Chapter 20 - Genomics

Question 1

Most scientists expected the genome to code for 100K - 200K genes, but the number is closer to __K. In fact, humans have barely __% more genes than Drosophila; and __ have more genes than humans.

Answer 1

22K.

50%

Grapes

Question 2

The human genome contains three genes for enolase (α, β, γ), whereas yeast contains just one gene for enolase. The three human enolase genes are \_\_ of each other, whereas the human and yeast enolase genes are \_\_ of each other.
A. allelic variants; homologs
B. orthologs; paralogs
C. paralogs; orthologs
D. orthologs; homologs

Answer 2

C. paralogs; orthologs

Question 3

Which of the following is NOT true regarding impacts of the human genome project?
A. It has led to development of more efficient and less expensive sequencing technologies.
B. It has helped identify and locate many genes related to diseases.
C. It has helped scientists understand basic biological processes.
D. It has led to widespread use of genetic tests by health insurers to assess people’s risk of developing disease.
E. Comparing other sequenced genomes to the human genome has helped further our knowledge of evolution.

Answer 3

D. It has led to widespread use of genetic tests by health insurers to assess people’s risk of developing disease.

Question 4

We have discussed several methods for mapping genes. Which of the following is ranked correctly lowest to highest resolution?
A. microsatellites; genetic recombination; restriction fragment length polymorphism (RFLP); SNPs
B. genetic recombination; restriction fragment length polymorphism (RFLP); microsatellites; SNPs
C. SNPs; genetic recombination; restriction fragment length polymorphism (RFLP); microsatellites
D. restriction fragment length polymorphism (RFLP); genetic recombination; microsatellites; SNPs
E. All of the above have similar levels of resolution.

Answer 4

B. genetic recombination; restriction fragment length polymorphism (RFLP); microsatellites; SNPs

Question 5

What is the rational for studying non-primate animals and applying knowledge to humans?

Answer 5

Humans share genetic homology with other animals.

Question 6

Metagenomics is __-__: it focuses on the genes in a __ rather than a specific species.

Answer 6

gene-centric; community

Question 7

The __ Genomes Project gathered genomic data from over 2500 individuals from 26 populations; this kind of data will help determine who will __ better to a specific treatment.

Answer 7

1000s; respond

Question 8

The Genome ___ Consortia has gathered nearly __K human genomes and determined that there is __ variant for every __ bp.

Answer 8

Aggregation; 150K; 1; 8

Question 9

Developing genetic profiles of patients and their responses to drugs will help predict which drugs work best for whom; this is called __.

Answer 9

Pharmacogenomics

Question 10

An example of personalized medicine will be a genetic tests that looks at your ability to __ common medications.

Answer 10

breakdown

Question 11

__ is an attempt to use engineered microbes to perform special functions, such as remove toxic waste. This is also called __ biology.

Answer 11

Bioremediation; synthetic

Question 12

__ genomics seeks to do 2 things:
1. ID all __ molecules transcribed from the genome (aka the __).
2. ID all of the __ encoded from the genome (aka the __).
Bottom line, __ genomics seeks to ID the biological function of __.

Answer 12

Functional;

RNA; transcriptome
Proteins; proteome

functional; proteins.

Question 13

Homologous genes are __ related. __ are homologs in different species; __ are homologs within the same species that arose due to gene __.
Sometimes the function of a novel protein can be predicted by its __ to one or more __ in a DNA or protein database.

Answer 13

evolutionarily.
Orthologs; paralogs; duplications.

homology; orthologs

Question 14

Protein __ can sometimes provide significant insight into the function of an unknown protein.

Answer 14

domains

Question 15

The __ to __ paradigm looks for clues to a gene whose expression differs between normal and diseased cells. It involves __: data mining of the human genome databases. The idea is to search for a way to interfere with the activity of a target gene or its __.

Answer 15

gene to drug; bioinformatics

product

Question 16

A __ gene is a gene whose activity is easy to monitor. Common examples include __ __ __ (GFP) or _-__ (the lacZ gene product of E. coli.)

Answer 16

reporter

green fluorescence protein; β-galactosidase

Question 17

In the gene to drug paradigm, scientists might look for a small __ that interacts with the protein product of a gene in order to cause __ when it (the gene or its __) is implicated in a disease process.

Answer 17

molecule; interference; product

Question 18

Use of a __ gene allows precise identification of tissues expressing a transgene that have been tagged with the __ gene.

Answer 18

reporter; reporter

Question 19

__ __ __ is used to systematically test a collection of various small molecules (uses __). Companies such as __ Florida has a library of more than 1M small molecules.

