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
supersecondary structural elements can also be ___, and combine several superseoncary elements, including both alpha helices and beta sheets
mixed
tertiary structure is determined by…
primary and secondary structures combined with interactions between R groups and the environment (most important interaction is hydrophobic exclusion***)
- others are van der Waals, hydrogen bonding, disulfide, ionic
proteins composed of multiple polypeptide chains = ___
name the 2
oligomers
homooligomers- identical subunits
heterooligomers- nonidentical subunits
proteins may be ________…. 1/3 of all proteins in higher eukaryotes may lack fixed tertiary structure entirely or at least contain unstructured sections or regions- diversity in binding
intrinsically unstructured
name one homooligomer and one heterooligomer
E. coli B clamp (homodimer)
hemoglobin
due to a toxin called ___ produced by streptococcus auerus, beta barrel can form pores in the ___ and kill the cell
hemolysin
cell membrane
in a nucleotide- the nitrogenous base is linked to the ___’ carbon or ribose/deoxyribose and the phosphate group is linked to the ___’ carbon
1’
5’
is the transfer of information into RNA irreversible?
no
the double helix of DNA under physiological conditions is in what form?
B form
What is more stable, G-C or A-T, why?
G-C (3 hydrogen bonds, not 2)
T or F:
all nucleic acids with complementary sequences can form duplexes
true
deoxiribose differs from ribose by having
one less oxygen
the DNA double helix always has a uniform diameter because ___, which have one ring always pair with ___, which have two rings
pyrimidines
purines
Which molecules form the backbone of DNA?
deoxyribose (sugar) and phosphate
primary structure of proteins is maintained by ___ bonds
peptide
