one bearing the original mutation that it suppresses. They sometimes work by changing the way the mRNA is translated. They can also work through gene interactions.
27
What are the three factors that influence mutation rates
they depend on the frequency with which changes in the DNA take place.
The probability that when an alteration in DNA takes place, it will be repaired.
The probability that a mutation will be detected.
28
What are mechanisms that keep mutation rates low
Reduced mutation rates occur in DNA sequences associated with nucleosomes. This could be because DNA associated with nucleosomes is less exposed to mutagens, nut could also be explained by the effect of nucleosomes on DNA repair, recombination, or replication, all of which influence the rate of mutation
29
What is the difference between spontaneous and induced mutations
spontaneous mutations result under normal conditions
induced mutations results from changes caused by environmental chemicals
30
How can strand slippage cause insertions/deletions and nucleotide repeat expansion
Strand slippage occurs when one nucleotide strand forms a small loop.
If the looped-out nucleotides are on the newly synthesized strand, it will cause an insertion.
If the looped-out nucleotides are on the template strand, it will cause a deletion.
Nucleotide repeat expansion occurs when repeats of nucleotides cause a hairpin structure to form on the newly synthesized strand (strand slippage). The more strand slippage happens, the more likely it is to occur again, causing expanding nucleotide repeats.
31
How does unequal crossing-over cause insertions and deletions
Misaligned pairing can cause unequal crossing over that results in one DNA molecule with an insertion and the other with a deletion.
32
how does depurination cause base substitutions
depurination is the loss of a purine base form a nucleotide. This creates an apurinic site. In the absence of a base an incorrect nucleotide is incorporated into the newly synthesized DNA (usually adenine)
33
How can base analogs cause mispairing during replication
base analogs are a class of chemical mutagens with chemical structures similar to those of any of the 4 standard bases of DNA. If base analogs are present during replication, they may be incorporated into newly synthesized DNA molecules. If incorporated, it will pair with the wrong base, and then in the next replication, it will lead to a permanent mutation.
34
How do intercalating agents result in a frameshift mutation. What is an example of an intercalating agent
intercalating agents produce mutations by sandwiching (intercalating) themselves between adjacent bases in DNA. This distorts the 3D structure of the DNA helix causing single nucleotide insertions and deletions in replication. These often produce frame shift mutations (since only one base is added or deleted)
Ethidium bromide is an intercalating agent
35
what are the two types of radiation and what mutations do they cause
Ionizing radiation (X-rays, gamma rays, and cosmic rays): dislodge electrons from the atoms they encounter, changing stable molecules into free radicals and reactive ions, which alter the structures of bases and break phosphodiester bonds in DNA. It also frequently results in double strand breaks in DNA
UV light: pyrimidine bases readily absorb UV light causing chemical bonds to from between adjacent pyrimidines on the same strand of DNA, creating pyrimidine dimers. These are bulky lesions that distort the configuration of DNA and often block replication.
36
what are transposable elements
also called transposons, they are DNA sequences that can move about the genome and they are often causes of mutations. Because they can move around they are also called jumping genes.
37
what can transposons cause
gene mutations and chromosome rearrangements
38
There are _________ _________ that repair errors and there is __________ between the mechanisms with respect to the types of ________ they repair.
There are several mechanisms that repair errors and there is overlap between the mechanisms with respect to the types of mutations they repair.
39
What is mismatch repair
- mismatched bases distort DNA structure
- distorted sections are cut out and replaced
40
what is direct repair
- altered bases gets repaired directly, without removal of the base or nucleotide
41
How can genetic disease associated with defective repair pathways increase the incidence of cancer
These diseases are often associated with high incidences of specific cancers because defects in DNA repair lead to increased rates of mutation.
42
What is recombinant DNA technology
it is a set of molecular techniques for locating, isolating, altering, and studying DNA segments. The goal is usually to to combine DNA from 2 distinct sources.
43
What is a restriction enzyme
also called a restriction endonuclease. They recognize specific nucleotide sequences in DNA and make double-stranded cuts at those sequences (called restriction sites).
44
what is the origin of a restriction enzyme and how are their names derived
They are produced naturally by bacteria to use as a defense against viruses.
The name of each restriction enzyme begins with an abbreviation that signifies its bacterial origin.
45
What are the two types of cuts restriction enzymes can make
Staggered cuts or blunt cuts
Staggered cuts produce single-stranded cohesive (sticky ends). These ends can spontaneously pair to connect the fragments.
Cuts straight across produce blunt ends.
