Genomics Exam Materials
Course Introduction
Genomics explores the structure, function, evolution, and mapping of genomes, which are the complete sets of DNA within organisms. This course covers foundational concepts such as the organization and regulation of genes, genome sequencing technologies, and bioinformatics tools used to analyze large-scale genetic data. Students will examine advancements in personalized medicine, biotechnology, and evolutionary biology, while learning how genomic information impacts areas like health, agriculture, and disease research. Emphasis is placed on case studies and current applications, equipping students with both the theoretical background and practical skills to interpret and utilize genomic data in a variety of scientific and medical contexts.
Recommended Textbook
Concepts of Genetics Books a la Carte Edition 11th Edition by William S. Klug
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Chapter 1: Introduction to Genetics
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Q1) What is meant by complementarity in terms of the structure of DNA?
Answer: base pairing of A with T,and G with C
Q2) What is meant by the term genetic code?
Answer: The genetic code consists of a linear series of three adjacent nucleotides present in mRNA molecules.
Q3) In many species,there are two representatives of each chromosome.In such species,the characteristic number of chromosomes is called the ________ number.It is usually symbolized as ________.
A) haploid; n
B) haploid; 2n
C) diploid; 2n
D) diploid; n
E) None of the answers listed are correct.
Answer: C
Q4) Research dealing with which human blood disorder was instrumental in linking the genotype to a specific phenotype,and what conclusion was reached?
Answer: The work on sickle-cell anemia was instrumental in showing that a mutant gene produced a mutant protein molecule.
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Chapter 2: Mitosis and Meiosis
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Q1) List in order of occurrence the phases of (a)mitosis and (b)prophase I of meiosis.
Answer: (a)prophase,prometaphase,metaphase,anaphase,telophase (b)leptonema,zygonema,pachynema,diplonema,diakinesis
Q2) What is the name of the membranous structure that compartmentalizes the cytoplasm of eukaryotic organisms?
A) ribosome
B) mitochondria
C) cytosol
D) endoplasmic reticulum
E) nucleoid
Answer: D
Q3) S phase is the part of interphase when DNA duplication takes place.
A)True
B)False
Answer: True
Q4) Homologous chromosomes are those that can be matched by virtue of their similar structure and function within a nucleus.Which chromosomes making up a genome do not follow the same characteristics of homology?
Answer: sex-determining chromosomes
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Chapter 3: Mendelian Genetics
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Sample Questions
Q1) Albinism,lack of pigmentation in humans,results from an autosomal recessive gene
(a).Two parents with normal pigmentation have an albino child.
a) What is the probability that their next child will be albino?
b) What is the probability that their next child will be an albino girl?
c) What is the probability that their next three children will be albino?
Answer: (a)1/4
(b)1/4 × 1/2 = 1/8
(c)1/4 × 1/4 × 1/4 = 1/64
Q2) Assuming independent assortment,what proportion of the offspring of the cross will have the aabbccdd \[A a B b C c D d \times A a b b C C d d\] genotype?
Answer: zero
Q3) Albinism,lack of pigmentation in humans,results from an autosomal recessive gene (a).Two parents with normal pigmentation have an albino child.What is the probability that their next three children will be albino?
Answer: 1/4 × 1/4 × 1/4 = 1/64
Q4) The nonfunctional form of a gene is called a wild-type allele.
A)True
B)False
Answer: False
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Chapter 4: Extensions of Mendelian Genetics
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Q1) A conditional mutant is one whose expression is influenced by some environmental condition.
A)True
B)False
Q2) What term is used to express the idea that several genes exert influence over the same characteristic?
A) coextension
B) co-adhesion
C) terminal interaction
D) gene interaction
E) transformation
Q3) Assume that a mutation occurs in the gene responsible for the production of hexosaminidase A,such that only about 50% of the enzyme activity is found in the heterozygote compared with a homozygous normal individual.If heterozygotes are phenotypically normal,we would say that the mutant allele is recessive to its normal allele.
A)True
B)False
Q4) Provide an example of sex-influenced inheritance.
Q5) How many different alleles can a gene have?
6
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Chapter 5: Chromosome Mapping in Eukaryotes
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Q1) (a)In a three-point mapping experiment,what three general classes of offspring are expected (assuming crossovers occur)? (b)How many different genotypic classes are expected?
Q2) Assume that a cross is made between AaBb and aabb plants and that the offspring fall into approximately equal numbers of the following groups: AaBb,Aabb,aaBb,aabb.These results are consistent with the following circumstance:
A) independent assortment.
B) alternation of generations.
C) complete linkage.
D) incomplete dominance.
E) hemizygosity.
