Introductory Topica Flashcards
delta g =
-RTlnK
fraction of molecules with E> free energy of transition state
what delta G tells us how far we are from equilibrium?
RTln(B/A)
dielectric constant
ability of solvent to disperse charge - dependent of solvent
at 25 celsius, every 1.4 kcal/mol change in G correponds to
10fold change in K
hydrogen bonds specify structure because
- short range
- directional: strongest when parallel to bond axis
what noncovalent forces dominate energetics of protein?
Hydrogen bonds
vdv
electrostatic
torsional
torsional energies: E vs. conformation
anti - minima
gauche, minimum with intermediate energy
eclipsed- highest energy maximum
van der vall interaction goes like
10-12 - 10-6
repulsion - attraction
not directional, small range
entropy changes with change in:
particles
available space
number of conformations
hydrophobic effects of water and hphob
entropy: unfavorable because water restricted at surface of hydrophobic
enthalpy:is H bond stronger at surface or free?
yes or no depending on temperature
favorable binding
shape complementarity
charge/dipole complements
hydrophobicity
conformational: minimise torsion
wavelengths of
peptide bonds
tryptophan/tyrosine
210 nm
A280
pka of carboxyl group in asp, glu, backbone
4
pka of arginine
12
pka of lysine
10-11
pka of histidine
6-7
pka of thiol
9
pka of tyrosine
10
how to measure size/polarity
- octanol water partitioning with Nacetyl amides: how much folded in water?
- calculate from np s area
peptide backbone: phi
+ or -
Calpha and N
only no +phi-psi
peptide backbone: psi
+ or -
C alpha and C
+ and -
glycine ramachandran
symmetric bc not chiral
many outliers, span all quadrants
conformationally special amino acids
alanine - alpha helix - y?
glycine- most flexible - all ramachandran
proline- restricted phi bc no h bond with amide/link to N
cysteine-disulfide
proline is different from other aa becaus
R links to backbone
lower E difference btwn cis and trans -> can isomerize between
cis/trans: is R group facing or away from carbonyl
mass spec steps
- fragment/ionize
- evap with hi velocity spray
- p/m ration separation
ID protein sequence by :
- bits of data of protein: sequence bits, masses after proteolysis, whole mass
- match to pdbases
definitnion of protein loops
not a helix, beta strand, beta turn
regular secondary structure characterized by
repeated torsion angles
supersecondary structure
connect secondary structures together:
turns and loops
why secondry structure
relaxed torsion, h bonds max
compact
BUT nucleation takes E because entropically unfavorable
a helix structure
Nh and C=o aligned along helix
bonding: O- and Hi+4 above
R tends to point towards N terminus
right anded start with C (down) end with N (up)
a helix lengths
100 degrees per residue
3.6 residues per turn
40degrees over reaching
which residues are on the same side of helix?
i +4 +3 +4 +3 etc
310 helix
triangular: i+3 h bond
longer per A acid
b sheets
peptide bondspoint in opposite directions:
c=0 up down up down; NH up down up down etc
no intrastrand bonding
ends:
- serine can take of main C=O H bonding
- hairpin must be rigid molecule
supersecondary turns
1-2 residues (short), rigid; minimize unHbonded
gamma turns: i binds with i+2:
unbonded NH: either have serine/asp/asn (C-C=O) h bond with it or
proline- no H on N
beta turn: i binds with i+3
i+1 and +2 are not h bonded- asn or asp h bond with
has more types: 1(XX) 1;(GG) 2(XG) 2’(GX)
supersecondary loops
highly variable length, irregular, not rigid
b sheet formation
nucleation from turn - cooperative (all or none)
definiton of 3 structure of protein
protein fold of a
domain
description of path of polypeptide backbone of domain
unit of ‘stand-alone’ protein structure-usually assoc with function
definition o 3 structure of protein
a folding/motif motif
well-defined collection of interacting secondary structure connected by supersecondary
signiture sequence pattern - indicate function
sequence alignment
alignment = match of 1 sequence - quantify relatedness
=sequence identity (identical seq)
+sequence homology (close match based on chem/genetic similarity_
homologs have evolutionary implications
NO- only similar sequence
isoform
protein with same bio function, slight different sequences
ortology/paralong
ortholog-different organism, same function
paralog- same biochem activity, different function
similar folds -> hi r low sequence identity
but similar function, ev relatedneess
tertiary structure classification
class- mostly alpha, mix ab, irreg
architecture- relative positioning of 2 structure
topology- how 2 structure connect
homologous superfamily - evolved from same
architecture of 3 stranded beta sheet-how many?
3
topology of 3 stranded beta sheet-how many?
symmetry-> redundant-> less structures
12
evolutionary relationship between different depends , of same - usually same
evolution of oligodimers
1 gene express subunit - aggregate later
duplication:subunits get expressed together gene
quaternary structure: filament
2 interaction serfaces that interact head to tail
usually superhelical
characterization of filament superhelix
helicity: monomer per turn
translation per monomer (helical pitch)
quaternary structure:
homooligomer:
head to tail interaction or head to head;
closes a ring
interfacial active sites
when more than one monomer donates residues to form 1 active site
regulates activity
hetero oligomer types
asymmetric multimer
pseudo-symmetric
(symmetric multimer of asymmetric multimers)
complex multimer
also has DNA
why form oligomers?
-increased stability/resistance to mut
regulation (allostery, checkboint)
higher specificity - larger interaction surface
architectural - can span larger areas
how is aggregation state determined ? (# units per particle)
- gell filtration
ultracentrifug - light scattering
4direct visualization
what defines oligemeric inerface
minimum buried surface area > 600A
charge distribution
type of interfaces in right area
