Reflections. Tales from the Genome. Lessons 5-6¶
import webbrowser
Glossary¶
Activator: transcription factors that bind to an enhancer and increase transcriptional activity
Adenine (A): a type of nitrogenous base that is typically used in both DNA and RNA (A basepairs with U or T)
Allele: Specific variant of a genetic sequence for which more than one variation exists, sometimes associated with a unique phenotype
Allele Frequency: the frequency of an allele is equal to the number of that allele divided by the total number of alleles in a given population
Amino Acid: the basic building blocks of proteins, combined by ribosomes during the process of translation; there are 20 different amino acids
Aneuploidy: a chromosomal aberration in which certain chromosomes are present in extra copies or are deficient in number
Autosome: a nuclear chromosome that is not a sex chromosome (X or Y)
Basepair: the phenomenon of nitrogenous bases in nucleic acid pairing with one another in double-stranded DNA or RNA, following the rules A:T, G:C in DNA and A:U, G:C in RNA
Behavioral Trait: any trait that concerns an organism's action or interaction with or within an environment, for example: aggressiveness
Bioethicist: someone who focuses on ethical issues relating to biological topics
Blending Inheritance: the idea that a particular trait in an offspring is a mix of the parents’ traits
Bottleneck: genetic drift resulting from the reduction of a population, typically by a natural disaster, such that the surviving population is no longer genetically representative of the original population
Chromosome: a super-coiled structure of organized DNA wrapped around histones; contains a single molecule of DNA
Coding DNA: sometimes referred to as "protein-coding DNA"; refers to any sequence in the genome that specifies amino acids and translation signals (initiation and termination codons)
Codon: a three-nucleotide sequence of mRNA that specifies a particular amino acid or termination signal
Combinatorial Regulation: the idea that transcription of most genes is controlled by more than one activator or repressor to achieve a particular level of activity
Computational Biologist: someone who applies their knowledge of computer science or computer coding to biological problems
Concordance: the presence of the same trait in both members of a pair of twins or set of individuals
Consensus Sequence: a single sequence that represents the most prevalent individual unit at each position, derived by comparing variants of the sequence from different sources
Correlation: refers to an observable relationship between any paired values
Cytochrome P450: a large and diverse group of enzymes that catalyze the oxidation (metabolism) of organic substances (drugs)
Cytoplasm: the interior of a cell, excluding the nucleus
Cytosine (C): a type of nitrogenous base that is typically used in both DNA and RNA (C basepairs with G)
Deoxynucleotides: the building blocks of DNA; there are four different bases used in deoxynucleotides: Adenine (A), Thymine (T), Guanine (G), and Cytosine (C)
Direct Selection: (see natural selection)
Director Of Clinical Operations: someone who designs and manages clinical trials
Dizygotic Twins: twins that came from two different fertilized eggs or zygotes; fraternal twins
DNA: deoxyribonucleic acid; the hereditary material of almost all cells that makes up their genomes
DNA Amplification: the in vitro replication of a DNA sequence to make many more copies
DNA Extraction: the isolation of DNA from a biological sample
DNA Sequence: a string of DNA letters (bases) in consecutive order
Dominant Trait: can mask the presence of a recessive allele or trait
Double Helix: the structure of DNA, referring to its two adjacent strands wound into a spiral shape and held together through basepairing
Duplicated Chromosome: the stereotypical structure in the shape of an "X" for a nuclear chromosome that appears only before cell division
Duplication: a replication error that doubles a large segment of DNA
Efficacy: a drug's ability to produce a therapeutic effect
Egg: female reproductive cell
Enhancer: a DNA sequence that binds certain transcription factors, activators, that can stimulate transcription of nearby genes
Enzyme: a class of proteins that enable chemical reactions without being consumed by the reaction
Exon: a sequence from a gene that is transcribed and remains in the mRNA after splicing and includes codes for amino acids
Founder Effect: a cause of genetic drift attributable to colonization by a limited number of individuals from a parent population
Frameshift: any mutation that results in changing the reading frame of translation
Gain-Of-Function Mutation: changes the gene product such that it gains a new and/or abnormal function
Gamete: sperm or egg cells; produce as a result of meiosis from germ cells
Gene: a discrete unit of hereditary information consisting of a specific deoxynucleotide sequence in DNA
