Transcript Genetic Research Lesson 4

LESSON 4:
Using Bioinformatics to Analyze Protein Sequences
PowerPoint slides to accompany
Using Bioinformatics:
Genetic Research
Chowning, J., Kovarik, D., Porter, S., Grisworld, J., Spitze, J., Farris, C., K. Petersen, and T.
Caraballo. Using Bioinformatics: Genetic Research. Published Online October 2012. figshare.
http://dx.doi.org/10.6084/m9.figshare.936568
Biological Anthropologist
Michael Crawford, PhD
Place of Employment:
University of Kansas
Type of Work:
DNA analysis to study the history of human
population and migrations
Science was something that I was always
excited about. I have one foot in anthropology
as an anthropological geneticist; therefore I’m
not strictly limited to a laboratory, but can go
into the field for my work reconstructing the
history of human populations and their origins
based on population genetics.
DNA is Complementary and Anti-Parallel
Gene or
coding strand
5’- CCGATGTCATAAGAC - 3’
DNA is Complementary and Anti-Parallel
Gene or
coding strand
5’- CCGATGTCATAAGAC - 3’
3’- GGCTACAGTATTCTG - 5’
Template or
non-coding strand
Translating DNA into Proteins
Gene or
coding strand
5’- CCGATGTCATAAGAC - 3’
3’- GGCTACAGTATTCTG - 5’
Template or
non-coding strand
Translating DNA into Proteins
Gene or
coding strand
5’- CCGATGTCATAAGAC - 3’
tRNAs
3’- GGC UAC AGU AUU CUG - 5’
mRNA
5’- CCGAUGUCAUAAGAC - 3’
3’- GGCTACAGTATTCTG - 5’
Template or
non-coding strand
How Do We Know Where to
Start Translation?
Gene or
coding strand
5’- CCGATGTCATAAGAC - 3’
tRNAs
3’- GGC UAC AGU AUU CUG - 5’
mRNA
5’- CCGAUGUCAUAAGAC - 3’
3’- GGCTACAGTATTCTG - 5’
Template or
non-coding strand
The Codon Table
Aspartic
Acid
(Asp / D)
Glutamic
Acid
(Glu / E)
Glycine
(Gly / G)
Phenylalanine
(Phe / F)
Leucine
(Leu / L)
Serine
(Ser / S)
Tyrosine
(Tyr / Y)
Alanine
(Ala / A)
STOP
Cysteine
(Cys / C)
Valine
(Val / V)
STOP
Tryptophan
(Trp / W)
Arginine
(Arg / R)
Leucine
(Leu / L)
Serine
(Ser / S)
Proline
(Pro / P)
Lysine
(Lys / K)
Methionine
(Met/ M)
Asparagine
(Asn / N)
Threonine
(Thr / T)
Isoleucine
(Ile/ I)
Arginine
(Arg / R)
Glutamine
(Gln / Q)
Histidine
(His / H)
Amino Acid Side Chains and Chemistry
Amino Acid Side Chain
(R-Group):
Amino Acid Backbone:
R
H2 N
CH
C
O
OH
Aspartic
Acid
(Asp / D)
Glutamic
Acid
(Glu / E)
Phenylalanine
(Phe / F)
Glycine
(Gly / G)
Leucine
(Leu / L)
Serine
(Ser / S)
Tyrosine
(Tyr / Y)
Alanine
(Ala / A)
STOP
Cysteine
(Cys / C)
Valine
(Val / V)
STOP
Tryptophan
(Trp / W)
Arginine
(Arg / R)
Step 1
Leucine
(Leu / L)
Serine
(Ser / S)
Step 2
Step 3
Lysine
(Lys / K)
Methionine
(Met/ M)
Asparagine
(Asn / N)
Threonine
(Thr / T)
Proline
(Pro / P)
Step 4
Isoleucine
(Ile/ I)
Arginine
(Arg / R)
Glutamine
(Gln / Q)
Histidine
(His / H)
DNA is Complementary and Anti-Parallel
Gene or
coding strand
5’- CCGATGTCATAAGAC - 3’
3’- GGCTACAGTATTCTG - 5’
Template or
non-coding strand
DNA is Complementary and Anti-Parallel
Gene or
coding strand
5’- CCGATGTCATAAGAC - 3’
3’- GGCTACAGTATTCTG - 5’
Template or
non-coding strand
What are Reading Frames?
“Gene” Sequence: thecatatetherat.
Reading Frame +1 starts at the first letter:
the cat ate the rat.
Reading Frame +2 starts at the second letter:
t hec ata tet her at.
Reading Frame +3 starts at the third letter:
th eca tat eth era t.
Reading Frames -1, -2 & -3 would be like reading the sentence “backwards.”
The period at the end of the sentence is like a stop codon.
Open Reading Frame: the cat ate the rat.
How Do We Know Where to
Start Translation?
Reading Frame +1
5’- CCGATGTCATAAGAC - 3’
3’- GGCTACAGTATTCTG - 5’
How Do We Know Where to
Start Translation?
Reading Frame +1
P
M
S
STOP
5’- CCGATGTCATAAGAC - 3’
3’- GGCTACAGTATTCTG - 5’
How Do We Know Where to
Start Translation?
R
Reading Frame +2
C
H
K
5’- CCGATGTCATAAGAC - 3’
Reading Frame +1
P
M
S
STOP
5’- CCGATGTCATAAGAC - 3’
3’- GGCTACAGTATTCTG - 5’
How Do We Know Where to
Start Translation?
R
Reading Frame +2
C
H
K
5’- CCGATGTCATAAGAC - 3’
Reading Frame +1
P
M
S
STOP
5’- CCGATGTCATAAGAC - 3’
3’- GGCTACAGTATTCTG - 5’
Reading Frame -1
R
H
STOP
L
V
Biological Anthropologist
Michael Crawford, PhD
Place of Employment:
University of Kansas
Type of Work:
DNA analysis to study the history of human
population and migrations
Science was something that I was always
excited about. I have one foot in anthropology
as an anthropological geneticist; therefore I’m
not strictly limited to a laboratory, but can go
into the field for my work reconstructing the
history of human populations and their origins
based on population genetics.
CAREERS IN SPOTLIGHT:
Biological Anthropologist
What do they do?
Also called Physical Anthropologists, Biological Anthropologists study the
development of the human species in the context of other primates and fossils.
They:
• compare and contrast traits among species
• study why and when certain traits evolved or disappeared
What kind of training is involved?
Bachelor’s or Master’s degree to work in the field. PhD to run your own lab.
What is a typical salary for a Biological Anthropologist?
Bachelor’s Degree: $35,000 to $40,000 ($17.50–$19.00/hour)
PhD, Full Professor: up to $150,000/year ($72.00/hour)
Source: Bureau of Labor and Statistics