Amino Acids and Peptides Chapter 3. Why is it important to specify the three dimensional structure...

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Transcript of Amino Acids and Peptides Chapter 3. Why is it important to specify the three dimensional structure...

  • Slide 1
  • Amino Acids and Peptides Chapter 3
  • Slide 2
  • Why is it important to specify the three dimensional structure of amino acids? Three dimensional structure of amino acids -carbon has amino group and carboxyl group R-group identity to amino acid Also bond to hydrogen
  • Slide 3
  • What is Stereochemistry? Nonsuperimposable mirror images Chiral All protein-derived amino acids have at least one stereocenter (the -carbon) and are chiral (stereoisomers) except glycine Two stereoisomers of amino acids are designated L- or D-
  • Slide 4
  • Amino acid structures (figure 3.3) The position of amino group on left or right side of alpha carbon determines the L or D designation L-amino acids are found in all proteins; D- amino acid image found in proline D-amino acids are found in nature Three letter or one-letter codes refer to amino acids Memorize table 3.1
  • Slide 5
  • Why are amino acid side chains so important? Side chains classification of amino acids Polar and nonpolar nature of side chain Acidic or basic group in side chain Nature of functional groups in side chains Side chain simplest in glycine Can be larger and complex Carbon atoms -, -, -, - and - carbons (refer to lysine in figure 3.3)
  • Slide 6
  • Which amino acids have nonpolar side chains? (Group 1) Nonpolar side chains Ala, Val, Leu, Ile, Pro, Phe, Trp and Met Ala, Val, Leu, Ile. Pro aliphatic hydrocarbon group- (absence of a benzene ring) - Proline has cyclic aliphatic structure
  • Slide 7
  • Which amino acids have nonpolar side chains? (Group 1) Phenylalanine hydrocarbon is aromatic (contains cyclic group similar to benzene ring) Trp aromatic indole ring side chain Met Sulfur + aliphatic hydrocarbon groupings in side chain
  • Slide 8
  • Which amino acids have electrically neutral polar side chains? (group 2) Neutral polar side chains electrically neutral (uncharged) at neutral pH Ser, Thr, Tyr, Cyc, Glu, Asn
  • Slide 9
  • Which amino acids have electrically neutral polar side chains? (group 2) Ser, Thr polar hydroxyl (-OH) group Tyr hydroxyl group bonded to aromatic hydrocarbon group Cys thiol group (-SH) Gln, Asn amide bonds
  • Slide 10
  • Which amino groups have carboxyl groups in their side chains? (Group 3) Acidic side chains Glutamic acid (Glu) and Aspartic acid (Asp) Carboxyl group (in addition to one already present) Lose a proton to form carboxylate anion Negatively charged at neutral pH
  • Slide 11
  • Which amino acids have basic side chains? Basic side chains His, Lys, Arg Positively charged at or near neutral pH Lys NH3 group is attached to an aliphatic hydrocarbon chain Arg Guanidino group His Imidazole group
  • Slide 12
  • Amino acid summary carbon present in 20 amino acids amino group is primary (19 aa) and secondary in proline carbon is stereo centre in all except glycine Isoleucine and threonine second stereo center Letter codes in table 3.1
  • Slide 13
  • Uncommon amino acids Why some amino acids are found less commonly in proteins? Produced by modification of parent amino acid in posttranslation
  • Slide 14
  • Uncommon amino acids Why amino acids are found less commonly in proteins? Hydroxylysine and Hydroxyproline differ from parent by having hydroxyl groups on their side chains- found in connective-tissue proteins-collagen Thyroxine has extra iodine-containing aromatic group- found in thyroid glands
  • Slide 15
  • What are zwitterions? Amino acids without charged groups on their side chains exist in neutral solution zwitterions - with no net charge Zwitterions have equal positive and negative charges at neutral pH electrically neutral
  • Slide 16
  • Why aminoacids can act as both acids and bases? The pKa values of carboxyl groups are 2 The pKa values of amino group are 9 to 10.5 The classification of aa as acidic or basic depends on pKa of side chain as well as chemical nature of group
  • Slide 17
  • Why aminoacids can act as both acids and bases? Histidine, Lysine and arginine basic aa amino group - high pKa Aspartic acid and glutamic acid acidic aa carboxylic side chains low pKa Have titratable protons. Some side chains do as well
  • Slide 18
  • What happens when we titrate an amino acid? Titration curve indicates reaction of each functional group with hydrogen ion
  • Slide 19
  • Titration of alanine with NaOH At low pH uncharged carboxyl group and positively charged amino group Alanine has a positive charge of 1 As base is added, carboxyl group loses proton negatively charged carboxylate group and pH increases
  • Slide 20
  • Titration of alanine with NaOH Alanine has no net charge pH increases with addition of base aminogroup loses it proton Alanine has negative charge of 1 Diprotic acid
  • Slide 21
  • What is Isoelectric point? Positive and negative charges are equal no net charge Isoelectric point or pH pI = pKa1 + pKa2 2 Determines properties of amino acids and proteins
  • Slide 22
  • Which groups on amino acids react to form a peptide bond? Individual amino acids can be linked by forming covalent bonds PEPTIDE (amide) bond is formed between carboxyl group of one amino acid and amino group of another amino acid Dipeptide, tripeptide, polypeptide (> 100 amino acids)
  • Slide 23
  • Geometry of peptide bond The four atoms of a peptide bond joined by two alpha carbon atoms lie in planar plane with bond angles of 120 about C and N Represented as a hybrid of two contributing structures resonance structures
  • Slide 24
  • What are some biological functions of small peptides? Marked physiological effects in organisms Naturally occurring dipeptide carnosine is found in muscle tissue Glutathione scavanger of oxidizing agents Oxytocin and vasopressin hormones Enkephalins naturally occurring painkillers
  • Slide 25
  • Carnosine Carnosine has alternative name beta alanyl-L-histidine
  • Slide 26
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  • Slide 27
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