Q3) Positive interference occurs when a crossover in one region of a chromosome reduces crossovers in nearby regions.
A)True
B)False
Q4) Assume that there are 12 map units between two loci in the mouse and that you are able to microscopically observe meiotic chromosomes in this organism.If you examined 200 primary oocytes,in how many would you expect to see a chiasma between the two loci mentioned above?
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Chapter 6: Genetic Analysis and Mapping in Bacteria and Bacteriophages
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Q1) Bacteriophages that cannot undergo lysogeny but can infect bacteria are called
Q2) Lysogeny is a process that occurs during transformation and conjugation.
A)True
B)False
Q3) Temperate phages are those that can enter either the ________ or ________ cycle.
A) lytic; lysogenic
B) virulent; avirulent
C) functional; nonfunctional
D) former; nonformer
E) complementing; competing
Q4) What is a significant difference between a lytic and a lysogenic cycle?
Q5) In a bacterial cross in which the donor (Hfr)is a b and the recipient strain (F )is a b ,it is expected that recombinant bacteria will all be a b .
A)True
B)False
Q6) What is meant by the term cotransformation?
Q7) Lysogeny is most likely associated with transduction.
A)True Page 8
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Chapter 7: Sex Determination and Sex Chromosomes
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Q1) An individual with Turner Syndrome has no Barr bodies.
A)True
B)False
Q2) In Drosophila,an individual female fly was observed to be of the XXY chromosome complement (normal autosomal complement)and to have white eyes as contrasted with the normal red eye color of wild type.The female's father had red eyes,and the mother had white eyes.Knowing that white eyes are X-linked and recessive,present an explanation for the genetic and chromosomal constitution of the XXY,white-eyed individual.It is important that you state in which parent and at what stage the chromosomal event occurred that caused the genetic and cytogenetic abnormality.
Q3) Dosage compensation is accomplished in humans by inactivation of the Y chromosome.
A)True
B)False
Q4) A small part of the human Y chromosome contains the gene that is responsible for determining maleness.What is the name of this gene?
Q5) Under what condition might a human female have the XY sex chromosome complement?
Q6) List three abnormalities involving numbers of X chromosomes.
Q7) Describe three distinct genetic regions of the human Y chromosome.
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Chapter 8: Chromosome Mutations: Variation in Number and Arrangement
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Q1) Inversions suppress crossing over by providing a chemical imbalance because of breakpoints within certain genes.
A)True
B)False
Q2) A paracentric inversion is one whose breakpoints do not flank the centromere.
A)True
B)False
Q3) A pericentric inversion includes the centromere.
A)True
B)False
Q4) The condition known as cri-du-chat syndrome in humans has a genetic constitution designated as ________.
A) 45, X
B) heteroplasmy
C) 46, 5p-
D) triploidy
E) trisomy
Q5) Colchicine is an alkaloid derived from plants.What is its effect on chromosome behavior?
Q6) In what way might gene duplication play a role in evolution? Page 11
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Chapter 9: Extranuclear Inheritance
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Q1) Researchers in the late 1950s isolated multiple antibiotic-resistant strains of the bacterium Shigella,which causes dysentery.Such resistance was caused by nonchromosomal R factors that originated in E.coli.Which of the following forms of extrachromosomal heredity-maternal effect,organelle heredity,infectious heredity-would you consider most closely related to the transfer bacterial antibiotic-resistant strains?
Q2) How do mitochondria and chloroplasts determine phenotypes? Which characteristics of mitochondria and chloroplasts allow such phenotypes to be inherited? Provide specific examples to illustrate your response.
Q3) It appears as if the direction of shell coiling in Lymnaea peregra is influenced by the orientation of the first cleavage division.
A)True
B)False
Q4) Why is variegation in four o'clock plants determined by the phenotype of the ovule source?
Q5) Which three classes of macromolecules are encoded by mtDNA?
Q6) Name two human disorders that appear to be transmitted extrachromosomally.
Q7) What is the meaning of the term endosymbiotic theory?
Q8) In what way do mitochondrial mutations influence phenotype?
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Chapter 10: DNA Structure and Analysis
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Q1) The transforming principle discovered by Griffith is RNA.
A)True
B)False
Q2) Experiments conducted in the 1920s by Frederick Griffith involving the bacterium Diplococcus pneumoniae demonstrated that a substance from one bacterial strain could genetically transform other bacterial strains.What was the name of the substance capable of such transformation,and who finally determined its identity?
Q3) Describe four major functions of DNA in a cell.
Q4) In the 1860s,a Swiss chemist,Friedrich Miescher,isolated an acidic substance from cell nuclei.What was the name of this substance,and what was its significance?
