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Genomics is an interdisciplinary field that focuses on the structure, function, evolution, mapping, and editing of genomes the complete set of DNA within a single cell of an organism. This course provides a comprehensive overview of the key principles and technologies in genomics, including genome sequencing, analysis, annotation, and comparative genomics. Students will explore applications of genomics in medicine, agriculture, and biotechnology, and will learn how computational tools and bioinformatics are used to interpret complex genomic data. Emphasis is placed on current advances, ethical considerations, and the potential impact of genomics on society.
Recommended Textbook
Concepts of Genetics Books a la Carte Edition 11th Edition by William S. Klug
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Q1) Until the mid-1940s,many scientists considered proteins to be the likely candidates for the genetic material.Why?
Answer: Proteins are the most abundant,universally distributed components in cells.They were considered likely candidates because of their great structural and functional diversity.
Q2) Bioinformatics is a discipline involved in the development of both hardware and software for processing,storing,and retrieving nucleotide and protein data.
A)True
B)False
Answer: True
Q3) Name one of the botanists who,in 1900,rediscovered the work of Gregor Mendel.
Answer: Carl Correns,Hugo de Vries,Erich Tschermak
Q4) What term is applied to a variety of projects whereby genome sequences are deposited in databases for research purposes?
Answer: genomics
Q5) Alternative forms of a gene are called ________.
Answer: alleles
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Q1) The horse (Equus caballus)has 32 pairs of chromosomes,whereas the donkey (Equus asinus)has 31 pairs of chromosomes.How many chromosomes would be expected in the somatic tissue of a mule?
Answer: 63
Q2) What hypothesis concerns the evolutionary origin of eukaryotic organelles?
A) endosymbiont hypothesis
B) homologous hypothesis
C) analogous hypothesis
D) evolutionary hypothesis
E) Darwinian hypothesis
Answer: A
Q3) Two terms,reductional and equational,generally refer to which stages of meiosis (I or II)?
Answer: meiosis I and meiosis II,respectively
Q4) A bivalent at pachytene contains four chromatids.
A)True
B)False
Answer: True
Q5) What is meant by the term chiasma?
Answer: areas where chromatids intertwine during meiosis
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Q1) 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
Q2) 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 child will be an albino girl?
Answer: 1/4 × 1/2 = 1/8
Q3) The nonfunctional form of a gene is called a wild-type allele.
A)True
B)False
Answer: False
Q4) 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
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Q1) Pattern baldness and hen/cock feathering in fowl are examples of X-linked inheritance.
A)True
B)False
Q2) Assume that a dihybrid cross (AaBb × AaBb)is made in which the gene loci are autosomal,independently assorting,and incompletely dominant.What phenotypic ratio would you expect from such a cross? Just provide the ratio,not the phenotypes.
Q3) With both incomplete dominance and codominance,one expects heterozygous and homozygous classes to be phenotypically identical.
A)True
B)False
Q4) A 9:7 ratio indicates incomplete dominance.
A)True
B)False
Q5) A typical epistatic ratio is 9:3:4. A)True
B)False
Q6) How many different alleles can a gene have?
Q7) Name three modes of inheritance that are influenced by the sex of individuals.
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Q1) Positive interference occurs when a crossover in one region of a chromosome reduces crossovers in nearby regions.
A)True
B)False
Q2) What two terms apply to the fusion of cultured human and mouse cells that produces cell lines that are useful in assigning a gene to a particular human chromosome?
A) forward and reverse
B) lod score and pod score
C) heterokaryon and synkaryon
D) single and double
E) positive and negative
Q3) Restriction fragment length polymorphisms (RFLPs),microsatellites,and single-nucleotide polymorphisms (SNPs)were used by Morgan and Sturtevant to discover linkage in Drosophila.
A)True
B)False
Q4) What are two commonly used DNA landmarks for mapping human genes?
Q5) If interference is complete,what would be the frequency of double crossovers?
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Q6) Provide a brief definition for positive interference.
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Q1) What are the roles of the recBCD genes?
