Flashcards in bio chap 15 Deck (27)
Differentiate between a genotype and a phenotype
A genotype refers to the genetic composition of a cell or organism, which can vary based on the nucleotide sequence in the region(s) of interest. Although there can be many different forms (alleles) of a gene or sequence, each cell or individual normally has only two copies of each sequence, and they can either be identical to one another (homozygous) or different from one another (heterozygous). A phenotype of a cell or organism refers to its observable features, which are determined in part by its genotype, but can also be influenced by environmental factors. Some phenotypes are easily seen and vary widely among individuals, like natural hair color or height, but a phenotype may also involve less easily observable characteristics like blood type, which fall into a few distinct groups.
Describe common effects of mutations on an organism, and provide an example of each
Beneficial mutations are those that provide some sort of advantage to the organism in its environment, such as the Δ32 allele of the CCR5 gene which can reduce HIV infection rates in exposed individuals and delay progression to AIDS after HIV infection has occurred. The PiZ allele of the gene encoding α1AT is an example of a harmful mutation because it results in reduced levels of α1AT which, in the homozygous state, can lead to the development of emphysema due to increased breakdown of elastin in the lungs. Neutral mutations provide neither benefit nor harm to the individual, such as the AVI allele present in PTC non-tasters since the inability to taste this chemical does not affect the survival or reproductive capacity of the individual.
Explain why it is sometimes an oversimplification to consider a mutation harmful, beneficial, or neutral.
Designating a mutation as simply beneficial, harmful or neutral does not account for the influence of the environment on the organism, which may determine how the mutation ultimately affects the individual’s fitness. For example, when an individual is heterozygous for the S allele of β-globin, they may have mild symptoms of blood disease (which would be considered harmful), but these individuals are also partially protected from malaria, which is highly beneficial for individuals in regions where malaria is widespread.
Describe two types of genetic polymorphism that are useful in DNA typing.
Differences in the amount of DNA or point mutations that alter restriction enzyme recognition sites are two types of differences in DNA sequences that can be used to uniquely identify an individual. Variable number tandem repeats (VNTRs) are generated by the repetition of short stretches of DNA one after another in a particular region of a given chromosome. The size of the fragment generated by PCR amplification of these regions can reveal differences in the number of repeats within the region of interest. Point mutations in a DNA sequence can also introduce or disrupt a recognition site for a restriction endonuclease, so the pattern of restriction fragments that are generated by digestion of the region of interest can be used to determine whether a polymorphism exists in that region. Since each of these types of polymorphisms occur at many different regions within the genome, the combination of the alleles at several positions can be used to distinguish the DNA of one individual from another.
Define the term “SNP” and explain why researchers are interested in detecting SNPs
A SNP is a single nucleotide polymorphism, or in other words, a difference between two sequences at a single nucleotide position within a DNA sequence (point mutation). By definition, SNPs must be common enough to be found at least once in a random sample of 50 individuals, but the effect of a given SNP on phenotype can vary widely. Some SNPs are neutral, whereas others are beneficial or can increase disease risk. SNPs that correlate with disease risk or incidence are of particular interest to researchers as a potential way to identify those that are at-risk for particular diseases before the onset of symptoms so that preventative treatment or early medical interventions can be initiated.
Explain how SNPs and CNVs are detected in a population of individuals.
DNA microarrays can be used to detect both SNPs and copy number variation (CNV). This technology relies on the ability of complimentary DNA sequences to hybridize to one another under favorable conditions. To detect SNPs, a microarray chip is covered with short, single-stranded DNA oligonucleotides that, in different regions of the chip, differ from one another by a single nucleotide to represent all four possible SNPs that might be present at one particular position within the sequence. The chip is then incubated with single-stranded, fluorescently-labeled DNA from one individual, which will hybridize to the chip only where the sequence is exactly complimentary. The pattern of fluorescence on the chip can then be used to determine which allele(s) of the SNP are present in individual samples. CNVs are detected in a similar manner except that the oligonucleotides adhered to the chip represent different regions of a larger stretch of DNA and the intensity of the signal for each region reflects the number of copies of that sequence that are present in the sample DNA.