Gene Expression: the process by which information from a gene is used in the synthesis of a functional gene product
Genetic Counselor: someone who explains and discusses personal genetic information with individuals and families
Genetic Genealogist: someone who uses genetic information to determine and catalog family relationships and uncover ancestry
Genome: the complete complement of an organism's genetic material
Genome Wide Association Study (GWAS): GWAS seek to correlate, in populations, the association of specific alleles with the trait or disorder being studied
Genotype: the genetic makeup of an organism, specifically the composition of alleles
Germ Cell: the type of the cell in the body that makes gametes; this is the only cell type where mutations affect the next generation of an organism
Guanine (G): a type of nitrogenous base that is typically used in both DNA and RNA (G basepairs with C)
Hidden Trait: any trait that is not apparent through outward observation
Histone: a protein that is used to organize and fold DNA like a string on a spool
Heterozygous: having two different alleles for a given gene
Heterozygote Advantage: describes the case in which the heterozygous genotype has a higher relative fitness than either the homozygous dominant or homozygous recessive genotype
Heritability: the proportion, between 0 and 1, of observable differences in variation of a trait between individuals within a population that is due to genetic differences
Homozygous: having two identical alleles for a given gene
Human Geneticist: someone who studies human genetics and inheritance
Hybridization: the process of basepairing that can occur between any types of nucleic acids (DNA:DNA, DNA:RNA, or RNA:RNA)
Identity By Descent (IBD): genetic sequence shared through ancestry
Identity By Descent (IBD): genetic sequence shared through ancestry
Identity By State (IBS): genetic sequence that is identical between two individuals
Inheritance: the passing down of traits from one generation to the next, at the level of the cell or the organism
Innate Trait: any trait that is in-born, for example: your pancreas secreting enzymes that break down the food in your gut
Intron: a sequence from a gene that is transcribed but cut out of the mRNA by splicing and typically does not code for any amino acids
Learned Trait: any trait that is not in-born and instead acquired through environmental (typically cognitive) influence, for example: belief in a particular religion
Loss-Of-Function Mutation: results in the gene product having less or no function
Meiosis: a two-stage type of cell division in germ cells that results in gametes with half the chromosome number of the original cell
Mitochondrial DNA: a circular DNA molecule that can only be found in the mitochondria of all cells in the body and is inherited only from the mother
Mitosis: the normal chromosome doubling and division that all somatic (body) cells do to maintain the same number of chromosomes at the end of each division
Missense/Non-Synonymous Mutation: a mutation that changes an amino acid
Monogenic Trait: traits that are significantly influenced by a single gene
Monozygotic Twins: twins that came from the same fertilized egg or zygote; identical twins
Multifactorial Trait: a trait that is controlled by many genes and is also influenced by the environment
Mutation: a change in the genetic sequence
Natural Selection: the process by which traits become either more or less common in a population because of pressures directly affecting the reproductive fitness of individuals carrying particular alleles; also considered "direct selection" due to pressures that directly affect the fitness of particular alleles
Non-coding DNA: any sequence that does not specify amino acids and translation signals (initiation and termination codons)
Non-Duplicated Chromosome: a non-"X"-shaped nuclear chromosome;
Nonsense Mutation: a mutation that changes an amino acid codon to a STOP codon
Nuclear Genome: the complete set of 23 pairs of chromosomes that reside within the nucleus of the cell
Nucleotide: building block of DNA and/or RNA consisting of a base, a ribose or deoxyribose sugar and a phosphate group; there are five different bases used in nucleotides: Adenine (A), Thymine (T) in DNA or Uracil (U) in RNA, Guanine (G), and Cytosine (C)
Nucleus: a separate, membrane-bound compartment of eukaryotic cells that houses the DNA and separates it from the rest of the cell; this is where transcription occurs
Particulate Inheritance: the idea that characteristics can be passed down from generation to generation through discrete particles, i.e. genes
Pedigree: organized way of illustrating (drawing) family relations and traits
Penetrance: the degree to which a particular allele causes a trait
Personal Genome: the entirety of your own individual DNA
