Lecture 10

Question 1

Hierarchal approach

Answer 1

start with 3 mil base pairs, chunk it to 200,000 and clone those chunks with bacterial artificial chromosomes, sequence and look for overlapping sequences, shotgun it at 500 bp
-slow method that uses BAC intermediates
-repetitive sequences wont affect this

Question 2

shotgun

Answer 2

6 mil base pairs and shotgun the whole thing
-this approach works well for small bacteria bc smaller have less repetitive sequences
-it is bad if there is a repetitive sequence
-sanger

Question 3

anotating sequence

Answer 3

editing and analyzing data

Question 4

what is half the human genome?

Answer 4

repeating sequences

Question 5

What percent of RNA is transcribed to RNA

Answer 5

28%
-only 1.1 to 1.4 is transcribed to proteins

Question 6

ORF

Answer 6

protein encoding genes
-25,000
-starts at the start codon
-DNA/ RNA sequence without stop codon

Question 7

theory supporting evolution?

Answer 7

most genes are in all of life and there are only a few differences in things like vertebrates
-2 people are 99.9% genetically identical
-1 in 1250 nucleotides are different

Question 8

mRNA will be identical to what strand?

Answer 8

the sense strand

Question 9

where are the genes that encode?

Answer 9

on both strands
-we can also have genes on the opposite strand that encode backward in the 5 to 3 direction
-each gene can encode multiple proteins

Question 10

how can small genomes encode?

Answer 10

they can encode the same DNA chunk in the opposite direction at the same time

Question 11

Proof the recombination frequencies are not uniforma cross a chromosome?

Answer 11

the closer the least likely theyare to separate and recombine

Question 12

do more genes make an organism more complex

Answer 12

no they dont
-worms have more genes than people
-complexity is due to gene regulation (how the genome is organized)

Question 13

how do we know where genes are

Answer 13

after examining many mutations we can build recombination frequency based on genetic map of where genes are in respect to each other. this is a classical sturtecantian genetic map but we cant do this with people because we would need families with thousands of kids

Question 14

Do all ppl w BRACA 1 mutation have the same mutaiton?

Answer 14

no, they all have a different mutation at BRACA 1

Question 15

methods of human gene mapping

Answer 15

-genome wide association screen
-positional cloning: can happen in a family

Question 16

positional cloning

Answer 16

frequency between DNA markers and causative allele
-goal is the find gene marker so you can measure the distance between the mutation and the gene which will let you isolate the mutation, sequence it or analyze it for a pattern of expression

Question 17

polymorphism

Answer 17

a sequence that varies between individuals in a population
-some of the sequences will have phenotypes some will be random and do nothing
-the variations are DNA markers
-can be SNP or SSR

Question 18

genome wide association screening

Answer 18

a large population not closely related
-lets us look at the association between DNA marker and causative allele
-basically what marker the affeted individuals share

Question 19

SNP polymorphism

Answer 19

-single nucleotide polymorphism
-ex: at the same site on person has a T and one person has a G while everything else is the same

Question 20

SSR polymorphism

Answer 20

-simple sequence repeat (microsatellite)
-a repeating sequence that repeats a different amount of times in different people

Question 21

does the marker cause the problem?

Answer 21

NO it just helps you find it

Question 22

what happens to the marker as generations pass?

Answer 22

mutations will always be near the same polymorphism and may become linked to the polymorphism

Question 23

How can we detect SSR?

Answer 23

PCR
-the SSR can be long (many repeats) or short
-PCR primers will be on both ends of the SSR
-you can be homo for long or short SSR marker or hetero
-we can also use a southern blot

Question 24

does the marker cause the phenotype?

Answer 24

NO

Question 25

How can we detect SNP

Answer 25

RFLP
-use a DNA probe that complements the SNP region

Question 26

Microarray

Answer 26

chip w spots that show DNA position/ gene location
-for polymorphism= infinium
-we aneel the sequence to the array and add flourecent ddNTP
-can give genotype of the whole genome

Question 27

RFLP

Answer 27

-cut the DNA w enzymes where the SNP is
-compare the lengths of the fragments w gel and look for location of SNP

Question 28

Can a polymorphism be outside the coding sequence?

Answer 28

yes it can also be in the UTR or intron

Question 29

the smaller the population

Answer 29

the less reliable the data is
-accuracy of data is based on LOD score
-increase LOD increase accuracy