Dna Sequencing And Beyond

Question 1

Chain termination

Answer 1

When ddtp is incorporated into a DNA strand, it no longer synthesizes

Question 2

What consists of DNA automated sequence?

Answer 2

Primer ( DNA polymerase), a single stranded template, all four nucleotides
Also has four dideoxyribonucleotides

Question 3

Downsides of Sanger sequencing

Answer 3

Individual sequencing reaction of 600 bp
Primers must anneal to the template ( slow down results)

Question 4

Benefits of next gen sequencing

Answer 4

Millions of templates can be sequenced in a single reaction.
Can use one primer for all

Question 5

Roche 454 sequencing steps in order

Answer 5

1. Isolate DNA
2. Fragment DNA into small pieces
3. Fragments are lighted to adaptors
4. Adaptors base pair with complementary sequences on beads
5. Individual beads are emulsified in droplets and amplified
6. Droplets are deposited into individual wells

Question 6

Are primers complementary or uncomplementary to adaptors?

Answer 6

Complementary

Question 7

Genome

Answer 7

Total genetic composition of an organism

Question 8

What are contigs?

Answer 8

Overlapped pieces of DNA that are put together by computer programs to create longer stretches of continuous DNA sequences

Question 9

A fully assembled contig would correspond to what?

Answer 9

An entire chromosome

Question 10

Genome annotation

Answer 10

Finding out gene functions and functional sequences within the genome.

Question 11

Gene prediction

Answer 11

The process of identifying regions of DNA that encode genes

Question 12

Computer programs use two strategies, de novo and homology based to locate genes. What are they?

Answer 12

De novo: identify genes based on raw sequences
homology based: similarity to known genes

Question 13

Open reading frame

Answer 13

Lacks stop codons,can be read right to left

Question 14

Two biological features are what? If share they what?

Answer 14

Homologus; common ancestor

Question 15

Orthologs

Answer 15

Homologous genes that arise from speciation

Question 16

paralogs

Answer 16

Homologous sequences that arose by gene duplication and exist in the same genome

Question 17

Gene family

Answer 17

Two or more copies of homologous genes of a single organism

Question 18

Conserved site

Answer 18

Identical or similar across multiple homologs

Question 19

Tips represent what?

Answer 19

Individual species

Question 20

What are nodes?

Answer 20

Common ancestors of particular groups of species

Question 21

What is the root?

Answer 21

The common ancestor of all of the species

Question 22

What are characters?

Answer 22

Nucleotides that differ between spaces

Question 23

Ancestral characters

Answer 23

Same nucleotide found in common ancestral gene

Question 24

Derived characters

Answer 24

New nucleotide differs from common ancestor due to a mutation

Question 25

Synapomorphies

Answer 25

Two species share the same mutation in a group of that species and it is a derived character, the two species are closely related to earn other then to the others