Biochemistry- Chapter 4 - Mississippi State University

Protein molecules adopt a specific

three-dimensional conformation.

The structure is able to fulfill a specific ___________, and is called ___________.

biological function; native fold or native conformation

The native fold has________ within the protein.

a large number of favorable interactions

What kind of cost is it to folding the protein into one specific native fold?

entropy

Limited number of conformations predominate under

biological conditions.

Conformations

thermodynamically the most stable, that is, lowest free energy (G).

Native

proteins in any functional, folded conformations. Has a large number of favorable interactions within the protein.

stability

tendency of a protein to maintain a native conformation.

Unfolded proteins have

high conformational entropy.

Chemical interactions does what to conformational entropy? (Ex.strong disulfide[covalent] bond and weak [noncovalent] bond)

stabilize.

disulfide bonds are

uncommon

there are _____ weak interactions such as:

numerous; hydrogen bonds, hydrophobic effect, ionic interactions.

Protein structures are stabilized by

noncovalent interactions and forces.

Formation of a thermodynamically favorable structure depends on

the influences of the hydrophobic effect, hydrogen bonds, ionic interactions, and van der Waals forces.

Natural protein structures are constrained by

peptide bonds, whose configurations can be described by the dihedral angles φ and ψ.

Favorable interactions in proteins include

hydrophobic effect, hydrogen bonds, London dispersion, and electrostatic interactions.

hydrophobic effect

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

hydrogen bonds

Interaction of N−H and C=O of the peptide bond leads to local regular structures such as helices and [beta] sheets.

London dispersion

Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein.

electrostatic interactions

-long-range strong interactions between permanently charged groups.


- Salt bridges, especially those buried in the hydrophobic environment, strongly stabilize the protein.

Four Levels of Protein Structure

primary, secondary, tertiary, quaternary

All proteins HAVE

primary, secondary, and tertiary structure

All protein do not HAVE

quaternary structure.

Primary Structure has what kind of arrangement?

linear

The order of amino acids is______ to its _____

crucial; function

Polypeptides consist of amino acids

linked by a peptide bond.

A protein consists of one or more polypeptides folded into a

specific 3D structure.

The peptide bond is also called

amide bond.

Each amino acid in a protein is called

residue.

Peptide bond

the linkage between two amino acids.

A peptide bond is

an amide linkage between the carboxyl group of amino acid and the amino group of the next.

What is removed in order for an amide bond to form?

water

The structure of the protein is partially dictated by the

properties of the peptide bond.

The peptide bond is a resonance hybrid of

two canonical structures.

The resonance causes the peptide bonds

to be less reactive, to be quite rigid and nearly planar, to exhibit a large dipole moment in the favored trans configuration

Rotation around the peptide bond is

inhibited by resonance.

C-N bond in peptide bond is shorter than

the C-N bond in a simple amine.

Peptides are

linear polymers of amino acids.

Dipeptides

have two linked amino acids.

Oligopeptides

have 4-20 amino acids.

Polypeptides

contain 20 or more peptides linked together.

Proteins

tend to be greater than 50 amino acids.

A polypeptide chain has

directionality

The amino terminal end is taken as the

beginning of the polypeptide chain.

The carboxyl terminal end is the

end of the polypeptide chain.

The primary structure is always written from

left to right.

The polypeptide chain consists of a repeating part called

the backbone.

variable part

amino acid side chains.

The backbone has hydrogen-bonding potential because

both the nitrogen and oxygen atoms of the peptide bond can participate in hydrogen-bond formation.

cis- configuration

the two α-carbon atoms are on the same side of the peptide bond. (exception: Proline)

trans- configuration

the two α-carbon atoms are on the opposite side of the peptide bond. (Exception: Proline)

In some proteins, the polypeptide chain can be cross-linked by

disulfide bonds

What are disulfide bonds formed by?

the oxidation of two cysteine.

two linked cysteine

cystine

Average molecular weight of an amino acid

110 daltons (g/mol)

Rotation is permitted about the

N-Cα bond [the phi (Φ)bond) and about the Cα-carbonyl bond (the psi (ψ) bond].

torsion angle

The rotation about the Φ and ψ bonds.

The torsion angle determines the

path of the polypeptide chain.

Torsion angles are also called

Ramachandran angles

Dihedral angles

4 points

What controls protein folding?

torsion angles.