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1 Lecture 3: Introduction to Proteins; Amino Acids, the Building Blocks of Proteins [PDF] Reading: Berg, Tymoczko & Stryer: Chapter 2, pp ; Appendix to chapter 2, pp (visualizing protein structures) See also posted general chemistry review for acid-base concepts, and online website on amino acids for excellent way to learn the amino acid structures and properties. Updated on: 1/14/06 at 9:30 pm Key Concepts 4 levels of protein structure: Primary (1 o ) Secondary (2 o ) Tertiary (3 o ) Quaternary (4 o ) 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 There's an excellent website on amino acids developed here in the Department of Biochemistry and Molecular Biophysics; there are links to various very useful parts of it here in these notes, and parts of it may be used in class. 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, side chain ( 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, sulfurcontaining, 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 the 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). 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. Protein structure: covalent structures = linear polymers of amino acids Page 1 of 11

2 macromolecules, usually amino acid residues per chain (M.W. ~ ,000) Some proteins are assemblies of multiple chains. individual chains = polypeptides building blocks = 20 different amino acids side chains -- many different functional groups (some modified after protein synthesized in cell) Some proteins also have non-amino acid constituents: added after biosynthesis (post-translational modification of proteins) e.g., metal ions or small organic or organometallic molecules (e.g., heme in hemoglobin) correct "folding" of polypeptide chain --> final 3-dimensional structure (complex but well-defined) determined by sequence of amino acids Protein function: depends on 3-dimensional structure specific BINDING of other molecules -- other protein molecules, DNA, small molecules, inorganic ions. Binding depends on 3-D structure COMPLEMENTARITY (shape and chemistry) between the 2 molecules. FLEXIBILITY of 3-D structure often required for binding -- PROTEIN STRUCTURES ARE NOT "ROCKS"! Berg, Tymoczko & Stryer Fig. 2.3: Lactoferrin (a protein) -- slightly different 3-D structure when it binds iron Result: Other molecules can distinguish between iron-free and iron-bound forms of lactoferrin. Biological Roles of Proteins (examples) Page 2 of 11

3 1. Catalysis (enzymes) 2. Transport (hemoglobin - O 2 transport in blood; transport of ions across cell membranes ) 3. Storage (e.g., myglobin - oxygen storage in muscle; seed proteins - storage of nutrients ) 4. Coordinated motion (muscle, cilia, flagella ) 5. Mechanical support (collagen ) 6. Protection (immune system - antibodies; blood clotting proteins ) 7. Regulation and communication (hormones, receptors, gene activation and repression, control of enzyme activity ) 8. Generation and transmission of nerve impulses 9. Toxins (bacterial, plant, snake, insect ) 4 Levels of Protein Structure Primary structure (1 structure): sequence of amino acids, linked together by peptide bonds (amide linkages) 2. Secondary structure (2 structure): local, regular/recognizable conformations observed for parts of the peptide backbone of a protein e.g, α-helix, β conformation, collagen helix 3. Tertiary structure (3 structure): 3-dimensional conformation of whole polypeptide chain in its folded state 4. Quaternary structure (4 structure): 3-dimensional relationship of different polypeptide chains (subunits) the way the subunits fit together and their symmetry relationships only in proteins with more than one polypeptide chain 4 levels of protein structure [Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed. (2004) Fig. 3-16] AMINO ACIDS α-amino acids: carboxylic acids, so "α", "β" "γ", etc. refer to the order of additional C atoms on the carboxyl group. central C atom (the "α" carbon), with 4 substituents: α-carboxyl group (the "α" carboxyl group because it's a substituent on the α C) α-amino group (the "α" amino group because it's a substituent on the α C) H atom (the "α"-hydrogen atom) R group (different structures for the 20 different amino acids) Stereochemistry: α carbon a chiral center (asymmetric C, 4 different substituents) 2 possible stereoisomers that are non-superimposable mirror images (enantiomers), D and L (We'll use "D" and "L" terminology in this course as the textbooks generally do, because RS Page 3 of 11

4 terminology is rarely needed for the basics.) Berg, Tymoczko & Stryer, 6th ed., Fig. 2.4: D & L isomers of amino acids, complete mirror images As you "travel" ONward in L- amino acids, from the carbonyl C toward the N of the amino group, the R group is on the left. L-amino acids = the naturally occurring enantiomers found in all proteins. Naturally occurring D-amino acids in some bacterial cell wall peptide structures, in some peptide antibiotics, etc., but not in proteins.. Ionization: α-amino group (amino group substituent on the αc) and α-carboxyl group (carboxyl substituent on the αc) both ionizable. α-cooh group: a weak acid, can DONATE its proton, with a pk a of about 2-3. What's the conjugate base form of the carboxyl group? Which form is charged, and is it a positive or a negative charge? α-nh 2 group: a weak base (there's an unshared pair of electrons on the :N; the neutral amino group can ACCEPT a proton). What's the conjugate acid form of the amino group? Which form is charged, and 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 a chain of amino acids, i.e., a peptide or protein. Berg, Tymoczko & Stryer, 6th ed., Fig. 2.6: Ionization state of amino acids as a function of ph Page 4 of 11

