Question

1. why is the word polypeptide not synonymous with the word protein?
2. the image to the right represents the basic structure of an amino acid. on the image circle and label the two functional groups that all 20 amino acids have. then, box the variable side chain, which differs between each amino acid.
3. r groups can be classified by their chemical properties. identify the three classifications for r groups and then discuss how the r groups affect the structure and function of a protein.
4. when a protein is folded, which classification of r groups would orient outward (toward the surface/aqueous cellular environment)? which would orient inward (away from the aqueous cellular environment)? why?
5. examine the three pairs of amino acids below. which pair of amino acids is in the optimal position to form a dipeptide? justify your choice by identifying and describing the reaction that takes place to form peptide bonds.

Explanation:

1. A polypeptide is a linear chain of amino - acids linked by peptide bonds. A protein is a functional molecule that may consist of one or more polypeptides that have folded into a specific three - dimensional structure through processes like secondary, tertiary and sometimes quaternary folding. So, polypeptides are just the building blocks or precursors of proteins.
2. The two functional groups in all 20 amino acids are the amino group ($-NH_2$) and the carboxyl group ($-COOH$). The variable side - chain is the R group.
3. R groups can be classified as non - polar (hydrophobic), polar uncharged, and charged (either acidic or basic). Non - polar R groups tend to cluster together in the interior of a protein away from the aqueous environment, contributing to the protein's three - dimensional shape. Polar uncharged R groups can form hydrogen bonds and interact with water. Charged R groups can form ionic bonds and also interact with water and other charged molecules, influencing protein function and stability.
4. Polar and charged R groups would orient outward towards the surface/aqueous cellular environment because they are hydrophilic and can interact favorably with water. Non - polar R groups would orient inward away from the aqueous environment because they are hydrophobic and seek to minimize contact with water.
5. The pair of amino acids in the optimal position to form a dipeptide is the one where the carboxyl group of one amino acid is adjacent to the amino group of the other amino acid. This allows for a dehydration synthesis reaction (also called a condensation reaction) to occur. In this reaction, the hydroxyl group from the carboxyl group of one amino acid and a hydrogen atom from the amino group of the other amino acid are removed as a water molecule, and a peptide bond ($-CO - NH-$) is formed between the two amino acids.

Answer:

1. A polypeptide is an amino - acid chain, while a protein is a functional, folded structure often made of one or more polypeptides.
2. Circle and label amino group ($-NH_2$) and carboxyl group ($-COOH$), box the R group.
3. Non - polar (hydrophobic), polar uncharged, charged (acidic or basic). Non - polar R groups cluster inside, polar uncharged form H - bonds, charged form ionic bonds and interact with water.
4. Polar and charged R groups outward; non - polar R groups inward due to hydrophobicity/hydrophilicity.
5. The pair with carboxyl and amino groups adjacent. Dehydration synthesis/condensation reaction removes water to form peptide bond.