46
How can restriction enzymes be used to produce recombinant DNA
DNA molecules cut with the same restriction enzyme have complementary sticky ends that pair if fragments are mixed together
Nicks in the sugar-phosphate backbone of the two fragments can be sealed by DNA ligase
47
How is CRISPR-Cas9 used for genome editing
- Scientists have engineered crRNA from bacteria with a sequence that is specific to the target sequence of interest
- The other part of the crRNA contains a sequence that pairs with CAS9 protein which creates a crRNA/Cas9 complex
- This complex finds and binds to to the target DNA sequence
- Cas9 makes double-stranded cuts within the target DNA sequence
- The cells DNA repair mechanisms kick in to try and repair the cut-- 2 things can happen
1. Nonhomologous end joining is a repair pathway that repairs chromosome breaks but often causes insertions/deletions within the process -- this would inactivate the gene
2. Donor DNA can be inserted into the cell with ends complementary to the break sequence-- homologous recombination would insert this sequence to repair the gene
48
How can CRISPR-Cas9 be used in gene therapy
By changing the sequence of the sgRNA precise edits can be made almost anywhere in the genome. CRISPR-Cas9 also has the ability to be used in intact cells.
It has the potential for treating infectious diseases by eliminating viral DNA from human cells.
It will enable genetic modification of crops and animals to create specific alterations that benefit yield and produce characteristics that improve cultivation
49
How can gel electrophoresis be used to separate DNA fragments by size
Gel electrophoresis separates molecules on a basis of size and electrical charge. DNA fragments are placed in the wells of the gel and an electrical current is passed through the gel (negative next to DNA positive at the bottom)
DNA fragments move toward the positive end of the gel (because DNA is negatively charged). The smaller the DNA fragment the faster it moves.
50
what is a probe
A DNA or RNA molecule with a base sequence complementary to a sequence in the gene of interest. The bases on the probe will only pair with the bases on a complementary sequence, so a suitably labeled probe can be used to locate a specific gene or an other DNA sequence.
51
What is PCR
Polymerase Chain Reaction. It is the amplification of a DNA fragment
52
What are 5 components of a PCR reaction
- Taq polymerase (DNA polymerase)
- dNTPs
- Template DNA
- Primers
- Magnesium ions (to mimic cellular conditions)
53
What are the steps in a PCR cycle
1. DNA is heated to 90-100 C to separate the two strands
2. The DNA is quickly cooled to 30-65 C to allow short single-stranded primers to anneal to their complementary sequences
3. The solution is heated to 72 C; DNA polymerase synthesizes new strands, creating two new double-stranded DNA molecules
4. The entire cycle is repeated. Each time the cycle is repeated the amount of target DNA doubles
54
What is gene cloning, and what is the process for it in bacteria
Produces identical copies of genes.
WHAT IS THE PROCESS??
55
What is a cloning vector and what are its 3 elements
a cloning vector is a stable, replicating DNA model to which a foreign DNA fragment can be attached for introduction into the cell.
1. an origin of replication recognized in the host cell so that it is replicated along with the DNA that it carries
2. It needs to carry selectable markers -- traits that enable cells containing the vector to be selected or identified
3. A single cleavage site for each of one or more restriction enzymes used
56
What are plasmids
circular DNA molecules that exist naturally in bacteria. They are commonly used as vectors for cloning DNA fragments in bacteria.
57
How can a foreign DNA fragment be inserted into a plasmid
1. The plasmid and the foreign DNA are cut by the same restriction enzyme
2. when mixed, the sticky ends anneal, joining the foreign DNA and plasmid
3. Nicks in the sugar-phosphate bronds are sealed by DNA ligase.
57
What is transformation
the mechanism where bacterial cells take up DNA from the external environment. Inside the cell, the plasmids replicate and multiply as the cells themselves multiply
58
How can a foreign DNA fragment be inserted into a plasmid
1. foreign DNA is inserted into the partial lacZ gene
2. Bacteria that are lacZ- are transformed by the plasmid
3. Bacteria with an original (nonrecombinant) plasmid produce B-gal, which cleaves X-gal and makes the colonies blue
4. Bacteria with a recombinant plasmid do not synthesize B-gal. Their colonies remain white
5. Bacteria without a plasmid will not grow
59
1. Cell with no plasmid: amp resistant?, B-gal?, color?
2. Cell with intact plasmid: amp resistant?, B-gal?, color?
3. Cell with recombinant plasmid: amp resistant?, B-gal?, color?
1. will not grow
2. not amp resistant, B-gal, blue,
3. amp resistant, no B-gal, white
60
What is meant by "expression of a foreign gene"
to not just replicate the gene but also produce the protein it encodes.
- special vectors are required to express a foreign gene (expression vectors), and they need to have sequences that allow the gene to be transcribed and translated in addition to being replicated.
61
How does next-generation sequencing work, specifically Illumina sequencing
Most next-generation sequencing technologies do sequencing in parallel, meaning millions of DNA fragments can be sequenced simultaneously.
Illumina sequencing is the most widely used sequencing technology today.
