Homework Answers

1
Homework Answers

• May 31, 2008

2
1. Write the other strand for this sequence 5'
G A T T A T G A T G T T G G G C C A T T C A T T 3'
3
1. Write the other strand for this sequence 5'
G A T T A T G A T G T T G G G C C A T T C A T T
3' 3' C T A A T A C T A C A A C C C G G T A A G T
A A 5'
4
1. Write the other strand for this sequence 5'
G A T T A T G A T G T T G G G C C A T T C A T T
3' 3' C T A A T A C T A C A A C C C G G T A A G T
A A 5' Now write the bottom strand you just
wrote in the 5' to 3' direction.
5
1. Write the other strand for this sequence 5'
G A T T A T G A T G T T G G G C C A T T C A T T
3' 3' C T A A T A C T A C A A C C C G G T A A G T
A A 5' Now write the bottom strand you just
wrote in the 5' to 3' direction. 5 A A T G A A T
G G C C C A A C A T C A T A A T C 3'
6
1. Write the other strand for this sequence 5'
G A T T A T G A T G T T G G G C C A T T C A T T
3' 3' C T A A T A C T A C A A C C C G G T A A G T
A A 5' Now write the bottom strand you just
wrote in the 5' to 3' direction. 5 A A T G A A T
G G C C C A A C A T C A T A A T C 3 Why did we
ask you to do this exercise?
7
2. According to the animation, what are the
ingredients in a PCR reaction? And what role
does each ingredient play?
8
2. According to the animation, what are the
ingredients in a PCR reaction? And what role
does each ingredient play? Key Ingredients Taq
Polymerase heat stable DNA Polymerase
9
2. According to the animation, what are the
ingredients in a PCR reaction? And what role
does each ingredient play? Key Ingredients Taq
Polymerase heat stable DNA Polymerase Primers
provide 3- hydroxyl groups bracketing the
target DNA
10
2. According to the animation, what are the
ingredients in a PCR reaction? And what role
does each ingredient play? Key Ingredients Taq
Polymerase heat stable DNA Polymerase Primers
provide 3- hydroxyl groups bracketing the
target DNA Deoxynucleoside triphosphates the
four building blocks of DNA
11
2. According to the animation, what are the
ingredients in a PCR reaction? And what role
does each ingredient play? Key Ingredients Taq
Polymerase heat stable DNA Polymerase Primers
provide 3- hydroxyl groups bracketing the
target DNA Deoxynucleoside triphosphates the
four building blocks of DNA Target DNA the DNA
that is to be amplified
12
2. According to the animation, what are the
ingredients in a PCR reaction? And what role
does each ingredient play? Key Ingredients Taq
Polymerase heat stable DNA Polymerase Primers
provide 3- hydroxyl groups bracketing the
target DNA Deoxynucleoside triphosphates the
four building blocks of DNA Target DNA the DNA
that is to be amplified
http//marinebiotech.net/workshop/bioinformatics/S
aturdays/19_pcr.swf
13
Inserting gaps ( - ) where necessary, line up
these three sequences to maximize the
similarities in the columns of letters.
Which two of those three sequences are
most similar (which have the most similarities
after you align them)? How did you decide
which were the most similar?
14
Inserting gaps ( - ) where necessary, line up
these three sequences to maximize the
similarities in the columns of letters.
15
Inserting gaps ( - ) where necessary, line up
these three sequences to maximize the
similarities in the columns of letters.
16
Inserting gaps ( - ) where necessary, line up
these three sequences to maximize the
similarities in the columns of letters.
Which two of those three sequences are
most similar (which have the most similarities
after you align them)?
17
Inserting gaps ( - ) where necessary, line up
these three sequences to maximize the
similarities in the columns of letters.
Which two of those three sequences are
most similar (which have the most similarities
after you align them)?
18
Inserting gaps ( - ) where necessary, line up
these three sequences to maximize the
similarities in the columns of letters.
Which two of those three sequences are
most similar (which have the most similarities
after you align them)?
19
Inserting gaps ( - ) where necessary, line up
these three sequences to maximize the
similarities in the columns of letters.
Which two of those three sequences are
most similar (which have the most similarities
after you align them)?
20
Inserting gaps ( - ) where necessary, line up
these three sequences to maximize the
similarities in the columns of letters.
Which two of those three sequences are
most similar (which have the most similarities
after you align them)? How did you decide
which were the most similar?
21

• You may or may not wish to attempt this question
  it was hard to come up with a question that
  matched the technology Simona was using.
• To the right is a sequencing gel read the gel
  and provide the
• DNA sequence it represents.
• The three-letter code of the protein it encodes.
• The single-letter code of the protein it encodes.
• Describe how dideoxy sequencing works.
• Remember, the smallest fragments are at the
  bottom of the gel so assume that is where the
  sequence begins!

22

• You may or may not wish to attempt this question
  it was hard to come up with a question that
  matched the technology Simona was using.
• To the right is a sequencing gel read the gel
  and provide the
• DNA sequence it represents.
• The three-letter code of the protein it encodes.
• The single-letter code of the protein it encodes.
• Describe how dideoxy sequencing works.
• Remember, the smallest fragments are at the
  bottom of the gel so assume that is where the
  sequence begins!

