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mcb 124 > Introductory Topica > Flashcards

Introductory Topica Flashcards

(58 cards)

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1
Q

delta g =

A

-RTlnK

fraction of molecules with E> free energy of transition state

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2
Q

what delta G tells us how far we are from equilibrium?

A

RTln(B/A)

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3
Q

dielectric constant

A

ability of solvent to disperse charge - dependent of solvent

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4
Q

at 25 celsius, every 1.4 kcal/mol change in G correponds to

A

10fold change in K

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5
Q

hydrogen bonds specify structure because

A
  • short range

- directional: strongest when parallel to bond axis

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6
Q

what noncovalent forces dominate energetics of protein?

A

Hydrogen bonds
vdv
electrostatic
torsional

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7
Q

torsional energies: E vs. conformation

A

anti - minima
gauche, minimum with intermediate energy
eclipsed- highest energy maximum

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8
Q

van der vall interaction goes like

A

10-12 - 10-6
repulsion - attraction

not directional, small range

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9
Q

entropy changes with change in:

A

particles
available space
number of conformations

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10
Q

hydrophobic effects of water and hphob

A

entropy: unfavorable because water restricted at surface of hydrophobic

enthalpy:is H bond stronger at surface or free?
yes or no depending on temperature

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11
Q

favorable binding

A

shape complementarity
charge/dipole complements
hydrophobicity
conformational: minimise torsion

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12
Q

wavelengths of
peptide bonds
tryptophan/tyrosine

A

210 nm

A280

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13
Q

pka of carboxyl group in asp, glu, backbone

A

4

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14
Q

pka of arginine

A

12

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15
Q

pka of lysine

A

10-11

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16
Q

pka of histidine

A

6-7

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17
Q

pka of thiol

A

9

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18
Q

pka of tyrosine

A

10

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19
Q

how to measure size/polarity

A
  1. octanol water partitioning with Nacetyl amides: how much folded in water?
  2. calculate from np s area
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20
Q

peptide backbone: phi

+ or -

A

Calpha and N

only no +phi-psi

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21
Q

peptide backbone: psi

+ or -

A

C alpha and C

+ and -

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22
Q

glycine ramachandran

A

symmetric bc not chiral

many outliers, span all quadrants

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23
Q

conformationally special amino acids

A

alanine - alpha helix - y?
glycine- most flexible - all ramachandran
proline- restricted phi bc no h bond with amide/link to N
cysteine-disulfide

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24
Q

proline is different from other aa becaus

Study These Flashcards
A

R links to backbone
lower E difference btwn cis and trans -> can isomerize between

cis/trans: is R group facing or away from carbonyl

25
mass spec steps
1. fragment/ionize 2. evap with hi velocity spray 3. p/m ration separation
26
ID protein sequence by :
1. bits of data of protein: sequence bits, masses after proteolysis, whole mass 2. match to pdbases
27
definitnion of protein loops
not a helix, beta strand, beta turn
28
regular secondary structure characterized by
repeated torsion angles
29
supersecondary structure
connect secondary structures together: | turns and loops
30
why secondry structure
relaxed torsion, h bonds max compact BUT nucleation takes E because entropically unfavorable
31
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)
32
a helix lengths
100 degrees per residue 3.6 residues per turn 40degrees over reaching
33
which residues are on the same side of helix?
i +4 +3 +4 +3 etc
34
310 helix
triangular: i+3 h bond | longer per A acid
35
b sheets
peptide bondspoint in opposite directions: c=0 up down up down; NH up down up down etc no intrastrand bonding ends: 1. serine can take of main C=O H bonding 2. hairpin must be rigid molecule
36
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)
37
supersecondary loops
highly variable length, irregular, not rigid
38
b sheet formation
nucleation from turn - cooperative (all or none)
39
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
40
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
41
sequence alignment
alignment = match of 1 sequence - quantify relatedness =sequence identity (identical seq) +sequence homology (close match based on chem/genetic similarity_
42
homologs have evolutionary implications
NO- only similar sequence
43
isoform
protein with same bio function, slight different sequences
44
ortology/paralong
ortholog-different organism, same function | paralog- same biochem activity, different function
45
similar folds -> hi r low sequence identity
but similar function, ev relatedneess
46
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
47
architecture of 3 stranded beta sheet-how many?
3
48
topology of 3 stranded beta sheet-how many?
symmetry-> redundant-> less structures 12 evolutionary relationship between different depends , of same - usually same
49
evolution of oligodimers
1 gene express subunit - aggregate later | duplication:subunits get expressed together gene
50
quaternary structure: filament
2 interaction serfaces that interact head to tail | usually superhelical
51
characterization of filament superhelix
helicity: monomer per turn | translation per monomer (helical pitch)
52
quaternary structure: | homooligomer:
head to tail interaction or head to head; | closes a ring
53
interfacial active sites
when more than one monomer donates residues to form 1 active site regulates activity
54
hetero oligomer types
asymmetric multimer pseudo-symmetric (symmetric multimer of asymmetric multimers)
55
complex multimer
also has DNA
56
why form oligomers?
-increased stability/resistance to mut regulation (allostery, checkboint) higher specificity - larger interaction surface architectural - can span larger areas
57
how is aggregation state determined ? (# units per particle)
1. gell filtration ultracentrifug 3. light scattering 4direct visualization
58
what defines oligemeric inerface
minimum buried surface area > 600A charge distribution type of interfaces in right area

mcb 124 (3 decks)

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