How to build a macromolecule?
Condensation reactions, remove water
How to break up a biopolymer?
Hydrolysis reactions, add water
How are proteins linked and what do they form?
linked by amide linkages to form peptide bonds
How to make up proteins?
Bunch of amino acids
Is the backbone of a peptide bond hydrophilic or hydrophobic?
hydrophilic
Which direction do you read a protein? (C/N terminis)
Read from positive amino (N) to negative carboxy (C)
What is primary structure?
linear sequence of amino acids
What is secondary structure?
regularly repeating folding patterns
What is tertiary structure?
overall three dimensional fold
What is quaternary structure?
assembly of subunits
What does aliphatic mean?
side chains made up of just carbon and hydrogen
What is phosphorylation and what amino acids are impacted?
hydroxyl replaced by phosphate group
ex: tyrosine kinases
Impacts: Ser, Thr, Tyr
What is hydroxylation and which amino acids are impacted?
Stabilization of structures
Ex: Collagen
Impacts: Pro, Lys
What is methylation and which amino acids are impacted?
Cell marker
Examples: Histones
Impacts: Lys, Arg, His
What is ubiquitination?
a protein can be modified through a chemical linkage to a second protein called ubiquitin
occurs at a lysine residue
How are secondary structures primarily stabilized?
hydrogen bonding
What are the phi and psi angles?
phi: C-N
psi: C-C
What is the structure of alpha helicies?
extensive hydrogen bonding between residues n and n+4
core is tightly packed to protect the hydrogen bonding
What is the difference in spacing (in angstroms) between alpha helices and beta sheets?
1.5 angstroms vs 3.5 angstroms between residues
What are the two types of beta sheets and which is more stable?
antiparallel (opposite N-C direction) and parallel (same N-C direction)
antiparallel is more stable because the H-bonding is linear
In terms of a Ramachandran plot, which amino acid is most and least sterically hindered?
Proline is the most sterically hindered because of the proline ring, and glycine is the least sterically hindered
In terms of a Ramachandran plot, which secondary structure has more possibilities?
Beta sheets have higher possibilities because it is spread out compared to the specific H-Bonding that needs to occur for an alpha helix
What are reverse turns for and where are they found?
used to turn a protein 180 degrees, found on the protein surface
n and n + 3
What is the differences between a Type I and II reverse turn?
Type I: carbonyl and R group are facing away
Type II: carbonyl and R group are facing the same side (usually forcing the R group to be Glycine)
