Amino Acids, Peptides & Proteins (Chapter 3)

™Proteins from all living organisms are biopolymers of 20 α-amino acids.

To understand the properties, functions & structures of proteins it is
imperative to understand the general & individual properties of the
building blocks of proteins – amino acids.
3.1 The Amino Acids in Proteins
-fundamental chemical structure, stereochemistry, acid-base chemistry &
classification of amino acids
3.2 Polypeptides & Proteins
-amino acids are linked by covalent peptide bonds to form polypeptides
3.3 Protein Function
-proteins are classified according to their diverse biological roles
3.4 Structural Properties of Proteins
-proteins are classified according to size, composition & solubility
-the four levels of protein structure are primary (amino acid sequence),
secondary (local structure), tertiary (overall compact structure) &
quaternary (subunit organization) structure
3.5 Studying Protein Structure & Function
-proteomics, isolating & purifying proteins, primary structure determination,
DNA sequencing & amino acid sequence homology
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3.1 The Amino Acids in Proteins

Learning Objectives: know the structural, chemical & biological properties of the α-amino
acids present in proteins.
Amino Acid –

α-Amino Acid –

™Special Features of Amino Acids

Zwitterion –

™EXAMPLE: Why are many amino acids considered

chiral?
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Classification of the 20 Common Amino Acids

™Based on the Amino Acid Side Chain (R group)
1) Nonpolar Amino Acids (Hydrophobic)

2) Polar, Uncharged Amino Acids (Neutral)

3) Acidic Amino Acids (Net Negative Charge at pH 7)

4) Basic Amino Acids (Net Positive Charge at pH 7)

™EXAMPLE: Draw the structures of the 20 amino acids at pH 7 three times.

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Nine Nonpolar Amino Acids at pH 7

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Six Polar Uncharged Amino Acids at pH 7

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Three Basic & Two Acidic Amino Acids at pH 7

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Common Amino Acids & Abbreviations

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Acid-Base Chemistry of Amino Acids

™Amino Acids are Diprotic & Triprotic Weak Acids

Isoelectric Point –
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pKa Values of Common Amino Acids

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Diprotic Amino Acid Titration Curve

™EXAMPLE: Draw the structures of the 20 amino acids at pH 1 (the fully

protonated from). Then draw each ionic form that exists of that amino acid as
pH is increased to 14 (the fully deprotonated form).
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Optical Activity & Stereochemistry of Amino Acids

™The Chirality of Life: Most active biomolecules are chiral (only one
enantiomer is biologically active)
Enantiomers –

™(D,L) Nomenclature Systems for Chiral Molecules

™L-Amino Acids are predominantly used as building blocks for proteins

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3.2 Polypeptides & Proteins

Learning Objectives: understand how amide bonds are formed & link amino acids into
polypeptides & proteins.
™Amino acids polymerize to form long chains called peptides through
formation of covalent peptide bonds
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3.3 Protein Function

Learning Objectives: know the primary categories of proteins when classified according to
biological function.
™Proteins are the Agents of Biological Function

Enzymes –

Structural Proteins –

Immunology (Defense) Proteins –

Transport & Storage Proteins –

Regulatory & Receptor Proteins –

Muscle Contraction & Mobility Proteins –

™EXAMPLE: For each classification above, list two protein examples.

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3.4 Structural Properties of Proteins

Learning Objectives: be able to describe the four levels of protein structure.
™Protein Terminology
Monomeric Protein –
Oligomeric Protein –

™EXAMPLE: What is the difference between simple proteins

& conjugated proteins?

™Three Classes of Proteins:

-Fibrous proteins

-Globular proteins

-Membrane proteins
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Four Levels of Protein Structure

1° Structure

2° Structure

3° Structure

4° Structure
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3.5 Studying Protein Structure & Function

Learning Objectives: describe experimental steps necessary to purify & analyze a protein
™EXAMPLE: What is the proteome?

™EXAMPLE: Describe how ion-exchange, gel-filtration & affinity

chromatography work?

™EXAMPLE: What is the purpose of SDS in gel

electrophoresis?

™EXAMPLE: What two experimental techniques

can reveal the 1° structure of a protein?