lecture 3- proteins Flashcards
proteins are…
polypeptides made of amino acids attached to each other via peptide bonds
___ are the building blocks of proteins and have these 4 groups
amino acids
amino (NH3), carboxyl (COO-), hydrogen, R group
name the nonpolar, alipathic amino acids
glycine
alanine
proline
valine
leucine
isoleucine
methionine
name the 3 nonpolar, aromatic amino acids
tyrosine
phenylalanine
tryptophan
name the polar, uncharged amino acids
serine
threonine
cysteine
asparagine
glutamine
name the polar, positively charged amino acids
lysine
histidine
arginine
name the polar, negatively charged amino acids
aspartate
glutamate
R groups of the amino acids next to each other face opposite direction- ___ conformation most common
trans
list the structures getting to a protein
primary structure (linear sequence of aa’s) — secondary structure — tertiary (protein) — quaternary
describe secondary structure
regular repeats resulting from hydrogen bonds involving the backbone
1- alpha helix (coil, 10-15 aa long)
2- beta pleated sheet (a fold, 3-10 aa long)
What sequences of amino acids form alpha helices?
- no consecutive bulky or long R groups
- no consecutive like-charged R groups
- few with polar R groups, especially: Serine, threonine, asparagine, aspartate (these destabilize the helix)
- infrequent glycine (very flexible) or proline (not flexible)
describe beta sheets
parallel (n terminuses on same side and C terminuses on same side)
or antiparallel
- beta sheets consist of at least two beta strands
name three supersecondary structural elements involving alpha helices
1- helix-turn-helix
2- coiled-coil
3- four-helix bundle
describe helix-turn-helix
in proteins, the HTH is a major structural motif capable of binding DNA
- C terminal binds to major groove, N terminal helps to position the complex
name three supersecondary structural elements involving beta sheets
1- beta hairpin
2- antiparallel B sheet
3- B barrel