1. Primers, DNA polymerase, and dNTPs are added to the flow cell. The primer attaches to the template
2. The first nucleotide is incorporated into the new strand. The tag is excited with a laser and fluoresces
3. The fluorescence is recorded by a computer. Thousands of fragments are sequenced and imaged simultaneously.
4. The tag and the terminator are removed
5. New dNTPs and polymerase are added
6. The next nucleotide is incorporated and excited with a laser
62
What is DNA fingerprinting
It is a technique used to identify individuals by examining their DNA sequences.
63
What type of sequence is analyzed in DNA fingerprinting
Most DNA fingerprinting uses microsatellites or short tandem repeats (STRs)
64
How does DNA fingerprinting work
DNA samples are collected and subjected to PCR. The fragments are separated by gel electrophoresis. Different-sized fragments appear as different bands.
13 core STRs are used for DNA fingerprinting
65
How can RNAi be used to turn off a gene
RNAi can be used to silence genes by 1. designing siRNAs that will be recognized and cleaved by Dicer. The complementary sequence must be unique to the target mRNA and must not be found on other mRNAs. Next, the double-stranded siRNA is delivered to the target cells. The RNAi sequence has the potential to become a permanent part of the cell's genome and be passed on to progeny
66
A geneticist uses a cloning plasmid that contains the lacZ gene and a gene that confers resistance to penicillin. She inserts a piece of foreign DNA into a restriction site located within the lacZ gene and uses the plasmid to transform bacteria. She then grows the bacteria on selective media containing penicillin and X‑gal. Explain how the geneticist can identify bacteria that contain a plasmid with the foreign DNA.
- Bacteria with the desired plasmid produce both blue and white colonies.
- Bacteria with the desired plasmid produce blue colonies.
- Bacteria with the desired plasmid produce white colonies.
- Only bacteria with the desired plasmid produce living colonies.
Bacteria with the desired plasmid produce white colonies.
67
The vehicle that carries a piece of foreign DNA to be cloned into a bacterial cell is called:
a vector
a fragment
a restriction enzyme
an insert
a vector
68
Restriction mapping of a linear piece of DNA reveals the following EcoRI restriction sites.
In each of the scenarios described, DNA is cut by EcoRI and the resulting fragments are separated by gel electrophoresis. The gel image is pictured below. Match each of the scenarios to the lane on the gel that would result after digestion and gel electrophoresis (A,B,C,D,or E)
Digestion with EcoRI
If a mutation that alters EcoRI site 1 occurred
If mutations occurred that alter EcoRI sites 1 and 2
If 1000 bp of DNA are inserted between the two restriction sites
If 500 bp of DNA are deleted between the two restriciton sites
Digestion with EcoRI: C
If a mutation that alters EcoRI site 1 occurred: A
If mutations occurred that alter EcoRI sites 1 and 2: B
If 1000 bp of DNA are inserted between the two restriction sites: E
If 500 bp of DNA are deleted between the two restriciton sites: D
69
Which one of the statements accurately describes gel electrophoresis?
-Larger DNA fragments move more quickly than smaller fragments.
-Fragments can be visualized by use of infrared light.
-DNA moves through the gel toward the positive electrode
-It requires the use of DNA probes.
DNA moves through the gel toward the positive electrode
70
Why is Taq polymerase used as the DNA polymerase in the polymerase chain reaction (PCR)?
- it allows for longer DNA sequences to be copied than with DNA polymerases from other species
- it is less prone to making replication errors than DNA polymerases from other species
- it does not require DNA primers as a starting point for replication to copy a single strand of DNA
- it is a thermostable protein that can withstand the heat needed to denature the DNA strands
it is a thermostable protein that can withstand the heat needed to denature the DNA strands
71
What is a restriction enzyme?
- enzymes that bind to DNA synthetase molecules to prevent DNA from being replicated
- bacterial enzymes that regulate levels of mitosis‑promoting factor to limit the rate of cell division
- enzymes that dissociate proteins in the nuclear membrane after mRNA strands exit the nucleus
- enzymes that can cut DNA molecules at or near a specific nucleotide sequence
enzymes that can cut DNA molecules at or near a specific nucleotide sequence
72
What is the purpose of the polymerase chain reaction (PCR)?
- measure changes in gene expression
- purify a specific piece of DNA
- separate DNA based on charge
- generate copies of a DNA fragment
generate copies of a DNA fragment
73
A certain restriction enzyme recognizes a 6 base pair restriction site that begins with 5' TAG 3'. What is the complete restriction site recognized by this enzyme?
5' ATCGAT 3'
5' TAGTAG 3'
5' TAGCTA 3'
5' GATGAT 3'
5' TAGGAT 3'
5' TAGCTA 3'
74
What would be the effect of leaving dNTPs out of the PCR reaction?
