Study Guide Lec 16

Question 1

A ___ map locates genes or markers based on genetic recombination frequencies.

Answer 1

genetic

Question 2

A ___ map locates genes or markers based on the physical length of DNA sequence

Answer 2

physical

Question 3

Because recombination frequencies vary from one region of the chromosome to another, ____ maps are approximate.

Answer 3

genetic

Question 4

Which maps have lower resolution and why?

Answer 4

genetic maps because recombination is difficult to observe between loci that are very close to each other.

Question 5

True or false?
Physical maps based on DNA sequences or restriction maps have much greater accuracy and resolution, down to a single base pair of DNA sequence.

Answer 5

true

Question 6

The following concerns are regarding what:
Ethical concerns arise about the privacy of an individual person’s genetic information and how such information will be used. If an individual’s genome can be sequenced, and polymorphisms associated with risks for genetic diseases or traits considered undesirable by some segments of society, will such information be used to discriminate against these individuals, deny them health insurance, or limit their opportunities for certain careers? The Genetic Information Nondiscrimination Act addresses some of these concerns by prohibiting employers and health insurers from using genetic information as the basis for employment and health insurance decisions. Other issues remain on the table. How will this information, even if kept private, affect people’s reproductive choices? How will genetic testing applied to the unborn (embryos fertilized in vitro or prenatal screening of fetuses) affect people’s decisions about whether to have children and what kinds of children to have? Ultimately, will such information lead people to have “designer” babies, or select those embryos with desirable traits? Given that genes interact with each other and the environment, and complex interactions lead to incomplete penetrance and expressivity, will people receive adequate counseling to properly interpret their genetic profiles?

Answer 6

Human Genome Project

Question 7

What is a SNP?

Answer 7

single base-pair differences in the sequence of a particular region of DNA from one individual compared to another of the same species or population

Question 8

How are SNPs used in genomic studies?

Answer 8

as molecular markers for mapping and pedigree analysis and may themselves be associated with phenotypic differences.

Question 9

A _____ is a particular set of neighboring SNPs or other DNA polymorphisms observed on a single chromosome or chromosome region.

Answer 9

haplotype

Question 10

How do haplotypes arise?

Answer 10

They tend to be inherited together as a set because of linkage. Meiotic recombination within the chromosomal region can split the haplotype and create new recombinant haplotypes.

Question 11

What is linkage disequilibrium?

Answer 11

Linkage disequilibrium is the association of certain genetic variants (alleles) with each other via linkage on the same chromosome, so that these allelic combinations occur more frequently in the population than expected based on random assortment.

Question 12

How does linkage disequilibrium result in haplotypes?

Answer 12

Distinct haplotypes occur because modern human populations have not undergone enough recombination to thoroughly shuffle the allelic combinations.

Question 13

___ ___ variation is the occurrence of more or less than the usual diploid copy number for a DNA sequence of longer than 1000 bp.

Answer 13

Copy number

Question 14

How does copy-number variation arise?

Answer 14

Such copy number variations could arise through deletion or duplication of a segment of chromosomal DNA.

Question 15

Computer algorithms (and humans) recognize or predict genes within genomic sequences by analysis of what?

Answer 15

(1) The presence of matching cDNA or EST sequences in a database
(2) Open reading frames (ORFs)
(3) Sequences characteristic of promoters upstream of a start codon of an open reading frame
(4) Homology (sequence similarity) to previously characterized genes in the same or other species

Question 16

_____ are sequences in different species that are descended from a sequence in a common ancestral species. _____ are sequences in the same species that originated by duplication of an ancestral sequence and subsequently diverged

Answer 16

Orthologs; paralogs

Question 17

Homologous sequences are derived from what?

Answer 17

a common ancestor

Question 18

Name the following method for inferring the function of a gene by examining DNA sequence:
For protein-coding genes, the DNA sequence is translated conceptually into the amino acid sequence of the protein. The amino acid sequence of the protein then may yield clues to its function if it is similar to another protein of known function. For example, it is quite easy to recognize histones because their amino acid sequences are highly conserved among eukaryotes. Even if the whole protein is not similar, it may have regions, or domains, that are similar to other domains with known functions or properties. Finally, the amino acid sequence may contain small motifs or signatures that are characteristic of proteins with certain enzymatic activities or properties or subcellular localizations.

Answer 18

homology and sequence similarity

Question 19

Name the following method for inferring the function of a gene by examining DNA sequence:
The coordinated absence or presence of clusters of genes in various species implies that the genes in the cluster have related functions. For example, genes required for nitrogen fixation would all be present in nitrogen-fixing species but absent in other species.