ATTGACATAGACTGGGAGCTTCTC
23

• You may or may not wish to attempt this question
  it was hard to come up with a question that
  matched the technology Simona was using.
• To the right is a sequencing gel read the gel
  and provide the
• DNA sequence it represents.
• The three-letter code of the protein it encodes.
• The single-letter code of the protein it encodes.
• Describe how dideoxy sequencing works.
• Remember, the smallest fragments are at the
  bottom of the gel so assume that is where the
  sequence begins!

ATTGACATAGACTGGGAGCTTCTC ATT GAC ATA GAC TGG GAG
CTT CTC AT TGA CAT AGA CTG GGA GCT TCT C A
TTG ACA TAG ACT GGG AGC TTC TC
24

• You may or may not wish to attempt this question
  it was hard to come up with a question that
  matched the technology Simona was using.
• To the right is a sequencing gel read the gel
  and provide the
• DNA sequence it represents.
• The three-letter code of the protein it encodes.
• The single-letter code of the protein it encodes.
• Describe how dideoxy sequencing works.
• Remember, the smallest fragments are at the
  bottom of the gel so assume that is where the
  sequence begins!

ATTGACATAGACTGGGAGCTTCTC ATT GAC ATA GAC TGG GAG
CTT CTC AT TGA CAT AGA CTG GGA GCT TCT C
Stop A TTG ACA TAG ACT GGG AGC TTC TC
Stop
25

• You may or may not wish to attempt this question
  it was hard to come up with a question that
  matched the technology Simona was using.
• To the right is a sequencing gel read the gel
  and provide the
• DNA sequence it represents.
• The three-letter code of the protein it encodes.
• The single-letter code of the protein it encodes.
• Describe how dideoxy sequencing works.
• Remember, the smallest fragments are at the
  bottom of the gel so assume that is where the
  sequence begins!

ATTGACATAGACTGGGAGCTTCTC ATT GAC ATA GAC TGG GAG
CTT CTC I D I D W E L L AT TGA CAT
AGA CTG GGA GCT TCT C Stop A TTG ACA TAG
ACT GGG AGC TTC TC Stop
26
4. The six DNA sequences below represent the same
piece of a gene from 6 different organisms. Three
sequences are from three different individuals of
species A. The other three sequences are from
three different species (B, C, and D). Species D
is the most distantly related to species A.
Which sequences are from species A and which is
from species D? 1 AATGCGTTTGAAGGATTATGATGTTGGGCCA
TTTATTGGCCTAGTGGTAACAATTTTATG 2
AATGCGTTTGAAGGATTATGATGTTGGTCCATTTATTGGCCTAGTGGTAA
CAATTTTATG 3 AATGCGTTTGAAGGATTATGATGTTGGGCCATTCATT
GGCCTAGTGGTAACAATTTTATG 4 AATGCGTTTGAAGGATCGCGATGT
TGGTAAATTCATTGGCCTAGTGGTAACAATTTTATG 5
AATGCGTTTGAAGGATCGCGATGTTGGTAAATTCATTCCCCTAGTGGTAA
CAAAATTATG 6 AATGCGTTTGACGGATCGCGATGGTGGGAAGTTTACT
GGCCTTGTCGTACCAAAATCATG
27
4. The six DNA sequences below represent the same
piece of a gene from 6 different organisms. Three
sequences are from three different individuals of
species A. The other three sequences are from
three different species (B, C, and D). Species D
is the most distantly related to species A.
Which sequences are from species A and which is
from species D?
28
4. The six DNA sequences below represent the same
piece of a gene from 6 different organisms. Three
sequences are from three different individuals of
species A. The other three sequences are from
three different species (B, C, and D). Species D
is the most distantly related to species A.
Which sequences are from species A and which is
from species D?
29
4. The six DNA sequences below represent the same
piece of a gene from 6 different organisms. Three
sequences are from three different individuals of
species A. The other three sequences are from
three different species (B, C, and D). Species D
is the most distantly related to species A.
Which sequences are from species A and which is
from species D?
On the tree below put the number of the sequence
next to the letter of the species.
_____________D6 __________C5 ________B4
__A3 ___A2 _A1
30
(No Transcript)
31
HOMEWORK PART II
32
How are alignments scored?
33
In early 1990s large dataset of highly conserved
local multiple alignments of short segments of
proteins from SWISS-PROT database were used. The
sequence blocks were clustered into groups
according to similarity if they exceeded a
specified threshold for percentage identity (for
example 62). Substitution frequencies for all
possible pairs of amino acids were then
calculated between the clustered groups and used
to calculate BLOck Substitution Matrix scores
(BLOSUM). In the late 1960s Margaret Dayhoff
and her colleagues began using scoring matrices
for alignments based on observation of amino acid
substitution rates in alignments of whole
proteins known to be homologous (gt85 identical).
Her matrices, based on actual evolution, turned
out to be more reliable than substitution
matrices based only on physicochemical or genetic
similarities of amino acids.
Blosum-62
What is the probability that one amino acid will
mutate into another?
PAM 120