Answer 19

High throughput screening; robotics.

Scripps

Question 20

__ analysis is an analytic technique based on the tech used to make chips. Microscopic droplets of DNA are “__” onto a glass slide (each spot is a “__” of DNA). This technique allows for analysis of changes in gene __ with the additional benefit of analyzing thousands of genes in a __ experiment.

Answer 20

Microarray
“printed”.
“microdot”.
expression; single

Question 21

__ analysis was used to evaluate the expression patterns of 25K genes of women with a specific breast cancer (some whose cancer had metastasized, others who were in remission). After evaluation, the expression pattern of 70 genes could accurately __ whether a new patient would experience a metastatic form of the disease.

Answer 21

Microarray.

predict

Question 22

T or F: SNPs produce phenotypic variation.

Answer 22

Mostly false; they don’t typically cause phenotypic differences.

Question 23

A __ is a combination of alleles OR a set of SNPs that tend to be inherited __ and/or found on the same __.

Answer 23

haplotype; together; chromosome

Question 24

Homologous chromosomes of individual humans are identical for most of the DNA sequence except for variation in a single bases called __. These __ combinations are equivalent / analogous to different __ of a gene.

Answer 24

SNPs.

SNPs; alleles

Question 25

__ is the only technology at this time that enables sequence analysis of minute starting samples (e.g. one __). For this reason, and because DNA is remarkably __ in the environment, it is used in forensics.

Answer 25

PCR; cell.

stable.

Question 26

__ __ __ __ (CODIS) is a national DNA database that includes genetic profiles of arrestees and forensic cases. It uses a set of 20 highly __ sites of __ __ __ (STRs) in the human genome.

Answer 26

COmbined DNA Indexing System;

polymorphic; short tandem repeats.

Question 27

__ analysis seeks to ID all of the __ within a specific __ type to understand how they interact with each other. The idea is to understand the __ basis of the disease in order to better treat it. The Human __ Project was initiated to catalog all of the proteins in each of the 200+ __ types of humans.

Answer 27

Proteomic; proteins; cell.

molecular.

Proteome; cell

Question 28

Proteomic analysis includes isolation of proteins using __-PAGE Gel (or liquid __ for proteins at very low concentrations). Once isolated, the proteins are digested with __, and fragments are analyzed using mass __ to determine __-__-__ ratios, then comparing them to a database of known protein profiles.

Answer 28

SDS; chromatography.

Protease; spectrometry; charge-to-mass

Question 29

Evaluation of proteins’ charge-to-mass ratios with SDS uses a a process called __ focusing. This process first separates proteins by __ along one axis, then by __ along another axis. It produces a series of __ on the gel each of which is a separate __.

Answer 29

isoelectric.

charge; mass.

spots; protein.

Question 30

A series of dots on an SDS gel has the same mass, but ranges in charge from 5.5 to 6.0. What might this be?

Answer 30

The same protein (based on mass), but different amounts of phosphorylation (affecting its charge).

Question 31

Microarray analysis is used for DNA analysis as well as protein analysis. What might one be able to examine in each?

Answer 31

DNA microarray: can examine / compare gene expression, such as the genes of normal cells vs. cancerous cells.
Protein microarray: can examine protein-protein interactions, such as a protein that is resistant do a specific enzyme.

Question 32

Approx 4M gene “__” (small __ RNAs) have been identified that mediate interactions between the environment and genetics; and they begin to shed light on why ID twins become less __ as they age.

The NIH calls the DNA coding for these __ RNAs the __ __ of the Human Genome.

Answer 32

switches; regulatory; identical

regulatory; Dark Matter

Question 33

__ medicine focuses on complex diseases (e.g. cancer, depression, etc.) that involve the __ of proteins that are encoded by a __ number of genes.

__ medicine will continue to advance as __ becomes cheaper and as technology and ___ continue to advance.

Answer 33

Personalized; interaction; large.

Personalized; sequencing; metagenomics

Question 34

__ __ is a treatment approach that seeks to ‘reprogram’ the patient’s immune system to attack the cancer.

Answer 34

Cancer immunotherapy

Question 35

List the 3 bacterial systems that have been used to edit complex genomes in order from least to most precise.

Answer 35

1. Restriction endonucleases
2. Taq polymerases
3. CRISPR/cas9

Question 36

Learning about our genome has provided a __ into the __. For example, some scientists have speculated that human culture may have emerged from a sudden mutation of the __ gene as little as 50,000 years ago.

Answer 36

window; past.

FOXP2