Q2) Compare and contrast bacteriophage lysis and lysogeny.
Q3) What is a merozygote?
Q4) An Hfr cell can initiate chromosome transfer from one E.coli to another.
A)True
B)False
Q5) A symbiotic relationship between a phage and a bacterium apparently occurs in the process of lysogeny.
A)True
B)False
Q6) R plasmids often contain genes for antibody production.
A)True
B)False
Q7) Lysogeny is most likely associated with transduction.
A)True
B)False

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Q8) Cotransduction of genes is an indication that the genes are linked.
A)True
B)False
Q9) What is a form of recombination in bacteria that involves the F plasmid?
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Q1) Normally in humans,all the sons of a male showing a sex-linked phenotype will inherit the trait.
A)True
B)False
Q2) Although triple-X human females typically have normal offspring,what kinds of gametes,with respect to the X chromosomes,would you expect from such XXX females? Draw meiotic stages that show the gametes that are expected to be produced.
Q3) Give the sex of the following organisms assuming that the autosomes are present in the normal number.
\(\begin{array}{lll}
\text {Sex Chromosome } && \text {Organism } \\
\text { Complement } & \text {Humans } & \text { Drosophila } \\
\hline \text { XX } & \underline { \quad\quad\quad}& \underline { \quad\quad\quad} \\
\text { XY } & \underline { \quad\quad\quad} & \underline { \quad\quad\quad} \\
\text { XO } & \underline { \quad\quad\quad} & \underline { \quad\quad\quad} \\
\text { XXX } & \underline { \quad\quad\quad} & \underline { \quad\quad\quad} \\
\text { XXY } & \underline { \quad\quad\quad}& \underline { \quad\quad\quad}
\end{array}\)
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Q1) Although the most frequent forms of Down syndrome are caused by a random error,nondisjunction of chromosome 21,Down syndrome occasionally runs in families.The cause of this form of familial Down syndrome is ________.
A) an inversion involving chromosome 21
B) a chromosomal aberration involving chromosome 1
C) too many X chromosomes
D) a translocation between chromosome 21 and a member of the D chromosome group
E) a maternal age effect
Q2) Familial Down syndrome is caused by a translocation involving chromosome 21.
A)True
B)False
Q3) 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
Q4) Describe Bar mutations in Drosophila melanogaster.
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Q1) Kearns-Sayre syndrome (KSS)results in progressive loss of vision and hearing,as well as heart defects.What is the genetic basis for this disease?
Q2) What is the expression pattern of dominant-negative mutations in petite strains of yeast?
A) Expression of wild-type mitochondria is enhanced.
B) Expression of mutant mitochondria resembles expression of wild-type mitochondria.
C) Mitochondria show enhanced capacity of oxidative phosphorylation.
D) The function of wild-type mitochondria is suppressed.
E) Mitochondrial membranes become hyperpolarized.
Q3) What is the meaning of the term endosymbiotic theory?
Q4) 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
Q5) An example of organelle heredity involves pigmentation in Mirabilis jalapa.
A)True
B)False
Q6) List three organisms that provide examples of organelle heredity.
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Q1) Reverse transcriptase is an enzyme found in association with retroviral activity.It has the property of ________.
A) synthesis of DNA from an RNA template
B) synthesis of RNA from a DNA template
C) requiring no template
D) translation
E) most lysozymes
Q2) List two major differences between RNA and DNA at the level of the nucleotide.
Q3) Regarding the structure of DNA,the covalently arranged combination of a deoxyribose and a nitrogenous base would be called a(n)________.
A) nucleotide
B) ribonucleotide
C) monophosphate nucleoside
D) oligonucleotide
E) nucleoside
Q4) What was the Avery et al.(1944)contribution to the understanding of molecular biology?
Q5) What is meant by the term antiparallel?
Q6) What is the name of the precursor molecule used in nucleic acid synthesis?
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Q1) G-quartets are G-rich single-stranded tails that loop back on themselves forming G-G double stranded sections.Such looping is involved in aligning chromosomes for homologous recombination.