Diagram how nondisjunction in meiosis I or II can result in extra or missing chromosomes in reproductive cells (gametes).
look up either in book/online/youtube
Describe the consequences of an extra copy of chromosome 21 (Down syndrome).
Individuals with Down syndrome have three copies of chromosome 21, so they have an additional copy of the genes and elements present on this chromosome. Although the exact gene(s) responsible for this syndrome are still unknown, the increased dosage of chromosome 21 results in a group of traits which are characteristic of Down syndrome including mild to moderate mental disability, short stature, unique facial features and shorter life expectancy.
SNPs arise from:
Genetic studies have identified an allele (Δ32) that seems to provide protection against AIDS. Which of the following would most likely explain the reason why our population has this mutation?
This mutation likely benefited the human population against some other early pathogen.
Only polymorphisms that add or remove restriction sites can be useful in DNA typing
You are working in a medical research lab and have to determine if a patient is heterozygous or homozygous for a particular restriction site. You isolate a region of DNA from each chromosome, the middle of which could contain the restriction site, if the patient has it. If you treat the DNA with the restriction enzyme, how many fragments will be produced if the patient is heterozygous for the presence of the restriction site?
Which of the following explains the difference between VNTRs and RFLPs?
In VNTRs, we are looking at the number of times a sequence is repeated; in RFLPs we are looking at size differences resulting from different restriction sites being present.
The number of tandem repeats in an individual:
will vary from chromosome to chromosome.
Imagine that you know two sisters―Rose and Sam―both of whom smoke. Furthermore, Rose has a mutation in the gene for alpha-1 antitrypsin, whereas Sam does not. Which of the following statements is true regarding these sisters?
It is possible that neither Rose nor Sam will develop emphysema; however, the fact that both sisters smoke―added to the mutation that Rose carries―increases their chances of developing this disease.
The ability to perceive a bitter taste from certain chemicals including PTC has been linked to certain alleles. Which of the following would provide an explanation for the fact that almost all nonhuman primates have the "taster" phenotype, whereas the human population has a significant percentage of "nontaster" phenotypes?
The advantage to being able to taste bitter compounds would keep you from eating poisonous compounds, an advantage not needed in the human population anymore.
Up until 20–30 years ago, people with cystic fibrosis (CF) wouldn't live long enough to reproduce. CF is a homozygous recessive condition, leading researchers to think that over time the incidence of CF would decrease because the allele would be removed from the gene pool. The results actually indicate that the rate of CF is on the rise. Based on what you know about why certain genotypes and phenotypes persist in a population, which of the following could be a likely explanation for why the rate of CF is on the rise?
The heterozygous condition is beneficial, much like what we see with sickle cell trait.
Imagine that you are a detective who has identified a potential suspect in a homicide. You acquire a small amount of blood from the crime scene and hand it over to your lab. The lab carries out PCR for one polymorphism, and it returns as a match to your suspect. Is this enough to arrest your suspect?
No, your lab should assess additional polymorphisms―a single polymorphism does not constitute a genetic fingerprint.
A single nucleotide polymorphism (SNP) and a point mutation are the same thing
false, a snp is a base pair mutation
In microarrays, the oligonucleotides that are attached have the fluorescent tag, whereas the DNA fragments being tested do not.
false, the DNA fragments have the flurosence, while the ognucleotides have complementary base pairs.
After doing PCR on the same region between two individuals, you notice that each person's DNA yielded pieces of different sizes. Which of the following is the most likely explanation?
This is an example of VNTRs*******why is this?
can be subject to environmental conditons
Which of the following is an advantage of DNA typing?
only small samples of DNA are needed
Which of the following is true regarding RFLPs?
A polymorphism results in one site being recognized by a restriction enzyme, but not in others.
Which of the following statements explains why restriction enzymes are not useful for genome-wide studies of genetic variation?
Using restriction enzymes will only tell us differences in sequence variation in restriction sites.
SNPs within a gene called FOXO correlate with increased longevity in humans. You are a researcher in a lab and wish to determine if you possess this SNP. Which of the following techniques would allow you to accomplish this