Introduction to Proteins; Amino Acids, the Building Blocks of Proteins

Transcription

1 Lecture 3 Introduction to Proteins; Amino Acids, the Building Blocks of Proteins Reading: Berg, Tymoczko & Stryer: Chapter 2, pp Appendix to Chapter 2, pp (visualizing protein structures) See also posted General Chemistry Review notes for acid-base concepts, and online website on amino acids (linked in lecture notes directory) for excellent way to learn the amino acids structures and properties: Lecture may skip portions of these notes and use website, or go back and forth. Key Concepts 4 levels of protein structure: 1. Primary (1 ) 2. Secondary (2 ) 3. Tertiary (3 ) 4. Quaternary (4 ) Properties of the 20 amino acids that occur in peptides and proteins are crucial to the structure and function of proteins Stereochemistry Relative hydrophobicity or polarity Hydrogen bonding properties Ionization properties Other chemical properties Chemical Properties 1

2 Learning Objectives Explain the 4 levels of protein structure: primary, secondary, tertiary, and quaternary. Draw the structure of a typical amino acid, indicating the following features: α-carbon, α-carboxyl group, α-amino group, sidechain ( R group ), and ionic forms that predominate at acidic (say, ph 1), neutral (ph 7), and basic (ph 13) ph values. Classify each of the 20 common amino acids found in proteins according to side chain type (aliphatic, aromatic, sulfur-containing, aliphatic hydroxyl, basic, acidic, amide, hydrophilic (polar), hydrophobic (nonpolar). (These categories overlap extensively, e.g., glutamate is acidic and it s very polar.) Learn the structure of each of these 20 amino acids, with its full name and 3-letter abbreviation. DO THIS NOW DON T PUT IT OFF. You won't have to draw detailed structures of arginine, histidine, or tryptophan, but you should be able to recognize them, and draw the simpler structures, with the ionization reactions of ionizable groups (see below). Learning Objectives, continued Be very familiar with the approximate ( typical ) pk a values of the 7 ionizable R groups (side chains) and also the α- amino and α-carboxyl groups in peptides and proteins; note that numerical values of these "generic " pk a values for the ionizable functional groups in peptides and proteins will be on the cover sheet of Exam 1, but the pk a values are of little use if you don't know the chemical nature of the groups (see below). You do NOT need to know the pk a values for the ionizable groups on the free amino acids. Write out the ionization (protonation/deprotonation) reactions for the 9 ionizable functional groups (7 side chains plus terminal α-amino and α-carboxyl groups), with appropriate structures; understand the charge properties of each form (conjugate acid and conjugate base) of each group. Chemical Properties 2

3 Protein Structure -- Overview Primary structure: linear sequence of amino acids polymer of amino acid residues (~ ) linked by peptide bonds (covalent, amide linkages) Terminology: amino acid residue, polypeptide (chain) Building blocks: 20 amino acids (different side chains) Protein function depends on correct 3-D folding of polypeptide 3-D folded structure determined by AA sequence Most proteins functions involve binding other molecules Shape complementarity (steric, van der Waals interactions) Chemical complementarity (hydrogen bond donors/acceptors, charge complementarity, etc.) Often the hydrophobic effect is important in binding. Flexibility in structure (proteins are not rocks!) Structure of lactoferrin changes when it binds iron (common phenomenon, induced fit) ribbon diagram, just backbone atoms of polypeptide chain (easier to trace chain from one end to the other) Space-filling structure, all atoms of polypeptide chain Berg et al., Fig. 2-3 Chemical Properties 3

4 Biological Roles of Proteins (examples) 1. Catalysis (enzymes) 2. Transport (e.g., hemoglobin - O 2 transport in blood; transport of ions across cell membranes) 3. Storage (e.g., myoglobin - oxygen storage in muscle; seed proteins - storage of nutrients) 4. Coordinated motion (e.g., in muscle, cilia, flagella) 5. Mechanical support (e.g., collagen) 6. Protection (e.g., immune system - antibodies; blood clotting proteins) 7. Regulation and communication (e.g., hormones, receptors, gene activation and repression, control of enzyme activity) 8. Generation and transmission of nerve impulses 9. Toxins (bacterial, plant, snake, insect) Levels of Protein Structure 1. Primary structure (1 structure): sequence of AAs linked by peptide bonds (amide linkages) 2. Secondary structure (2 structure): local, regular/recognizable conformations observed for parts of peptide backbone of a protein e.g, α-helix, β conformation, collagen helix 3. Tertiary structure (3 structure): 3-dimensional conformation of whole folded polypeptide chain 4. Quaternary structure (4 structure): 3-dimensional relationship of different polypeptide chains (subunits) how the subunits fit together and their symmetry relationships only in proteins with more than 1 polypeptide chain Chemical Properties 4