Q5) What was the Avery et al.(1944)contribution to the understanding of molecular biology?
Q6) Deoxyribonuclease is an enzyme that adds 3 -hydroxyl groups to RNA.
A)True
B)False
Q7) All other factors being equal,the renaturation of the three classes of complementary nucleic acid sequences occurs in what order,from fastest to slowest?
Q8) What does it mean to say that double-stranded nucleic acids are antiparallel?
Page 14
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Chapter 11: DNA Replication and Recombination
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Q1) DNA replication occurs in the 5 to 3 direction; that is,new nucleoside triphosphates are added to the 3 end.
A)True
B)False
Q2) DNA replication in vivo requires a primer with a free 3 end.What molecular species provides this 3 end,and how is it provided?
Q3) Which structural circumstance in DNA sets up the requirement for its semidiscontinuous nature of replication?
Q4) As unwinding of the helix occurs during DNA replication,tension is created ahead of the replication fork.Describe the nature of this tension and state the manner in which this tension is resolved.
Q5) Telomerase is an RNA-containing enzyme that adds telomeric DNA sequences onto the ends of linear chromosomes.
A)True B)False
Q6) What term is used to describe genetic exchange at equivalent positions along two chromosomes with substantial DNA sequence homology?
Q7) Describe the function of the RecA protein.
Page 15
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Chapter 12: DNA Organization in Chromosomes
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Q1) When native chromatin is digested with micrococcal nuclease,what significant result occurs?
Q2) Compare and contrast the chromosome structure of viruses,bacteria,and eukaryotes.
Q3) What is unusual about the amino acid composition of histones? How is the function of histones related to the amino acid composition? Of which histones are nucleosomes composed?
Q4) In instances in the eukaryotic genome,DNA sequences represent evolutionary vestiges of duplicated copies of genes.What are such regions called and what are their characteristics?
Q5) In addition to highly repetitive and unique DNA sequences,a third category of DNA sequences exists.What is it called,and what types of elements are involved in it?
A) composite DNA; telomeres and heterochromatin
B) dominant DNA; euchromatin and heterochromatin
C) multiple gene family DNA; hemoglobin and 5.0S RNA
D) moderately repetitive DNA; SINEs, LINEs, and VNTRs
E) permissive DNA; centromeres and heterochromatin
Q6) How does a polytene chromosome differ from a typical eukaryotic chromosome?
Q7) Describe the chromosomal conformations of X174 and polyomaviruses.
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Chapter 13: The Genetic Code and Transcription
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Q1) A 5 -cap describes the addition of a base,usually thymine,to the 5 end of a completed peptide.
A)True
B)False
Q2) It has been recently determined that the gene for Duchenne muscular dystrophy (DMD)is more than 2000 kb (kilobases)in length; however,the mRNA produced by this gene is only about 14 kb long.What is a likely cause of this discrepancy?
A) The exons have been spliced out during mRNA processing.
B) The DNA represents a double-stranded structure, whereas the RNA is single-stranded.
C) There are more amino acids coded for by the DNA than by the mRNA.
D) The introns have been spliced out during mRNA processing.
E) When the mRNA is produced, it is highly folded and therefore less long.
Q3) A base at the first position of an anticodon on the tRNA would pair with a base at the ________ position of the mRNA.
Q4) Describe the direction of information flow in living systems.Use appropriate,scientific terms in your description.
Q5) What is a nonsense mutation?
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Chapter 14: Translation and Proteins
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Q1) Describe each of the following parameters that relate to the structure and function of tRNA:
(a) four functional domains
(b) Wobble hypothesis
Q2) Which class of protein functions primarily by lowering the energy of activation during a reaction?
Q3) Below are several phenomena relating to protein structure.Clearly describe each phenomenon,the conditions under which each occurs,and the probable influence each has on protein structure.
(a) hydrophobic interactions
(b) hydrogen bonds
(c) disulfide bridges
Q4) The primary structure of a protein is composed of the sequence of amino acids in that protein.
A)True
B)False
Q5) Electrophoretic separation of HbA from HbS is based on a difference in their
Q6) What are polyribosomes?
Q7) What is the structure of fetal hemoglobin (HbF)?
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Chapter 15: Gene Mutation,dna Repair,and Transposition
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Q1) Under which condition(s)might one have an amino acid substitution in a protein that does not result in an altered phenotype?
Q2) All insertion sequences (IS elements)contain two structural elements that are essential for their movement.What are these two elements?
A) transposase and inverted terminal repeats
B) integrase and pseudogenes
C) integrase and oncogenes
D) proto-oncogenes and oncogenes
E) transposase and oncogenes
Q3) Describe the action of the enzyme transposase.
