Chapter 16b: Genomics

Question 1

What information can we use to
annotate genes in a genome?
A. Determine which sequences are transcribed into
mRNA
B. Predict which sequences can encode proteins based
on “open reading frames” (ORFs)
C. Determine which sequences are evolutionarily
conserved across species
D. All of the above
E. None of the above

Answer 1

All of the above

Question 2

What is the purpose of the oligo-dT
primers when synthesizing cDNA?
A. Reverse transcription of all of the RNA
B. Reverse transcription of mRNA from the 3’ end
C. Degradation of the remaining RNA
D. Synthesis of the 2nd strand of cDNA
E. All of the above are true

Answer 2

Reverse transcription of mRNA from the 3’ end

Question 3

What kind of functional sequence is easiest
to annotate in a newly sequence genome?
A. Protein coding sequence
B. Transcribed non-coding RNAs
C. Transcriptional regulatory sequence (e.g., enhancers)
D. It’s all a piece of cake.

Answer 3

Protein coding sequence

Question 4

The largest class of predicted genes based on
whole-genome sequencing of eukaryotes falls
into which of the following categories?

a) nutrient metabolism
b) transcription
c) cell division cycle
d) function unknown

Answer 4

function unknown

Question 5

What do you expect to differ between the
genomes of two closely related species?
A. Individual nucleotides
B. Gene copy number
C. Gene order
D. All of the above
E. None of the above

Answer 5

All of the above

Question 6

What are the most common differences
between the genomes of different people?

A. Single nucleotide polymorphisms (SNPs)
B. Duplicated/deleted sequences, i.e., copy number
variants (CNVs)
C. Trisomy/monosomy
D. They are all equally common

Answer 6

Single nucleotide polymorphisms (SNPs)

Question 7

What is cDNA?

Answer 7

Complementary DNA synthesized from mRNA using reverse transcriptase.

Question 8

What is an ORF?

Answer 8

An open reading frame—a stretch of DNA that could encode a protein.

Question 9

What does RNA-seq measure?

Answer 9

Expression levels of all genes in the genome.

Question 10

How does RNA-seq quantify expression?

Answer 10

By aligning reads to the genome and measuring coverage.

Question 11

What do heatmaps in functional genomics show?

Answer 11

Gene expression changes over time or conditions (e.g., cell cycle).

Question 12

What is synteny?

Answer 12

Genes located on the same chromosome.

Question 13

What is conserved synteny?

Answer 13

Genes remain on the same chromosome in different species.

Question 14

How frequent are SNPs in humans?

Answer 14

1 per 1,000 bp (~3 million differences between two individuals).

Question 15

What are CNVs?

Answer 15

Regions of DNA that are duplicated or deleted.

Question 16

What do phylogenetic trees represent?

Answer 16

Evolutionary relationships among genes or species.

Question 17

What are orthologs?

Answer 17

Genes in different species that evolved from a common ancestor and retain the same function.

Question 18

What are paralogs?

Answer 18

Genes within the same species that arose by duplication and may have new functions.