Biochemistry Lecture 4

What is the structure of an amino acid?

An amino acid consists of a central carbon atom bonded to a hydrogen atom, an amino group (-NH2 or -NH3+), a carboxyl group (-COOH or -COO-), and a variable side chain (-R).

Why are amino acids typically ionized?

At physiological pH (pH=7.4), amino acids exist predominantly in ionized forms because the ambient pH is higher than the carboxyl group's pKa and lower than the amino group's pKa.

What are the typical functional groups of amino acids and their pKa?

The -amino group typically has a pKa between 9 and 11, and the -carboxyl group typically has a pKa between 1.9 and 2.5. Side chain functional groups have variable pKa values.

What is the zwitterionic form?

The zwitterionic form is the dipolar ionic state of an amino acid where the amino group is protonated (-NH3+) and the carboxyl group is deprotonated (-COO-), resulting in a net neutral charge.

Why are side chains significant in amino acid structure?

Side chains determine the specific chemical characteristics (polarity, charge, size) of each amino acid and drive the non-covalent interactions and folding patterns of proteins.

How is the amino group affected at high pH?

At a high pH (9-11), the amino group is deprotonated, shifting from its positively charged ammonium form (-NH3+) to a neutral amine form (-NH2).

How is the carboxyl group affected at low pH?

At a low pH (1.9-2.5), the carboxyl group is protonated, shifting from its negatively charged carboxylate form (-COO-) to a neutral carboxylic acid form (-COOH).

What is Tyrosine?

Tyrosine is an amino acid featuring an aromatic phenol side chain containing a hydroxyl group with a pKa of approximately 10.

How do different pH levels affect Tyrosine?

At low pH (pH<2), tyrosine is fully protonated with a net charge of +1. At neutral pH (2<pH<9.5), the carboxyl group is deprotonated and the amino group is protonated, giving a net charge of 0. At high pH (pH>10), the amino group and phenolic side chain are also deprotonated, resulting in a net charge of -2.

Which functional group is deprotonated first as the pH rises?

The -carboxyl group is deprotonated first as the pH rises because it possesses the lowest pKa (around 2).

What is the isoelectric point (pI)?

The isoelectric point (pI) is the specific pH of an amino acid solution at which the molecule carries no net electrical charge.

How to determine the pI in steps?

Step 1: List out the ionizable groups. Step 2: Determine the net charge state from lowest to highest pH. Step 3: Calculate the pI using the formula pI = (pKa1 + pKa2) / 2.

How does the titration curve for Tyrosine work as pH increases?

The titration curve features three distinct buffering plateaus corresponding to the sequential deprotonation of its three ionizable groups as equivalents of OH- are added.

What are peptides and oligopeptides?

Peptides are chains formed by linking multiple amino acids together. Oligopeptides refer to short chains composed of a small number of amino acid residues.

What are peptide bonds?

Peptide bonds are covalent chemical bonds that link amino acids together within a peptide or protein chain.

What is the N-terminus and C-terminus?

The N-terminus is the starting end of a peptide with a free amino group, and the C-terminus is the terminal end with a free carboxyl group.

How to draw polypeptides in steps?

Step 1: Determine the type and number of amino acids present.

Step 2: Count the number of necessary peptide bonds using the formula (N − 1), where N is the number of amino acids.

Step 3: Draw the repeating backbone from the N-terminus: H₂N − Cα − C(=O) − NH.

Step 4: Once all amino acids are connected, end at the C-terminus: − Cα − C(=O) − OH

How to fill side chains for amino acids in steps?

Step 1: Find the alpha carbon for each amino acid. Step 2: Attach the correct side chain to each alpha carbon. Step 3: Adjust protonation states based on pKa values.