Chapter 2: Protein Composition and Structure

Exam 1

Amino acid

An organic compound containing an amino group, a carboxyl group, and a unique functional group that are each bonded to a common carbon atom

Alpha carbon (-carbon)

The central carbon of an amino acid, linked to an amino group, a carboxylic acid group, a hydrogen atom, and a side chain.

Side chain/R group

The distinctive variable group bonded to the α-carbon atom of an amino acid

Chiral

The property of asymmetry in which a structure and its mirror image are not superimposable

Dipolar ion/zwitterion

an ion carrying both a positive and a negative charge 

Peptide bond/amide bond

covalent linkage formed between the alpha-carboxyl group of one amino acid and the alpha-amino group of another 

residue

each amino acid unit in a polypeptide 

main chain/backbone

regularly repeating part of a polypeptide including the amino group, alpha-carbon and carbonyl groups 

protein

a biological macromolecule built of chains of amino acids 

Oligopeptide/peptide

polypeptide chains made of small numbers of amino acids 

Dalton

A unit of mass equal to one atomic mass unit, or very nearly equal to that of a hydrogen atom

amino acids w/ionizable side chains

1. aspartic acid/aspartate

2. glutamic acid/glutamate

3. lysine

4. arginine

5. histidine

6. cysteine

7. tyrosine

disulfide bond

covalent bond formed by the oxidation of 2 sulfhydryl groups 

primary structure

amino acid sequence of a protein 

Torsion angle/dihedral angle

measure of the rotation about a bond 

Ramachandran plot

demonstrates possible psi and phi values due to steric collisions between atoms 

phi

angle of rotation around the N-C alpha bond

psi

angle of rotation around the C alpha - C bond

secondary structure

the spatial arrangement of amino acid residues that are near one another in the linear sequence

• due to regular pattern of h-bonding of backbone N-H and O=C

alpha-helix

a tightly coiled backbone forms the inner part of the rod and the side chains extended outward in a helical array 

• h-bond pattern is i + 4

• 1.5 A rise, 3.6 residues per turn (every 3-4 AA)

beta-pleated sheet (beta-sheet)

composed of 2+ polypeptide chains called beta-strands lying next to one another through hydrogen bonds

• 3.5 A between adjacent residues

• side chains in opposite direction

• can be parallel or anti-parallel

beta strand

A polypeptide chain that is almost fully extended rather than being tightly coiled as in the α helix

parallel h-bonding

slightly distorted/angled h-bond, 1 amino acid from strand A h-bonds to 2 amino acids on strand B

antiparallel h-bonding

virtually straight h-bonds between strands, 1 amino acid on strand A h-bonds 1 amino acid on strand B

Reverse turn/beta turn/hairpin turn

a short segment of residues where the polypeptide chain reverses direction

loop

a segment of residues where the polypeptide chain reverses direction, usually longer and more elaborate than a reverse turn 

tertiary structure

the overall course of the polypeptide chain (3D folding)

globular protein

a protein that forms a tightly packed structure, usually water soluble and devoid of overall symmetry

• protein folding is driven by hydrophobic effect

myoglobin

interior consists of non-polar residues

outside consists of both NP and P residues

amphipathic

have both hydrophobic/polar side + hydrophilic/non-polar side

Motif/supersecondary structure

certain combinations of secondary structure present in many proteins which frequently exhibit similar functions

• patterns of secondary structure in tertiary structure

• ex: helix-turn-helix

domain

an independently folded unit in the tertiary structure of a polypeptide chain, often connected to other similar regions by a flexible polypeptide segment 

fibrous protein

a protein that adopts a long, extended structure with repeated sequences 

• structural/support role

• insoluble

• use special type of helices that facilitate formation of long fibers that serve a structural role

alpha-keratin

single alpha-keratin polypeptide strand is an alpha-helix

• 2 right-handed alpha-helices intertwined to form a left handed coiled-coil

• contains a heptad repeat b/c 3.5 residues per turn (instead of 3.6)

collagen

rod-shaped

• single polypeptide contains left-handed helical structure

• 3 helical polypeptide chains wrap around each other to form right-handed superhelix

• lacks hydrogen bonding

• proline and hydroproline help stabilize structure

quaternary structure

proteins containing more than one polypeptide chain

subunit

individual polypeptide chain within a protein that contains multiple chains 

denatured protein

a protein that has lost its natural three-dimensional shape and biological function due to external stress, but keeps its primary sequence of amino acids intact

native protein

a protein in its original active and folded form 

cooperative transition

post-translational modification

covalent chemical changes made to a protein after it has been translated from mRNA

Valine and isoleucine tend to be present in β strands

• Branching at the β-carbon atom tends to destabilize α helices because of steric clashes

Cooperative transition

In protein folding, an “all-or-none” process where conditions that lead to the disruption of any part of a protein structure are likely to unravel the entire protein completely