5 Levels of Protein Structure Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed., Fig α-amino Acids carboxylic acids, so "α", "β" "γ", etc. designate order of additional C atoms on carboxyl group. α carbon = central C atom, with 4 different substituents: 1. α-carboxyl group 2. α-amino group 3. hydrogen atom 4. R group = side chain (different structures for 20 different amino acids) Stereochemistry: D vs. L α carbon chiral (4 different substituents) Enantiomers (non-superimposable complete mirror images) All AAs in naturally occurring proteins are L-isomers. R Chemical Properties 5

6 α-amino Acids, Stereochemistry Berg et al., Fig. 3-4 UA s BMB Biology Project website on amino acids As you "travel" ONward, from carbonyl C toward N of amino group, in L-amino acids R group is on left. Are there naturallyoccurring D-amino acids? α-amino Acids, Ionization α-carboxyl group α-amino group Berg et al., Fig. 2-6 Chemical Properties 6

7 α-cooh group: a weak acid can DONATE its proton pk a ~ 2-3 What's the conjugate base form of the carboxyl group? Which form is charged? Is it a positive or a negative charge? α-nh 2 group: a weak base unshared pair of electrons on the :N neutral amino group can ACCEPT a proton. pk a ~9-10 What's the conjugate acid form of the amino group? Which form is charged? Is it a positive or a negative charge? pk a s of α-amino and α-carboxyl groups are different for different amino acids, and also are altered if they're the terminal groups on chain of AAs, i.e., a peptide or protein. Amino Acid Ionization, continued Besides the α-carboxyl and α -amino groups, 7 of the 20 AAs have ionizable side chains. Structures and Properties of AA side chains Biology Project website on amino acids, highly recommended for studying: Categories of AA side chains (ONE way to classify them) Aliphatic side chains Aromatic side chains Hydroxyl-containing side chains Sulfur-containing side chains Basic side chains Acidic side chains Amide side chains Chemical Properties 7

8 Amino Acids with Aliphatic Side Chains (nonpolar) Which of the 20 amino acids is achiral (has no asymmetric C)? Which aliphatic AA has 2 chiral centers? Amino Acids with Aromatic Side Chains Which of the aromatic side chains would be the least polar (the most hydrophobic)? Do any of the aromatic side chains have an ionizable group (the ability to dissociate a proton)? Which? Approx. pk a? Chemical Properties 8

9 Amino Acids with Hydroxyl-Containing Side Chains Does either of the hydroxyl-containing amino acids have 2 chiral centers? Which? Amino Acids with Sulfur-Containing Side Chains Which of the two S-containing side chains would be more hydrophobic? Chemical Properties 9

10 Amino Acids with Basic Side Chains (Structures are those that predominate at ph 7) Why is the His side chain (imidazole group) called basic if the predominant form at ph 7 is unprotonated? Amino Acids with Acidic Side Chains and their Amides (Structures are those that predominate at ph 7) Are the amide side chains of glutamine and asparagine ionizable, i.e. can they gain or lose a proton? Why or why not? Chemical Properties 10

11 Proton Dissociation Reactions of Amino Acids with Ionizable Groups in Proteins [side chain carboxyls] [imidazole group] Berg et al., Table 2-1 Proton Dissociation Reactions of Amino Acids with Ionizable Groups in Proteins [thiol group] [aromatic hydroxyl group] [ε-amino group] [guanidino group] Berg et al., Table 2-1 Chemical Properties 11

12 Titration of an amino acid with a non-ionizable R group (Gly) Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed., Fig Titration of an amino acid with an ionizable R group (His) Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed., Fig. 3-12b Chemical Properties 12

13 Classification of AA side chains by chemical properties Nonpolar but rather H 2 O-soluble (not hydrophobic): Gly, Pro Nonpolar, hydrophobic Ala, Val, Leu, Ile, Met, Phe, (Trp), (Cys) Polar, uncharged at ph 7: Amide-containing: Asn, Gln Hydroxyl-containing: aliphatic OH: Ser, Thr aromatic OH: Tyr Aromatic: Phe, Tyr, Trp Chemical Properties 13

14 Classification of AA side chains by chemical properties Charged (at ph 6-7), polar: Acidic ( ): Asp (carboxyl), Glu (carboxyl) Basic (+): Lys (ε-amino), Arg (guanidino), (His) (imidazole) Ionizable but predominantly uncharged at ph 7: Cys (thiol), Tyr (phenolic OH) Sulfur-containing: Cys (thiol), Met (thioether) Chemical Properties 14