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LESSON 4: Using Bioinformatics to Analyze Protein Sequences

LESSON 4: Using Bioinformatics to Analyze Protein Sequences. PowerPoint slides to accompany Using Bioinformatics : Genetic Research.

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LESSON 4: Using Bioinformatics to Analyze Protein Sequences

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  1. 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

  2. Biological AnthropologistMichael 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.

  3. DNA is Complementary and Anti-Parallel Gene or coding strand 5’- CCGATGTCATAAGAC - 3’

  4. DNA is Complementary and Anti-Parallel Gene or coding strand 5’- CCGATGTCATAAGAC - 3’ 3’- GGCTACAGTATTCTG - 5’ Template or non-coding strand

  5. Translating DNA into Proteins Gene or coding strand 5’- CCGATGTCATAAGAC - 3’ 3’- GGCTACAGTATTCTG - 5’ Template or non-coding strand

  6. Translating DNA into Proteins Gene or coding strand 5’- CCGATGTCATAAGAC - 3’ 3’- GGCTACAGTATTCTG - 5’ 3’- - 5’ Template or non-coding strand GGC UAC AGU AUU CUG tRNAs 5’- CCGAUGUCAUAAGAC - 3’ mRNA

  7. How Do We Know Where to Start Translation? Gene or coding strand 5’- CCGATGTCATAAGAC - 3’ 3’- GGCTACAGTATTCTG - 5’ 3’- - 5’ Template or non-coding strand GGC UAC AGU AUU CUG tRNAs 5’- CCGAUGUCAUAAGAC - 3’ mRNA

  8. The Codon Table

  9. Phenyl-alanine (Phe / F) Glycine (Gly / G) Aspartic Acid (Asp / D) Glutamic Acid (Glu / E) 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)

  10. Amino Acid Side Chains and Chemistry Amino Acid Side Chain (R-Group): R H2N CH C OH Amino Acid Backbone: O

  11. Phenyl-alanine (Phe / F) Glycine (Gly / G) Aspartic Acid (Asp / D) Glutamic Acid (Glu / E) Leucine (Leu / L) Serine (Ser / S) Tyrosine (Tyr / Y) Alanine (Ala / A) STOP Cysteine (Cys / C) Valine (Val / V) Step 1 STOP Tryptophan (Trp / W) Step 2 Arginine (Arg / R) Leucine (Leu / L) Serine (Ser / S) Step 3 Step 4 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)

  12. DNA is Complementary and Anti-Parallel Gene or coding strand 5’- CCGATGTCATAAGAC - 3’ 3’- GGCTACAGTATTCTG - 5’ Template or non-coding strand

  13. DNA is Complementary and Anti-Parallel Gene or coding strand 5’- CCGATGTCATAAGAC - 3’ 3’- GGCTACAGTATTCTG - 5’ Template or non-coding strand

  14. What are Reading Frames? “Gene” Sequence: thecatatetherat. Reading Frame +1 starts at the first letter: the cat ate the rat. Reading Frame +2starts at the second letter: t hec ata tet her at. Reading Frame +3starts 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.

  15. How Do We Know Where to Start Translation? Reading Frame +1 5’- CCGATGTCATAAGAC - 3’ 3’- GGCTACAGTATTCTG - 5’

  16. How Do We Know Where to Start Translation? Reading Frame +1 P M S STOP 5’- CCGATGTCATAAGAC - 3’ 3’- GGCTACAGTATTCTG - 5’

  17. How Do We Know Where to Start Translation? Reading Frame +2 R C H K 5’- CCGATGTCATAAGAC - 3’ Reading Frame +1 P M S STOP 5’- CCGATGTCATAAGAC - 3’ 3’- GGCTACAGTATTCTG - 5’

  18. How Do We Know Where to Start Translation? Reading Frame +2 R 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

  19. Biological AnthropologistMichael 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.

  20. 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

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