protein structure Flashcards
What are proteins?
Proteins are linear polymers of amino acids joined
by peptide bonds.
What is the smallest protein length? What is the average protein length? What is the largest known protein?
The smallest proteins are ~40 amino acids in
length. The “average” protein is ~300-400 amino acids in
length. The largest known protein is the muscle protein titin: ~30,000 amino acids!
What is the specific sequence of amino acids in a
protein called?
The specific sequence of amino acids in a protein is
called the protein’s primary structure.
Do linear polymers of amino acids form straight
rod-like structures?
No, but fold into definite 3-D structures
depending on the sequence of amino acids.
What determines the functions of a protein?
The functions of a protein are determined by :
-its overall shape (i.e., specific folding pattern driven by amino acid sequence)
-the distribution throughout that overall shape of the amino acid side chains with their distinctive chemical properties.
What are the two major classes of amino acid side
chains?
Hydrophilic and Hydrophobic.
What is the charge distribution of hydrophilic side
chains?
They have a polar electronic charge distribution.
What is the charge distribution of hydrophobic side
chains?
They have a non-polar charge distribution.
What is the hydrophobic effect?
Water molecules surrounding hydrophobic molecules dispersed in water
adopt a constrained, cage-like organization (low entropy).
If hydrophobic molecules coalesce, constrained water molecules is reduced, and this net increase in entropy
ultimately drives the formation of separate hydrophobic and aqueous phases.
What type of interactions favor the coalescence of
hydrophobic molecules?
Weak non-covalent van der Waals intermolecular
interactions.
What is the “Oil drop” model of protein folding?
It is a model that takes into account the hydrophobic
and hydrophilic side chains of amino acids and their
interactions in an aqueous solution.
What determines the overall shape of the molecule?
specific, local, structural interactions, called secondary
and tertiary, determine the path of the peptide “backbone”
through space and hence, the overall shape of the molecule.
What dictates protein structure and function?
The amino acid sequence
What is the relationship between DNA and protein
function?
DNA indirectly determines protein function through
its determination of the amino acid sequence.
How do amino acids link together? (Process)
The amino acids of a polypeptide are attached to their neighbors by covalent bonds known as a peptide bonds. Each bond forms in a dehydration synthesis (condensation) reaction. The carboxyl group of the amino acid chain reacts with the amino group of an incoming amino acid, releasing a molecule of water. The resulting bond between amino acids is a peptide bond
What is the directionality of amino acids in a protein
chain?
it has two ends that are chemically distinct from one another. At one end, the polypeptide has a amino group, and this end is called the amino terminus (or N-terminus). The other end, which has a carboxyl group, is known as the carboxyl terminus (or C-terminus).
What is the secondary structure of polypeptides?
local conformations of the
peptide chain backbone.
