Lecture 8

Question 1

Genome

Answer 1

An organisms complete set of DNA including all its genes

Question 2

Genetics

Answer 2

The study of individual genes and their functions

Question 3

Genomics

Answer 3

Methods for studying the entire genome of a microbe

Question 4

What method of DNA sequencing did Walter Gilbert come up with

Answer 4

Chemical Degradation Method

Question 5

What method of DNA sequencing did Sanger invent? What are the different names this

Answer 5

Sanger method, dideoxy method, chain termination method or enzymatic method.

Question 6

Whats the difference between Ribose, deoxyribose and dideoxyribose sugars

Answer 6

Ribose has OH at C2 & C3, Deoxyribose has OH at only C3, and dideoxyribose has OH at neither C2 nor C3.

Question 7

What makes RNA more unstable than DNA

Answer 7

The presence of the OH at C2, which makes more unstable phosphodiester linkages.

Question 8

What are the four components needed for dna sequencing

Answer 8

template dna, primer, dna polymerase & nucleotides

Question 9

The smaller the fragment, the closer it is to the ____ of the strand

Answer 9

bOTTOM

Question 10

How long of a chain can Sanger method sequence

Answer 10

700-1000 bp

Question 11

How long is the smallest bacterial genome?

Answer 11

169 kBp

Question 12

The automated methods of sanger method replaced radioactive labels with _____ labels

Answer 12

Fluorescent

Question 13

What is it called when you use repeated rounds of sequencing with primers complementary to the end of the last segment sequenced?

Answer 13

Primer Walking

Question 14

What can you do to make the sanger method achieve longer sequences?

Answer 14

Primer Walking

Question 15

Pyrosequencing is a type of _____ ____ Sequencing

Answer 15

Next Generation

Question 16

Explain how pyrosequencing works

Answer 16

Every time a phosphodiester bond is formed by adding a nucleotide to a dna chain, pyrophosphate is released. Pyrophosphate + APS under the action of ATP-sulfurylase gives rise to ATP. ATP under the action of luciferase gives rise to light. So thats how you see the sequencing

Question 17

What’s faster and whats cheaper, sanger or pyrosequencing method?

Answer 17

Pyrosequencing is both faster and cheaper

Question 18

How many Base Pairs can pyrosequencing sequence?

Answer 18

300 - 500 Base Pairs

Question 19

What’s another name for whole genome sequencing?

Answer 19

Shotgun Sequencing

Question 20

How does whole genome shotgun sequencing work?

Answer 20

It sequences the entire genome at once.

1) DNA is physically sheared
2) Fragments are sequenced by some next-gen sequencing
3) Software aligns the sequences and removes overlapping sequences

Question 21

How many Base Pairs can shotgun sequencing do?

Answer 21

25 - 500 bp

Question 22

Shotgun sequencing is veryyy fast, but what is one downside of it?

Answer 22

It may need 10x the total genome length inputted into it for it to sequence successfully.

Question 23

Define bioinformatics

Answer 23

Analysis of large data sets of sequencing data

Question 24

What are Open Reading Frames (ORFs)?

Answer 24

ORFs are spots in the genome that allow us to easily determine the start and stop points of a particular gene

Question 25

What is functional genomics

Answer 25

When both the sequence and the function of genes are determined

Question 26

What is "a collection of cloned DNA fragments that represents the entire genome of an organism"

Answer 26

A genetic library

Question 27

What is the formula that can determine the number of cloned fragments needed to encompass an entire genome?

Answer 27

N = ln (1 - P)/ ln (1 - f) Where N = number of clones P = Probability of generating complete library f = average size of each clone divided by the total size of the genome.