Answer 19

phylogenetic profile

Question 20

Name the following method for inferring the function of a gene by examining DNA sequence:
In some species, genes of related function have undergone a fusion event to form a single multifunctional polyprotein. Then similar but separate component genes in other species can be presumed to have similar functions.

Answer 20

Gene fusions

Question 21

Name the following method for inferring the function of a gene by examining DNA sequence:
In bacteria, genes in metabolic or functional pathways are often clustered together into an operon. Therefore, all the genes that are co-transcribed into a single polycistronic mRNA should have related functions.

Answer 21

Gene clusters or operons

Question 22

A _____ consists of thousands of DNA fragments spotted onto glass slides in an ordered grid (gene chips) or even proteins or peptides arrayed onto glass slides (protein chips). The identity of the DNA or peptide at each location is known.

Answer 22

microarray

Question 23

How are microarray gene chips used to obtain information about gene function?

Answer 23

Gene chips are typically used in hybridization experiments with labeled mRNAs or cDNAs to survey the levels of transcript accumulation for thousands of genes, or even whole genomes, at one time. Peptide or protein chips can be used to identify protein-protein interactions or enzymatic activities or other properties of proteins.

Question 24

Explain how a reporter sequence can be used to provide information about the expression pattern of a gene.

Answer 24

A reporter sequence is fused to a gene in such a way that the native gene regulatory sequences drive expression of the recombinant gene: reporter fusion product. Typically, a segment of genomic DNA that includes the upstream promoter region and other cis-acting regulatory sequences is ligated to the reporter gene sequence. This construct may then be used to create a transgenic organism expressing the recombinant reporter gene fusion. The reporter may have enzymatic activity (like β- galactosidase) that is detectable with a substrate that forms a colored product, or with an antibody to the reporter protein, or the reporter may itself be fluorescent (like green fluorescent protein). The gene’s own regulatory sequences specify the developmental pattern of expression of the reporter as they would the native gene. If the protein-coding region of the gene is also included, in part or in full, the resulting translational fusion product can be used to study the subcellular localization of the protein.

Question 25

Briefly outline how a mutagenesis screen is carried out.

Answer 25

After random mutagenesis with chemicals or transposons, the mutant progeny are screened for phenotypes of interest. The mutant gene can be identified by cosegregation with molecular markers or by sequencing the position of transposon insertion. To verify that the mutation identified is truly responsible for the phenotype, the same mutation can be introduced into a wild-type copy of the gene via site-directed mutagenesis and the phenotype observed in the offspring.

Question 26

DNA content varies considerably among different multicellular organisms. Is this variation closely related to the number of genes and the complexity of the organism? If not, what accounts for some of these differences?

Answer 26

The “complexity” of an organism is not well-defined and thus difficult to quantify. DNA content can vary widely among related species, so there appears to be little relation between the “complexity” of an organism, the number of genes, and the DNA content. Large differences in DNA content may arise from differences in the frequency and size of introns, the abundance of DNA derived from transposable elements, and duplication of the whole or substantial parts of the genome in the evolutionary history of the species.

Question 27

A duplication involving a relatively large (greater than 1000 bp) stretch of chromosomal DNA sequence is called what?

Answer 27

segmental duplication

Question 28

The human genome does not encode substantially more protein domains than do invertebrate genomes, yet it encodes many more proteins. How are more proteins encoded when the number of domains does not differ substantially?

Answer 28

The human genome contains proteins with many more combinations of domains, often featuring multiple domains on a single protein.

Question 29

____ is the study of the content, organization, function, operation, and evolution of whole genomes.

Answer 29

genomics

Question 30

how does structural genomics differ from functional genomics?

Answer 30

Structural genomics deals largely with the DNA sequence itself and its physical organization; functional genomics deals largely with the functions of the sequences in the genome, through RNA or protein molecules.

Question 31

_____ genomics analyzes the similarities and differences among genomes to achieve insights into genomic or organismal evolution or relationships between groups of genes and physiological functions.

Answer 31

comparative

Question 32

How does proteomics differ from genomics?

Answer 32

Whereas genomics is the analysis of whole genome DNA sequences and their organization, expression, and function, proteomics focuses on the complete set of proteins made by an organism. Unlike the genome, which is constant from cell to cell, the proteome varies within a species from cell type to cell type, with stage of development, and with time in response to signals and other environmental stimuli. Proteins also undergo numerous modifications that affect protein localization and function.