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Transcript
Lecture One: Amino acids [Based on Chapter 2 – Berg, Tymoczko & Stryer] (Figures in Red are for the 7th Edition) Amino acids Amino acids are the building blocks of proteins FIVE elements are used in amino acids Hydrogen Carbon _______ _______ _______ Together with Phosphorus these are the fundamental elements of life Figure 2-5, page 27 (2-5, page 27) This figure represents an -amino acid Consists of C => The Central carbon atom NH2 => Amino group COOH => Carboxyl (acid) group H => Hydrogen atom R => ____________________ Usually amino acids exist as a ___________ Known as a Zwitterion Depends on pH Figure 2-6, page 27 (2-6, page 27) Different ionisation states are found at different pHs pH = 1 ==> Positively charged pH = 7 ==> Dipolar ion (neutral) pH = 11 ==> Negatively charged Figure 2-4, page 27 (2-4, page 27) There are FOUR different atoms attached to the -carbon Amino acids exist as optically active pairs L-Isomer D-Isomer Only the _________ amino acids are found in proteins Twenty different amino acids are found in proteins Twenty different side chains Key features of the different side chains ____ ______ ______ Hydrophobic Character Hydrogen Bonding Capacity Chemical Reactivity Nomenclature There are three ways of referring to amino acids Full Name Three Letter Abbreviation The first three letters (with EXCEPTIONS) One Letter Abbreviation The first letter (again, with EXCEPTIONS) It is IMPORTANT to know all three nomenclature forms Figure 2-7 & Figure 2-8 pages 28 & 29 (2-7, page 29) Aliphatic amino acids Glycine ===> Methionine Increasing Size Increasing Hydrophobicity Hydrophobicity => Water hating Usually found away from the water Inside proteins in the CORE Methionine contains Sulphur Figure 2-9, page 29 (2-7, page 29) Proline => Unique with a cyclic side chain Often found at bends in protein structures Figure 2-10, page 30 (2-7, page 29 and 2-8, page 30) Aromatic amino acids All contain a phenyl ring All are ____________ Tyrosine is less hydrophobic since it has an OH group The side chains become increasingly bulky in size Tryptophan = Trp = W = Widest amino acid The electron clouds allow for interaction with other systems This enables electron transfer to take place Figure 2-13, page 31 (2-8, page 30) Cysteine also contains Sulphur This amino acid is _____________ This is because of the SH group Figure 2-11, page 31 (2-8, page 30) Serine and Threonine Similar to Alanine and Valine respectively Serine also similar to Cysteine However, the OH group makes them more Hydrophilic Hydrophilic => _____________ Usually found on the protein surface Figure 2-14, page 32 (2-9, page 31) Basic amino acids Lysine and Arginine have the longest side chains of the amino acids and terminate with positively charged group at pH 7 Figure 2-14 & Figure 2-15, page 32 (2-9 and 2-10, page 30) Histidine The charge on the side chain of histidine varies with the local pH Very Important for ______________ Figure 2-16, page 33 (2-11, page 32) Acidic amino acids Aspartic acid and Glutamic acid Also referred to as Aspartate and Glutamate Usually negatively charged at physiological pH Figure 2-12, page 31 (2-8, page 30) Uncharged derivatives Asparagine and Glutamine NH2 replaces a side chain Oxygen in the Carboxylate group Table 2-1, page 33 (Table 2-1, page 32) There are Seven amino acids with ionisable side chains Aspartic acid Glutamic acid _________ Cysteine Tyrosine Lysine _________ The terminal carboxyl group and the terminal amino group can also be ionised Table 2-2, page 33 (Table 2-2, page 32) This table summarises the nomenclature used for amino acids These abbreviations are integral to biochemistry Summary of Lecture One: There are Twenty common amino acids used in proteins Two possible isomers L-Isomer & D-Isomer Only the L-Isomer is found in proteins Six key features Size, Shape, Charge, Hydrogen Bonding Capacity, Hydrophobic Character and Chemical Reactivity Seven ionisable side chains Histidine important as side chain charge varies at near physiological pH Nomenclature Three formats for amino acids Full name, Three & One letter abbreviations INTEGRAL TO BIOCHEMISTRY & MANY OTHER RELATED DISCIPLINES