Pharmacodynamics: the target effects of a drug; what a drug does to the body
Pharmacogenetics/Pharmacogenomics: the study of how different drugs interact with the body in different ways based on genetic variation
Pharmacokinetics: how a drug is metabolized; what the body does to a drug
Pharmacology: the study of drugs and their origins, as well as how they interact with the body of a living organism
PharmGKB: Pharmacogenomics Knowledge Base is an interactive tool for researchers to investigate how genetic variation affects drug response, both with regards to pharmacodynamics and pharmacokinetics
Phenotype: the physical makeup, or appearance, of an organism or individual trait
Physical Trait: any trait that concerns our material makeup
Polygenic Trait: a trait that is the result of multiple gene interactions with very little environmental impact
Population: a group of individuals of one species that live in a particularly defined area
Promoter: a region of DNA at which transcription of a particular gene is initiated
Protein: a large chain or combination of multiple chains of amino acids
Promoter: a region of DNA at which transcription of a particular gene is initiated
Qualitative Trait: a trait that is described by either its presence or absence
Quantitative Trait: a trait that varies continuously over a range of measurements and displays a normal distribution (bell curve)
Random Selection: the process by which traits become either more or less common in a population due to random chance, not because of pressures directly affecting the reproductive fitness of particular alleles; it is random because the pressures do not directly affect the fitness of particular alleles
Recessive Trait: masked by the presence of a dominant allele or trait
Recombination: a special process during meiosis that can swap pieces of your maternal and paternal chromosome copies
Relative Risk: an individual's risk based on family or genetic background compared to the general population
Repressor: transcription factors that bind to a silencer and inhibit transcriptional activity
Ribosome: a molecular machine that translates, or reads, the genetic code within the mRNA sequence and synthesizes a corresponding chain of amino acids
RNA and mRNA: ribonucleic acid; A type of nucleic acid, usually single-stranded, consisting of nucleotides with the nitrogenous bases of A, C, G, and U
RSID: reference SNV identification
Sex Chromosome: a nuclear chromosome that distinguishes the sexes: XY - male, XX - female, and can affect sex-specific traits
Silencer: a DNA sequence capable of binding transcription regulation factors, called repressors, and inhibit transcriptional activity
Silent/Synonymous Mutation: a mutation that does not change the amino acid sequence
Single Nucleotide Variation (SNV): single base change in DNA; SNVs (also known as single nucleotide polymorphisms, or SNPs) are one of the smallest kinds of mutations and are responsible for a large number of differences among humans
SNV Genotyping: determining the base at any given position in a genome, not through total genome sequencing
Somatic Cell: any cell of the body that is not a germ cell (not directly responsible for carrying the information passed on to the next generation)
Splicing: the process of removing introns and combining exons in a mRNA sequence after transcription
TATA-Box: the TATAAA sequence that can be found in the promoter of many genes and is essential to initiate transcription
Thymine (T): a type of nitrogenous base that is typically used in DNA (T basepairs with A)
Toxicity: the degree to which a drug causes negative effects
Trait: any distinguishing feature of an individual
Transcription: the step of gene expression in which a particular segment of DNA is copied into RNA
Transcription Factor: any protein that joins the transcription process by binding to DNA or to other proteins that bind DNA to regulate transcription
Translation: the process by which ribosomes read the mRNA sequence and connect the amino acids in the order specified by the sequence
Translocation: rearrangement of a large sequence of genetic information, typically transferring from one chromosome to another through DNA breakage and resealing
Uracil (U): a type of nitrogenous base that is typically used in RNA (U basepairs with A)
Variant: version of a genetic sequence or gene for which more than one version exist
Variation: diversity among members of a population
Visible Trait: any trait that is apparent through outward observation
X Chromosome: one of two mammalian sex chromosomes that can be found in both males (XY) and females (XX)
Y Chromosome: the mammalian sex-determining chromosome that can only be found in males (XY) and is passed from father to son
Lesson 5 ¶
from IPython.display import Image
Image(filename='cm05.jpg')
Genotype and Phenotype¶
For every characteristic we have 2 forms of a gene - one from our mother, the other from our father.
