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Biochemistry Test 1 > chapter 6 > Flashcards

chapter 6 Flashcards

1
Q

Folding energetics is a sum of ______ _______.

A

Contributing Factors

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2
Q

What is the free energy equation

A

ΔG=ΔH-TΔS

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3
Q

What are the thermodynamic factors of protein folding

A

Conformational entropy, Charge-Charge interaction, Internal hydrogen bonds, van der waals interactions, the hydrophobic effect

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4
Q

Describe the role of conformational entropy in protein folding

A

The folding of a protein results in a decrease in entropy, and thus a positive ΔS term.

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5
Q

What can break salt bridges between Amino acids in a protein?

A

A pH sufficiently high or low to cause one or both of the amino acids to loose their charge.

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6
Q

The change in enthalpy for folding is dominated by the differences in _____ ______ interactions between the unfolded and folded states, and is given by the equation ΔH(U>F)=_____-_______.

A

Noncovalent bonding, ΔH(U->F)=H(Folded)-H(unfolded)

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7
Q

One thermodynamic consideration between folded an unfolded proteins solvated in water that can negativly effect the change in enthalpy is?

A

The loss of noncovalent interactions between water and the elongated amino acid chain.

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8
Q

The stability of a of the folded structure of a globular protein depends on the interplay of three factors, they are?

A

The unfavorable conformational entropy change, which favors the unfolded state. The favorable enthalpy contribution arising from intramolecular interactions. The favorable entropy change arising from the burying of hydrophobic groups within the molecule.

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9
Q

How many years would it take to go through all of the possible conformations for a 100 AA chain?

A

10^50

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10
Q

In cases where the denaturation of a proteins differ from those that do in 2 ways.

A

The proteins are usually larger, and start folding before the protein is completely folded.

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11
Q

New proteins with different functions can be created without a new gene code by _____?

A

the interactions of multiple domains, each with a role to play

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12
Q

What are two examples of all alpha helix proteins

A

Cytochrome b, and HGH

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13
Q

What are two examples of all beta sheet motifs

A

Immunoglobulin folds, and 8-stranded beta barrel (retinol binding protein),

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14
Q

What are oligomeric proteins?

A

Those with more than one separate polypeptide chains

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15
Q

what are protomers?

A

structural unit of an oligomeric protein

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16
Q

Protomers are usually _____arranged?

A

symmetrically

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17
Q

Are disulfide bonds necessary for correct folding, why or why not?

A

No, experiments have demonstrated that when denatured proteins with disulfide bridges are allowed to refoldand the bridges are reoxideized the number of correctly formed bridges approaches 100%, much higher than would be expected through chance.

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18
Q

What effect do disulfide bonds have on the entropy of an unfolded protein

A

A molecule containing disulfide bridges has fewer possible conformations than one without the bonds, consequently the entropy for the unfolded protein with disulfide bonds is decreased.

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19
Q

What effect do disulfide bridges have on the ΔG (F>U) t

A

Because of the decreased entropy of the unfolded protein the ΔS term is larger relative to a protein without the disulfide bridges. Consequently the difference in free energy is larger and more unfavorable than for a molecule without disulfide bonds.

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20
Q

What are the two ways to increase the thermodynamic stability of a protein?

A

Making the free energy of the folded state more negative, or making the free energy of the unfolded state more positive.

21
Q

Is protein folding a random process, yes or no and why

A

No, RNase A is able to fold in vitro in less than a minute despite that there are about 10^50 possible conformations.

22
Q

What is the molten globule, and what does it seek to explain?

A

It is an intermediate structure of a folded protein in which the secondary structures, and backbone folding topology are formed, but lacks the defined features of a tertiary structure. This intermediate seeks to resolve levinthal’s paradox.

23
Q

How does the energy landscape model seek to resolve levinthal’s paradox?

A

Any molecule folding only has to sample a fraction of the possible conformations to reach the final state.

24
Q

Why are enzymes sometimes necessary to aid in the folding of proteins?

A

To correct incorrect cis trans isomerization of proline, and incorrectly formed disulfide bridges formed in off-pathway states.

