Chapter 15: Genomics and Proteomics

Question 1

What are omics?

Answer 1

• Field of biology aims at the collective characterization and qualification of pools of biological molecules that translate into the structure, function, and dynamics of an organism
• Large-scale

Question 2

What are genomics?

Answer 2

Attempts to understand the content, organization, function, and evolution of the genetic information contained in whole genomes

Question 3

What are genetic maps?

Answer 3

• Rough approximation of the locations of genes relative to the locations of other known genes
• Based on the genetic process of recombination

Question 4

What are physical maps?

Answer 4

Based on the direct analysis of DNA (physical distance measured in base pairs)

Question 5

How are distances on a genetic map measured?

Answer 5

CentiMorgans

Question 6

What was the first free-living organism to be sequenced?

Answer 6

The bacteria Haemophilas

Question 7

How do physical maps compare to genetic maps?

Answer 7

Physical maps generally have a higher resolution and are more accurate than genetic maps

Question 8

What are collinear relationships?

Answer 8

• Comparing a genome with little known information to other genomes helps determine their origins, and their genomic characteristics
• Concerns species that are linked in evolution
• Many genes are present in the same order in related genomes

Question 9

Provide an example of a collinear relationship.

Answer 9

• Rice was compared to Brachypodium, which was then used to uncover characteristics about Sorghum
• Sorghum was difficult to characterize

Question 10

What are homologous sequences?

Answer 10

Sequences that are evolutionarily related

Question 11

What are orthologs?

Answer 11

Homologous sequences found in different species

Question 12

What are paralogs?

Answer 12

Homologous genes in the same species that arise from gene duplication

Question 13

What were the overall steps to determining the human genome?

Answer 13

1) Map-based sequencing
2) Flow cytometry
3) Partial digestion of each chromosome
4) DNA fragments are cloned
5) Large-insert clones are put together in the correct order based on their overlapping features

Question 14

What is map-based sequencing?

Answer 14

• Short sequenced fragments are assembled into a whole-genome sequence
• By first creating detailed genetic and physical maps of the genome, which provide known locations of genetic markers at regularly spaced intervals
• These markers are later used to help align the short sequenced fragments in the correct order

Question 15

What is flow cytometry?

Answer 15

Used to separate individual chromosomes from a single unique cell

Question 16

What is partial digestion?

Answer 16

• Restriction enzymes are allowed to act for only a limited time
• Produces a set of large overlapping DNA fragments

Question 17

What is a contig?

Answer 17

A set of two or more overlapping DNA fragments that form a contiguous stretch of DNA

Question 18

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 18

B) A set of overlapping fragments that form a continuous stretch of DNA

Question 19

What is whole-genome shotgun sequencing?

Answer 19

The entire genome is assembled based on sequence overlap

Question 20

What is a single-nucleotide polymorphism?

Answer 20

A site in the genome at which individual members of a species differ in a single base pair

Question 21

What is a haplotype?

Answer 21

• The specific set of SNPs and other genetic variants observed on a single chromosome or part of a chromosome
• Each haplotype is made up of a particular set of alleles at each SNP

Question 22

Why are SNPs used as a marker for linkage studies in diseased states?

Answer 22

• When a SNP is physically close to a disease-causing locus, it will tend to be inherited along with the disease-causing allele
• People with a diseased tend to have different SNPs than healthy people

Question 23

How do SNPs compare to RFLPs?

Answer 23

There are many more SNPs, providing a dense set of variable markers covering the entire genome

Question 24

What is the transcriptome?

Answer 24

All the RNA molecules transcribed from a genome

Question 25

What are microarrays?

Answer 25

Rely on nucleic acid hybridization, in which a known DNA fragment is used as a probe to find complementary sequences

Question 26

What information can microarrays provide?

Answer 26

• Information about gene expression (which RNA molecules are synthesized)
• How gene expression changes in the course of biological processes (development, or disease)

Question 27

What do red and green fluorescence indicate in microarrays?

Answer 27

• Red: overexpression of a gene in a cancer cell

- Green: overexpression of a gene in a non-cancer cell

Question 28

What is mass spectrometry used for?

Answer 28

Method to determine the precise molecular mass of a molecule

Question 29

Mass spectrometry separates molecules on the basis of their _________ ratio

Answer 29

mass-to-charge

Question 30

What are the dimensions of two-dimensional acrylamide gel electrophoresis?

Answer 30

• One dimension separates based on charge

- Another dimension separates based on mass

Question 31

What method may be utilized to analyze protein-protein interactions?

Answer 31

Protein microarrays

Question 32

What are some of the limitations of genetic maps?

Answer 32

Accuracy and resolution

Question 33

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.

Answer 33

D) Orthologs are in different organisms; paralogs are in the same organism.