Q4) Under certain conditions,the rate of mutation of a particular gene may be determined in humans.What three properties of the mutation would favor the most direct determination of mutation rate in humans?
Q5) When treating an organism with a mutagen,although it is possible that homozygous mutations will occur,it is more likely that most new mutations will be heterozygous or hemizygous.
A)True
B)False
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Chapter 16: Regulation of Gene Expression in Prokaryotes
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Q1) Monod discovered that if tryptophan is present in relatively high quantities in the growth medium,the enzymes necessary for its synthesis are repressed.How does this occur?
Q2) Regarding the lactose utilization system in E.coli,a gratuitous inducer is a molecule that is chemically analogous to lactose and induces the operon,but is not a substrate for the enzymes of the lac operon.
A)True
B)False
Q3) Regarding regulation of the trp operon,what might one appropriately call the amino acid tryptophan?
Q4) Certain mutations in the regulator gene of the lac system in E.coli result in maximal synthesis of the lac proteins ( -galactosidase,etc.)even in the absence of the inducer (lactose).Provide an explanation for this observation.
Q5) Attenuation is known to occur in the lac operon.
A)True
B)False
Q6) What is an allosteric molecule?
Q7) What is the function of the lacY gene in the lac operon?
Q8) Present an overview of prokaryotic regulation in terms of growth efficiency.
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Chapter 17: Regulation of Gene Expression in Eukaryotes
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Q1) Two modular elements that appear as consensus sequences upstream from RNA polymerase II transcription start sites are ________.
A) microsatellites and transposons
B) rDNA and nucleolar organizers
C) TATA and CAAT
D) TTAA and CCTT
E) enhancers and telomeres
Q2) One of the earliest steps in the RNAi pathway involves the association of siRNA or miRNA molecules with an enzyme complex composed mainly of reverse transcriptase.
A)True
B)False
Q3) The term spliceopathy would be a reasonable term to signify a genetic condition caused by a defect in the regulation of RNA splicing.
A)True
B)False
Q4) Transcription factors appear to be important molecules relating to the regulation of gene activity.Two general classes of transcription factors exist in eukaryotes.Briefly describe each.
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Chapter 18: Developmental Genetics
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Q1) During development,many genes act in such a way as to decrease the number of alternative developmental pathways that a cell can follow.Usually there are two alternative developmental paths for a cell to follow.What is the term given to genes that act in this fashion?
Q2) Experiments involving nuclear transplantation in amphibians indicate that nuclei derived from blastula are more likely to support development of complete and normal adults compared with those derived from later stages of development.What do these experiments tell us about the process of development?
Q3) How does determination relate temporally to differentiation?
Q4) In Drosophila,maternal-effect genes are influential in determining the anterior-posterior organization of the developing embryo.
A)True
B)False
Q5) Which class of genes controls the developmental identity of segments along the anterior-posterior axis?
Q6) What kinds of general observations cause one to conclude that development is the result of variable gene activity?
Q7) In Drosophila,what is the order of function of the segmentation genes?
Page 22
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Chapter 19: Cancer and Regulation of the Cell Cycle
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Q1) The gene p53 is called the "guardian of the genome" because it corrects mutations in the spindle apparatus before nondisjunction can occur.
A)True
B)False
Q2) Much has been written about p53 in terms of cancer biology.What is p53,and what is its significance?
Q3) List at least three environmental agents or factors that are known to cause cancer.
Q4) Which three stages or transitions in the cell cycle seem to serve as points of control (checkpoints)?
Q5) Provide a simple definition of a carcinogen.
Q6) A tumor-suppressor gene normally functions to suppress cell division. A)True
B)False
Q7) Why do cancer researchers study molecular events associated with mitosis?
Q8) If someone has a predisposition to cancer,what genetic circumstance likely exists?
Q9) What is the significance of CDK?
Q10) Describe the general relationship that may exist between mutations and cancer.
Page 23
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Chapter 20: Recombinant DNA Technology
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Q1) Restriction endonucleases typically recognize palindromic DNA sequences and often generate "sticky ends" or single-stranded DNA overhangs at cut sites.
A)True
B)False
Q2) What might be a reasonable function of restriction endonucleases in a bacterium,distinct from their use by molecular biologists?
Q3) In the context of molecular genetics,reverse transcription PCR (RT-PCR)refers to ________.
A) assembling a DNA sequence from an mRNA
B) assembling an RNA sequence from a DNA sequence
C) translating in the 3 to 5 direction
D) transcribing first, then translating
E) making an amino acid sequence from a DNA sequence
Q4) In a typical PCR,primers are used to cleave specific regions of the DNA template.
