Download Basic Biochemistry

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
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