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Chem 237 > Protein Structure and folding > Flashcards

Protein Structure and folding Flashcards

1
Q

what are the 4 elements of secondary structure ?

A

Alpha helix
beta sheet
beta turns
loops

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2
Q

what are the 4 structural feature of alpha helix?

A
  1. right handed helix with 3.6 residues per turn
  2. 5.4 Armstrong (A) (0.54 nm) per turns
  3. held together by hydrogen bonds
  4. amino acids point outwards from axis
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3
Q

what is a primary sturcture

A

the amino acid sequence in a poly peptide chain

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4
Q

what are 4 beta sheet important structural feautres ?

A
  1. two or more stands of poly peptide have sections where they interact via h bonds
  2. 2 orientations, can be mixed
    antiparallel - straight h bonds
    parallel not straight hydrogen bonds
  3. can turn between strands
  4. amino acids in beta sheets point out at rgiht angles to the plane
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5
Q

what are beta tight turns called and AA is there type 1 and type 2

A

it is called b turns and pro at postiion 2 in type 1(rare) and gly in postion 3 in type 2

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6
Q

what are loops

A

the are very long and include helices

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7
Q

what connects the strands in beta sheet

A

tight turns or large loops

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8
Q

what can side chains do to secondary strutures

A

it can disrupt or distort the structure

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9
Q

how can the sequence affect the helix

A

it can affect the stablilty as small hydrophoic AAs like Ala and Leu are strong helix formers while
Pro bc of rotation and Gly bc of R groups are a helix breaker

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10
Q

what is CD aka circular dichroism Analysis

A

it measure the molar absorption difference (delta e) of circular polarized light
chromophores produce signal that signal peptide bonds depending on the conformation of the chain and allows us to determine the perctage of different secondary structures on a protein

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11
Q

what are the two things secondary structure can make up

A

they can form fibrous protein and globular proteins

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12
Q

what is a tertiary structure?

A

it refers to the overall spatial arrangement of atoms in a polypeptide chain/ protein

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13
Q

what are the two major classes of tertiery structures ?

A

fibrous proteins and globular proteins

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14
Q

what is the make up of fibrous proteins and example ?

A

usually insoluble. and is made from a single secondary structure
keretin

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15
Q

what is the make up of globular proteins and example

A

water & lipid soluble
spherical as the polypeptide fold back
enzymes are globular (myoglobobin)
helices and sheet are closer together

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16
Q

what is a example of an alpha and beta fibrous tertiarty structure ?

A

alpha keritan
silk fibrion
collegan

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17
Q

whats alpha keratin and where is it found ?

A

it is a coiled coil of 2 alpha helixes left handed 3.5 residue per turn it is found in mammal hair and nails etc

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18
Q

what is the beta sheet fibrous protein silk fibroin and what are its interaction

A

it is silk used for moth and spiders , has anti parallel beta sheet with Ala and Gly with both H-bonding, hydrophobic and London dispersion interaction

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19
Q

what is collagen ?

A

a 3 alpha helices structure that is a left handed helix 3 residue per turn

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20
Q

what 2 things do 4 hydroxy proline do ?

A

increase stability of collegen and increase electrostatic interaction

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21
Q

what makes the globular teteriary structure more stable ?

A

proteins folding

22
Q

how do secondary structural elements become activated ?

A

the are activated via a fold to form an active conformation

23
Q

what are structural motifs?

A

they are small parts of proteins that are repeated therefore protein with similar function have similar structure

24
Q

what is a rossman fold ?

A

it is motif that is found in nucleotide binding domains 56 families have this

25
what are the design principles of globular proteins ?
it has is polar residue facing the outside and hydrophobic facing inwards towards the protein
26
what are the 3 types of globular motion in order from slowest to fastest and the number of displace
1. atomic vibrations 0.01- 1 A 2. collective motions 0.01 -5 A 3 (fastest) enzymic triggered conformation changes 0.5 -10A
27
what is are domains and what are 2 examples?
a independently folded part of a larger protein and binds specific things 1. SH2 2. Kringle
28
what are 3 examples of a quaternary structure ?
1. hemo globin 2. o2 carrying protein 3. a2b2 structure
29
what are 6 key things about a protein having the quaternary structure and why for each
1. Stability: interaction increase the stability of the subunit 2. Activity: the active site is created at the subunit interface 3. Regulation of activity: cooperativity of substrate improves binding efficiency 4, distal binding site for activators and enhancers increases sensitivity to molecules 5. genetic fidelity: each chain coded for by a different gene , if one goes wrong other one compensates 6. gene efficiency: one gene many subunits may combinations
30
what 4 intermolecular interaction allow for the stability of tertiary (3) and (4) quaternary proteins
1. electrostatic forces 2. van der walls ( London disperson ) 3, h bonds 4. hydrophobic interaction
31
what 3 things holds proteins together
the hydrophobic effect- majority contribution h bonds ( 40% contribution) salt bridge (small contributions
32
why is the hydrophobic the most effective and what its driving force
ex in myoglobin all the hydrophobic residues are on one side for both helices and they are buried between layers in the structure , entropy is the driving force
33
what is the interior of the protein
it has an hydrophobic core and charged side chains buried in hydrophobic pockets and buried salt bridges
34
class example if we have a hydrophobic core of ASp , glu which are negatively charged AAs and we have lysine with a pka of 10 what will happen to the pka
the pka will increase from 10 to a higher number as it is more favourable to have that postive opposing the negative hydrophobic core to maintain good interaction and visa versa if it has positive hydrophobic centre
35
class example if you have the neutral phe, leu ille val in the hydrophobic core with lysine again with pka 10 ( + charge what will happen to pka
as they are neutral it wants be deprotated towards neutrality so pka will drop
36
what is a mutation
changes in amino acid that can change the structure of protein
37
what happens if a val is mutated to ala
not much will happen as val and ala is quiet similar
38
what happens if you change serline to proline in helic
it will drastically change bc proline is a know helix breaker
39
what are the 5 techniques to determine a protein stucture
CD x ray nmr spectroscopy cryo electron microscopy modelling
40
what is protein denaturing?
disrupting the forces that hold the native structure together and unfolding the protein
41
what are 4 chemical ways a protein can be denatured ?
1. heat/cold 2. ph extremes 3. organic solvents 4. chaotropic agents
42
what is the main driving force of protein folding by itself
the hydrophobic affect and entropy
43
what happens if you remove denature reagents urea and mercaptoethanol to ribonulease
when you remove the denaturing reagetns the proteins is able to fold up back to its native state
44
what is nucleation condensation model ?
where when unfolding the proteins has partially folded intermediates
45
what the two protein helpers ?
1. protein disulfide isomerase 2. molecular chaperones
46
what is protein disulfide isomerase
it is an enzyme that correct inccorect disulfide bridges and reforms new ones
47
how does groel and groes work
1. atp binds to groel 2. chamber opens and atp is hydrolyze 2. and the new folded protein is releaeed to the other side
48
what are molecular chaperones
heat shock protein and groel and groes
49
what is alzeimers caused by ?
a normal folded peptide in the brain where unfolding cause a beta sheet conformation and cause plaque in brain
50
what is p53 tumour suppresssion
mutations in the core of protein destabilizing the structure causing it to unfold and not bind to dna
51
what is cystic fibrous
deletion of the AA phe 508 and it destabilizes the structure of the protein

Chem 237 (12 decks)

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