- The reaction would progress as expected.
- The DNA would not denature.
- The new DNA strand would not be able to elongate.
- The primers would not be able to bind to the template strand.
The new DNA strand would not be able to elongate.
75
A geneticist wants to use the CRISPR-Cas9 system to edit a gene in a eukaryotic cell. Specifically, she wants the cell to use the nonhomologous end joining system to repair the DNA after it is cut. Which of the following is a component the geneticist would need to add to the cell? Select all that apply.
- sgRNA complementary to the target gene
- Cas9
- sgRNA complementary to the Cas9 gene
- donor DNA
- sgRNA complementary to the target gene
- Cas9
76
Which of the following is an important component of a dNTP used in a next-gen sequencing reaction? Select all that apply.
- DNA polymerase
- fluorescent tag
- reversible terminator
- irreversible terminator
- fluorescent tag
- reversible terminator
77
DNA fingerprinting was performed to assess paternity. Normally 13 loci must be used to determine paternity, but this test only used 5 loci. What can be said based on this data?
- It is highly improbable that the alleged father is the biological father of the child.
-Nothing can be determined because only 5 loci were analyzed.
-The alleged father cannot be ruled out as the biological father.
It is highly improbable that the alleged father is the biological father of the child.
78
What is genomics
genomics is the field of genetics that attempts to understand the content, organization, function, and evolution of genetic information contained in whole genomes
79
What is the difference between genetic maps and physical maps
genetic maps provide a rough approximation of the locations of genes relative to the locations of other known genes.
they are based on the process of recombination. They are measured in centimorgans
genetic maps are low in details and they do not always correspond to physical distances between genes (there are sometimes discrepancies.
Physical maps are based on the direct analysis of DNA and they place genes in relation to distances measured in number of base pairs. They generally have higher resolution and are more accurate than genetic maps.
80
What are some problems associated with sequencing an entire genome
only small fragments (500-700 bp) can be sequenced at a time.
must fragment the genome into millions of small overlapping fragments for sequencing.
difficulty ordering the sequenced genome
81
What were some goals of the Human Genome project
develop sequencing technology
sequence genomes of model organisms
determine the sequence of the human genome (3.2 billion bp)
identify all genes in the human genome (around 20-25,000)
82
What is the percent similarity between two humans
99.9% identical
83
what is Single Nucleotide Polymorphisms and haplotype
single nucleotide polymorphism is a site in the genome where individual members of a species differ in a single base pair (SNP)
The specific set of SNPs and other genetic variants observed on a single chromosome or part of a chromosome is called a haplotype.
84
How can SNPs can be used for genome-wide association studies
genome-wide association studies use numerous SNPs scattered across the genome to find genes of interest. SNPs have been used in genome-wide association studies to successfully locate genes that influence many additional traits, such as height, body mass index, the age of puberty, etc.
The genes identified often explain only a modest proportion of the genetic influence on the trait.
85
what are bioinformatics
an interdisciplinary field that combines molecular biology and computer science; it centers on the development of databases, computer-search algorithms, gene-prediction software, and other analytical tools that are used to make sense of DNA-, RNA-, and protein-sequence data.
85
what are bioinformatics
an interdisciplinary field that combines molecular biology and computer science; it centers on the development of databases, computer-search algorithms, gene-prediction software, and other analytical tools that are used to make sense of DNA-, RNA-, and protein-sequence data.
86
How can bioinformatics be used to identify a gene
there are two general approaches to finding genes.
ab initio approach scans the sequence, looking for features that are usually found within a gene. Specific sequences mark the splice sites at the beginnings and ends of introns; other specific sequences are present in promoters immediately upstream of start codons. It looks for similarities between a new sequence and a sequence of all known genes.
87
what is annotation as it applies to bioinformatics
annotation means linking its sequence information to other information about its function and expression, the protein it encodes, and similar genes in other species.
88
what are metagenomics and briefly explain why this field exists
metagenomics is an emerging field in which the genome sequences of an entire group of organisms that inhabit a common environment are sampled and determined.
it mostly applies to microbial communities. It provides the ability 1) the identification and study of microbes that cannot be cultured in the laboratory and 2) the study of the community structure of microorganisms.
89
what is transcriptome and proteome
transcriptome of a genome are all the RNA molecules transcribed from a genome and all the proteins encoded by the genome, called the proteome.
90
what is homology search, and explain how this can be used to understand the function of a gene
homology search is used to determine gene function. It relies on comparisons of DNA and protein sequences from the same species and from different species. Homologous genes are genetically related genes
91
what is the difference between orthologs and paralogs
orthologs are homologous genes found in different species that evolved from the same gene in a common ancestor
paralogs are homologous genes in the same species
92
What are 2 techniques that can be used to study the expression of a gene
Microarrays: rely on nucleic acid hybridization
RNA sequencing: provides detailed information about gene expression, including the types and number of RNA molecules produced by transcription, the presence of alternatively processed RNA molecules, differential expression of the two alleles in a diploid individual, and different RNA molecules generated by bidirectional or overlapping transcription of DNA sequences.
