Protein Structure, Amino Acids, and pH: Foundations of Biochemistry

Protein Structure and Function

Introduction to Proteins

Proteins are essential macromolecules in all living cells, responsible for a vast array of biological functions. Their diverse roles stem from their complex structures and the chemical properties of their building blocks, the amino acids.

• Proteins are linear, heteropolymers of amino acids.

• They are the most abundant macromolecules in cells.

• Proteins exhibit variable size and physical properties, accounting for their diversity in structure and function.

• The final product of most genes is a protein.

Key Concept: The function of a protein is determined by its structure, which in turn is dictated by the sequence and properties of its amino acids.

Protein Function and Interactions

• The essence of a protein's function lies in its interaction with other molecules.

• Protein function is always determined by its three-dimensional structure.

• Critical questions include:

  • What determines the 3D shape of a protein?

  • What forces stabilize that shape?

  • What mediates interactions between proteins and other substances?

Proteins and pH

Protons in Equilibrium and Acid-Base Chemistry

The ionization state of amino acids and proteins is highly dependent on pH, which affects their structure and function.

• General acid dissociation equilibrium:

$HA \rightleftharpoons A^- + H^+$

• At high pH, the deprotonated form ($A^-$) predominates; at low pH, the protonated form ($HA$) predominates.

• When $[HA] = [A^-]$, $pH = pK_a$ (half-dissociated point).

$K_a = \frac{[A^-][H^+]}{[HA]}$

$pK_a = -\log_{10} K_a$

• Above $pK_a$: acid is mostly deprotonated (conjugate base).

• Below $pK_a$: acid is mostly protonated.

pKa Values of Functional Groups in Proteins

Functional Group	Ionization Reaction	pKa
Carboxyl (-COOH)	$-COOH \rightleftharpoons -COO^- + H^+$	~2
Amino (-NH3+)	$-NH_3^+ \rightleftharpoons -NH_2 + H^+$	~9.5
Sulfhydryl (-SH)	$-SH \rightleftharpoons -S^- + H^+$	~9
Hydroxyl (-OH)	$-OH \rightleftharpoons -O^- + H^+$	varies

Ionization State of Amino Acids

• The charge of an amino acid changes with pH due to the ionization of the amino and carboxyl groups.

• At pH 7, most amino acids exist as zwitterions (equal positive and negative charges).

• At low pH, amino acids are fully protonated (net positive charge); at high pH, they are fully deprotonated (net negative charge).

Zwitterions

• A zwitterion is a molecule with both positive and negative charges but is overall electrically neutral.

• For amino acids, this occurs at intermediate pH values (typically around pH 7 for most).

Practice Example

At which pH will half the molecules in solution be in the monohydrogen phosphate form and half in the phosphate form?

• Answer: At the $pK_a$ of the relevant equilibrium (for $H_2PO_4^-$ to $HPO_4^{2-}$, $pK_a = 7.2$).

The Amino Acids

Structure of Amino Acids

• All amino acids have an amino group and a carboxylate group attached to a central (alpha, $C_\alpha$) carbon.

• The 20 common amino acids differ only at the R group (side chain).

• At neutral pH, the amino group is protonated ($NH_3^+$) and the carboxyl group is deprotonated ($COO^-$).

Chirality of Amino Acids

• With the exception of glycine, all amino acids are chiral (the $C_\alpha$ is bonded to four different groups).

• Proteins are made exclusively from L-amino acids (as defined by the CORN rule).

• The CORN rule: Looking from the hydrogen through the $C_\alpha$ bond, the groups CO-R-N in a clockwise direction indicate the L-form.

Classification of Amino Acids

Amino acids are classified based on the properties of their R groups:

• Non-polar amino acids: Aliphatic and aromatic side chains, hydrophobic.

• Polar (uncharged) amino acids: Side chains with hydroxyl, thiol, or carboxyamide groups, hydrophilic but uncharged at pH 7.

• Charged amino acids: Side chains are ionized at pH 7 (either positive or negative charge).

Non-Polar Amino Acids

• Hydrophobic side chains, mainly hydrocarbons.

• Examples: Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Phenylalanine (Phe), Tryptophan (Trp), Methionine (Met), Proline (Pro), Glycine (Gly).

• Aromatic amino acids (Phe, Trp) absorb UV light.

• Proline has a distinctive cyclic structure; glycine is achiral and very small.

Polar (Uncharged) Amino Acids

• Contain polar functional groups (hydroxyl, thiol, carboxyamide).

• Examples: Serine (Ser), Threonine (Thr), Cysteine (Cys), Asparagine (Asn), Glutamine (Gln), Tyrosine (Tyr), Glycine (Gly).

• Ser, Thr, and Cys are often involved in enzymatic reactions.

• Cys can form disulfide bridges (cystine) under oxidizing conditions.

• Tyrosine and cysteine have ionizable R groups (pKa values between 1-14).

Charged Amino Acids

• Side chains are ionized at pH 7.

• Negatively charged (acidic): Aspartate (Asp), Glutamate (Glu).

• Positively charged (basic): Lysine (Lys), Arginine (Arg), Histidine (His; can be charged or uncharged at pH 7).

• These amino acids are very polar and often participate in ionic interactions and hydrogen bonding.

Special Properties and Modifications

• Some amino acids can be modified after incorporation into proteins (post-translational modification).

• Uncommon amino acids may arise as metabolic intermediates or derivatives.

Practice and Application

• Be able to draw the structure of all 20 amino acids at different pH values (1, 7, 14).

• Classify amino acids based on their side chain properties.

• Understand the importance of amino acid properties for protein structure and function.

Summary Table: Amino Acid Classification

Class	Examples	Key Properties
Non-polar	Ala, Val, Leu, Ile, Phe, Trp, Met, Pro, Gly	Hydrophobic, mainly hydrocarbon side chains
Polar (uncharged)	Ser, Thr, Cys, Asn, Gln, Tyr, Gly	Hydrophilic, contain polar groups, uncharged at pH 7
Charged	Asp, Glu, Lys, Arg, His	Side chains ionized at pH 7, very polar

Additional info: The notes above are based on standard introductory biochemistry content, with expanded explanations and context for clarity and completeness.