Deck 19: Genomics and Proteomics

Question 1

Both genetic and physical maps provide information about the relative positions and distances between genes, molecular markers, and chromosome segments. Genetic maps are based on rates of recombination and are measured in percent recombination, or centimorgans. Physical maps are based on physical distances and are measured in base pairs.
-What are some of the limitations of genetic maps?

Answer 1

Accuracy and resolution

Question 2

Sequencing a genome requires breaking it up into small overlapping fragments of which the DNA sequences can be determined in a sequencing reaction. In map-based sequencing, sequenced fragments are ordered into the final genome sequence with the use of genetic and physical maps. In whole-genome shotgun sequencing, the genome is assembled by comparing overlap in the sequences of small fragments.

-A contig is

A) a set of molecular markers used in genetic mapping.
B) a set of overlapping fragments that form a continuous stretch of DNA.
C) a set of fragments generated by a restriction enzyme.
D) a small DNA fragment used in sequencing.

Answer 2

a set of overlapping fragments that form a continuous stretch of DNA.

Question 3

In addition to collecting genomic-sequence data, genomic projects are collecting databases of nucleotides that vary among individual organisms (single-nucleotide polymorphisms, SNPs), variations in the number of copies of sequences (copy-number variations), and markers associated with transcribed sequences (expressed-sequence tags, ETSs).
-What was the goal of the HapMap Project?

Answer 3

To catalog and map SNPs and other human genetic variants

Question 4

Bioinformatics is a interdisciplinary field that combines molecular biology and computer science. It develops databases of DNA and protein sequences and tools for analyzing those sequences.

-The ab initio approach finds genes by looking for

A) common sequences found in most genes.
B) similarity in sequence with known genes.
C) mRNA with the use of in situ hybridization.
D) mutant phenotypes

Question 5

The function of an unknown gene can sometimes be determined by finding genes with similar sequence whose function is known. A gene's function may also be determined by identifying functional domains in the protein that it encodes.

-What is the difference between orthologs and paralogs?

A) Orthologs are homologous sequences; paralogs are analogous sequences.
B) Orthologs are more similar than paralogs.
C) Orthologs are in the same organism; paralogs are in different organisms.
D) Orthologs are in different organisms; paralogs are in the same organism.

Question 6

Genomewide mutagenesis screening coupled with positional cloning can be used to identify genes that affect a specific characteristic or function.

-Which is the correct order of steps in a mutagenesis screen?

A) Positional cloning, mutagenesis, identification of mutants, verification of genetic basis.
B) Mutagenesis, positional cloning, identification of mutants, verification of genetic basis.
C) Mutagenesis, identification of mutants, verification of genetic basis, positional cloning.
D) Identification of mutants, positional cloning, mutagenesis, verification of genetic basis.

Question 7

Comparative genomics compares the content and organization of whole genomic sequences from different organisms. Prokaryotic genomes are small, usually ranging from 1 million to 3 million base pairs of DNA, with several thousand genes. Prokaryotes with the smallest genomes tend to occupy restricted habitats, whereas those with the largest genomes are usually found in complex environments. Horizontal gene transfer has played a major role in bacterial genome evolution.
-What is the relation between genome size and gene number in prokaryotes?

Question 8

Genome size varies greatly among eukaryotic species. For multicellular eukaryotic organisms, there is no clear relation between organismal complexity and amount of DNA or gene number. A substantial part of the genome in eukaryotic organisms consists of repetitive DNA, much of which is derived from transposable elements. Vast regions of DNA may contain no genes or other functional sequences. Many eukaryotic genomes have homologous genes in common, and genes are often in the same order in the genomes of related organisms.

-Segmental duplications play an important role in evolution by

A) giving rise to new genes and multigene families.
B) keeping the number of genes in a genome constant.
C) eliminating repetitive sequences produced by transposition.
D) controlling the base content of the genome

Question 9

The proteome is the complete set of proteins found in a cell. Techniques of protein separation and mass spectrometry are used to identify the proteins present within a cell. Affinity capture and microarrays are used to determine sets of interacting proteins. Structural proteomics attempts to determine the structure of all proteins.
-Why is knowledge of a protein's structure important?