Lecture 14 - Hierarchy of Protein Structure Flashcards
a peptide bond results from the linkage of:
the carboxyl group of one amino acid and the amino group of another amino acid with the ELIMINATION of water
what is the orientation of the peptide bond?
the peptide bond is planar
what are the positive amino acids?
Lysine (Lys, K), Arginine (Arg, R) and Histidine (His, H)
what are the negative amino acids?
Glutamic acid (Glu, E) and Aspartic acid (Asp, D)
how will acidic and basic amino acids behave above and below their pKa?
•Acidic side chains will be NEGATIVELY charged ABOVE their pKa
•Basic side chains will be POSITIVELY charged BELOW their pKa
when do hydrogen bonds form in proteins?
a hydrogen bond occurs when two electronegative atoms, such as nitrogen and oxygen, interact with the same hydrogen
where do hydrogen bonds form in proteins?
in proteins hydrogen bonds form between main chain and also side chains
definition of secondary structure:
Secondary structure is defined by the phi and psi angles (BACKBONE TORSION ANGLES) of the backbone atoms of the amino acid residues, and the hydrogen bonds between main chain atoms.
what are alpha-helix and beta-strands classed as?
alpha-helixes and beta-strands are “units of secondary structure”
what amino acids make good & poor helix formers?
•Ala, Glu, Leu and Met are good helix formers
•whereas Pro, Gly and Tyr are poor helix formers
a. series of beta strands hydrogen bond to form…
… pleated sheets where the R-groups point alternately up and down
beta strands can either be:
parallel or anti-parallel
beta-sheet formers:
they are large bulky side chains
simply plain, large Tyr, Trp (Phe) bulky
and awkward due to branched beta carbon: Ile, Val, Thr
large S carbon on beta carbon - Cys
secondary strucutre breakers
many amino acids have side chain which disrupt the secondary strucutre and are known as secondary strucutre breakers
beta-turn:
•H-bond between carbonyl oxygen and amide hydrogen of residue three positions down
•Forces reverse of direction of chain
