Proteins and Amino Acids Overview

Study Notes

Proteins

Composed of linear chains of amino acids.
Classified as heteropolymers consisting of alpha amino acids.

Amino Acids (General)

All amino acids are chiral except for glycine.
Proteins exclusively use L amino acids.
Four essential properties support various biological functions:
- Capacity to polymerize
- Useful acid-base properties
- Varied physical properties
- Varied chemical properties

Structure of Amino Acids

Common backbone structure with variations primarily in the R group.
Four substituents within each amino acid:
- Carboxyl group (COO-)
- Amino group (NH3+)
- R group (side chain)
- Hydrogen atom (H)

Classification of Amino Acids

Grouped based on R substituents:
- Nonpolar, aliphatic (7 types)
- Aromatic (3 types)
- Polar, uncharged (5 types)
- Positively charged (3 types)
- Negatively charged (2 types)

Ionization of Amino Acids

Carboxylic acid displays an acidic pKa, becoming protonated in low pH conditions.
Amino group shows basic pKa, remaining protonated until high pH is reached.

pH Effects on Amino Acids

At low pH, amino acids exist primarily as cations (positively charged).
At high pH, they predominantly take the form of anions (negatively charged).

Zwitterion Form

Amino acids exist as zwitterions between pKa values of amino and carboxyl groups, featuring both positive and negative charges.

Isoelectric Point (pI)

For amino acids without ionizable side chains, pI calculates as:
- pI = (pK1 + pK2) / 2
At pI, the amino acid has a net charge of 0, is least soluble in water, and does not move in an electric field.

Buffering Capacity

Amino acids can function as buffers due to their ability to accept or donate protons.

Uncharged Side Chains

Example: Glycine with two pKa values:
- Alpha carboxyl group: pKa 2.34
- Alpha amino group: pKa 9.60

Ionizable Side Chains

Ionizable side chains influence pI and can also act as buffers.
These side chains can be titrated.

Calculation of pI with Ionizable Side Chains

Steps to calculate pI:
- Identify species with a net zero charge.
- Find pKa value defining acid strength of the zwitterion.
- Find pKa value defining base strength of the zwitterion.
- Average these two pKa values.

Peptide Formation

Amino acids polymerize to create peptides, which are short chains of amino acids linked by peptide bonds.

Peptide Nomenclature

Peptides are named starting from the N-terminal using three-letter abbreviations (e.g., Ser-Gly-Tyr-Ala-Leu).

Functions of Peptides

Peptides serve various roles such as:
- Hormones (e.g., insulin, oxytocin)
- Neuropeptides (e.g., substance P)
- Antibiotics (e.g., polymyxin B, bacitracin)
- Protective toxins (e.g., amanitin, conotoxin)

Composition of Proteins

Proteins consist of polypeptides formed from covalently linked alpha amino acids and may include:
- Cofactors (metal ions, organic molecules)
- Coenzymes (e.g., NAD+ in lactate dehydrogenase)
- Prosthetic groups (e.g., heme in myoglobin)
- Other modifications (e.g., phosphorylation, glycosylation)

Description

Explore the fundamentals of proteins and amino acids in this quiz. Learn about their structures, classifications, and significant properties essential for biological functions. Perfect for students studying biochemistry or molecular biology.

Proteins and Amino Acids Overview

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Questions and Answers

What are proteins made of?

All amino acids are chiral except glycine.

What are some properties of amino acids that contribute to their biological functions?

What determines the classification of amino acids?

What is the value of pKa for the alpha carboxyl group of glycine?

What is the isoelectric point of amino acids without ionizable side chains calculated as?

What do amino acids polymerize to form?

What is the pKa value for the alpha amino group of glycine?

What are the peptide ends?

Amino acids can act as __________.

Name one function of peptides.