QUIZ

Class 3 quiz

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Flag question: Question 1

Question 1 1 pts

What is difference between genetics and genomics?

Group of answer choices

a. Genetics follows mutations in genes while Genomics follows genes during evolution.

b. Genetics studies individual genes. Genomics studies all of an organism's DNA together.

c. Genomics and Genetics are essentially the same thing, with genomics only possible recently because of technological advances.

d. Genomics studies individual genes. Genetics studies all of an organism's genes together.

 

Flag question: Question 2

Question 2 1 pts

How many different sequences are possible for a DNA segment with length of N bases?

Group of answer choices

a. N to the 4'th power.

b. Depends on N and, to some extent, the organism you're looking at.

c. 4 times N

d. 4 to the N'th power.

 

Flag question: Question 3

Question 3 1 pts

For a 4Mb genome, how often would you expect any 10-mer on average (Note: 4 ^ 10 = 1,048,576)?

Group of answer choices

a. About 4 times

b. About once

c. About 10 times

d. Depends on the organism so you cannot generally predict this.

 

Flag question: Question 4

Question 4 1 pts

How evenly distributed is the occurrence of N-mers in genomes of higher organisms, like the human genome?

Group of answer choices

a. Generally like a normal, bell-shaped (Gaussian) distribution.

b. Pretty flat distribution, with each base occurring at a pretty constant rate (for any given organism)

c. Strongly skewed, with some sequences being very common and some being very rare.

d. Distribution is dependent on the choice of N and the organism so it is not possible to generalize this.

 

Flag question: Question 5

Question 5 1 pts

What factors contribute to the distribution of N-mer frequencies in a genome?

Group of answer choices

a. Codon frequency of gene usage, as determined by the organism, is the main factor.

b. Repeats make some N-mers very rare, while other factors make some N-mers highly common.

c. It's pretty much random drift acted upon by evolution so that some N-mers are more / less common than others.

d. Repeats make some N-mers very common, biological constraints make some N-mers very rare.

 

Flag question: Question 6

Question 6 1 pts

What is DNA hybridization and melting temperature, Tm?

Group of answer choices

a. DNA hybridization is opposite of DNA melting, where duplexes break up. Tm is the melting temperature where hybridization breaks down.

b. DNA hybridization is the pairing of two complementary, single-strand sequences together. Tm is the temperature where 50% of a DNA sequence is hybridized.

c. DNA hybridization is process where sequences match. Tm is the temperature where nearly all DNA is single stranded, eg. 99%.

d. DNA hybridization is the joining of two sequences together. Tm is the temperature where this joining reaction is complete.

 

Flag question: Question 7

Question 7 1 pts

How does Tm depend on sequence?

Group of answer choices

a. Tm is a measured quantity that must be deduced from experiments. GC rich sequences consistently have high Tm.

b. Tm depends mainly on sequence length and GC. Shorter sequences always have lower Tm than longer ones.

c. Tm depends mainly on sequence length and GC. For a given length, more GC raises Tm.

d. Tm depends mainly on sequence length and GC. For a given length, more GC lowers Tm.

 

Flag question: Question 8

Question 8 1 pts

How is understanding of Tm useful for assay design?

Group of answer choices

a. Tm is useful to know when you look at assay readout via hybridization reactions.

b. Assay target locations can be changed so that all targets have similar Tm

c. To achieve even hybridization, assay sequence lengths can be adjusted longer for GC-poor targets and shorter for GC-rich targets.

d. All of the above

 

Flag question: Question 9

Question 9 1 pts

What best describes a multiplex genotyping assay?

Group of answer choices

a. Any assay or test that can readout multiple information channels at once, for example with different colors.

b. A genotyping assay that is run multiple times to improve genotype accuracy.

c. An assay where multiple components are used together to determine multiple genotypes simultaneously.

d. Any assay requiring multiple oligonucleotide component parts.

 

Flag question: Question 10

Question 10 1 pts

How would you identify specific genotypes given different readouts for each allele? For example, assume allele-1 gives Red and allele-2 gives Green signals.

Group of answer choices

a. Heterozygous samples show only Red. Homozygous allele 1 shows Red or Green. Homozygous allele 2 shows only Green.

b. Heterozygous samples show only Green. Homozygous allele 1 shows Red and Green. Homozygous allele 2 shows Green.

c. Heterozygous samples show only Red. Homozygous allele 1 shows only Green. Homozygous allele 2 shows only Yellow.

d. Heterozygous samples show both readouts. Homozygous allele 1 shows only Red. Homozygous allele 2 shows only Green.

 

Flag question: Question 11

Question 11 1 pts

How can OLA (Oligonucleotide Ligation Assay) be used for genotyping?

Group of answer choices

a. OLA uses differently-labeled, allele-specific probes together with a ligase enzyme to distinguish genotypes via labeled products.

b. OLA uses differently-labeled, allele-specific PCR primers to distinguish genotypes via labeled products.

c. OLA uses multiple assay components and a polymerase to yield different colors for different genotypes

d. OLA, or Oligo Ligation Assay, is very similar to PCR, allowing genotyping with a different enzyme.

 

Flag question: Question 12

Question 12 4 pts

What are SNPs, InDels and CNVs and how do these differ from "mutations"?

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Flag question: Question 13

Question 13 4 pts

Describe PCR in simple terms. What components are needed? How do genome uniqueness and thermodynamics influence design?