Week 4: Structures - Protein and RNA

Assigned readings: Krane Chapter 7 & Appendix 1

Key Topics:

Amino Acids

Polypeptide Composition

Secondary Structure

Tertiary and Quaternary Structure

Algorithms for Modeling Protein Folding

Structure Prediction

Creating and Executing Computer Programs

Variables and Values

Program Control

Readability and Data Structures

Regular Expressions

Day 1: Text based readings, questions and hands-on activities

Chapter 7 Odd-numbered Problems and Appendix 1

Day 2: Web based readings, questions, and hands-on activities, 3-4 websites, 1-2 handouts, 5-8 powerpoint slides

Amino Acids :

Polypeptide Composition :

Secondary Structure :
What Protein Are You? Game

Tertiary and Quaternary Structure :

Algorithms for Modeling Protein Folding :

Structure Prediction :

Creating and Executing Computer Programs :
Notes on appendix 1

Variables and Values :

Program Control :

Readability and Data Structures :

Regular Expressions :

Perl Class
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BioPerl.org

Ultra Conserved element:
TGATCCCGGACTCTATGAATTATTGATGAGATATGAGCGTTGATTTCCCCTTTCAG
GATGCAAACTCCATTATATTGTTAAAATGGCGATTTAATCGTTGAGAATAGCTTTG
GTGTGGGTTTTTTCCCCCAACTCATTTGCGCCTCCTTCCTTTTCATTTAACTCTCT
TAATTAAATCCTTTAACAGATTTTAATCACTTTTTGGAG

Analysis of a Gene that confers resistance to HIV: USCS Genome Browser
CCR5 normal sequence:
ATGGATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGCCAAAAAATCA
ATGTGAAGCAAATCGCAGCCCGCCTCCTGCCTCCGCTCTACTCACTGGTGTTCATCTTTGGTTTTGTGGG
CAACATGCTGGTCATCCTCATCCTGATAAACTGCAAAAGGCTGAAGAGCATGACTGACATCTACCTGCTC
AACCTGGCCATCTCTGACCTGTTTTTCCTTCTTACTGTCCCCTTCTGGGCTCACTATGCTGCCGCCCAGT
GGGACTTTGGAAATACAATGTGTCAACTCTTGACAGGGCTCTATTTTATAGGCTTCTTCTCTGGAATCTT
CTTCATCATCCTCCTGACAATCGATAGGTACCTGGCTGTCGTCCATGCTGTGTTTGCTTTAAAAGCCAGG
ACGGTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAA
TCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACAGTCAGTA
TCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTCATG
GTCATCTGCTACTCGGGAATCCTAAAAACTCTGCTTCGGTGTCGAAATGAGAAGAAGAGGCACAGGGCTG
TGAGGCTTATCTTCACCATCATGATTGTTTATTTTCTCTTCTGGGCTCCCTACAACATTGTCCTTCTCCT
GAACACCTTCCAGGAATTCTTTGGCCTGAATAATTGCAGTAGCTCTAACAGGTTGGACCAAGCTATGCAG
GTGACAGAGACTCTTGGGATGACGCACTGCTGCATCAACCCCATCATCTATGCCTTTGTCGGGGAGAAGT
TCAGAAACTACCTCTTAGTCTTCTTCCAAAAGCACATTGCCAAACGCTTCTGCAAATGCTGTTCTATTTT
CCAGCAAGAGGCTCCCGAGCGAGCAAGCTCAGTTTACACCCGATCCACTGGGGAGCAGGAAATATCTGT
GGGCTTGTGA

CCR5 mutant sequence:
ATGGATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGCCAAAAAATCA
ATGTGAAGCAAATCGCAGCCCGCCTCCTGCCTCCGCTCTACTCACTGGTGTTCATCTTTGGTTTTGTGGG
CAACATGCTGGTCATCCTCATCCTGATAAACTGCAAAAGGCTGAAGAGCATGACTGACATCTACCTGCTC
AACCTGGCCATCTCTGACCTGTTTTTCCTTCTTACTGTCCCCTTCTGGGCTCACTATGCTGCCGCCCAGT
GGGACTTTGGAAATACAATGTGTCAACTCTTGACAGGGCTCTATTTTATAGGCTTCTTCTCTGGAATCTT
CTTCATCATCCTCCTGACAATCGATAGGTACCTGGCTGTCGTCCATGCTGTGTTTGCTTTAAAAGCCAGG
ACGGTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAA
TCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACATTAAAGA
TAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTCATGGTCATCTGCTACTCGGGAATCCTAAAAACTCT
GCTTCGGTGTCGAAATGAGAAGAAGAGGCACAGGGCTGTGAGGCTTATCTTCACCATCATGATTGTTTAT
TTTCTCTTCTGGGCTCCCTACAACATTGTCCTTCTCCTGAACACCTTCCAGGAATTCTTTGGCCTGAATA
ATTGCAGTAGCTCTAACAGGTTGGACCAAGCTATGCAGGTGACAGAGACTCTTGGGATGACGCACTGCTG
CATCAACCCCATCATCTATGCCTTTGTCGGGGAGAAGTTCAGAAACTACCTCTTAGTCTTCTTCCAAAAG
CACATTGCCAAACGCTTCTGCAAATGCTGTTCTATTTTCCAGCAAGAGGCTCCCGAGCGAGCAAGCTCAG
TTTACACCCGATCCACTGGGGAGCAGGAAATATCTGTGGGCTTGTGA

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