CH 306 Chapter 3 Flashcards
Proteins are quite stable. The life- time of a peptide bond in aqueous solution is nearly 1000 years. However, the free energy of hydrolysis of proteins is negative and quite large. How can you account for the stability of the peptide bond in light of the fact that hydrolysis releases considerable energy?
The energy barrier that must be crossed to go from the polymerized state to the hydrolyzed state is large even though the reaction is thermodynamically favorable.
Table 3.1 gives the typical pKa values for ionizable groups in proteins. However, more than 500 pKa values have been determined for individual groups in folded proteins. Account for this discrepancy.
This observation demonstrates that pKa values are affected by the environment. A given amino acid can have a variety of pKa values, depending on the chemical environment inside the protein.
Why is rotation about the peptide bond prohibited, and what are the consequences of the lack of rotation?
The peptide bond has partial double-bond character, which prevents rotation. This lack of rotation constrains the conformation of the peptide backbone and limits possible structures.
Forms between two cysteine amino acids
Disulfide bond
A rodlike structure with a tightly coiled backone
a-helix
Angle of rotation about the bond between the N atom and the a-carbon atom
phi-angle
Fully extended poly- peptide chain
B-strand
Formed by hydrogen bonds between parallel or antiparallel chains
B-pleated sheet
Regular repeating three-dimensional structures
Secondary structure
The bond responsible for primary structure
Peptide (amide) bond
Sequence of amino acids in a protein
Primary structure
Angle of rotation between the a-carbon atom and the carbonyl carbon atom
psi-angle
A plot of phi and psi angles
Ramachandran plot
What is meant by the term polypeptide backbone?
The (nitrogen–a carbon–carbonyl carbon) repeating unit
Define the term side chain in the context of amino acid or protein structure.
Side chain is the functional group attached to the a-carbon atom of an amino acid.
Differentiate between amino acid composition and amino acid sequence.
Amino acid composition refers simply to the amino acids that make up the protein. The order is not specified. Amino acid sequence is the same as the primary structure—the sequence of amino acids from the amino terminal to the carboxyl terminal of the protein. Different proteins may have the same amino
acid composition, but amino acid sequence identifies a unique protein.
List some of the benefits of knowing the primary structure of a protein.
The primary structure determines the tertiary structure. Knowing the primary structure helps to elucidate the function of the protein. Knowledge of the primary structure of mutated proteins enables an understanding of the biochemical basis of some diseases. Primary structure can reveal the evolutionary history of the protein.
Differentiate between amino acid composition and amino acid sequence.
Amino acid composition refers simply to the amino acids that make up the protein. The order is not specified. Amino acid sequence is the same as the primary structure—the sequence of amino acids from the amino terminal to the carboxyl terminal of the protein. Different proteins may have the same amino acid composition, but amino acid sequence identifies a unique protein.
What are the levels of protein structure? Describe the type of bonds characteristic of each level.
Primary structure—peptide bond; secondary structure—local hydrogen bonds between components of the polypeptide backbone; tertiary structure—various types of noncovalent bonds between R groups that are far apart in the primary structure; quaternary structure—various noncovalent bonds between R groups on the surface of subunits.
List some of the differences between an a helix and a b strand.
The helix is a condensed, coiled structure, with the R groups bristling outward from the axis of the helix. The distance between two adjacent amino acids is 1.5 Å. The strand is a fully extended polypeptide chain, and the side chains of adjacent amino acids point in opposite directions. The distance between adjacent amino acids is 4.5 Å. Both structures are stabilized by hydrogen bonding between components of the polypeptide backbone.
Basic component of quaternary structure
Subunit
Proteins that in whole or in part lack discrete three-dimensional structure under physiological conditions
Intrinsically unstructured protein
Refers to the spatial arrangement of amino acid residues that are far apart in the sequence
Tertiary structure
Proteins that exist in an ensemble of structures of approximately equal energy that are in equilibrium
Metamorphic protein
An energy landscape
Folding funnel
Compact regions that may be connected by a flexible segment of polypeptide chain
Domain
Refers to the arrangement of subunits and the nature of their interactions
Quaternary structure
Cause of spongiform encephalopathies
Prion
Combinations of secondary structure are present in many proteins
Supersecondary structure
