Lecture 3 Flashcards
(35 cards)
What does the way proteins fold depend on?
on the backbone interactions, and the interactions of the side chains with each other and with the surrounding solvent.
What does the variety in a structure depend on?
the sequence of the amino acid residues in a protein chain
Why does water have an extremely high boiling point?
due to its strong tendency to self associate through extensive hydrogen bonding - occurs in both the solid and liquid phase
Hydrogen bondings affects on water (3):
- Gives water an unusually high melting and boiling point
- Water can H-bond to polar molecules dissolved in it
- Influences how nonpolar molecule interact with it
How many H-bonds does each molecule in ice form compared to liquid water?
4 H-bonds : 3.6 H-bonds
Why don’t water and oil mix?
the hydrophobic effect.
What interactions maximize the number of energetically favourable H-bonds
water-water interactions
what is the goal of the hydrophobic effect?
the drive to maximize the number of stabilizing hydrogen bonds between water molecules
Where are polar residues found compared to non polar residues?
Outside (surface) vs. inside
What interactions occurs due to packing of the atom’s residues
Van der Waals interactions
What angle do side chains have in alpha helices?
Downward
What orientation do side chains have in beta sheets?
Because the orientation of each residue is flipped 180 degrees relative to its neighbour, the positions on the side chains make an alternating pattern.
What side chains do aliphatic amino acids have?
consist solely of carbon and hydrogen and are not aromatic
True or false: The smaller the hydrocarbon side chain, the more hydrophobic it is
False, The larger the hydrocarbon side chain, the more hydrophobic it is
List five amino acids with aliphatic side chains and their structure
Glycine: hydrogen atom
Alanine: methyl group
Valine: three carbon chain
Leucine: four carbon chain - T shape
Isoleucine: four carbon chain - isomer of leucine
List five amino acids with polar uncharged side chains and their structure
Serine: alcohol - methyl alcohol
Threonine: alcohol - ethyl alcohol
Asparagine: amides - two carbon + oxygen & amine - short arm (little extra distance)
Glutamine: amide - three carbon + oxygen & amine - longer arm (more distance)
Cysteine: thiol - methyl sulfur
how can you recognize fibrous proteins? (4)
- Have long extended structures
- Tend to be composed of a single secondary structure type
- Tend to have repeat sequences of residues that gives them their repeat structures
- Tend to use just a few types of residues
Examples of alpha keratin
Cat has whiskers, claws, and fingernails made up of alpha-keratin
describe structure of alpha keratin
Two alpha helices wrap around each other as a coiled coil - the helices are arranged in a parallel fashion, with the two N-termini at the same end
What is the interaction surface between the two helices formed by?
from nonpolar amino acid side chains that occur every 3rd or 4th residue along each helix
What forms a disulphide bond?
Oxidation of a pair of adjacent cysteine residues forms a covalent bond
Example of fibroin
Silk
What is the fibroin structure made up of?
beta sheets on top of each other
Examples of collagen
major structural protein of skin, tendon, and connective tissue
