CHAPTER 3 Amino Acids, Peptides, Proteins
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1 CHAPTER 3 Amino Acids, Peptides, Proteins Learning goals: Structure and naming of amino acids Structure and properties of peptides Ionization behavior of amino acids and peptides Methods to characterize peptides and proteins
2 Proteins: Main Agents of Biological Function Catalysis enolase (in the glycolytic pathway) DNA polymerase (in DNA replication) Transport hemoglobin (transports O 2 in the blood) lactose permease (transports lactose across the cell membrane) Structure collagen (connective tissue) keratin (hair, nails, feathers, horns) Motion myosin (muscle tissue) actin (muscle tissue, cell motility)
3 Proteins serve a wide range of biological functions
4 Amino Acids: Building Blocks of Protein Proteins are linear heteropolymers of α-amino acids Amino acids have properties that are well-suited to carry out a variety of biological functions Capacity to polymerize Useful acid-base properties Varied physical properties Varied chemical functionality
5 Amino acids share many features, differing only at the R substituent
6 Most α-amino acids are chiral The α-carbon always has four substituents and is tetrahedral All (except proline) have: an acidic carboxyl group a basic amino group an α-hydrogen connected to the α-carbon The fourth substituent (R) is unique In glycine, the fourth substituent is also hydrogen
7 Amino Acids: Atom Naming Organic nomenclature: start from one end Biochemical designation: start from α-carbon and go down the R-group
8 All amino acids are chiral (except glycine) Proteins only contain L amino acids
9 Amino Acids: Classification Common amino acids can be placed in five basic groups depending on their R substituents: Nonpolar, aliphatic (7) Aromatic (3) Polar, uncharged (5) Positively charged (3) Negatively charged (2)
10
11 These amino acid side chains absorb UV light at nm
12 These amino acids side chains can form hydrogen bonds. Cysteine can form disulfide bonds.
13
14
15 Uncommon Amino Acids in Proteins Not incorporated by ribosomes except for Selenocysteine Arise by post-translational modifications of proteins Reversible modifications, especially phosphorylation, are important in regulation and signaling
16 Modified Amino Acids Found in Proteins
17 Reversible Modifications of Amino Acids
18 Ionization of Amino Acids At acidic ph, the carboxyl group is protonated and the amino acid is in the cationic form. At neutral ph, the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; such ions are called Zwitterions. At alkaline ph, the amino group is neutral NH 2 and the amino acid is in the anionic form.
19 Cation Zwitterion Anion
20 Chemical Environment Affects pk a Values α-carboxy group is much more acidic than in carboxylic acids α-amino group is slightly less basic than in amines
21 Amino acids can act as buffers Amino acids with uncharged side chains, such as glycine, have two pk a values: The pk a of the α-carboxyl group is 2.34 The pk a of the α-amino group is 9.6 It can act as a buffer in two ph regimes.
22 Buffer Regions
23 Amino acids carry a net charge of zero at a specific ph (the pi) Zwitterions predominate at ph values between the pk a values of the amino and carboxyl groups For amino acids without ionizable side chains, the Isoelectric Point (equivalence point, pi) is pk 1 + pk pi = 2 2 At this point, the net charge is zero AA is least soluble in water AA does not migrate in electric field
24 Ionizable side chains can show up in titration curves Ionizable side chains can be also titrated Titration curves are now more complex pk a values are discernable if two pk a values are more than two ph units apart Why is the side chain pk a so much higher?
25
26 How to Calculate the pi When the Side Chain is Ionizable Identify species that carries a net zero charge Identify pk a value that defines the acid strength of this zwitterion: (pk 2 ) Identify pk a value that defines the base strength of this zwitterion: (pk 1 ) Take the average of these two pk a values What is the pi of histidine?
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