Protein Structure and Function – Chapter 19 Study Notes

Protein Structure and Function

Introduction

Proteins are essential macromolecules in all living organisms, playing critical roles in structure, function, and regulation of the body's tissues and organs. This chapter explores the chemistry of proteins, their building blocks (amino acids), and the principles underlying their structure and function.

Functions of Proteins

Overview of Protein Functions

• Proteins are polymers made from 20 different amino acids.

• Their characteristics and functions depend on the sequence of amino acids.

• Proteins form structural components (e.g., cartilage, muscles, hair, nails).

• They act as enzymes to regulate biological reactions such as digestion and metabolism.

• Proteins like hemoglobin and myoglobin are involved in transport and storage of molecules.

Classification of Proteins by Function

Proteins are classified based on their biological roles. The following table summarizes major classes, their functions, and examples:

Protein	Function	Examples
Structural	Provide structural components	Collagen (tendons, cartilage), Keratin (hair, skin, wool, nails)
Contractile	Make muscles move	Myosin, Actin
Transport	Carry essential substances throughout the body	Hemoglobin (oxygen transport), Lipoproteins (lipid transport)
Storage	Store nutrients	Casein (milk), Ferritin (iron storage)
Hormone	Regulate body metabolism and the nervous system	Insulin (blood glucose regulation), Growth hormone
Enzyme	Catalyze biochemical reactions in cells	Sucrase (hydrolysis of sucrose), Trypsin (protein hydrolysis)
Protection	Recognize and destroy foreign substances	Immunoglobulins (antibodies)

Amino Acids

Structure of Amino Acids

• Amino acids are the molecular building blocks of proteins.

• Each amino acid contains a central α carbon bonded to:

  • An ammonium group ($-NH_3^+$)

  • A carboxylate group ($-COO^-$)

  • A hydrogen atom

  • An R group (side chain, unique for each amino acid)

• The α carbon is a chiral center (except for glycine).

• Only the "L" form of amino acids is metabolized by the body.

Amino Acids at Physiological pH

• At physiological pH (~7.4), amino acids exist as zwitterions, with both the ammonium and carboxylate groups ionized.

• This gives the molecule a balance of positive and negative charges.

Example: Glycine at pH 7.4: $^+H_3N-CH_2-COO^-$

Classification of Amino Acids

By Polarity of the Side Chain

• Hydrophobic (water-fearing): Non-polar neutral side chains (alkyl or aromatic R groups).

• Hydrophilic (water-loving):

  • Polar neutral side chains (alcohol, thiol, or amide R groups)

  • Acidic side chains (negatively charged, carboxylate R groups)

  • Basic side chains (positively charged, ammonium R groups)

Nonpolar Amino Acids

• R group is H, alkyl, or aromatic.

• Examples: Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Phenylalanine (Phe, F), Methionine (Met, M), Proline (Pro, P), Tryptophan (Trp, W)

Polar Amino Acids, Neutral R Groups

• R group is an alcohol, thiol, or amide.

• Examples: Serine (Ser, S), Threonine (Thr, T), Tyrosine (Tyr, Y), Cysteine (Cys, C), Asparagine (Asn, N), Glutamine (Gln, Q)

Polar Acidic Amino Acids (Negative Charges)

• R group contains a carboxylate ($-COO^-$) group.

• Examples: Aspartate (Asp, D), Glutamate (Glu, E)

Polar Basic Amino Acids (Positive Charges)

• R group contains an ammonium ($-NH_3^+$) group.

• Examples: Histidine (His, H), Lysine (Lys, K), Arginine (Arg, R)

Peptide Bonds and Protein Structure

Formation of Peptide Bonds

• Proteins are polymers of amino acids joined by peptide bonds.

• A peptide bond is an amide bond formed between the α-amino group of one amino acid and the carboxyl group of another, with the elimination of water.

Equation for Peptide Bond Formation:

$\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Peptides, Polypeptides, and Proteins

• Peptides: Short chains of amino acids (typically < 50 residues).

• Polypeptides: Longer chains (50–100 residues).

• Proteins: Very long chains (> 100 residues).

• The N-terminal amino acid is written on the left, and the C-terminal on the right.

Drawing Peptides

• Peptides are linear polymers of amino acids connected by amide bonds.

• To draw a peptide:

  1. Draw each amino acid starting from the N-terminus.

  2. Remove an O atom from the carboxylate group of the N-terminal amino acid and two H atoms from the ammonium group of the next amino acid to form the peptide bond.

  3. Repeat until the C-terminus is reached.

Example: Naming and Drawing Peptides

• Example 1: For the tripeptide shown (Phe–Cys–Ala):

  • N-terminus: Phenylalanine (Phe)

  • C-terminus: Alanine (Ala)

  • Name: Phe–Cys–Ala

• Example 2: Drawing Gly–Ser–Met:

  1. Draw the structures for Glycine, Serine, and Methionine in sequence.

  2. Form peptide bonds as described above.

Practice: Drawing a Tripeptide at Physiological pH

• Draw the chemical structure of the tripeptide Ala–Gly–Val at pH 7.4.

• At this pH, the N-terminus is protonated ($-NH_3^+$) and the C-terminus is deprotonated ($-COO^-$).

General Structure:

$^+H_3N-CH(CH_3)-CO-NH-CH_2-CO-NH-CH(CH(CH_3)_2)-COO^-$

Additional info: For full peptide structures, always show the correct ionization states at physiological pH.