Unit 4 (chap 18, 19, 20, 25, 26)

Question 1

A nucleotide in a DNA strand was depurinated. What type of DNA repair mechanism could be used to repair this nucleotide?

Answer 1

direct repair

Question 2

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

Answer 2

in frame mutation

Question 3

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.

Answer 3

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

Question 4

Which of the following can be mutagenic? Select all that apply.
transposons
ionizing radiation
base analogs
UV radiation
intercalating agents

Answer 4

transposons
ionizing radiation
base analogs
UV radiation
intercalating agents
(all of them)

Question 5

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

Answer 5

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

Question 6

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

Answer 6

Deletion of a single nucleotide

Question 7

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 _______.

Answer 7

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

Question 8

Strand slippage can cause: (select all that apply)
deletions
insertions
trinucleotide repeats
frameshift mutation
base substitutions

Answer 8

deletions
insertions
trinucleotide repeats
frameshift mutation

Question 9

Define mutation

Answer 9

an inherited change in the DNA sequence of genetic information

Question 10

what is the difference between a germline mutation and a somatic mutation

Answer 10

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

Question 11

what is the difference between a gene mutation and a chromosome mutation

Answer 11

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

Question 12

what is a base substitution

Answer 12

an alteration of a single nucleotide in the DNA. It can be a transition or a transversion

Question 13

what is the difference between a transition and a transversion

Answer 13

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

Question 14

what are insertions and deletions, and what type of mutations do these cause

Answer 14

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.

Question 15

what are in-frame insertions and deletions and how do they arise

Answer 15

insertions or deletions consisting of any multiple of 3 nucleotides leaves the reading frame intact.

Question 16

what are expanding nucleotide repeats

Answer 16

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.

Question 17

How can strand slippage cause the expansion of nucleotide repeats

Answer 17

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.

Question 18

how can expanding nucleotide repeats correspond to anticipation

Answer 18

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)

Question 18

what are the three effects base substitutions can have on the amino acid sequence

Answer 18

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

Question 19

what is the difference between a forward mutation and a reverse mutation

Answer 19

a forward mutation alters the wild-type phenotype to a mutant
a reverse mutation changes a mutant phenotype back into the wild type.

Question 20

what is a neutral mutation

Answer 20

a missense mutation that alters the amino acid sequence of a protein but does not significantly alter its function.

Question 21

What is a loss of function mutation

Answer 21

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.

Question 22

what is a gain of function mutation

Answer 22

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.

Question 23

what is a conditional mutation

Answer 23

conditional mutations are expressed only under certain conditions

Question 24

what are lethal mutations

Answer 24

mutations that cause premature death.

Question 25

Define Suppressor mutation

Answer 25

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

Question 26

What is the difference between intragenic and intergenic suppressor mutations and how may each one occur

Answer 26

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.

Question 27

What are the three factors that influence mutation rates

Answer 27

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.

Question 28

What are mechanisms that keep mutation rates low

Answer 28

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

Question 29

What is the difference between spontaneous and induced mutations

Answer 29

spontaneous mutations result under normal conditions
induced mutations results from changes caused by environmental chemicals

Question 30

How can strand slippage cause insertions/deletions and nucleotide repeat expansion

Answer 30

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.

Question 31

How does unequal crossing-over cause insertions and deletions

Answer 31

Misaligned pairing can cause unequal crossing over that results in one DNA molecule with an insertion and the other with a deletion.

Question 32

how does depurination cause base substitutions

Answer 32

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)

Question 33

How can base analogs cause mispairing during replication

Answer 33

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.

Question 34

How do intercalating agents result in a frameshift mutation. What is an example of an intercalating agent

Answer 34

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

Question 35

what are the two types of radiation and what mutations do they cause

Answer 35

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.

Question 36

what are transposable elements

Answer 36

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.

Question 37

what can transposons cause

Answer 37

gene mutations and chromosome rearrangements

Question 38

There are _________ _________ that repair errors and there is __________ between the mechanisms with respect to the types of ________ they repair.

Answer 38

There are several mechanisms that repair errors and there is overlap between the mechanisms with respect to the types of mutations they repair.

Question 39

What is mismatch repair

Answer 39

• mismatched bases distort DNA structure
• distorted sections are cut out and replaced

Question 40

what is direct repair

Answer 40

• altered bases gets repaired directly, without removal of the base or nucleotide

Question 41

How can genetic disease associated with defective repair pathways increase the incidence of cancer

Answer 41

These diseases are often associated with high incidences of specific cancers because defects in DNA repair lead to increased rates of mutation.

Question 42

What is recombinant DNA technology

Answer 42

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.

Question 43

What is a restriction enzyme

Answer 43

also called a restriction endonuclease. They recognize specific nucleotide sequences in DNA and make double-stranded cuts at those sequences (called restriction sites).

Question 44

what is the origin of a restriction enzyme and how are their names derived

Answer 44

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.

Question 45

What are the two types of cuts restriction enzymes can make

Answer 45

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.