A)True
B)False
Q2) Assume that you were growing cells in culture and had determined the cell-cycle time to be 24 hours.You introduce ³H thymidine and prepare autoradiographs of metaphase chromosomes after 48 hours.Of the chromosomes that are labeled,you expect two classes: one class that had completed one S phase in the label,and a second class that had completed a cellular division and an additional S phase in the label.Draw the DNA (double-stranded)labeling pattern for each chromosome that you would expect to find in these two types of metaphase chromosomes.(Use a broken line {- - -} for labeled single strands of DNA and a solid line for unlabeled single strands of DNA.)
(a)metaphase chromosome having replicated once in label
(b)metaphase chromosome having gone through two S phases in label
Q3) Meselson and Stahl determined that DNA replication in E coli is semiconservative.What additive did they initially supply to the medium in order to distinguish "new" from "old" DNA?
Q4) During DNA replication,what is the function of RNA primase?
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Q1) Compare and contrast the chromosome structure of viruses,bacteria,and eukaryotes.
Q2) What similarities do bacterial chromosomes have with eukaryotic chromosomes?
Q3) What are histones,and how are they arranged in nucleosomes?
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) Approximately how much of the mammalian genome is composed of repetitive DNA?
Q6) List the components of a nucleosome.
Q7) In situ hybridization allows one to "visualize" the location of labeled RNA or DNA in a tissue or cell.
A)True B)False
Q8) Telomerase is an enzyme involved in the replication of the ends of eukaryotic chromosomes.
A)True B)False
Q9) List several configurations that characterize different viral chromosomes.
Q10) What is meant by SINE in terms of chromosome structure? By LINE? Why are they Page 15
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Q1) Describe a difference between the RNA polymerases of eukaryotes and prokaryotes.
Q2) The relationship between a gene and a messenger RNA is that ________.
A) genes are made from mRNAs
B) mRNAs are made from genes
C) mRNAs make proteins, which then code for genes
D) all genes are made from mRNAs
E) mRNA is directly responsible for making Okazaki fragments
Q3) Suppose that in the use of polynucleotide phosphorylase,nucleotides A and C are added in a ratio of 1A:5C.What is the probability that an AAA sequence will occur?
Q4) What is one particular function that the codons (UAA,UGA,or UAG)serve during protein synthesis?
A) UAA, UGA, and UAG are initiator codons, not termination codons.
B) They allow the mRNA to assume a variety of linear conformations.
C) These triplets cause frameshift mutations, but are not involved in termination.
D) They provide a substrate for the addition of the initiator amino acid.
E) They act in chain termination.
Q5) Describe the function of N-formylmethionine in prokaryotes.
Q6) What is polycistronic mRNA?
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Q1) The secondary structure of a protein includes ________.
A) gamma and delta
B) alpha and gamma
C) -helix and -pleated sheet
D) hydrophobic clusters
E) disulfide bridges
Q2) What are polyribosomes?
Q3) The one-gene:one-enzyme hypothesis emerged from work on which two organisms?
A) E. coli and yeast
B) Drosophila and humans
C) Neurospora and Drosophila
D) E. coli and humans
E) All of the answers listed are correct.
Q4) The primary structure of a protein is determined by ________.
A) the sequence of amino acids
B) hydrogen bonds formed between the components of the peptide linkage
C) a series of helical domains
D) pleated sheets
E) covalent bonds formed between fibroin residues
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Q5) What is the structure of fetal hemoglobin (HbF)?
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Q1) Assuming one mutational event in a gene,on average,which of the following mutagens or mutational conditions would be expected to cause the most damage to a protein synthesized by such a mutagenized gene: 5-bromouracil,2-amino purine,ethylmethane sulfonate,or frameshift?
Q2) A missense mutation causes premature chain (protein)termination. A)True B)False
Q3) In general,mutation rates in humans occur in the range of ________ (frequency)per gamete per generation.
Q4) Recombinational repair is activated when damaged DNA has escaped repair and the distortion disrupts the process of replication.Which gene is responsible recombinational repair?