25
Q

Why are chaperones needed?

A

While proteins are able to fold spontaneously in vitro, this is not always the case in vivo…Chaperones essentially serve to keep the protein out of trouble by preventing improper folding or aggragation.

26
Q

What do Φ and Ψ represent

A

Phi represents the angle between N-C, while Psi represents the angle C-COOH

27
Q

Describe Amphiphillic secondary structures

A

Amphiphillic secondary structures are structures in which one side is hydrophilic and one is hydrophobic. In an alpha helix this is accomplished through alternating hydrophilic or hydrophobic ratios every 3-4 residues.

28
Q

What are the 4 principles for secondary structures set forth by linus pauling?

A

Bond length + Bond angles should be distorted as little as possible. No 2 atoms should approach closer than van der waals ratio. Amide group must remain planar trans, rotation only possible about alpha carbon. Non-covalent bonding necessary to stabilize regular folding. The preferred conformation maximizes hydrogen bonding without violating the other three rules.

29
Q

How is the pi helix formed?

A

Through insertion of amino acid into the alpha helix.

30
Q

The polyproline II helix is composed of ____proline, and is ____handed.

A

1/3, left.

31
Q

Describe alpha keratin

A

Pairing coil-coil due to AA sequence because AA sequence is nonpolar hydrophobic every 3-4 residues. Contains higher than average cysteine, and has disulfide bridges.

32
Q

What are 4 types of fibrous proteins

A

alpha keratin, fibroin, collagen, elastin.

33
Q

Describe Actin, and Tubulin.

A

Helicaly aranged globular subunits

34
Q

What is an interesting feature of glycine

A

Has a much larger range of phi and psi values because of the lack of an R group

35
Q

Describe Fibroin

A

Long regions antiparallel beta sheets, Exclusively made up of repetitions of the same sequence, flexible because the e sheets not covalently bound.

36
Q

Describe Collagen

A

Makes up ~1/3 of total protein mass in most vertabrates, base unit is topocollagen (tripple helix of 3 repetitive chains ~1000 residues in length. every 3rd residue can only be a glycine.

37
Q

What does scurvy cause?

A

Ascorbic acid is necessary for enzymes that hydroxylate proline. Scurvy is caused by failure to hydroxylate propine and lysine. Hydrogen bonding between hydroxylated residues increases the stability.

38
Q

Describe the aging process on collagen

A

Oxidation of lysine side chain to aldehyde derivatives which condense into cross linkages. This process continues throughout life and contributes to the brittleness of collagen.

39
Q

What are the 4 domain classes?

A

Mainly alpha, mainly beta, alpha plus beta, and few secondary structures.

40
Q

What are the two levels architecture

A

alpha beta alpha sandwich, and alpha beta barrel.

41
Q

Describe domain and architecture of the rossman fold

A

The rossman fold is in the alpha +beta domain, with a alpha beta alpha sandwich architecture.

42
Q

Describe Globular proteins

A

Compact, charged polar r groups hydrated on outside, hydrophobic nonpolar R groups buried hiden from water, driving force is mainly hydrophobic and partly electrostatic.

43
Q

What is a domain

A

compact locally folded region of tertiary structure, different domains perform differing structure functions, distinct structural motifs,

44
Q

What is the motif in collagen

A

gly-x-y. Where x is proline, and why is 3 hydroxy proline

45
Q

What is the rossman folds common function?

A

Binding NAD

46
Q

What are the rules for tertiary folding?

A

all globular proteins have defined inside and outside, beta sheets are usually twisted into barrel structrues, polypeptide chain can turn corners in a number of ways, not all parts of globular proteins can be classified as beta sheet helix or turn.

47
Q

What are some tertiary structural motifs?

A

Beta/Alpha/Beta, Beta/Beta/Beta, Alpha/Alpha.

48
Q

What are the types of symmetry?

A

Cyclic (C2,C3) Dihedral (D2,D4) Icsohedral, helical, and cubic

Biochemistry Test 1 (6 decks)

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