Question 46

How can restriction enzymes be used to produce recombinant DNA

Answer 46

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

Question 47

How is CRISPR-Cas9 used for genome editing

Answer 47

• 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

Question 48

How can CRISPR-Cas9 be used in gene therapy

Answer 48

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

Question 49

How can gel electrophoresis be used to separate DNA fragments by size

Answer 49

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.

Question 50

what is a probe

Answer 50

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.

Question 51

What is PCR

Answer 51

Polymerase Chain Reaction. It is the amplification of a DNA fragment

Question 52

What are 5 components of a PCR reaction

Answer 52

• Taq polymerase (DNA polymerase)
• dNTPs
• Template DNA
• Primers
• Magnesium ions (to mimic cellular conditions)

Question 53

What are the steps in a PCR cycle

Answer 53

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

Question 54

What is gene cloning, and what is the process for it in bacteria

Answer 54

Produces identical copies of genes.
WHAT IS THE PROCESS??

Question 55

What is a cloning vector and what are its 3 elements

Answer 55

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

Question 56

What are plasmids

Answer 56

circular DNA molecules that exist naturally in bacteria. They are commonly used as vectors for cloning DNA fragments in bacteria.

Question 57

How can a foreign DNA fragment be inserted into a plasmid

Answer 57

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.

Question 57

What is transformation

Answer 57

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

Question 58

How can a foreign DNA fragment be inserted into a plasmid

Answer 58

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

Question 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?

Answer 59

1. will not grow
2. not amp resistant, B-gal, blue,
3. amp resistant, no B-gal, white

Question 60

What is meant by “expression of a foreign gene”

Answer 60

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.

Question 61

How does next-generation sequencing work, specifically Illumina sequencing

Answer 61

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

Question 62

What is DNA fingerprinting

Answer 62

It is a technique used to identify individuals by examining their DNA sequences.

Question 63

What type of sequence is analyzed in DNA fingerprinting

Answer 63

Most DNA fingerprinting uses microsatellites or short tandem repeats (STRs)

Question 64

How does DNA fingerprinting work

Answer 64

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

Question 65

How can RNAi be used to turn off a gene

Answer 65

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

Question 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.

Answer 66

Bacteria with the desired plasmid produce white colonies.

Question 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

Answer 67

a vector

Question 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

Answer 68

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

Question 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.

Answer 69

DNA moves through the gel toward the positive electrode

Question 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

Answer 70

it is a thermostable protein that can withstand the heat needed to denature the DNA strands

Question 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

Answer 71

enzymes that can cut DNA molecules at or near a specific nucleotide sequence

Question 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

Answer 72

generate copies of a DNA fragment

Question 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’

Answer 73

5’ TAGCTA 3’

Question 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.

Answer 74

The new DNA strand would not be able to elongate.

Question 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

Answer 75

• sgRNA complementary to the target gene
• Cas9

Question 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

Answer 76

• fluorescent tag
• reversible terminator

Question 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.

Answer 77

It is highly improbable that the alleged father is the biological father of the child.

Question 78

What is genomics

Answer 78

genomics is the field of genetics that attempts to understand the content, organization, function, and evolution of genetic information contained in whole genomes

Question 79

What is the difference between genetic maps and physical maps

Answer 79

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.

Question 80

What are some problems associated with sequencing an entire genome

Answer 80

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

Question 81

What were some goals of the Human Genome project

Answer 81

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)

Question 82

What is the percent similarity between two humans

Answer 82

99.9% identical

Question 83

what is Single Nucleotide Polymorphisms and haplotype

Answer 83

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.

Question 84

How can SNPs can be used for genome-wide association studies

Answer 84

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.

Question 85

what are bioinformatics

Answer 85

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.

Question 85

what are bioinformatics

Answer 85

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.

Question 86

How can bioinformatics be used to identify a gene

Answer 86

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.

Question 87

what is annotation as it applies to bioinformatics

Answer 87

annotation means linking its sequence information to other information about its function and expression, the protein it encodes, and similar genes in other species.

Question 88

what are metagenomics and briefly explain why this field exists

Answer 88

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.

Question 89

what is transcriptome and proteome

Answer 89

transcriptome of a genome are all the RNA molecules transcribed from a genome and all the proteins encoded by the genome, called the proteome.

Question 90

what is homology search, and explain how this can be used to understand the function of a gene

Answer 90

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

Question 91

what is the difference between orthologs and paralogs

Answer 91

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

Question 92

What are 2 techniques that can be used to study the expression of a gene

Answer 92

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.

Question 93

How can microarrays be used to examine gene expression

Answer 93

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.

Question 94

What is the process of RNA seq

Answer 94

• collect total RNA from cells
• isolate mRNA
• reverse transcribed into cDNA
• fragment cDNA
• sequence with next-gen sequencing
• assemble sequences into RNA transcripts

Question 95

What are population genetics

Answer 95

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

Question 96

what are mendelian population and gene pool

Answer 96

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.

