Lecture 3 Flashcards
Protein Structure
What are the four main parts of an amino acid?
Amino group (-NH₃⁺), carboxyl group (-COO⁻), hydrogen (H), R group (side chain).
Does every amino acid have a central chiral carbon?
No, glycine is the only amino acid without a chiral carbon because its R group is a hydrogen atom.
What is a zwitterion?
A molecule with both a positive and negative charge but is overall neutral.
Why does the zwitterion form predominate under cellular conditions?
At pH 7.4, the amino group is protonated (+) and the carboxyl group is deprotonated (-), making the molecule stable.
How does pH affect the ionization of amino acids?
Low pH: Both groups are protonated (positively charged). Neutral pH: Zwitterion form. High pH: Both groups are deprotonated (negatively charged).
What is an R group/side chain?
The variable part of an amino acid that determines its properties and interactions.
Which type of R groups are found in hydrophobic (nonpolar) amino acids?
Mostly carbon (C) and hydrogen (H), making them water-repelling. Examples: Alanine, Valine, Leucine.
Which type of R groups are found in hydrophilic (polar & charged) amino acids?
Contain oxygen (O), nitrogen (N), or sulfur (S) to form hydrogen/ionic bonds with water. Examples: Serine, Glutamate, Lysine.
Where do hydrophilic vs. hydrophobic amino acids localize in a protein?
Hydrophilic → Surface (interacts with water). Hydrophobic → Core (avoids water).
What happens if you swap hydrophobic and hydrophilic amino acids?
Protein misfolds, loses stability, or aggregates, leading to dysfunction.
What is a peptide bond?
A covalent bond between the carboxyl (-COO⁻) of one amino acid and the amino (-NH₃⁺) of another.
What are the N-terminus and C-terminus of a polypeptide?
N-terminus: Free amino (-NH₃⁺) end. C-terminus: Free carboxyl (-COO⁻) end.
What are the four levels of protein structure?
Primary – Amino acid sequence (peptide bonds). Secondary – Alpha helices & beta sheets (hydrogen bonds). Tertiary – 3D folding (hydrogen, ionic, van der Waals, disulfide bonds). Quaternary – Multiple polypeptides interacting.
How do hydrogen bonds
van der Waals forces
What is protein denaturation?
Loss of protein structure due to heat, pH changes, or chemicals, making it nonfunctional.
Which protein structures are affected by heat?
Secondary, tertiary, and quaternary structures (hydrogen, ionic, and van der Waals bonds break).
Which structure is not affected by heat?
Primary structure, because peptide bonds are very strong.
Can protein denaturation be reversed?
Sometimes. If the correct environment is restored, some proteins can refold properly.
Can a cooked egg be returned to raw by refrigeration?
No. Heat permanently changes protein structure.
What did Anfinsen’s experiment show?
Amino acid sequence alone determines protein folding.
Why does the order of urea removal matter in Anfinsen’s experiment?
If urea is removed first, the protein refolds correctly. If oxidation happens first, incorrect disulfide bonds form.
What are molecular chaperones?
Proteins that assist in the proper folding of other proteins.
What are heat-shock proteins (HSPs)?
Chaperones that help refold proteins after heat stress.
How does Hsp70 work?
Binds to unfolded proteins to prevent incorrect folding.
What are chaperonins?
Protein complexes that provide a safe chamber for folding.
How does the GroEL-GroES system work?
GroEL acts as a chamber, and GroES caps it to allow correct folding.
What happens if chaperones fail and proteins misfold?
Misfolded proteins clump, leading to diseases like Alzheimer’s & Parkinson’s.
How does the cell remove misfolded proteins?
Ubiquitin-proteasome system tags and degrades them. Autophagy digests large protein aggregates.
What amino acid change causes sickle cell disease?
Glutamic acid (hydrophilic) → Valine (hydrophobic) in hemoglobin.
What happens due to this mutation?
Hemoglobin clumps, forming sickle-shaped red blood cells, causing poor oxygen transport and blockages.
