CHEM130A: protein primary & secondary structures

There are 4 levels of protein structure. What does each level consist of?

1° primary is the amino acid sequence

2° secondary is the small local α-helix structure driven by H-bonding in the backbone

3° tertiary is a polypeptide chain driven by R-group interactions

4° quaternary are assembled complexes with multiple proteins or subunits associating

What are the two main methods of amino acid sequencing?

mass spectrometry (modern method): ionization and fragmentation of proteins or peptides into gas-phase ions.

Edman degradation (old method): N-term amino acid is labeled, cleaved, and identified by chromatography or electrophoresis

What are consensus sequences?

Define what the following symbols in consensus sequencing mean: [ ], { }, x(#), big letter, small letter

consensus sequences are protein regions with some function that usually have similar sequence

[ ] → common amino acid

{ } → amino acids that are not allowed because they break proteins

x(#) → that # amino acid is not restricted and can be anything

big letter → amino acid happens often

little letter → amino acid does not happen often

What is sequence alignment?

Define what the following symbols in sequence alignment mean: *, :, ⋅, ( ), -

sequence alignment is the alignment between homologs, which can reveal evolutionary conserved regions

* → conserved sequence (identical)

: → conservative mutation (chemically similar)

⋅ → semi-conservative mutation (chemically similar)

( ) → non-conservative mutation (blank and not chemically similar)

What is the relationship between conserved sequence and mutations?

↑ conservation → mutations there are very bad → might be what’s causing disease

What are the 7 weak interactions that make a protein?

dipole-dipole, Van der Waals, hydrophobic effect, hydrogen bonding, disulfide bond, π interactions for Tyr and Trp, and ionic interactions for charged amino acids

The peptide bond

NA

What are the two main types of peptide bonds?

phi (ɸ) bonds: planes between carbonyl carbons

psi (ψ) bonds: planes between nitrogen

What is the Ramachandran plot? What are the axes? How do you read it?

a method to calculate and graph ψ (y-axis) and ɸ (x-axis) angles for every peptide bond in a protein.

dark green → many observations of angle combinations (less restricted)

light green → few observations of angle combinations (more restricted)

white → no observations of angle combinations (forbidden space)

steric interference between adjacent residues → such angle combinations are not allowed due to Van der Waals

In a protein secondary structure, what kind of helices is there and its properties?

α-helices

hydrogen bonding between backbone of amine donor and carbonyl acceptor → holds structure together

chirality of either right handed helix (most common for L-amino acids) or left-handed helix