Genes are part of chromosomes. Differing forms of a gene are called ALLELES, e.g. the alleles for the gene for eye colour are blue, green, brown etc.
PHENOTYPE is the physical appearance resulting from the inherited information. e.g. someone with blue eyes has the phenotype blue eyes.
Genes or alleles can be said to be DOMINANT (shows up in the phenotype) or RECESSIVE (hidden when it is present along with the dominant gene).
Dominant alleles are always expressed in a cell’s phenotype. Only one copy of the dominant allele needs to be present for that characteristic to be expressed.
Dominant alleles are represented by a capital letter, e.g. Brown eyes would be B since brown eyes are dominant to blue eyes.
Recessive alleles are represented by a lower case e.g. blue eyes would be b. They are only expressed when two copies of the allele are present. If only one is present then it becomes ‘masked’ by the dominant allele, e.g. brown eyes is dominant so Bb would show the brown eye characteristic (phenotype).
Blue eyes will only be expressed if the genotype is bb.
Genotype The genotype of an organism demonstrates the alleles present for a particular characteristic.
For example:
Genotype Phenotype
BB Brown eyes Same phenotype as below but different genotype
Bb Brown eyes Same phenotype as above but different genotype
bb Blue eyes Different phenotype and genotype from both above
When two of the same alleles for a gene are present, the genotype is said to be homozygous e.g. BB or bb. But if different alleles are present for the same gene, e.g.. Bb, then they are said to be heterozygous.
Meiosis¶
Meiosis is the process by which gametes with a single set of chromosomes are produced. This process takes place in the testes for men and the ovaries for women.
During the process of meiosis a type of body cell called a gamete mother cell divides to form four sex cells Each gamete mother cell contains two sets of chromosomes (23 pairs) and each sex cell contains one set of chromosomes (23) Immediately before gamete production each chromosome in a gamete mother cell uncoils and undergoes DNA replication forming two identical chromatids Shuffling of Chromosomes Each gamete produced from a gamete mother cell receives one chromosome from each pair in the mother cell The separation of the members of a pair of chromosomes is totally at random - therefore there is a huge number of combinations possible. This 'shuffling' of matching pairs of chromosomes is also described as random assortment of chromosomes.
Problem set 5 ¶
Image(filename='bio0501.jpg')
#3¶
Two first cousins marry, and their first child has the rare autosomal recessive disease galactosemia (inability to process galactose, leading to muscle, nerve, and kidney malfunction). Assuming that the genetic disease is a result of inbreeding, indicate which members of the following pedigree MUST be heterozygous for this to be true. Explain.¶
- -/-
- +/- & +/-
- +/- and +/-
- +/- or +/-
Image(filename='bio0502.jpg')
#5¶
See the following pedigree for a rare genetic disease trait. Which of the following is the most likely mode of inheritance? Why?¶
- Recessive or Dominant
- Autosomal or Sex-linked or Maternal #### not maternal ( not only 1 maternal line) and not sex-linked (both sexes are equally affected) recessive (skip generations)
Image(filename='bio0503.jpg')
#7¶
Fill in the blank.¶
An individual unaffected by a recessive trait cannot be homozygous for the causative allele, whereas an individual affected by a dominant trait must at least be heterozygous for the dominant allele.¶
[Word bank: dominant, recessive, homozygous, heterozygous, affected, unaffected]¶
#8¶
A man with KearnsSayre syndrome is affected by many musclerelated deficiencies by the age of 25. At this point the man already has four children. If his syndrome follows a pattern of maternal inheritance, how many of his children would you expect to be affected by KearnsSayre syndrome? Enter a number.¶
0¶
#9¶
For a dominant trait like achondroplasia (most common cause of dwarfism), which of thefollowing are true? Select any and all that apply. Why?¶