93
How can microarrays be used to examine gene expression
used with cDNA, microarrays can provide information about the expression of thousands of genes, enabling scientists to determine which genes are active in particular tissues.
A microarray consists of DNA probes fixed to a solid support, such as nylon membrane or glass slide. Each spot consists of a different DNA probe. Cancer and noncancer cells are removed from 78 women with breast cancer cells. mRNA from the cells is converted into cDNA and labeled with red or green nucleotides. The cDNAs are mixed and hybridized to DNA probes on a chip. The chip is scanned by spot. Yellow indicates equal expression of the gene in both types of cells.
The microarray scan is converted to a heat map. Each spot represents the expression of one gene in one patients tumor compared with the expression of that gene in noncancer cells.
94
What is the process of RNA seq
- collect total RNA from cells
- isolate mRNA
- reverse transcribed into cDNA
- fragment cDNA
- sequence with next-gen sequencing
- assemble sequences into RNA transcripts
95
What are population genetics
the genetic compostion of a population and how it changes over time. It can be described by the frequencies of genotypes and alleles in the population
96
what are mendelian population and gene pool
the gene pool of a population can be described in terms of allelic frequencies. The types and numbers of alleles, rather than genotypes, have real continuity from one generation to the next and make up the gene pool of a population.
97
what are two things that characterize a gene pool
frequencies of genotypes and alleles in the population
98
How do you calculate genotypic frequencies
f(AA)= number of AA individuals/ N
f(Aa)= number of Aa individuals/N
f(aa)= number of a individuals/N
N= individuals possessing a genotype and divide by the total number of individuals in the sample
99
Define Hardy-Weinberg Law
mathematical model that evaluates the effect of reproduction on genotypic and allelic frequencies
100
what are the assumptions and predictions of the Hardy-Weinberg law (for an autosomal locus with two alleles)
Assumptions:
-large population
- random mating
- not affected by mutation, migration, or natural selection
Predictions:
1. Allelic frequencies do not change
2. Genotypic frequencies stabilize after one generation in proportions: p^2 + 2pq + q^2
- when assumptions are met, reproduction alone does not alter allerlic or genotypic frequencies and allelic frequencies determine frequencies of genotypes
- Hardy-Weinberg law applies only to a single locus
101
How did the Hardy-Weinberg equilibrium originate
Mendels principle of segregation states that each individual organism possess two allels at a locus and that each of those two alleles has an equal probability of passing into a gamete.
If mating is random, the gametes will come together in random combinations, which can be represented by a punnet square
102
What is the difference between positive assortative mating and negative assortative mating
Positive assortative mating refers to a tendency for like individuals to mate
Negative assortative mating refers to the tendency for unlike individuals to mate
103
What is inbreeding and how does it affect a population
inbreeding is a form of nonrandom mating. It is preferential mating between related individuals.
It leads to a departure form the hardy weinebrg equilibrium frequencies. It leads to an increase in the number of homozygotes and a decrease in the number of heterozygotes in the population
104
how does nonrandom mating affect allelic and genotypic frequencies
positive assortative mating: tendency for like individuals to mate
negative assortative mating: tendency for unlike individuals to mate
assortative mating is only for a particular trait and affects only those genes associated with that trait.
(no affect on allelic frequency)
105
What are the 4 forces that change allelic frequencies
mutation, migration, genetic drift, and natural selection
106
how does mutation change allelic frequencies
mutation can influence the rate at which one genetic variant increases at the expense of another. Forward (G1 --> G2) and reverse mutations (G2 --> G1) go back and forth until eventually equilibrium is met. Increase in G1 = decrease in G2 and vice versa. At equilibrium the allelic frequencies do not change even though mutation in both directions continues
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what is migration (gene flow)
influx of genes from other populations. Most natural populations experience it. The overall effect is 1) it prevents populations from becoming genetically different from one another and 2) it increases genetic variation WITHIN populations.
108
What factors influence the change in allelic frequency due to migration
The amount of change is directly proportional to the amount of migration
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over time migration _______ the differences between populations
over time migration reduces the differences between populations
110
what is genetic drift
when population size is small, a limited number of gametes unite to produce the individuals of the next generation, and changes influence which alleles are present in this limited sample. These result in changes in allelic frequencies, which are deviations from the parental genetic pool.
