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mcb 124 > Introductory Topica > Flashcards

Introductory Topica Flashcards

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

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
Q

mass spec steps

A
  1. fragment/ionize
  2. evap with hi velocity spray
  3. p/m ration separation
26
Q

ID protein sequence by :

A
  1. bits of data of protein: sequence bits, masses after proteolysis, whole mass
  2. match to pdbases
27
Q

definitnion of protein loops

A

not a helix, beta strand, beta turn

28
Q

regular secondary structure characterized by

A

repeated torsion angles

29
Q

supersecondary structure

A

connect secondary structures together:

turns and loops

30
Q

why secondry structure

A

relaxed torsion, h bonds max
compact

BUT nucleation takes E because entropically unfavorable

31
Q

a helix structure

A

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
Q

a helix lengths

A

100 degrees per residue
3.6 residues per turn
40degrees over reaching

33
Q

which residues are on the same side of helix?

A

i +4 +3 +4 +3 etc

34
Q

310 helix

A

triangular: i+3 h bond

longer per A acid

35
Q

b sheets

A

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
Q

supersecondary turns

A

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
Q

supersecondary loops

A

highly variable length, irregular, not rigid

38
Q

b sheet formation

A

nucleation from turn - cooperative (all or none)

39
Q

definiton of 3 structure of protein
protein fold of a
domain

A

description of path of polypeptide backbone of domain

unit of ‘stand-alone’ protein structure-usually assoc with function

40
Q

definition o 3 structure of protein

a folding/motif motif

A

well-defined collection of interacting secondary structure connected by supersecondary

signiture sequence pattern - indicate function

41
Q

sequence alignment

A

alignment = match of 1 sequence - quantify relatedness

=sequence identity (identical seq)
+sequence homology (close match based on chem/genetic similarity_

42
Q

homologs have evolutionary implications

A

NO- only similar sequence

43
Q

isoform

A

protein with same bio function, slight different sequences

44
Q

ortology/paralong

A

ortholog-different organism, same function

paralog- same biochem activity, different function

45
Q

similar folds -> hi r low sequence identity

A

but similar function, ev relatedneess

46
Q

tertiary structure classification

A

class- mostly alpha, mix ab, irreg
architecture- relative positioning of 2 structure
topology- how 2 structure connect
homologous superfamily - evolved from same

47
Q

architecture of 3 stranded beta sheet-how many?

A

3

48
Q

topology of 3 stranded beta sheet-how many?

A

symmetry-> redundant-> less structures
12

evolutionary relationship between different depends , of same - usually same

49
Q

evolution of oligodimers

A

1 gene express subunit - aggregate later

duplication:subunits get expressed together gene

50
Q

quaternary structure: filament

A

2 interaction serfaces that interact head to tail

usually superhelical

51
Q

characterization of filament superhelix

A

helicity: monomer per turn

translation per monomer (helical pitch)

52
Q

quaternary structure:

homooligomer:

A

head to tail interaction or head to head;

closes a ring

53
Q

interfacial active sites

A

when more than one monomer donates residues to form 1 active site

regulates activity

54
Q

hetero oligomer types

A

asymmetric multimer
pseudo-symmetric
(symmetric multimer of asymmetric multimers)

55
Q

complex multimer

A

also has DNA

56
Q

why form oligomers?

A

-increased stability/resistance to mut
regulation (allostery, checkboint)
higher specificity - larger interaction surface
architectural - can span larger areas

57
Q

how is aggregation state determined ? (# units per particle)

A
  1. gell filtration
    ultracentrifug
  2. light scattering
    4direct visualization
58
Q

what defines oligemeric inerface

A

minimum buried surface area > 600A
charge distribution
type of interfaces in right area

mcb 124 (3 decks)

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