A. Affected adults must carry a dominant allele¶
B. Affected adults must carry a recessive allele¶
C. Unaffected adults must carry a dominant allele¶
D. Unaffected adults must carry a recessive allele¶
A, B, D ¶
only -/- will be unaffected for sure¶
Image(filename='bio0504.jpg')
Image(filename='bio0505.jpg')
#13¶
Duchenne muscular dystrophy is Xlinked and usually affects only males. Victims of the disease become progressively weaker, starting early in life. Assuming you are female, if only your father’s brother had the disease, what is the probability that you have receivedthe allele? Draw a pedigree if you need to for answering this question. Write your answer as a fraction, a decimal, or a percentage¶
0¶
#16¶
A man’s maternal grandfather had galactosemia, a rare autosomal recessive disease caused by the inability to process galactose. The man married a woman whose sister had galactosemia. The woman is now pregnant with their first child. In the pedigree, indicate all the individuals that should be shaded to indicate their affected status.¶
Image(filename='bio0506.jpg')
Image(filename='bio0507.jpg')
Image(filename='bio0508.jpg')
Image(filename='bio0509.jpg')
Image(filename='bio0510.jpg')
#21¶
Two genes (A and B) that are responsible for two very different traits can be found on the same chromosome. Based on what you know about recombination during meiosis, which one of the following depictions would most likely result in the maximum number of genotype combinations in gametes from an individual that is heterozygous for both genes? Assuming recombination occurs, what would be the maximum number ofgenotype combinations? Why?¶
4 (A+B+ A+B- A-B+ A-B-)¶
#22¶
There are four genes (W, X, Y, and Z) all located very close together on chromosome 3. They are so close together that they are considered linked and virtually no recombination can occur in between them. Assuming no recombination, if an individual is heterozygous for each gene, what is the maximum number of possible genotype combinations in the gametes after meiosis? Why?¶
2; Because there is no recombination¶
#23¶
Select the underlined word in the following sentence that is incorrect. Then write the correct word that should replace it.¶
Genetic variability achieved by sex, specifically chromosome recombination and independent assortment through meiosis, is undermined by inbreeding which allows forthe possibility of fewer(MORE) homozygous combinations than would be expected in the general population for typically rare recessive alleles.¶
Lesson 6 ¶
Image(filename='cm06.jpg')
webbrowser.open('http://content.udacity-data.com/course/bio110/Lesson_6_Concept_Map.pdf')
Bottlenecks and founder effects¶
Genetic drift can cause big losses of genetic variation for small populations.¶
Population bottlenecks occur when a population's size is reduced for at least one generation. Because genetic drift acts more quickly to reduce genetic variation in small populations, undergoing a bottleneck can reduce a population's genetic variation by a lot, even if the bottleneck doesn't last for very many generations. This is illustrated by the bags of marbles shown below, where, in generation 2, an unusually small draw creates a bottleneck. Reduced genetic variation means that the population may not be able to adapt to new selection pressures, such as climatic change or a shift in available resources, because the genetic variation that selection would act on may have already drifted out of the population.
An example of a bottleneck¶
Northern elephant seals have reduced genetic variation probably because of a population bottleneck humans inflicted on them in the 1890s. Hunting reduced their population size to as few as 20 individuals at the end of the 19th century. Their population has since rebounded to over 30,000 — but their genes still carry the marks of this bottleneck: they have much less genetic variation than a population of southern elephant seals that was not so intensely hunted.