111
what is sampling error
deviation from an expected ratio due to limited sample size
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What is effective population size (Ne)
the equivalent number of breeding adults (factors include: sex ratio, variation between individuals in number of offspring, fluctuations in population size, age structure, if mating is random)
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what is the relationship between the amount of genetic drift and the effective population size
The amount of change in allelic frequencies due to genetic drift is inversely related to the effective population size
114
Explain the 3 effects of genetic drift
1. Change in allelic frequency within a population -- change randomly from each generation since it is based solely on chance.
2. Loss of genetic variation -- an allele may eventually reach of frequency of 0 or 1
3. Different populations diverge genetically over time -- since genetic drift is random, the frequencies of different populations do not change the same way, so populations gradually acquire genetic differences
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What are the 3 causes of genetic drift and describe them
all genetic drift arises from smapling error but there are different ways sampling error can arise
1. a population may be reduced in size for a number of generations fie to limitations of critical resources. Genetic drift in small populations over multiple generations can significantly affect the composition of the population gene pool
2. founder effect: results from the establishment of a population by a small number of individuals
3. genetic bottle neck: develops when a population undergoes a drastic reduction in size.
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What is natural selection and how can it change allelic frequencies
natural selection is the differential reproduction of genotypes. It takes place when individuals with adaptive traits produce a greater number of offspring than do individuals not carrying such traits. A trait with reproductive advantages increase overtime.
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what is fitness
the relative reproductive success of a genotype
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What are the individual long term and short term effects of: mutation, migration, genetic drift, and natural selection
Short term for each one: change in allelic frequency
Long term:
- Mutation: equilibrium reached between forward and reverse mutations
- Migration: equilibrium reached when allelic frequencies of source and recipient populations are equal
- Genetic Drift: fixation of one allele
- Natural selection:
- directional selection: fixation of one allele
- overdominant selection: equilibrium reached
- underdominant selection: unstable equilibrium
119
what is evolution and explain the two steps involved
biological evolution refers only to a specific type of change: genetic change happening taking place in a group of organisms. This includes only genetic change and it takes place in groups never just an individual
step one: genetic variation arises
second step: change in the frequencies of genetic variants
120
what is the difference between anagenesis and cladogenesis
anagenesis is evolution taking places in a single lineage (a group of organisms connected by ancestry)
cladogenesis is the splitting of one lineage into two. When a lineage splits, the two branches no longer have a common gene pool and evolve independently of each other. This is how new species arise
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How do we observe genetic variation today
molecular variation: we can investigate evolutionary change directly by analyzing protein and nucleic acid sequences. Variation in protein and nucleic acid sequence is has a clear genetic basis and is easy to interpret.All organisms have certain molecular traits in common. These molecules offer a valid basis for comparisons among all organisms.
Molecular data is quantifiable, which facilitates the objective assessment of evolutionary relationships. It can also reveal clues about the process of evolution
122
what is the neutral mutation hypothesis
a theory for the extensive molecular variation observed in natural populations. It proposes that much molecular variation is adaptively neutral: individuals with different molecular variants have equal fitness. This suggests that most variations in DNA and protein sequences are functionally equivalent, natural selection doesn't differentiate, and their evolution is largely shaped by genetic drift and mutation. It suggests that when natural selection occurs, it's largely directions favoring the best allele while eliminating the others.
Natural selection is viewed as an evolutionary force that largely limits variation.
123
what is balancing selection
some genetic variation is maintained by natural selection. In these cases, genetic variants are not functionally equivalent; instead they result in phenotypic effects that cause differences in reproduction (fitness differences). Balancing selection is selection that maintains variation
124
what is the biological species concept
it is a widely used definition of a species. It defines species as a group of organisms whose members are capable of interbreeding with one another but are reproductively isolated from the members of other species.
