Question

Why does the primary structure impact all levels of protein structure? What is unique about the peptide bond that directly impacts protein structure? What intermolecular forces stabilize protein structure? Consider protein denaturation, what environmental forces can cause a protein to lose its structure? What types of interactions are they disrupting? Many proteins require chaperones to properly fold. How do chaperones help proteins fold? What potential problems might arise from a misfolded protein? (An example from the text may be useful but is not required.)

Answer 1

Solution:

Key points:

1. The sequence of amino acids linked in a polypeptide chain is called as primary Protein structure. This structure is when amino acids are linked together by peptide bonds to form polypeptide chains. This is the back bone.
2. The local folded structures that form within a polypeptide due interactions between atoms of the backbone other than R groups.
3. The 3D structure of a polypeptide is called as tertiary structure. Interaction between R groups of the amino acids of the protein is responsible for this structure.
4. Subunits of polypeptide chains come together and give the protein its quaternary structure.

a. Primary structure of the protein is the backbone where the amino acids are arranged. Based on the primary structure other structures such as secondary, tertiary and quaternary structures of protein is determined.

Hence the primary structure impact all levels of protein structure.

b. Amino acids are linked together by peptide bonds to form polypeptide chains. Each chain has its own set of amino acids, assembled in a particular order. Even change in just one amino acid in a protein's sequence can affect the overall protein's structure and its function.

Hence the peptide bond directly impacts the protein structure.

c. The intermolecular forces stabilize the protein structure is peptide bonds, hydrogen bonds, disulfide bridges, Van der Waals interactions and ionic bonds.

d. Environmental forces such as change in temperature, change in pH, exposure to chemicals can cause a protein to loose its structure.

e. Environmental forces can disrupt hydrogen bonds and non-polar hydrophobic interactions.

f. Chaperones protect proteins during their process of folding by shielding them from other proteins that might bind and hinder the folding process.

g. Potential problems such as improper degradation, mislocalization, dominant-negative mutations, structural alterations that establish novel toxic functions, and amyloid accumulation might arise from a misfolded protein. This can lead to disease such as Alzheimer's, Parkinson's, Huntington's, Creutzfeldt–Jakob, cystic fibrosis, Gaucher's, and neurodegenerative disorders.