Protein Structure & Function

Essential Cell Biology (6th Ed.) Chapter Four

amino acid

Organic molecule with an:

• H group

• a carboxyl group (-COOH)

• an amino group (-NH₂)

• an R group/side chain

all bonded to the same alpha carbon

protein

When polypeptides come together, the macromolecule that is formed is called a ________.

Polypeptide chain

amino acids linked together

sequence/order

The shape of a protein is determined by the _____ of its amino acids.

Peptide bonds

Amino acids are linked by …..

Noncovalent bonding

What type of bonding helps proteins fold?

Disulfide bonds

help stablize a favored protein conformation

Extracellular

Extracellular or Intracellular proteins?
Often stabilized by Covalent Cross-Linkages

Hydrophobic forces

Help proteins fold into compact conformations

Polar

Polar or Nonpolar?

• A.A. side chains displayed on surface

• interact with water

• form H bonds

Nonpolar

Polar or Nonpolar?

• packed into hydrophobic core region

• hidden from water

Hydrogen bonds

• form between adjacent regions of a folded polypeptide chain

• help stabilize a protein’s folded shape

• occur between:

  • backbone to backbone

  • backbone to side chain

  • side chain to side chain

lowest

Lowest or highest?

Proteins fold into a conformation of ____ energy.

Primary

Simple sequence of amino acids that make up the polypeptide

• no folding

• nothing fancy

Secondary

most common are structures include:

• α-helix

• β-pleated sheet

alpha-helix

Helix is held by hydrogen bonds between the oxygen atom in a carbonyl group of one amino acid and the H atom of the amino group that is just four amino acid units farther along the chain

Beta pleated sheet

Pleats are formed by similar hydrogen bonds between continuous sequences of carbonyl and animo groups that are further separated on the backbone of the polypeptide chain

Tertiary

Large-scale 3D shape

• Determined by interactions between A.A. residues that are far apart in the chain, such as disulfide bridges

Quaternary

• Contain more than one polypeptide chain

• Stabilized by weaker interactions

• e.g., hemoglobin

hydrophobic

The side chains of amino acids are ________.

hydrophilic

The polypeptide backbone of amino acids is ______.

coiled-coil alpha helix proteins

Helices wrap around each other to minimize exposure of hydrophobic amino acid side chains to aqueous environments

• found in:

  • a-keratin in hair

  • outer layer of skin

C-terminus

In parallel and antiparallel β sheets, the arrows point toward the _-_____ of the polypeptide chain.

Unstructured proteins

lack a stable, fixed 3D structure

• exist as flexible chains

• gains order upon binding partners

• play roles in:

  • cell signaling

  • gene regulation

lowest

Protein folding conformation represents the ________ energy state.

Hydrogen bonds

These bonds help stabilize the folded protein shape.

Hydrophobic

_______ interactions help proteins fold into compact shapes.

amyloid fibril

abnormal prion proteins propagate and aggregate to form …

Prions disease

Protein misfolding causes what type of disease?

• e.g., Mad cow disease