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Biochemistry I - Protein Structure

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    Study Guide Biochemistry I – Protein Structure 1. Amino Acids Amino acids are the basic building blocks of proteins . Although there are many different proteins in living cells, all proteins are made from the same 20 naturally occurring amino acids . These amino acids share a common basic structure , but differ in their side chains, which gives each amino acid unique properties. 1.1 General Structure of Amino Acids All amino acids contain: • An amino group ( – NH ₂ ) • A carboxyl group ( – COOH) • A hydrogen atom • A side chain (R group) All four are attached to a single central carbon atom called the alpha ( α) carbon . Because the amino group is attached to the α - carbon, the amino acids found in proteins are called α - amino acids . Figure 1 The R group (side chain) is different for each amino acid and determines its chemical behavior and role in proteins.

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    Study Guide 1.2 Stereochemistry of Amino Acids The amino acids found in proteins have a specific three - dimensional arrangement . In standard drawings, the amino group is shown on the left side of the α - carbon. This configuration is called the L - form (L for levo , meaning left). • All amino acids in proteins are L - α - amino acids • Biochemists usually describe amino acids using L and D notation , rather than R and S notation A few D - amino acids do occur in nature, but they are not found in cellular proteins . Some peptide antibiotics, such as bacitracin , contain D - amino acids. 1.3 Zwitterion Form of Amino Acids In water, amino acids exist mainly as zwitterions , meaning they carry both a positive and a negative charge at the same time. • The carboxyl group donates a proton (acts as an acid) • The amino group accepts a proton (acts as a base) This happens because: • Carboxyl groups are relatively strong acids (pKₐ ≈ 2) • Amino groups are relatively strong bases (pKₐ > 9) As a result, amino acids in solution have the general form: 1.4 Amino Acid Side Chains and Protein Diversity The side chains (R groups) give amino acids their chemical diversity. Proteins typically contain 100 – 1000 amino acids . Even with the smallest size (100 amino acids), the number of possible protein sequences is:

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    Study Guide 20¹⁰⁰ ≈ 10¹³⁰ This number is far greater than the number of particles in the universe. Clearly, not all possible proteins exist . Instead, proteins are related through evolution. Most proteins have homologues , meaning related proteins that share a common ancestor. These homologous proteins often have: • Identical short sequences • Substitutions involving chemically similar amino acids 1.5 Conservative Substitutions and Amino Acid Classes Amino acids can be grouped into six major classes based on their side chains. Replacing one amino acid with another from the same group is called a conservative substitution . Homologous proteins typically differ by conservative substitutions rather than drastic changes. Figure 2

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    Study Guide 1.6 Classification of Amino Acids 1. Aliphatic (Nonpolar) Amino Acids These amino acids have side chains made only of carbon and hydrogen : • Glycine • Alanine • Valine • Leucine • Isoleucine Glycine is unique: • Its side chain is just one hydrogen • It is not optically active • L and D forms do not apply to glycine

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    Study Guide Figure 3 2. Aromatic Amino Acids These contain ring structures :

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    Study Guide • Phenylalanine (benzyl ring) • Tyrosine (phenylalanine + hydroxyl group) • Tryptophan (two rings, one containing nitrogen) The nitrogen in tryptophan is not ionizable at physiological pH. 3. Basic (Positively Charged) Amino Acids These amino acids have side chains that can accept protons : • Histidine • Lysine • Arginine Histidine: • Has an imidazole ring • pKₐ ≈ 7 • Can easily gain or lose a proton • Commonly involved in enzyme catalysis Lysine and arginine: • Strongly basic • Almost always positively charged in cells 4. Acidic Amino Acids and Their Amides • Aspartic acid → Asparagine • Glutamic acid → Glutamine Aspartic and glutamic acids: • Have carboxylate side chains • pKₐ ≈ 4 • Negatively charged at physiological pH

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    Study Guide Asparagine and glutamine: • Contain amide groups • Are uncharged but polar 5. Hydroxyl - and Sulfur - Containing Amino Acids • Serine → hydroxyl group • Threonine → hydroxyl on β - carbon (optically active) • Cysteine → sulfhydryl group ( – SH) • Methionine → sulfur with a methyl group Threonine has two chiral centers , making it stereochemically unique. 6. The Cyclic Amino Acid: Proline Proline is unusual: • The amino group is part of a ring • The structure is rigid • Limits flexibility of protein chains

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    Study Guide 1.7 Peptide Bond Formation A peptide bond is formed between: • The carboxyl group of one amino acid • The amino group of another This is an amide bond , formed with the loss of water. Two amino acids can form: • Gly - Ala or • Ala - Gly These are different molecules. Peptide sequences are always written from: N - terminus → C - terminus

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    Study Guide 1.8 Peptide Bond Structure: Cis and Trans Forms Although the peptide bond is a single bond, it has partial double - bond character , making it: • Planar • Difficult to rotate Thus, peptide bonds exist in: • Trans form (most common) • Cis form (rare) Proline is special because: • Cis and trans forms are closer in energy • Special enzymes help convert between them

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