A)True
B)False
Q5) What is the fundamental purpose of creating a knockout organism?
Q6) Name at least two typical characteristics of a DNA cloning plasmid?
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Chapter 21: Genomics, bioinformatics, and Proteomics
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Q1) What is ELSI?
Q2) What appears to be the range of the number of protein-coding genes per genome in eukaryotes?
Q3) Explain the goal of the emerging discipline called systems biology.
Q4) What is comparative genomics?
Q5) In humans,no genes are larger than 2 kb.
A)True
B)False
Q6) What is meant by the term low gene density? Give an example of an organism with low gene density.
Q7) What is meant by the term pseudogene?
Q8) Present a general definition for a multigene family and how it relates to a superfamily.
Q9) Intron frequency varies considerably among eukaryotes.Provide a general comparison of intron frequencies in yeast and humans.What about intron size?
Q10) The dog (Canis familiaris)genome has recently been sequenced.About how many of the dog's genes are shared with humans?
Page 25
Q11) Present an overview of the gene organization in large-genome plants.
Q12) Describe the organization of the -globin gene in humans.
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Chapter 22: Applications and Ethics of Genetic Engineering and Biotechnology
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Q1) What term is used to describe the new field engaged to producing more specific,effective and personally customized drugs?
Q2) Describe the structure of a DNA microarray and its use.
Q3) How are gene therapy and recombinant DNA technology related?
Q4) The Genetic Testing Registry is designed to restrict public access to a variety of genetic processes.
A)True B)False
Q5) Direct-to-consumer provides an accurate assessment of physiological and behavioral circumstances within patients that will eventually replace the need for routine visits to the doctor.
A)True B)False
Q6) How is a microarray used to scan for mutations in a genome?
Q7) Amniocentesis is preferred over chorionic villus sampling because recombinant DNA screening can be achieved with amniocentesis but not with chorionic villus sampling.
A)True B)False
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Chapter 23: Quantitative Genetics and Multifactorial Traits
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Q1) Name two human traits that would be expected to have high concordance.
Q2) We often refer to the host of genetic factors in the genome that have an influence on a particular gene's expression as its genetic background.What influence does genetic background have over the phenotype of the organism?
Q3) Typically,one thinks of identical (MZ)twins being genetically identical.However,genomic differences do exist between MZ twins by epigenetic processes.What are epigenetic processes?
Q4) What are QTLs and RFLPs?
Q5) As used in twin studies in mammals,distinguish between the terms concordant and discordant.
Q6) Additive alleles are those that are epistatic over nonallelic genes that influence the same phenotypic characteristic.
A)True
B)False
Q7) Polygenes are involved in determining continuously varying or multiple-factor traits.
A)True
B)False
Q8) Name the three components of phenotypic variance.
Page 28
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Chapter 24: Neurogenetics
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Q1) What is the biochemical role of adenyl cyclase?
Q2) Huntington disease (HD)is a well-studied,autosomal dominant disorder that affects the nervous system.Symptoms usually appear after age 40,and victims usually die within 10 to 15 years after onset of the disease.It appears that at least in some cases of HD,"stutter" mutations occur.Such mutations are characterized by ________.
A) uncontrolled verbal capacity of patients
B) extra trinucleotide repeats within the HD gene
C) RNA polymerase imperfections leading to altered DNAs
D) repeated DNA polymerases generating too many coding symbols
E) links between monoamine oxidase A (MAOA) and hexokinase
Q3) Research on alcoholism indicates that at least in mouse and animal models,a single dominant gene is responsible.
A)True
B)False
Q4) Individuals with Huntington disease have a point mutation in a gene coding for the p53 protein.
A)True
B)False
Q5) Why is cyclic AMP considered important in behavioral studies?
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Chapter 25: Population and Evolutionary Genetics
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Q1) In directional selection,both phenotypic extremes are equally selected against.
A)True
B)False
Q2) Migration occurs when individuals move between populations.Considering a single pair of alleles,A and a,what formula is used to indicate the new frequency of A in one generation of migration?
Q3) What single event is probably common to all occurrences of speciation?
Q4) Evolution is dependent on genetic diversity in the evolving population.
A)True
B)False
Q5) What are the genetic consequences of inbreeding?
Q6) Assume that in a Hardy-Weinberg population,9% of the individuals are of the homozygous recessive phenotype.What percentage are homozygous dominant?
Q7) Natural selection occurs when there is nonrandom elimination of genotypes from a population due to differences in viability or reproductive success.
A)True
B)False
Q8) Contrast directional and stabilizing forms of selection.
Page 30
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