Folding, Globular &Fibrous proteins, Peptide sequencing

Question 1

Is the search for the lowest-energy conformation random?

Answer 1

Search for the minimum is not random because the direction toward the native structure is thermodynamically most favorable

Question 2

What is the Ken Dill’s folding funnel: hypothesis ?

Answer 2

Unfolded structures lie around the top. As the protein folds, it falls down the wall of the energy funnel to more stable conformations. The native, folded structure is at the bottom.

Question 3

What directs a protein’s folding into native conformation ?

Answer 3

A protein’s internal residues -Hydrophobic Effect

Question 4

What are motifs ?

Answer 4

• Specific arrangement of several secondary structure elements – All alpha-helix – All beta-sheet – Both
• Motifs can be found as reoccurring structures in numerous proteins
• Proteins are made of different motifs folded together

Question 5

Why must peptide chains fold?

Answer 5

Peptide chain must fold to “bury” most of the hydrophobic side chains, minimizing their contact with water residues

Question 6

Examples of fibrous (insoluble) proteins ?

Answer 6

Collagen and Elastin

Question 7

Fibrous proteins have an abundance of what type of AAs?

Answer 7

High abundance of amino acids with non-bulky side chains (glycine, alanine, serine, glutamate, and glutamine); exception high amount of proline in collagen and elastin.

Question 8

What is a coiled-coil motif?

Answer 8

• Pairs of helices twine about each other in left-handed coil (alpha helical coiled-coil) and bury the hydrophobic residues (stable structure)
• Helps alpha helices stick together

Question 9

Describe alpha keratin

Answer 9

• Mechanically durable and chemically nonreactive
• Hard alpha keratin (occur in birds and reptiles) – shells, fingernails, claws
• Soft alpha keratin (occur in mammals) – skin, hair, wool • High levels of cysteine and cross-links.
• Keratin fibers cross-link through disulphide bonds between cysteine residues on adjacent chains

Question 10

Describe silk fibroin structure

Answer 10

• b-sheet protein • Alternating sequence: Gly-Ala-Gly-Ala….
• Gly on one side – Ala (or Ser) on the other – Gly on one sheet to meshes with Gly on an adjacent sheet (same for Ala/Ser)

Question 11

Describe spider silk

Answer 11

• Used for webs, egg sacks, and wrapping the prey
• Extremely strong material – stronger than steel – can stretch a lot before
breaking
• A composite material – crystalline parts (fibroin-rich) – rubber-like stretchy
parts
• Comprised of 2 proteins – fibroin which gives structure – seracin acts like
glue or matrix • Overall composite material like carbon fibre – higher tensile
strength than steel

Question 12

Describe elastin

Answer 12

• Major component of connective tissue of lung and arteries allows these to
resume their shape after stretching or contracting
• Hydrophobic , insoluble, forms 3 D elastic network; Formed from loose and
unstructured polypeptide chains
• Conformation that of random coil –>permits the protein to stretch and recoil .
A variety of random coil conformations possible
• Can stretch in any direction, structure more elastic than rubber

Question 13

When can Edman Degradation (Classical method) be used when sequencing proteins?

Answer 13

When protein sequence is known.

Question 14

What can Mass Spectrometry (Modern) method be used for ?

Answer 14

Can be used to determine post-translational modifications

Question 15

Differences in protein sequences indicate what?

Answer 15

evolutionary divergences

Question 16

What type of bonds are important for keratin structure?

Answer 16

Disulfide bonds

Question 17

What residues are particularly abundant in collagen?

Answer 17

Gly residues

Question 18

What are protein domains?

Answer 18

Regions in the protein that can fold and function as an independent
entity from the whole protein