Theme 4 - Module 3

Question 1

How has PCR revolutionized the world of cellular and molecular biology?

Answer 1

Shed light on:

• diagnosis of genetic defects
• detection of viral DNA in cells
• producing large amounts of DNA from fossils containing trace amounts of DNA
• able to link specific individuals to DNA samples during forensic investigations

Question 2

Taq polymerase was first isolated from which bacterial species?

Answer 2

Thermus aquaticus

adapted to live in hot springs

Question 3

True or false: gel electrophoresis is a technique that can only be used with separated DNA fragments from PCR

Answer 3

False

Other sources (other than PCR) can also supply separated DNA fragments

Question 4

True or false: gel electrophoresis can only separate DNA fragments, not any other molecule

Answer 4

False

Can separate other macromolecules including RNA and proteins

Question 5

Why are DNA and RNA are negatively charged molecules?

Answer 5

Bc of their ionized phosphate groups along the phosphodiester backbone

Question 6

True or false: the bands would NOT be visible while separating in the gel electrophoresis apparatus

Answer 6

True

Question 7

True or false: gel electrophoresis can only be used on single size of DNA molecule

Answer 7

False

Can be used to separate and visualize a DNA sample containing a mixture of DNA fragments of different sizes

Question 8

What was a limitation to Sanger’s DNA sequencing technique?

Answer 8

It could only determine the sequence of small fragments of DNA

Question 9

What are the three phases of shotgun sequencing?

Answer 9

(after breaking the entire genome into different sized pieces)

Phase 1: Random sequencing of the DNA in each fragment

Phase 2: Identifying the regions of overlap between the generated fragments and assembling the sequence of nucleotides that makes up each chromosome

Phase 3: Annotating the sequences and identifying the coding regions, regulatory regions and non-coding regions

Question 10

What was the first bacterial whole genome to be sequenced?

Answer 10

Haemophilus influenza

Question 11

What was the first multicellular organism genome to be sequenced? The second?

Answer 11

1) C. elegans

2) Drosophila

Question 12

What was critical to the process of whole-genome sequencing?

Answer 12

The development of computational software capable of facilitating the assembly of the fragments

Question 13

What is the purpose of putting dideoxynucleotides within the tubes as well? (shotgun seq)

Answer 13

ddNTPs are missing the -OH group at the 3’ position. Therefore, would not allow for further elongation of a growing DNA strand and would terminate replication. Leads to a series of interrupted daughter strands.

Question 14

True or false: insertion of ddNTPs or the dNTPs is a organized and calculated process

Answer 14

False

It’s random process. Many fragments of many different sizes can potentially terminate at every possible nucleotide

Question 15

True or false: there is a smaller amount of ddNTPs that are added relative to the amount of dNTPs

Answer 15

True

Question 16

How do you distinguish all the chain terminators that are present in all the replicated DNA fragments?

Answer 16

By labelling each of the four ddNTPs with diff coloured fluorescent dyes

Question 17

What is a limitation to the Sanger dideoxy chain-termination method?

Answer 17

Can only determine the sequence of fragments of DNA up to several hundred nucleotides in length

Question 18

What are contigs?

Answer 18

Overlapping DNA segments that are assembled into a consensus region of DNA

Question 19

For any double-stranded DNA sequence, how many possible reading frames are there?

Answer 19

6

Question 20

What characteristics of a seq indicates that its a good reading frame?

Answer 20

Long, continuous triplets of nucleotides that specify the amino acids that will make up the protein. Lacks a stop codon and are flanked on either side by a start and stop codon

(also indicates that that may be the coding sequence)

Question 21

True or false: computer programs only look for coding regions

Answer 21

False

Also look for typical sequences that code for promoters, or other regulatory sites

Question 22

True or false: it’s hard to scan and identify regions of interest on both prokaryotic and euk seq DNA

Answer 22

False

Prokaryotic genomes can be easily scanned

Eukaryotic genomes need an array of different techniques to find the introns and exons especially

Question 23

How would you know if a particular sequence of DNA coded for tRNA?

Answer 23

tRNA molecules forms hairpin structures in which the molecule folds back on itself and undergoes complementary base pairing within itself

Therefore, look for nearby complementary sequences within the sequence

Question 24

True or false: 50% of the average eukaryotic genome consists of repeated sequences that do not code for functional gene products

Answer 24

True