Biophysics Lecture 5 Revision

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Ways that chaperonins help proteins fold properly

They can help fold proteins by catalyzing reactions in the folding process that would otherwise take a long time, bring molecules closer together, and provide an isolated environment with specific properties that facilitate folding into the native state.

Steric forces

Repulsive forces that arise from interactions between electron clouds of close atoms.

Aromatic and hydrophobic amino acids

Tryptophan and phenylalanine

Aromatic and hydrophillic amino acid

Tyrosine, because of the hydroxyl group it possesses.

Amino acids are divided into 3 main groups

Hydrophobic, uncharged polar (hydrophillic), and charged polar (hydrophillic), with charged amino acids being further subdivided into two categories: acidic (release protons and carry a negative charge) and basic (absorb protons and carry a positive charge).

Zwitterion

When amide and carboxyl groups ionize (addition of protons to amide groups and loss of protons in carboxyl groups), an ionized molecule with both negative and positive charges but a net neutral charge is formed. Ionized amino acids occur before binding together in physiological pH (7.35-7.45), and deionize once they bind, releasing water as a product (dehydration synthesis).

Carboxyl and amino groups with relation to acidity and pH

Amino groups during ionization accept protons, and are therefore basic. Carboxyl groups, on the other hand, donate protons during ionization and are acidic as a result.

Disulfide bonds

A type of covalent bond formed between the sulfurs of different cysteine residues, causing a release of 2 hydrogen protons (bc of the initial sulfhydryl group). They provide rigidity to the protein, making it able to withstand stress without disrupting its native state.

Peptide bond dipoles

The amine group and carbonyl group in amino acids are polar, forming a dipole. The amide group has a charge of 0.2 while the carbonyl group has a charge of 0.4. Together, they act as a single dipole in a peptide bond with their dipole moment (D) being approx. 0.7.

Dipole interaction

If lined up in a parallel configuration, they will repel. If lined up in an anti-parallel configuration, they will attract. In addition, dipoles lined up end to end (effectively the negative charge of one dipole faces the positive charge of another), they will treat each other as point charges, with the distance expressed as 1/r. This means that these attractions are much stronger and felt over a much longer distance in comparison to other interactions. Configurations with the peptide bonds lined up end to end may be favored over others during folding.

The polypeptide backbone…

-is flexible and determines what shapes are permitted for the protein to fold into. Though side chains provide some flexibility, the backbone itself is more important when it comes to this aspect.

Rotation in a polypeptide…

-is dependent on the bonds formed between alpha carbon and amine nitrogen (represented by symbol phi) and alpha carbon and the carbonyl carbon (represented by symbol psi). The bond between amide nitrogen and carbonyl carbon allows for no rotation because of the lone pair of electrons on the amide nitrogen, giving the bond a double bond character, restricting rotation.

The 2 biggest contributors for the limitation of psi and phi angles in polypeptides.

1) Steric hindrances (repulsion forces)

2) Dipole-dipole interactions from adjacent peptide bonds.

Sickle cell anemia is caused by…

A replacement in the sixth amino acid of the beta polypeptide chain in hemoglobin. Instead of glutamic acid, the amino acid present is valine, altering the shape of red blood cells.

About how many amino acids are present in hemoglobin?

Around 600; 150 in each of the alpha and beta polypeptide chains.

Alpha helices

Examples of secondary protein structure in which the carbonyl oxygen of one amino acid forms hydrogen bonds with the amino hydrogen of another amino acid 4 residues away (on the same strand), forming a helix shape. Each turn of the helix contains 3.6 amino acids (an alpha helix 36 amino acids long would form 10 turns). Remember that the structure repeats itself every 5.4 angstroms (a pitch of 5.4 angstroms).

Beta-pleated sheets

Are another type of configuration in secondary protein structure, where segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together via hydrogen bonds between strands. Each “beta strand” is apoximately 5-10 residues long. They may be parallel or antiparallel.

Which secondary structure is mostly found in proteins embedded in the lipid bilayer?

Right-handed alpha helices.

Why do proteins become denatured in low temperatures?

Typically, interaction between water molecules and the hydrophobic residues of a polypeptide chain are minimized, increasing entropy, as contact between the two is energetically unfavorable and decreases entropy. However, in colder temperatures, water becomes more ordered, so the minimization of contact between the water molecules and the hydrophobic residues is reduced as the entropy change is negligible, as water is already in a fairly ordered state.