Biochemistry I - Protein Structure - Quick Guides | Biochemistry

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Study GuideBiochemistry I–Protein Structure1.Amino AcidsAmino acids are thebasic building blocks of proteins. Although there are many different proteins inliving cells, all proteins are made from the same20 naturally occurring amino acids. These aminoacids share acommon basic structure, but differ in their side chains, which gives each amino acidunique properties.1.1General Structure of Amino AcidsAll amino acids contain:•Anamino group(–NH₂)•Acarboxyl group(–COOH)•Ahydrogen atom•Aside chain (R group)All four are attached to a single central carbon atom called thealpha (α)carbon. Because the aminogroup is attached to theα-carbon, the amino acids found in proteins are calledα-amino acids.Figure 1TheR group (side chain)is different for each amino acid and determines its chemical behavior androle in proteins.

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Study Guide1.2Stereochemistry of Amino AcidsThe amino acids found in proteins have aspecific three-dimensional arrangement. In standarddrawings, the amino group is shown on theleft sideof theα-carbon. This configuration is called theL-form(L forlevo, meaning left).•All amino acids in proteins areL-α-amino acids•Biochemists usually describe amino acids usingL and D notation, rather than R and SnotationA fewD-amino acidsdo occur in nature, but they arenot found in cellular proteins. Some peptideantibiotics, such asbacitracin, contain D-amino acids.1.3Zwitterion Form of Amino AcidsIn water, amino acids exist mainly aszwitterions, meaning they carryboth a positive and anegative chargeat the same time.•Thecarboxyl groupdonates a proton (acts as an acid)•Theamino groupaccepts 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:1.4Amino Acid Side Chains and Protein DiversityTheside chains (R groups)give amino acids their chemical diversity. Proteins typically contain100–1000 amino acids. Even with the smallest size (100 amino acids), the number of possible proteinsequences is:

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Study Guide20¹⁰⁰ ≈ 10¹³⁰This number is far greater than the number of particles in the universe. Clearly,not all possibleproteins exist. Instead, proteins are related through evolution.Most proteins havehomologues, meaning related proteins that share a common ancestor. Thesehomologous proteins often have:•Identical short sequences•Substitutions involving chemically similar amino acids1.5Conservative Substitutions and Amino Acid ClassesAmino acids can be grouped intosix major classesbased on their side chains.Replacing one amino acid with another from thesame groupis called aconservative substitution.Homologous proteins typically differ by conservative substitutions rather than drastic changes.Figure 2

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Study Guide1.6Classification of Amino Acids1. Aliphatic (Nonpolar) Amino AcidsThese amino acids have side chains made only ofcarbon and hydrogen:•Glycine•Alanine•Valine•Leucine•IsoleucineGlycine is unique:•Its side chain is justone hydrogen•It isnot optically active•L and D forms do not apply to glycine

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Study GuideFigure 32. Aromatic Amino AcidsThese containring structures:

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Study Guide•Phenylalanine(benzyl ring)•Tyrosine(phenylalanine + hydroxyl group)•Tryptophan(two rings, one containing nitrogen)The nitrogen in tryptophan isnot ionizableat physiological pH.3. Basic (Positively Charged) Amino AcidsThese amino acids have side chains that canaccept protons:•Histidine•Lysine•ArginineHistidine:•Has animidazole ring•pKₐ ≈ 7•Can easily gain or lose a proton•Commonly involved inenzyme catalysisLysine and arginine:•Strongly basic•Almost alwayspositively chargedin cells4. Acidic Amino Acids and Their Amides•Aspartic acid → Asparagine•Glutamic acid → GlutamineAspartic and glutamic acids:•Havecarboxylate side chains•pKₐ ≈ 4•Negatively charged at physiological pH

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Study GuideAsparagine and glutamine:•Containamide groups•Are uncharged but polar5. Hydroxyl-and Sulfur-Containing Amino Acids•Serine→ hydroxyl group•Threonine→ hydroxyl onβ-carbon (optically active)•Cysteine→ sulfhydryl group (–SH)•Methionine→ sulfur with a methyl groupThreonine hastwo chiral centers, making it stereochemically unique.6. The Cyclic Amino Acid: ProlineProline is unusual:•The amino group is part of aring•The structure isrigid•Limits flexibility of protein chains

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Study Guide1.7Peptide Bond FormationA peptide bond is formed between:•Thecarboxyl groupof one amino acid•Theamino groupof anotherThis is anamide bond, formed with the loss of water.Two amino acids can form:•Gly-Alaor•Ala-GlyThese are different molecules.Peptide sequences are always written from:N-terminus → C-terminus

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Study Guide1.8Peptide Bond Structure: Cis and Trans FormsAlthough the peptide bond is a single bond, it haspartial double-bond character, making it:•Planar•Difficult to rotateThus, 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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