Biomolecules - Amino Acids and Proteins Flashcards
How does epigenetic change gene expression?
methylation and histone modification
How is a peptide bond formed?
nucleophilic addition substitution between the C terminus of one AA and the N terminus of another
How are peptide bonds stabilized?
delocalization across the O and N on either side of the peptide bond
What is an AA in a polypeptide called?
residue
The N terminus is the?
amino group at the beginning
The C terminus is the?
carboxyl group at the end
What is pKa?
shows acid strength, lower the pKa the higher the acidity
Why is histidine useful to have an active sites?
Its side chain has a pKa of ~6.5 which is close to the physiological pH of ~7.4
Sensitive to pH change so it can stabilize or destabilize a substrate
pH < pKa
AA is protonated (+)
pH = pKa
mix of +/- AAs
pH > pKa
AA is deprotonated (-)
What’s weird about proline?
It has a 2* alpha amino group (side chain doubles back to bond with the N again)
This disrupts the alpha helix because the 2* alpha amino group causes kinks
What’s weird about glycine?
The simplest AA with side chain -H
Alpha carbon is no longer chiral (only nonchiral AA)
Disrupts the alpha helix because -H is so small which makes the molecule very flexible which causes kinks
What’s weird about cysteine?
Forms disulfide bridges if 2 get too close
CystEine vs cystine
Has the E if its reduced (SH)
No E if oxidized (S-)
Where are cysteine vs cystine?
extracellular = oxidizing = cystine
intracellular = reducing because of antioxidants = reduced = cystEine
How to determine L vs D AA?
With COOH at the top and R at the bottom
If the amino group is on the Left = L
Isoelectric point (pI)
the pH point where a molecule is net neutral
How to find pI
take the average of pKas of all functional groups
pH < pI
Everything is protonated = net +
pH = pI
zwitterion = net neutral
pH > pI
Everything is deprotonated = net -
How are proteins 3* structure stabilized?
H bonding, Van der Waals forces, disulfide bridges, and hydrophobic packing
solvation shell
the layer of solvent surrounding a protein which helps to stabilize (or destabilize) the outer layer
