Structure of Nucleotides (Figure 8.1) Purine and Pyrimidine Bases (Figure 8.2) DNA and RNA (Figure 8.7) Watson-Crick base pairing (Figure 8.11) A, B, and Z DNA, RNA structure (Figure 8.17 and 8.25) DNA denaturation (Figure 8.27)
Reading: Chapter 8, pp. 272-298 2 Lecture 4: Amino Acids Reading: Chapter 3, pp. 71-81
Structure of an amino acid 20 common amino acids Acid-base properties of amino acids Disulfide bonds Properties of amino acids 3 Gene Expression: Genes to Proteins Translation: mRNA is decoded by the ribosome and tRNA is used to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. Transcription: Creates a complementary RNA copy (messenger RNA, mRNA ) of a sequence of DNA (gene). http://en.wikipedia.org/wiki/Protein_biosynthesis http://en.wikipedia.org/wiki/Translation_(genetics) 4 Proteins Phenotype of an organism determined by proteins Three-dimensional structure of proteins defines function by interaction 5 The Protein Database http://www.rcsb.org/pdb/ 6 Two-dimensional gel showing more than 1,000 different proteins from E. coli (see Fig. 3-21 pp. 91) Proteins in a Cell 7 Ampholyte molecule contain both acidic and basic groups and will exist mostly as zwitterions (next slide) in a certain range of pH (a (alpha) carbon) (side chain, R) (Amino group, NH 2 /NH 3 + ) (Carboxyl group, COOH/COO - ) Amino Acids (AAs) 8 Zwitterion Form of Amino Acid at neutral pH Figure 3-9. Lehninger, 5 th Ed. 9 Charge of an Amino Acid The charge on an amino acid is dependent on the pH of the solution. Increasing pH 10 pI = pK a1 +log [ HA] [ HAH + ] pI = pK a2 +log [ A - ] [ HA] At the isoelectric point (pI = pH), average charge equals 0 HAH+ HA A- Two equilibrium dissociation reactions involve the zero charge species, The Henderson-Hasselbalch equation can be applied at pI for both equilibrium dissociations. Isoelectric Point of Amino Acids HAH + HA + H + A - + H + HA
] [HAH + ] The two Henderson-Hasselbalch equations can be added to solve for pI. HAH+ HA A- Cancelling out [HA] gives, Isoelectric Point of Amino Acids (cont.) 2pI=pK a1 + pK a2 +log [HA] [HAH + ] +log [A - ] [HA] = pK a1 +pK a2 +log [HA][A - ] [HAH + ][HA] pI = pK a1 +pK a2 2 @ pI, [A - ]=[HAH + ] so, Fig. 3-10. Lehninger, 5 th Ed. 12 Side Chains, R, Defines Amino Acid 20 common amino acids found in proteins (plus other uncommon AAs and AAs modified after translation) Differ in properties because of side chain, R R=H is the simplest amino acid, glycine Many ways to classify amino acids based on properties Size and shapes Charge(s) Polarity Hydrophilicity/Hydrophobicity (either attracts/excludes water) Aromaticity (stacking interactions) Conformation usually determined by side chain Propensity to adopt a particular conformation in proteins (a combination of the above) Memorize the structure (and properties) of the 20 amino acids
13 Tetrahedral carbon atom has 4 substituent groups. 4 different groups = chiral At least 2 of the 4 groups the same = achiral Chiral Achiral Molecular Asymmetry 14 Looking along the H-C a bond, with H atom closest to you and reading clockwise, the groups attached to the C a spell CORN The central carbon (C a - atom) is a chiral center Encoded proteins have the L-configuration at this chiral center L-configuration can be remembered as the CORN law Amino Acid Structure 15 Stereoisomers of a-amino acids 16 L- and D-Stereoisomers of a-amino acids 17 Structures at neutral pH These side chains are nonpolar and hydrophobic. Ala, Val, Leu and Ile tend to cluster together on the inside of proteins, stabilizing protein structure via hydrophobic interactions. Figure 3-5. Lehninger, 5 th Ed. AAs with nonpolar, aliphatic R groups 18 Structures at neutral pH Phe, Tyr and Trp are relatively hydrophobic. But the hydroxyl group of Tyr can form hydrogen bonds and plays an important functional role in some enzymes. AAs with aromatic R groups 19 Structures at neutral pH The R groups are more hydrophilic because their functional groups can form H bonds with water. Asn and Gln are amides of two other common amino acids, aspartate (Asp) and glutamate (Glu). Fig. 3-5. Lehninger, 5 th Ed. AAs with polar, uncharged R groups 20 Cysteine - Ionize the side chain at relatively high pH Pairs of cysteines can oxidize to form cystine through a disulfide bond (examples shown later). Cystine is non- polar and strongly hydrophobic. Bovine Pancreatic Trypsin Inhibitor Disulfide Bonds 21 Basic Amino Acids: Lys, Arg and His have significant positive charge at pH 7.0. Also His is the only amino acid with an ionizable side chain that has a pK a near neutrality. Therefore, His can serve as a proton donor or acceptor in many enzyme-catalyzed reactions. The most hydrophilic R groups are those that are either positively or negatively charged. Structures at neutral pH Fig. 3-5. Lehninger, 5 th Ed. AAs with positively charged R groups 22 Structures at neutral pH Acidic Amino Acids: Asp and Glu, have R groups (a second carboxyl group) with a net negative charge at pH 7.0. AAs with negatively charged R groups 23 Titration of Amino Acids with Ionizable Side Chains Fig. 3-12b. Lehninger, 5 th Ed. +1 -0.5 +0.5 0.0 pI =7.59 +1.5 x pK 1 =1.82
pK R =6.0 pK 2 =9.17
+2 +1 -1 0 Net charge 24 Detect the present of particular biomolecules and estimate concentration Characterization of Biomolecules by Light Absorption Using a Spectrophotometer 25 Fig. 5.6, Biochemistry, Mathews, Van Holde & Ahern UV Light Absorbance by Amino Acids and Proteins 26 a b g d 1 d 2
Carbon Labeling Convention in Amino Acids 27 Properties of Free Amino Acids 28 Properties of Free Amino Acids (cont.) 29 Alanine Ala A first amino acid (AA) alphabetically, ABC Cysteine Cys C only AA to start with C Aspartate Asp D asparDate (or if you prefer, asparDic acid) Glutamate Glu E gluEtamate (or gluEtamic acid) Phenylalanine Phe F Fenylalanine Glycine Gly G Just because its the easy G to remember! Histidine His H only AA starting with H Isoleucine Ile I only AA starting with I Lysine Lys K (K is near L in alphabet) Leucine Leu L alphabetically first of the AAs starting with L Methionine Met M only AA starting with M Asparagine Asn N asparagiNe Proline Pro P starts with P and is P-shaped (imino acid ring) Glutamine Gln Q Q-tamine Arginine Arg R R-ginine Serine Ser S only AA starting with S Threonine Thr T alphabetically first AA starting with T Valine Val V only AA starting with V Tryptophan Trp W tWyptophan (Elmer Fudd's favorite AA) Tyrosine Tyr Y tYrosine One and three letter codes for AAs 30 Dietary Needs Human diets must include adequate amounts of nine amino acids histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine These essential amino acids cannot be synthesized (de novo) from other precursors so are necessary for a healthy diet However, cysteine can partially meet the need for methionine (both contain sulfur) and tyrosine can partially substitute for phenylalanine
In addition, the following are considered conditionally essential arginine, cysteine, glutamine, glycine, tyrosine They are not normally required in the diet, but must be supplied to specific populations that do no synthesize adequate amounts