Ch 3/ Protein Structure and Function Flashcards
Non polar ameno acids letters
(London & Canada (C for cys)
Uncharged polar ameno acid letters
NQSTY
Quit The Nozzey Shit You
Basic ameno acid letters
(positve)
RKH
Kyle Rests Heavaly
acidic ameno acid letters
Negative
DE
Dead Earth
unique properties of water
given by H bonds
are thermal regulation and universal solvent
Disolves in water
ionic and polar
hydration shells
keeps ions seperage (also polar molecules), partal charge on O of water is attracted to ions making the schell
hydrophobic effect
nonpolar subsances excluded from solvation netwoek of water
hydrophobic results in few water milecules on scheel, therefore released and spontatious
nonpolar has an orderd water chage, unfavered
high number of hydrocarbons
non polar
protines add
functionality
functions of protines
structural, movement, defence, regulation, transport, catalusis
SM(all)
D(i)R(t)
T(i)K
each protine folds into a
stable conformatin
parts of ameno acid
Unchared polar
capable of forming H bonds
H & OH-
Nature prefers on __ over another
issomer
L ameno acids
D suggars
same with enzimes
chiral
4 differnt groups
Thalimonide
was racemic mixtre one form sedative other caused brith defects
not even just give one enantomer - because boddy convers it tothe other
___ site on enzimes (are chiral)
allosteric site
Peptide bond
covalent bond
connects two amino acids
amide linkage
e- is delocalized - exists as resonance
formation of peptide bond
type of reaction of peptide bond
condensation, dehydration,
Nuc. Acytl sub.
How peptide bond affects protine conformation
rigid and planer
partial double bond charatar (b/c resonance)
not rotate freely (1/3 of bonds in peptide backbone)
limits conformation possibilites of protines
Primary
linear ameno acid sequence
secondary
basic folding units (helices, sheets)
Common patterns
tertiary
3D structre of a folded prien (final)
Quaternary
contains more than one polypeptide chain
Priamary structure is listed from __ to __
N (amino) terminous to C (carboxyl) terminous
the backbone of the polpeptide excludes __
is a repeating __
r chains
repeating CCN
3D structure is determined by the
order of amino acids
alfa heliex Bondong:
R group:
philic:
hydrogen bonding between N-H and c=O groups in polypeptide backbone (every 4 amino acids)
Rgroup away from helix
one side is hydropobic other side is hydrifilic (amphipathic)
coiled coil
supper seoncdary
alpha helies wrap around each other to form a stable sturctre
two amphipathic come together (phobic binds w phobic phillic binds with phillic)
Betta sheet
when polpeptide chain segments line up side by side
each Betta sheet is fully extended and stabalized by H bonding between N-h and carboxl groups WITHIN the polypeptide backbone
also amphipathic - goes above and below the plane, the R groups alternate up and down
spider silk
stronger than steel
pick sequenct that could fom a strand in a amphipathic beta sheet
alternating polar and nonpolar ameno acids
tertiart structre
interacts of side chains/r groups
Protine domains
substucture
fold independantly into a stable compact structre
each doman is a specific function of the protien (and structure)
Globular protiens
soluable in H2O, compact structre, synamic function
Fibrous protines
structural protines, long rod shape, insoluable in water
Non covalent interactions include
vander wals
H bonding
electrostatic attractions
vander wals
weak fromed with in close range between non polar atoms
fluctuate electtral charges in close proximity
H bonding
between hydrogen attom and small highly electroneg attom
electrostatic attrations
salt bridges
attration between ionic groups of opposite charges (ex. ionic bonds between acid and basic)
Disulfide bridge/bond
forms when two cysteine residues are oxidized
SH SH to S S
Hemoglobin quaternary structure
2 alfa 2 beta chains
each has a heme group that binds to oxygen (like a “pocket”)
2 dimers slide past each other
indivdual subunits of multimeric complexts ___ associate to from a __
non-covalentaly (alows functionality because break and form eaisly)
a functional protine structure
problem of protine folding
cannot go though all possible conformations
protines take less than a second to fold inside cell or in test tube
Levinthal’s paradox
astronomcal numbers of conformations open to a protine in a denatured state
molten globule
protein states that are more or less compact, but are lacking the specific tight packing of amino acid residues which creates the solid state-like tertiary structure of completely folded proteins.
formation of tertiary strutures but not fully there
Native proteins
lowest energy form/ bottem of energy landscape model
intermediates of energy landscape model
are more stable
the folding code
themodynamic question of folding causes less disorder but it is spontanous (inc disorder in universe) how
protine structure prediction
predit proteins native structre froma ameno acids
the folding process
kientics
a lof of possible pathways, how does it know which to take
glibular proteins are __ proteins
soluble
hydrophobic groups together in aquesous enviorment
hydrophobic groups togerher, water gets released into surroundsings (from water schell), increasing disorder
Minimizing the nonpolar surface area
(bury nonpolar groups in interior of
folded protein) minimizes the
number of water molecules that become
ordered
water is freed, no longer organized aeound polpeptide
denaturing of albumin in egg goes from
soluable to insoluable
denaturing conditions
heat
reducing agents
detergents
high salt
mechanical stress
heat
disrups weak bonds such as H
Reducing agents
disulfide brige (covalant bond) is produced durring oxidation and removed with reduction
detergents
get more on thiss
amphipathic - hydrophobic and hydrophilic
high salts
distrupt ionic bonds
mechanical stress
ex. whisk egg white causes foam (with denatured protines)
ligand
substance bound by the protine
Indicate level(s) of protein structure to which
each of the following contributes:
a. hydrogen bond
b. beta pleated sheet
c. disulfide bond
d. amino acid sequence
a. secondary, tertiary (quantanry if accaplable)
b. secodary
c. tertairy (quant if apiciable)
d primary
disulfide bond is caused by
teo cistines reducing