Founder effects¶
A founder effect occurs when a new colony is started by a few members of the original population. This small population size means that the colony may have: *- reduced genetic variation from the original population,
- a non-random sample of the genes in the original population.* For example, the Afrikaner population of Dutch settlers in South Africa is descended mainly from a few colonists. Today, the Afrikaner population has an unusually high frequency of the gene that causes Huntington's disease, because those original Dutch colonists just happened to carry that gene with unusually high frequency. This effect is easy to recognize in genetic diseases, but of course, the frequencies of all sorts of genes are affected by founder events.
Natural Selection¶
Since more offspring are produced by every species than the environment can support, not all will survive long enough to reproduce.
The following factors may mean that members of the species will not survive:
Predators Disease Competition for light and space Competition for food Competition for a mate Survival of the fittest - those offspring whose phenotypes are better adapted to the environment have a better chance of survival and therefore a greater chance of passing on their genes to the next generation.
The offspring whose phenotypes are less well suited, die before reaching reproductive age, and therefore fail to pass on their genes.
Problem set 6 ¶
#1¶
Look at the following sequence from a human gene:¶
...GATCGAGCCGTGAGTCCATGC...¶
You discover that the sequence is altered in one individual to look like this:¶
...GATCGAGCCGTAACGAGTCCATGC...¶
Which of the following best describes the mutation?¶
A. Trinucleotide Repeat¶
B. Insertion¶
C. Duplication¶
D. SNV¶
E. Deletion¶
B ¶
#3¶
A single nucleotide addition and a single nucleotide deletion approximately 15 sites apart in the DNA cause a protein change in sequence from:¶
...Lys – Ser – Pro – Ser – Leu – Asn – Ala – Ala – Lys...¶
to¶
...Lys – Val – His – His – Leu – Met – Ala – Ala – Lys…¶
Based on the changes, enter one possible mRNA nucleotide sequence for the first chain of amino acids. (use the genetic code!)¶
What could be the old mRNA nucleotide sequence? (use the genetic code!)¶
Old: AA(A,G) AGU CCA UCA CUU AAU GCA GCU AA(A,G)¶
What could be the new mRNA nucleotide sequence? (use the genetic code!)¶
New: AA(A,G) GUC CAU CAC UUA AUG GCA GCU AA(A,G)¶
To get the new mRNA sequence, which nucleotide has been added and which has been deleted? (use only the RNA letters A, U, G, or C)¶
AAG-AGU-CCA-UCA-CUU-AAU-GCA-GCU-AAA ¶
#4 ¶
A single nucleotide addition and a single nucleotide deletion approximately 15 sites apart in the DNA cause a protein change in sequence from:¶
...Lys – Ser – Pro – Ser – Leu – Asn – Ala – Ala – Lys...¶
to¶
...Lys – Val – His – His – Leu – Met – Ala – Ala – Lys…¶
Based on the changes, enter one possible mRNA nucleotide sequence for the new chain of amino acids. (use the genetic code!)¶
## AAA-GUC-CAU-CAC-UUA-AUG-GCA-GCU-AAA ¶
#5 ¶
A single nucleotide addition and a single nucleotide deletion approximately 15 sites apart in the DNA cause a protein change in sequence from:¶
...Lys – Ser – Pro – Ser – Leu – Asn – Ala – Ala – Lys...¶
to¶
...Lys – Val – His – His – Leu – Met – Ala – Ala – Lys…¶
To get the new mRNA sequence, which nucleotide has been added and which has been deleted? (use only the RNA letters A, U, G, or C)¶
G,A ¶
#6 ¶
Which of the following mutations would be expected to be MOST likely to have a harmful effect on an organism? Why?¶
A. A single base change¶
B. A deletion of three bases near the middle of a gene¶
C. A single base deletion near the middle of an intron¶
D. A single base deletion close to the end of the coding sequence¶
E. A single base insertion near the start of the coding sequence¶
E .¶
It totally changes the coding sequence and producing the protein.¶
#7 ¶
Which of the following repeat errors within a coding sequence would be most likely to be tolerated (cause the least problems) by the individual? Why?¶
A. Dinucleotide repeats (repetition of a 2letter sequence)¶
