Lecture 15 - Genomics

Question 1

What is a genome?

Answer 1

The complete DNA sequence of an individual

Question 2

Does genome size always correlate with organism complexity?

Answer 2

No, some simple organisms have very large genomes

Question 3

What does the genome specify?

Answer 3

The transcriptome

Question 4

What does the transcriptome specify?

Answer 4

The proteome

Question 5

What are the base-pairing rules in DNA?

Answer 5

A–T and G–C

Question 6

What is DNA’s role in heredity?

Answer 6

It encodes phenotypes and differences between organisms

Question 7

What is a gene made of?

Answer 7

DNA

Question 8

What is the central dogma of molecular biology?

Answer 8

DNA → RNA → Protein (with reverse transcription possible)

Question 9

In which direction is RNA synthesized?

Answer 9

5′→3′ direction

Question 10

Which base is found in RNA but not DNA?

Answer 10

Uracil (replaces thymine)

Question 11

What is the sugar in RNA?

Answer 11

Ribose

Question 12

What are the main types of RNA genes?

Answer 12

mRNA, rRNA, tRNA, miRNA, and other noncoding RNAs

Question 13

What is the function of mRNA?

Answer 13

Codes for proteins

Question 14

What is the function of rRNA?

Answer 14

Forms ribosome core and catalyzes protein synthesis

Question 15

What is the function of tRNA?

Answer 15

Adaptor between mRNA and amino acids during protein synthesis

Question 16

What is the function of miRNA?

Answer 16

Regulates gene expression

Question 17

What are examples of other noncoding RNAs?

Answer 17

RNAs involved in splicing, telomere maintenance, and regulation

Question 18

What is genome size defined as?

Answer 18

The total number of base pairs in one complete set of chromosomes (1C)

Question 19

What is comparative genomics?

Answer 19

Studying variation between individuals or species to understand evolution

Question 20

How many base pairs are in the human genome?

Answer 20

Over 3 billion bp

Question 21

How many chromosomes are in the human genome?

Answer 21

23 pairs (46 total)

Question 22

How many protein-coding genes are in the human genome?

Answer 22

About 30,000

Question 23

What percentage of human DNA is protein-coding?

Answer 23

About 3%

Question 24

What is clone-based mapping?

Answer 24

Sequencing method using ordered overlapping clones assembled into contigs

Question 25

What is shotgun sequencing?

Answer 25

Sequencing method where DNA is randomly fragmented, sequenced, and assembled computationally

Question 26

What is sequencing coverage?

Answer 26

The number of times each base is read (e.g., 30–50x for accuracy)

Question 27

Why are repeats a challenge for genome assembly?

Answer 27

They cause ambiguities in aligning sequence fragments

Question 28

What role does bioinformatics play in genomics?

Answer 28

Software assembles fragments and resolves repeats into contiguous genome sequences

Question 29

What are the three main DNA sequencing approaches?

Answer 29

Sanger sequencing, next-generation sequencing, third-generation sequencing

Question 30

What is Sanger sequencing used for today?

Answer 30

Short DNA segments (<1,000 bp), small-scale projects

Question 31

What are limitations of Sanger sequencing?

Answer 31

Slow, expensive for whole genomes

Question 32

What is next-generation sequencing (NGS)?

Answer 32

Massively parallel sequencing of millions of DNA fragments simultaneously

Question 33

What was the approximate cost and time for a human genome using NGS?

Answer 33

$2 million and 2 months

Question 34

What are three types of NGS technologies?

Answer 34

Pyrosequencing, semiconductor sequencing, reversible chain-termination (Illumina)

Question 35

What is pyrosequencing based on?

Answer 35

Light emission from pyrophosphate release during nucleotide incorporation

Question 36

What is the main limitation of pyrosequencing?

Answer 36

Poor performance on homopolymer tracts

Question 37

What does semiconductor sequencing (Ion Torrent) detect?

Answer 37

pH changes from H+ release during nucleotide incorporation

Question 38

What limitation does semiconductor sequencing share with pyrosequencing?

Answer 38

Problems with homopolymer repeats

Question 39

What is reversible chain-termination sequencing (Illumina)?

Answer 39

Short-read NGS using fluorescently labelled, reversible terminator nucleotides

Question 40

What are the advantages of Illumina sequencing?

Answer 40

High throughput, cheap, no homopolymer issues

Question 41

How cheap has Illumina sequencing become for humans?

Answer 41

<$1,000 per genome in under 1 week

Question 42

What is third-generation sequencing?

Answer 42

Newest methods that sequence long DNA molecules in real time