TLDR; members of the same species have the biological potential to exchange genes, and members of other different species cannot exchange genes. Because different species do not exchange genes, each species evolves independently
125
what is the difference between prezygotic and postzygotic reproductive isolating mechanisms
Prezygotic: prevent gametes from two different species from fusing and forming a hybrid zygote. Includes 5 different types
Postzygotic: gametes of two species may fuse and form a zygote, but there is no gene flow between the two species, either because resulting hybrids are inviable/sterile or because reproduction breaks down in subsequent generations. 3 different types
126
what are the 5 prezygotic reproductive isolating mechanisms and describe them
1. Ecological isolation: members of 2 species do not encounter each other so they do not reproduce with each other (dif ecological niches)
2. Behavioral isolation: differences in behavior prevent interbreeding (ex: dif mating calls)
3. Temporal isolation: reproduction in different species takes place at different times of year
4. Mechanical isolation: results from anatomical differences that prevent successful exchange of gametes
5. Gametic isolation: mating between individuals of different species may take place, but the gametes do not form zygotes
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what are the 3 types of postzygotic reproductive isolating mechanisms and describe them
1. Hybrid inviability: incompatibility between the genomes of the two species prevents the hybrid zygote from developing. (ex: gamete forms but resulting embryos never complete development)
2. Hybride sterility: hybrid embryos complete development but are sterile, so that genes are not passed between the two parental species. (ex: donkeys and horses make mules but mules are sterile)
3. Hybrid breakdown: species are able to mate and produce viable and fertile F1 progeny but further crossing of the hybrids produces enviable or sterile offspring
128
What is speciation
the process by which new species arise. It comes through the evolution of reproductive isolating mechanisms
129
What are the 2 principal modes of speciation and describe them
Allopatric speciation: occurs when a geographic barrier splits the population into two groups and blocks the exchange of genes between them
Sympatric speciation: speciation that arises in the absence of any external barrier to gene flow, reproductive isolating mechanisms evolve within a single population
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What is phylogeny, phylogenetic tree, branches, nodes, rooted, and gene tree
Phylogeny: evolutionary relationships among a group of organisms
Phylogenetic tree: a graphical representation of phylogeny
Branches: evolutionary connections between organisms
Nodes: points where the branches split, representing a common ancestor that existed before divergence took place
Rooted: A tree is rooted when one node represents a common ancestor to all other nodes on the tree
Gene tree: shows evolutionary relationship among prolactin and somatropin genes in vertebrates (evolutionary relationship among a group of genes)
130
Different parts of genes evolve at ______ rates
different parts of genes evolve at different rates
the highest rates of nucelotide substitution are in sequences that have the lease effect on protein function.
the highest rates of change are found where changes have the least effect on function. This observation fits with the neutral-utation hypothesis.
131
How can the molecular clock be used to date evolutionary events
Relation between the rate of amino acid substitution and time since divergence
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what is the molecular clock
If the rate at which a protein evolves is roughly constant overtime, the amount of molecular change that a protein has undergone can be used as a molecular clock to date evolutionary events.
133
Genes found in the same organism and that arose by duplication of a single gene in the evolutionary past are called
-paralogs
-two of these answers are correct
-heterologous
- orthologs
paralogs
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Researchers used microarrays to examine the expression pattern of 25,000 genes from the primary tumor cells in women who had breast cancer. They determined that the gene expression patterns found in these tumor cells accurately predict the recurrence of cancer within five years after treatment. In this experiment, mRNA from cancer cells and noncancer cells was converted into cDNA and labeled with red fluorescent and green fluorescent markers, respectively.
Determine whether most of the genes represented on the microarray are overexpressed or underexpressed in cancer cells from patients who remained cancer free for five years after treatment, and select the reason why.
- Underexpressed, because green indicates genes that are expressed less in noncancer cells compared to cancer cells.
- Overexpressed, because green indicates genes that are highly expressed in noncancer cells compared to cancer cells.
- Overexpressed, because green indicates genes that are expressed less in noncancer cells compared to cancer cells.
- Underexpressed, because green indicates genes that are highly expressed in noncancer cells compared to cancer cells.
Underexpressed, because green indicates genes that are highly expressed in noncancer cells compared to cancer cells.
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A set of DNA polymorphisms on a single chromosome or chromosomal region is known as
- a hemizygote
- a contig
- a haplotype
- a single nucleotide polymorphism
-an interspecies mutation
a haplotype
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James Noonan and his colleagues (2005. Science 309:597–599) set out to study genome sequences of an extinct species of cave bear. They extracted DNA from 40000‑year‑old bones from a cave bear and used a metagenomic approach to isolate, identify, and sequence the cave bear DNA. Why did they use a metagenomic approach when their objective was to sequence the genome of one species, the cave bear?
- The cave bear samples could be heavily contaminated so scientists used metagenomics to sequence all of the DNA. They then compared the sequences obtained with modern bear DNA to identify which DNA fragments were from the cave bear.
- Even though the isolated cave bear DNA was pure, it had been highly degraded over time. Metagenomics is the only way to analyze highly degraded DNA.
- Metagenomics allows the study of a complex mixture of proteins. Because the cave bear remains had been present with other organisms in the cave, they used mass spectrometry to tell the difference between cave bear proteins and proteins from other organisms.
- The scientists wanted to see what other organisms were present in the cave samples.
The cave bear samples could be heavily contaminated so scientists used metagenomics to sequence all of the DNA. They then compared the sequences obtained with modern bear DNA to identify which DNA fragments were from the cave bear.