B. Trinucleotide repeats (repetition of a 3letter sequence)¶
C. Tetranucleotide repeats (repetition of a 4letter sequence)¶
D. Pentanucleotide repeats (repetition of a 5letter sequence)¶
B ¶
A multiple of three, then it does not lead to serious changes.¶
#9 ¶
Fragile X Syndrome, characterized by particular physical features as well as a range of cognitive deficits, is caused by a trinucleotide repeat expansion of the sequence CGG in a gene on the X chromosome. An unaffected individual has around 50 or fewer repeats whereas someone with over 230 is likely to be affected. What is the most likely cause of this sort of repeat expansion? Why?¶
A. Xray radiation¶
B. UV rays¶
C. Replication error¶
C ¶
UV and X rays causes of other types (the base substitutions and the DNA breaking).¶
#10 ¶
Amazingly, the expansion of the CGG sequence from 50 to over 230 repeats on the X chromosome (and causing Fragile X Syndrome) does not occur in the coding region of a gene. The increase in repeats actually occurs near the promoter, causing proteins to accumulate and silence the gene through a process called DNA methylation. If males are affected by one copy but females are not, would you consider this expanded repeat allele to be:¶
A. Dominant¶
B. Recessive¶
Why?¶
B ¶
The reason why only men affected - they have only one copy of X chromosome, so they will have a recessive allele in this case.¶
#11 ¶
Trinucleotide repeat expansions (TNREs) are associated with several different human inherited diseases. Certain types of TNREs produce a long stretch of Glutamines (an amino acid abbreviated as Gln) within the encoded protein. This long stretch of glutamines somehow inhibits the function of the protein, thereby causing a disorder.¶
When a TNRE exerts its detrimental effect by producing a glutamine stretch, which of the following statements could be TRUE? Select any and all that apply.¶
A. The TNRE is within the coding sequence of the gene¶
B. The TNRE affects the promoter preventing transcription¶
C. The trinucleotide sequence could be CAG¶
D. The trinucleotide sequence could be CCG¶
A, C ¶
#12 ¶
A position effect is described as a change in phenotype that occurs when the position of a gene is changed from one chromosomal site to a different location. Which of the following would be appropriately described as a position effect? Select any and all that apply.¶
A. A SNV mutation at the position 10 basepairs in front of the promoter region, blocking transcription¶
B. A translocation placing the coding sequence for a musclespecific gene next to an enhancer that is activated in nerve cells¶
C. A nonsense mutation that occurs in the nexttolast exon position of a gene¶
B ¶
#14 ¶
Select the underlined word in the following sentence that is incorrect. Then write the correct word that should replace it.¶
There are four main types of mutations that occur in coding regions.¶
Silent mutations do not alter the amino acid sequence.¶
Induced (Missense) mutations change one amino acid to another.¶
Nonsense mutations generate a STOP codon from a codon that used to code for another amino acid.¶
And frameshift mutations alter the reading frame such that many amino acids are change.¶
#15 ¶
In the United States, Phenylketonuria, an autosomal recessive metabolic disorder characterized by problems with brain development leading to progressive mental retardation, brain damage, and seizures, affects roughly 1 in every 10,000 newborn babies. Assume a population size of 300,000,000 people for the United States. If the allelic frequency of the Phenylketonuria recessive allele is 0.01, estimate how many individuals in the US would be carriers? Write your answer as a number (integer), and use a calculator if you need it!¶
(300000000 * (1 - 0.01) * 2) * 0.01
#17 ¶
An individual acquired a mutation in a skin cell caused by UV light that changes a Lysine (Lys) codon into a Glutamate (Glu) codon. Would this mutation be considered spontaneous or induced? What is the probability that this individual will pass this mutation on to their offspring? Write your answer as a fraction, percentage, or decimal.¶