Q5) Certain base analogs such as 5-bromouracil cause mutations by chemically altering nitrogenous bases in nonreplicating DNA. A)True B)False
Q6) 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?
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Q1) Attenuation is known to occur in the lac operon.
A)True
B)False
Q2) In the lac operon,the product of structural gene lacZ is capable of ________.
A) nonautonomous replication
B) forming lactose from two glucose molecules
C) replacing hexokinase in the early steps of glycolysis
D) splitting the -linkage of lactose
E) forming ATP from pyruvate
Q3) The trp and lac operons are both subject to forms of control that are typically called negative.
A)True
B)False
Q4) State whether the following statement is true or false,then give your reasoning.The terminating "hairpin" loop occurs in the trp operon when sufficient tryptophan is present.
A)True
B)False
Q5) Present a detailed description of the actions of the regulatory proteins in inducible and repressible enzyme systems.
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Q1) In some cases,genes undergo amplification (local,multiple duplications)when additional gene products are in high demand.Would you consider gene amplification as a form of genetic regulation in eukaryotes? Explain your answer.
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) Channels between chromosomes in the interphase nucleus are called ________.
A) extrachromosomal elements
B) localized zones
C) nonlocalized zones
D) interchromosomal compartments
E) subchromosomal territories
Q4) In what way is gene rearrangement related to gene regulation? Give an example.
Q5) List three general pathways in which eukaryotic mRNA is typically degraded in eukaryotes.
Q6) Describe how nucleosomes may influence gene transcription.
Q7) List at least three levels or types of genetic regulation in eukaryotes.
Q8) What is meant by the term helix-turn-helix (HTH)?
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Q1) Mutations that eliminate a contiguous region in the Drosophila embryo's segmentation pattern are called ________.
A) homeodomains
B) gap genes
C) compartment genes
D) linkage genes
E) segment genes
Q2) It is often said that development is a two-step process.What two steps are likely to be referred to here?
Q3) It is presently believed that the asymmetric distribution of substances in the egg,positioned by the mother,is responsible for establishing the determined state.Which general term describes such molecular positioning?
Q4) Genetic involvement in development appears to be achieved,at least in part,by variable gene activity.
A)True
B)False
Q5) What kinds of general observations cause one to conclude that development is the result of variable gene activity?
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Q1) The retinoblastoma protein (pRB),like p53,serves as a(n)________ in regulating the cell cycle.
A) tumor suppressor
B) tumor enhancer
C) up regulator
D) oncogene
E) pseudooncogene
Q2) The genome of humans is remarkably stable,so much so that there are no cancers known to result from genomic instability.
A)True
B)False
Q3) Chronic myelogenous leukemia appears to be associated with a chromosomal rearrangement.Which chromosome(s)is(are)involved,and what is the name of the rearrangement?
Q4) Provide a definition of cancer at the anatomical level.
Q5) In what way can loss of heterozygosity lead to cancer?
Q6) List three general categories of genetic changes that lead to the formation of oncogenes.
Q7) Describe the molecular nature of mutation,as related to cancer,in a ras gene.
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Q8) Provide a definition of cancer at the genetic level.
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Q1) List,in order,the steps usually followed in producing recombinant DNA molecules in a plasmid vector.
Q2) In general,the main goal of cloning is to include as many different genes as possible in a single cloning vector.
A)True
B)False
Q3) What is a cDNA molecule?
Q4) A ddNTP,used often in DNA sequencing,lacks a(n)________ at the ________ and ________ carbons.
A) OH; 2 ; 3
B) methyl; 2 ; 3
C) carboxyl; 5 ; 3
D) OH; 2 ; 5
E) None of the above is correct.
Q5) What is the specific application of reverse transcriptase in the preparation of cDNA?
Q6) If one wishes to clone a gene using typical restriction endonucleases,how does the restriction endonuclease recognize genes in the genome?
Q7) What is meant by the designation EcoRI?
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Q1) Typically,bacterial DNA contains less repetitive DNA than eukaryotic DNA.