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Categorize the terms to indicate if they belong to physical maps or genetic maps:
less accurate
higher resolution
map units
base pairs
recombination frequencies
Physical maps:
higher resolution
base pairs
Genetic maps:
less accurate
map units
recombination frequencies
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Which of the following is a part of RNA sequencing? Select all that apply.
fragmentation of the RNA
next-gen sequencing
Isolate total RNA from cells
PCR
isolate mRNA
reverse transcription
fragmentation of the RNA
next-gen sequencing
Isolate total RNA from cells
PCR
isolate mRNA
reverse transcription
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In the figure, each blue dot represents one copy of the A allele and each red dot represents one copy of the a allele
The frequency of the A allele in population II before migration is :
The frequency of the A allele in population II after migration is :
The frequency of the A allele in population II before migration is : 0.125
The frequency of the A allele in population II after migration is : 0.2
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Given the figure choose the statement that best explains the change in frequency of the A allele in population II after migration.
- Natural selection favors the migrants with the A allele from population I.
- The migrants came from a population with a much higher frequency of the A allele.
- The migrants came from a population with a much lower frequency of the A allele.
- The migrants from population I outnumbered the original population II.
The migrants came from a population with a much higher frequency of the A allele.
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Tay–Sachs disease is an autosomal recessive disorder. Homozygous recessive individuals lack a key enzyme called hexosaminidase A, which presents as progressive mental and motor deterioration until death occurs around age 5. Heterozygous individuals, called Tay–Sachs carriers, develop no symptoms of the disease. Tay–Sachs disease was historically more prevalent within populations of Ashkenazi Jews, Pennsylvania Dutch, southern Louisiana Cajuns, and eastern Quebec French Canadians. Today, individuals descended from these populations are more likely to be Tay–Sachs carriers, but genetic testing within these populations has largely eliminated the occurrence of Tay–Sachs disease.
For a randomly mating population, calculate the Tay–Sachs carrier frequency if 1 in 3600 individuals develops Tay–Sachs disease.
0.033
142
The Barton Springs salamander is an endangered species found only in a single spring in the city of Austin, Texas. There is growing concern that a chemical spill on a nearby freeway could pollute the spring and wipe out the species. To provide a source of salamanders to repopulate the spring in the event of such a catastrophe, a proposal has been made to establish a captive breeding population of the salamander in a local zoo. The zoo was asked to provide a plan for establishing this captive breeding population, with the goal of maintaining as much of the genetic variation of the species as possible in the captive population.
What factors are likely to lead to a loss of genetic variation in the captive population?
- a lack of inbreeding
- increased rate of mutation
- reduced genetic drift over time
- a founder effect
a founder effect
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The Barton Springs salamander is an endangered species found only in a single spring in the city of Austin, Texas. There is growing concern that a chemical spill on a nearby freeway could pollute the spring and wipe out the species. To provide a source of salamanders to repopulate the spring in the event of such a catastrophe, a proposal has been made to establish a captive breeding population of the salamander in a local zoo. The zoo was asked to provide a plan for establishing this captive breeding population, with the goal of maintaining as much of the genetic variation of the species as possible in the captive population.
What factors are likely to lead to a loss of genetic variation in the captive population?
- a lack of inbreeding
- increased rate of mutation
- reduced genetic drift over time
- a founder effect
a founder effect
143
Which statement best describes fitness?
- average lifespan of individuals of a given genotype
- relative reproductive success of a phenotype
-average lifespan of individuals of a given phenotype
- absolute reproductive success of a genotype, expressed in the number of offspring per breeding individual
- relative reproductive success of a genotype
relative reproductive success of a genotype
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Migration does not result in
- more genetic variation within populations.
- populations becoming more genetically similar.
- more genetic variation between populations.
- gene flow between populations.
more genetic variation between populations
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Nonrandom mating
- affects genotypic frequencies but not allelic frequencies.
- is always harmful when it occurs in populations.
- only occurs when relatives mate.
- affects allelic frequencies but not genotypic frequencies.
affects genotypic frequencies but not allelic frequencies.
146
Imagine a population of moths. By chance, three white moths are killed before they reproduce. Meanwhile, two black moths have four offspring, all of which survive to reproduce. Due to the chance event that killed the white moths, the next generation has more alleles for black coloration than the previous generation. Which evolutionary process does this scenario describe?
- natural selection
- mutation
- genetic drift
- migration
genetic drift
147
Phenylketonuria (PKU) is caused by homozygosity for a recessive allele and can cause a severe form of mental retardation if not detected early. The prevalence of PKU (genotype aa) is 1 per 15000 newborns in the United States, according to the National Institutes of Health (2001). Given that data, what is the expected allele frequency of the a allele?
0.008
148
If a population is in Hardy-Weinberg equilibrium and 51% of the population exhibits the dominant phenotype, what is the frequency of the dominant allele (assume there are 2 alleles). Answer as a decimal.
0.3
149
If a population is in Hardy-Weinberg equilibrium and the frequency of the dominant allele is 0.2, what percent of the population will exhibit the dominant phenotype (assume there are 2 alleles). Answer as a percent and not as a decimal.
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