Question 97

what are two things that characterize a gene pool

Answer 97

frequencies of genotypes and alleles in the population

Question 98

How do you calculate genotypic frequencies

Answer 98

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

Question 99

Define Hardy-Weinberg Law

Answer 99

mathematical model that evaluates the effect of reproduction on genotypic and allelic frequencies

Question 100

what are the assumptions and predictions of the Hardy-Weinberg law (for an autosomal locus with two alleles)

Answer 100

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

Question 101

How did the Hardy-Weinberg equilibrium originate

Answer 101

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

Question 102

What is the difference between positive assortative mating and negative assortative mating

Answer 102

Positive assortative mating refers to a tendency for like individuals to mate
Negative assortative mating refers to the tendency for unlike individuals to mate

Question 103

What is inbreeding and how does it affect a population

Answer 103

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

Question 104

how does nonrandom mating affect allelic and genotypic frequencies

Answer 104

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)

Question 105

What are the 4 forces that change allelic frequencies

Answer 105

mutation, migration, genetic drift, and natural selection

Question 106

how does mutation change allelic frequencies

Answer 106

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

Question 107

what is migration (gene flow)

Answer 107

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.

Question 108

What factors influence the change in allelic frequency due to migration

Answer 108

The amount of change is directly proportional to the amount of migration

Question 109

over time migration _______ the differences between populations

Answer 109

over time migration reduces the differences between populations

Question 110

what is genetic drift

Answer 110

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.

Question 111

what is sampling error

Answer 111

deviation from an expected ratio due to limited sample size

Question 112

What is effective population size (Ne)

Answer 112

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)

Question 113

what is the relationship between the amount of genetic drift and the effective population size

Answer 113

The amount of change in allelic frequencies due to genetic drift is inversely related to the effective population size

Question 114

Explain the 3 effects of genetic drift

Answer 114

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

Question 115

What are the 3 causes of genetic drift and describe them

Answer 115

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.

Question 116

What is natural selection and how can it change allelic frequencies

Answer 116

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.

Question 117

what is fitness

Answer 117

the relative reproductive success of a genotype

Question 118

What are the individual long term and short term effects of: mutation, migration, genetic drift, and natural selection

Answer 118

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

Question 119

what is evolution and explain the two steps involved

Answer 119

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

Question 120

what is the difference between anagenesis and cladogenesis

Answer 120

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

Question 121

How do we observe genetic variation today

Answer 121

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

Question 122

what is the neutral mutation hypothesis

Answer 122

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.

Question 123

what is balancing selection

Answer 123

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

Question 124

what is the biological species concept

Answer 124

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

Question 125

what is the difference between prezygotic and postzygotic reproductive isolating mechanisms

Answer 125

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

Question 126

what are the 5 prezygotic reproductive isolating mechanisms and describe them

Answer 126

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

Question 127

what are the 3 types of postzygotic reproductive isolating mechanisms and describe them

Answer 127

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

Question 128

What is speciation

Answer 128

the process by which new species arise. It comes through the evolution of reproductive isolating mechanisms

Question 129

What are the 2 principal modes of speciation and describe them

Answer 129

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

Question 130

What is phylogeny, phylogenetic tree, branches, nodes, rooted, and gene tree

Answer 130

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)

Question 130

Different parts of genes evolve at ______ rates

Answer 130

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.

Question 131

How can the molecular clock be used to date evolutionary events

Answer 131

Relation between the rate of amino acid substitution and time since divergence

Question 132

what is the molecular clock

Answer 132

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.

Question 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

Answer 133

paralogs

Question 134

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.

Answer 134

Underexpressed, because green indicates genes that are highly expressed in noncancer cells compared to cancer cells.

Question 135

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

Answer 135

a haplotype

Question 136

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.

Answer 136

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.

Question 137

Categorize the terms to indicate if they belong to physical maps or genetic maps:
less accurate
higher resolution
map units
base pairs
recombination frequencies

Answer 137

Physical maps:
higher resolution
base pairs
Genetic maps:
less accurate
map units
recombination frequencies

Question 138

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

Answer 138

fragmentation of the RNA
next-gen sequencing
Isolate total RNA from cells
PCR
isolate mRNA
reverse transcription

Question 139

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 :

Answer 139

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

Question 140

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.

Answer 140

The migrants came from a population with a much higher frequency of the A allele.

Question 141

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.

Answer 141

0.033

Question 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

Answer 142

a founder effect

Question 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

Answer 142

a founder effect

Question 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

Answer 143

relative reproductive success of a genotype

Question 144

Migration does not result in
- more genetic variation within populations.
- populations becoming more genetically similar.
- more genetic variation between populations.
- gene flow between populations.

Answer 144

more genetic variation between populations

Question 145

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.

Answer 145

affects genotypic frequencies but not allelic frequencies.

Question 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

Answer 146

genetic drift

Question 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?

Answer 147

0.008

Question 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.

Answer 148

0.3

Question 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.

Answer 149

36