5 Besides α-amino and α-carboxyl groups, 7 amino acids also have ionizable R groups (side chains). (See R group structures below.) Structures and Chemistry of Amino Acid R Groups: (tutorial on amino acids posted on the biochem/biology project website) NOTE: Structures drawn are in the state of ionization that PREDOMINATES at ph 7. States of ionization depend on 2 things: pk a of functional group ph of the solution/medium surrounding the group SEE POSTED REVIEW of general chemistry -- ph, pk a, Henderson-Hasselbalch Equation, and sample calculations involving ph, pk a, and what fraction of a group is in the form of the conjugate base or the conjugate acid at a given ph. Aliphatic side chains Cyclic side chain Page 5 of 11

6 Which of the 20 amino acids commonly found in proteins is achiral (has no asymmetric C atom)? Aromatic Side Chains Hydroxyl-containing Side Chains Sulfur-containing Side Chains Acidic and amide side chains Page 6 of 11

7 Basic side chains IONIZATION Page 7 of 11

8 Only 7 amino acids have ionizable side chains (R groups that can donate or accept a proton). Ionizable groups in peptides and proteins: 7 types of side chains ONE terminal α-amino in each peptide or protein ONE terminal α-carboxyl in each peptide or protein Titration of the α-carboxyl and α-amino groups of an amino acid with a nonionizable R group: Titration of Glycine [(Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed.(2004), Fig. 3-10] Blue-shaded areas show the ph range surrounding the two pk a values, regions where Gly would have the greatest buffering power. Page 8 of 11

9 Titration of an amino acid with a 3rd ionizable functional group, the R group: Titration of Histidine [Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed. (2004) Fig. 3-12b] Polarity/solubility of amino acid side chains (R groups): with only C and H atoms: non-polar longer chains = more hydrophobic (less H 2 O-soluble) Page 9 of 11

10 Ile, Leu, Val, Ala, (Pro), (Gly) Uncharged R groups with electronegative atoms: more polar (more H 2 O-soluble) e.g., Asn, Gln, Ser Charged R groups (forms that predominate at ph 7): the most H 2 O-soluble Asp, Glu, Lys, Arg, (His) aromatic functional groups: Phe, Tyr, Trp Phe: very hydrophobic Tyr & Trp have polar portions (OH group in Tyr, NH in Trp), so aren't very hydrophobic CLASSIFICATION OF AMINO ACID SIDE CHAINS Note that many amino acids fall into more than one category, e.g., Tyrosine is both aromatic and OHcontaining. 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 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) Aromatic: Phe, Tyr, Trp The 20 Standard Amino Acid Residues of Proteins, and Abbreviations Amino acid (or residue) 3-letter symbol 1-letter symbol Mnemonic help for 1-letter symbol Approximate pk a of R group (if it's ionizable) in peptides and proteins Alanine Ala A Alanine N.A. Arginine Arg R arginine ~ 12 Aspartate Asp* D aspardic acid ~ 4 Asparagine Asn* N asparagine N.A. Cysteine Cys C Cysteine ~ 8.5 Glutamate Glu** E gluetamic acid ~ 4 Glutamine Gln** Q Q-tamine N.A. Glycine Gly G Glycine N.A. Histidine His H Histidine ~ 6.5 Isoleucine Ile I Isoleucine N.A. Leucine Leu L Leucine N.A. Lysine Lys K (before L) ~ 10 Methionine Met M Methionine N.A. Proline Pro P Proline N.A. Phenylalanine Phe F Fenylalanine N.A. Serine Ser S Serine N.A. Page 10 of 11

11 Threonine Thr T Threonine N.A. Tryptophan Trp W two rings (or twyptophan) N.A. Tyrosine Tyr Y tyrosine ~ 10 Valine Val V Valine N.A. *Asx (B) = either acid or amide (when it isn't known which it is) ** Glx (Z)) = either acid or amide (when it isn't known which it is) Absorption of ultraviolet light by amino acid R groups Berg, Tymoczko & Stryer, 5th ed., Fig. 3-11: Absorption of ultraviolet light (aromatic AAs, esp. Trp) zieglerm@u.arizona.edu Department of Biochemistry & Molecular Biophysics The University of Arizona Copyright ( ) 2007 All rights reserved. Page 11 of 11