Induced. 0 ¶
#18 ¶
Although the phrase “gene pool” is sometimes used loosely to refer to genes in a group of individuals, technically it is defined as the collective genetic information contained within a population of sexually reproducing organisms. A large gene pool indicates immense genetic diversity of various alleles within a population that can withstand rounds of intense selection. With this in mind, which of the following have the net effect of reducing the gene pool? Select any and all that apply.¶
A. Meiosis¶
B. Extensive inbreeding¶
C. Population bottlenecks¶
D. Natural or random selection¶
E. Random mating¶
B, C, D ¶
#19 ¶
Consider the populations that have the genotype frequencies shown in the followingtable:¶
Population Genotype +/+ Genotype +/- Genotype -/-¶
1 1.0 0.0 0.0¶
2 0.0 1.0 0.0¶
3 0.0 0.0 1.0¶
4 0.25 0.5 0.25¶
What are the allelic frequencies in each population? Enter a number/decimal for each.¶
'+' 1 - 1.0, 2 - 0.5, 3 - 0.0, 4 - 0.5 ¶
'-' 1 - 0.0, 2 - 0.5, 3 - 1.0, 4 - 0.5 ¶
#20 ¶
Phenotypic, genotypic, and allelic frequencies can all be assessed for a population if enough information is known. Frequencies are measured from 0 to 1, with 0 being a complete absence in the population and 1 comprising the entirety of the population. For the autosomal recessive trait of lactose intolerance, heterozygous individuals are unaffected because one copy of the dominant allele is enough to be lactase persistent.¶
Out of a population of 10,000 where 2,000 are lactase persistent (dominant) and 8,000 are lactase non-persistent (recessive and lactose intolerant), there are 1,500 heterozygous individuals. Fill in the table for the phenotypic, genotypic, and allelic frequencies for the trait of lactase persistence.¶
Allelic
Phenotypic frequency ___ Lactase Persis: 0.2 Non-persis: 0.8 ¶
Genotypic frequency ___ +/+: 0.05 +/-: 0.15 -/- 0.8 ¶
Allelic frequency ___ + : 0.125 - : 0.875 ¶
#21 ¶
Not only can selection pressures (natural or random) alter allelic frequencies, but so can genetic drift. Genetic drift is simply the change in allelic frequencies in a population due to random sampling effects over the formation of successive generations. The expected population dynamics indicates that neutral alleles are predicted to eventually become fixed at zero or 100% frequency in the absence of other mechanisms affecting allele distributions. Which of the following examples show an instance where the dominant (+) allele is fixed at 0 or 100%? Select any and all that apply. Why?¶
A. 100% individuals with the dominant phenotype, 25% have two dominant alleles¶
B. 100% individuals with the dominant phenotype, 0% have one recessive allele¶
C. 100% individuals with the recessive phenotype, 100% have two recessive alleles¶
D. 50% individuals with the recessive phenotype, 0% have two dominant alleles¶
B, C ¶
#22 ¶
Fill in the blanks using words from the word bank.¶
Spontaneous mutations like those from replication errors can cause duplications, insertions, deletions , and individual SNVs. Induced mutations from X-rays can cause chromosomal translocations . No matter the source, mutations in germ cells get passed down to the next generation and have the potential to spread in a population in response to selection .¶
(Word bank: germ cells, induced, deletions, selection, population, spontaneous, replication errors, translocations)¶
#23 ¶
Achondroplasia is one of the most common forms of dwarfism caused by an autosomal dominant mutation in the coding region of a single gene. Out of 1,500,000 live births, the number of babies born with achondroplasia was 31. Among those 31 babies, 18 of them had one parent with achondroplasia. The remaining babies had two unaffected parents. For this group of 1,500,000 babies, which of the following is most likely the mutation rate? Which of the following is most likely the mutation frequency? Why?¶
Rate 31/1500000 31/3000000 18/1500000 18/3000000 13/1500000 13/3000000¶
Frequency 31/1500000 31/3000000 18/1500000 18/3000000 13/1500000 13/3000000¶
# Rate:
print (31-18), '/', (2*1500000)
# Frequency:
print 31, '/', (2*1500000)