A)True
B)False
Q2) Which two factors contribute significantly to the wide ranges of genome size among eukaryotes?
Q3) Introns are found only in prokaryotic genomes.
A)True B)False
Q4) Describe the relationship between introns (size and number)and organismic complexity in eukaryotes.
Q5) Name the two strategic methods that scientists are using to sequence genomes.
Q6) What is meant by the term low gene density? Give an example of an organism with low gene density.
Q7) Sequencing the dog genome has indicated that a single locus on chromosome 15 may play a major role in genetically distinguishing large dog breeds from small dog breeds.
A)True B)False
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Q8) In what way will the discipline called metagenomics contribute to human health and welfare?

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Q1) There is a fear that preconception genetic testing may lead to "designer babies." What historical practice comes to mind regarding the production of such babies?
Q2) Under strictly controlled conditions,a probe can be used that will hybridize only with its complementary sequence and not with other sequences that may vary by as little as one nucleotide.What are such probes called?
A) generation-specific probes
B) short, variable repeats
C) VNTRs
D) microsatellites
E) allele-specific oligonucleotides (ASOs)
Q3) Can human genes be patented?
Q4) The Genetic Testing Registry is designed to restrict public access to a variety of genetic processes.
A)True
B)False
Q5) Prenatal detection of human diseases has been greatly enhanced by two procedures.Name and briefly describe each.
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Q6) What process is effectively the true test of the functionally synthetic genome?
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Q1) Describe the value of using twins in the study of questions relating to the relative impact of heredity versus environment.
Q2) Quantitative inheritance involves the interaction of a number of gene loci.The pattern of genetic transmission typical of quantitative inheritance is ________.
A) discontinuous distributions such as 3:1
B) typical of Mendelian inheritance
C) continuous variation of phenotypic expression
D) a 9:3:3:1 ratio
E) usually a pattern that clearly reflects dominance and recessiveness
Q3) Provide a brief definition of the terms additive variance,dominance variance,and interactive variance.
Q4) Huntington disease is inherited in humans as an autosomal dominant gene.Affected individuals show progressive brain deterioration from cell death in the cerebral cortex.Onset of the disease usually occurs between ages 30 and 50.Give two possible reasons for the observed variation in the age of onset of this disease.
Q5) What is the term given to a random subset of individuals who are selected for measurement in a particular study?
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Q1) Determining the genetic influence on two fairly common human behavioral disorders has eluded researchers for many years.One involves passive deficits in thinking,language,feelings,and social skills; the other includes a variety of psychotic symptoms,perceptual disorders (hearing voices),and withdrawal from reality.Evidence from pedigrees and twins indicates that these two behaviors have a genetic component.Which behaviors are being described here?
Q2) Drosophila can learn and remember.
A)True
B)False
Q3) In studies attempting to determine a genetic basis for a given behavior,if the environment is held constant,and behavioral differences directly correlate with genetic differences,a genetic basis for the behavioral state is supported.
A)True
B)False
Q4) Much effort has been expended to understand genetic involvement in brain function in Drosophila.Why might this research be important in understanding the functioning of the human brain?
Q5) What is the biochemical role of adenyl cyclase?
Q6) Briefly describe the mutant status of the HD gene.
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Q1) One of the Hardy-Weinberg assumptions states that the population is infinitely large.What influence might a small population size have on a Hardy-Weinberg equilibrium?
Q2) What single event is probably common to all occurrences of speciation?
Q3) Which general term is used to group various biological and behavioral properties of organisms that act to prevent or reduce interbreeding?
A) phyletic evolution
B) allopatric speciation
C) reproductive isolating mechanisms
D) inbreeding
E) genetic divergence
Q4) In large random mating populations,random genetic drift is usually a significant factor in changing gene frequencies.
A)True
B)False
Q5) A certain form of albinism in humans is recessive and autosomal.Assume that 1% of the individuals in a given population are albino.Assuming that the population is in Hardy-Weinberg equilibrium,what percentage of the individuals in this population is expected to be heterozygous?
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