Peptides

Question 1

Why is a peptide bond shorter than a normal C-N bond?

What is the difference between the cis & trans config around a peptide bond?

Why is a cis config of peptide bonds less likely?

What is the omega angle? What is it in the trans configuration?

Answer 1

The peptide bond is mostly planar & rigid so there is only 40% resonance giving it double bond character (so 1.27A)

Trans = Ca on opposite sides of C-N
Cis = Ca on same side of C-N

Involves proline residues (cause steric hinderence) so omega angle would be 0

Angle between C-N in the peptide bond, 180

Question 2

What is the phi bond? What is its angle?

What is the psi bond? What is its angle?

Why are these bonds not always free?

In a Ramachandran plot, what does the light & dark bits represent?

What are the differences in the plot between proline & glycine?

In what config are the amino acids after a proline?

Answer 2

Angle between N of peptide & Ca - free

Angle between C of peptide & Ca - free

Steric hinderance of side chains

Light = steric hinderance
Dark = where combinations of phi & psi bonds allowed

Glycine = smallest side chain (H) so less steric hinderance & more combos phi & psi
Proline = little dark areas- most steric hinderance

Cis (normally trans)

Question 3

What are the sizes of:

dipeptide
oligopeptide
polypeptide
protein

How would you name a peptide with:
N, valine, aspartic acid, alanine, C

How do you calculate the molecular weight of a peptide?

What is the average mass of an amino acid residue in a peptide/protein? With this, what is the average mass of an amino acid residue on its own?

Answer 3

2AA long
<25 AA
<100 AA
>100 AA (more than 1 polypeptide chain)

Valyl-aspartyl-alanyl or H-Val-Asp-Ala-OH or VDA

Mass of amino acids & water (18)

110

110 + 18 = 128

Question 4

With what technique can you identify homologs? What does this allow you to do?

What are the definitions of:

homolog

ortholog

paralog

What is a sequence motif?

Answer 4

Multiple sequence alignment.
Build phylogenetic trees, trace evolutionary relationships, predict new members of protein families

Similarity attributed to descent from a common ancestor

Homologous sequence in different species which arose from common ancestral gene in speciation (may or may not have similar function)

Homologous sequence in single species arising from gene duplication (normally have different function)

short conserved sequence pattern associated with distinct functions of a protein or DNA