Chapter 4 (Section 2: Protein Structure)

Proteins can assume an _____ number of ______

uncountable, conformations

chemical or structural functions relate to unique ____-_____ ______

three-dimensional structures

What are the four levels of protein structure?

Primary, secondary, tertiary, quaternary

What is the primary structure of proteins made up of?

Amino acid residues

What is the secondary structure of proteins made up of?

alpha-helixes

What is the tertiary structure of proteins made up of?

a polypeptide chain

What is the quaternary structure of proteins made up of?

Assembled subunits

Unlike organic polymers, what is unique about the protein structure?

They take conformations necessary for the protein to undergo a specific biological function

What is the protein conformation called?

Native fold

The native fold has a large number of _____ ______ within the protein

favorable interactions

What is the cost for the folding the protein into specific native fold?

Entropy cost

What is entropy?

The measure of randomness and disorder

Folding protein is a ____ -dependent process

energy

Proteins conformation is stabilizes mostly by ____ interactions

Weak

Define stability

Tendency of a protein to maintain a native conformation

Unfolded proteins have ____ conformation energy

high

What types of chemical interactions (weak or strong) are numerous to stabilize native conformations? What strong bonds are not typically found in native conformations

Weak (noncovalent) interactions and forces are numerous. Strong disulfide (covalent) bonds are uncommon

What are the three chemical interactions and forces are present in stabilizing protein conformations?

Hydrogen bonds, hydrophobic effect, ionic interactions

What are the four favorable interactions in proteins?

Hydrophobic effect, Hydrogen bonds, London dispersion, electrostatic interactions

What is the hydrophobic effect in protein folding?

The release of water molecules from the structured solvent layer around the molecule as the protein folds which increases net entropy

What is the role of hydrogen bonds in protein folding and what structures do they lead to

They are interaction between N-H and C=O of the peptide bonds. Leads to structures such as alpha helices and beta sheets

What is the London Dispersion effect in protein folding?

Medium-range weak attraction between all atoms which contributes to the stability in the inside of the protein

What are electrostatic interactions in protein folding?

Long range strong interactions between permanently charged groups and salt bridges especially those buried in the hydrophobic environment which strongly stabilizes the protein

What is the primary structure of a peptide bond?

The peptide bond is a resonance hybrid of two canonical structures

The resonance causes peptide bonds to…….

1) Be less reactive compared with esters

2) To be quite rigid and nearly planar

3) To exhibit a large dipole moment in the favored trans configuration

Due to the resonance structure, rotation around the peptide bond is….

not permitted

In which case is rotation around bonds permitted ?

When connected to the alpha-carbon

What are the two angles of bonds that are connected to the alpha carbon called?

Phi (ϕ): amide nitrogen bond and Psi (ψ): carbonyl carbon bond

In a fully extended polypeptide, both phi and psi are what degree?

180

Why are some phi and psi combinations are more favorable?

There is the chance to form favorable H-bonding interactions along the backbone

Why are some phi and psi combinations unfavorable?

There is steric crowding of backbone atoms with other atoms in the backbone or side chains

What is a saltt-bridge?

Interaction of oppositely charged groups form an ion pair