LESSON 4 Using Bioinformatics to Analyze Protein Sequences

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LESSON 4Bioinformatics & Proteins: Slide #8Side chains or R-groups: Uniqueportions of an amino acid that givethe amino acid its chemical properties(such as hydrophobic, hydrophilic, acidic[negatively-charged], or basic [positivelycharged]).There are 20 different aminoacids specified by the genetic code.Hydrophobic: A substance that repelswater. From the Greek “hydro,” whichmeans water, and “phobos,” whichmeans fear. A synonym for nonpolar.The opposite of hydrophilic or polar.19. Tell students that this codon table also contains information about aminoacid chemistry.20. Show students Slide #9, which illustrates the amino acid side chains orR-groups, and the categories used to describe amino acid side chains.Bioinformatics & Proteins: Slide #9Nonpolar: A substance that repels water.A synonym for hydrophobic.Hydrophilic: A substance that isattracted to water. From the Greek“hydro,” which means water, and“philos” meaning love. A synonym forpolar. The opposite of hydrophobic ornonpolar.Using Bioinformatics: Genetic ResearchPolar: A substance that is attracted towater. A synonym for hydrophilic. Theopposite of hydrophobic or nonpolar.Acidic: Side chains of amino acids thatcan act as a proton donor (-COOH) andgive up a hydrogen, leaving a negativelychargedside chain (-COO - ). Acidic aminoacids are negatively charged.Basic: Side chains of amino acids thatcontain chemical groups, like aminogroups (-NH 2 ), that can accept ahydrogen (-NH3 + ). Basic amino acids arepositively charged.21. Tell students that these categories include:• Hydrophobic or nonpolar, which are amino acids with side chains thatrepel water.• Hydrophilic or polar, which are amino acids with side chains that areattracted to water.• Acidic or negatively-charged side chains, such as amino acids that containcarboxyl groups (-COO - ) as side chains.• Basic or positively-charged side chains, such as amino acids that containamine groups (-NH3+) as side chains.128©Northwest Association for Biomedical Research—Updated October 2012
LESSON 422. Show Slide #10, which is the same codon table as in Slide #8. Walkstudents through the example of the start codon AUG, encouraging them tofollow along on Student Handout—Codons and Amino Acid Chemistry. Clickthe space bar or forward arrow to advance the animation. A gray arrow willappear for each step.• Step 1: Start in the center of the table, in the “A” quadrant for the firstposition of the codon.• Step 2: From the A quadrant, move to the next outer ring and locate the“U” slice for the second position of the codon.• Step 3: From the U slice, move to the third ring outward to the thirdposition of the codon in the “G” slice.• Step 4: From the G slice, move to the outermost ring and locate theamino acid that corresponds to it – in this case methionine (M), which iscolored yellow because it is nonpolar/hydrophobic, also indicated by the“N” on the codon table.Bioinformatics & Proteins: Slide #1023. Importance of Side Chains:Explain to students that amino acids are often characterized by genetic researchersbased on the chemistry of their side chains or R-groups. When mutations changethe coding sequence and replace one amino acid with one that has differentchemical properties, the function of the protein can be reduced, or the proteinmay not function at all. This is called a non-conservative change. For example,some proteins are held together when the side chains of positive and negativeamino acids are attracted to each other. If a negatively-charged amino acid wereto be replaced with a positively-charged amino acid, the interaction would belost, and the protein may not hold its shape anymore. When mutations changethe coding sequence and replace one amino acid with one that has the samechemical properties, this is called a conservative change.24. Methionine:Tell students that methionine, like the other amino acids colored yellow onthe table, is hydrophobic (also called nonpolar, and noted with an “N” on thecodon table). This means that these amino acids do not like water, or repelwater. In proteins, these amino acids are often buried in the center to theprotein, away from water.Non-conservative: When amino acidchanges observed between two or moresequences do not share the same sidechain or R-group chemistry.Conservative: When amino acidchanges observed between two or moresequences do share the same side chainor R-group chemistry.[Note: During the Bio-ITEST Introductoryunit, Using Bioinformatics: GeneticTesting, the M1775R mutation studentslearned about in the BRCA1 proteinchanged the amino acid chemistry froma hydrophobic methionine (M) to apositively-charged arginine (R) at aminoacid position #1775.]Lesson 4 – Using Bioinformatics to Analyze Protein Sequences129©Northwest Association for Biomedical Research—Updated October 2012
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LESSON 4 Using Bioinformatics to Analyze Protein Sequences

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