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Biochemistry > Proteins > Flashcards

Proteins Flashcards

1
Q

Peptides are…

A

amino acids linked together by a peptide bond usually through dehydration reactions

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2
Q

Peptide bonds are…

A

an amide linkage between amino acids

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3
Q

Peptides are always named from the…

A

N-terminus to the C-terminus

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4
Q

T/F: peptides are not polyamphoteric

A

F

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5
Q

Polyamphoteric molecule:

A

polypeptide with one or more amino acids containing an ionizable side chain
- gives multiple pKa values

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6
Q

T/F: shifts in pH can greatly affect protein shape

A

T

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7
Q

Two possible forms of peptides:

A
  • trans: usually favored due to steric hindrance

- cis: possible but still not favored in proline

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8
Q

Enzymatic cleavage of peptides:

A
  • enzymes required to hydrolyze polypeptide since uncatalyzed hydrolysis is extremely slow at physiological pH
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9
Q

Digestive enzymes or proteases cleave…

A

peptide bonds at specific locations

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10
Q

Two types of chemical cleavage:

A
  • cyanogen bromide (CNBr)

- Edman degradation

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11
Q

Where does cyanogen bromide cleave?

A

cleaves after methionine amino acids

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12
Q

How/what does Edman degradation cleave?

A

amino acids are chemically cleaved from N-terminus one at a time

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13
Q

Rn-1 means that it cuts…

A

after amino acid listed

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14
Q

Rn means that it cuts…

A

before amino acid listed

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15
Q

Protease inhibitors function by blocking..

A

cleavage of specific materials in viral envelope and stops newly formed virus from maturing

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16
Q

Proteins have a defined sequence that dictates…

A
  • specific folding pattern

- structure of the protein

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17
Q

Structure of the protein enables protein to…

A

perform specific function

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18
Q

Primary structure is the..

A

amino acid sequence

- dictated by genetic code

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19
Q

Secondary structure is the…

A

local folding

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20
Q

Tertiary structure is the…

A

overall fold

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21
Q

Quaternary structure is the…

A

subunit association

- organization of multiple subunits/domains

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22
Q

Ramachandran Plot:

A

demonstrates the type of secondary structure that a particular amino acid is likely to form

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23
Q

Secondary structure describes the local fold of a protein and can be predicted from….

A

Ramachandran Plot

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24
Q

Alpha helix are found where…

A

amino acid angles psi and phi are about -50 degrees and -60 degrees
- corresponds with the bottom left quadrant of Ramachandran Plot

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25
Q

Alpha helix has _____ residues per turn

A

3.6

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26
Q

The H bonds between C’=O in the alpha helix have residue of…

A

n

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27
Q

N-H in alpha helix have residue of…

A

n+4

- fewer residues per turn compared to H bonds

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28
Q

Alpha helix have a dipole moment w/…

A

negative at C terminus and positive at N terminus

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29
Q

What makes alpha helix and beta sheet very stable and energetically favorable?

A
  • H bonds

- max separation of amino acid (residue) side chains

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30
Q

beta-pleated sheets are arranged either:

A
  • parallel

- antiparallel

31
Q

beta-pleated sheets are usually up to _____ residues long w/ psi and phi angles in the _______ quadrant of Ramachandran plot

A

5-10, upper left

32
Q

T/F: For beta-pleated sheets, H bonds that form between C’=O groups and the N-H groups are on the same strand

A

F, each are on their own strand

33
Q

T/F: beta-pleated sheets are pleated w/ alpha C above and below plane

A

T

34
Q

Loop regions (turns) usually connect…

A

two adjacent antiparallel beta strands

- proline is often found here

35
Q

Random coil is a term given to…

A

secondary structure which is neither helical or beta sheet

36
Q

Globular proteins have a defined…

A

inside and outside

37
Q

Beta sheets of globular proteins are…

A

usually twisted/wrapped into barrel structures

38
Q

Polypeptide chain of globular proteins can…

A

turn in a # of ways

39
Q

Helix-loop-helix motif is called…

A

EF HAND

40
Q

Protein stability is affected by:

A
  • pH
  • temp
  • chemicals
41
Q

T/F: electrostatic interaction that contributes to enthalpy stabilizes protein and reduces entropy

A

T

42
Q

pH can cause a change in _______ and alter _______

A

protonation state, H bonds

43
Q

pH will eventually cause ______

A

protein to denature

44
Q

Proteins are soluble at _____ pH, but insoluble near their ____

A

high and low, pl

45
Q

Proteins can denature due to change in:

A
  • temp (thermal denaturation)
  • chem (guanadinium hydrochloride/urea)
  • ionic strength
  • solvent nature (hydrophobic effect)
46
Q

Thermal denaturation:

A

increase in temp = increases unfolding

47
Q

Protein folding is driven by…

A

enthalpy

48
Q

An increase in [urea] leads to…

A

denaturization of proteins

49
Q

Ionic strength changes include:

A
  • salting in

- salting out

50
Q

Salting in:

A

soluble proteins by increasing ionic strength w/ type of ion that tends to result in solubilizing of proteins

51
Q

Salting out:

A

precipitate proteins by increasing ionic strength w/ type of on that tends to form protective ion shells
- repels protein molecules and decreases solubility

52
Q

Folding proteins will maximize:

A
  • # of H bonds

- buried nonpolar groups

53
Q

Folding proteins will minimize:

A
  • interstitial cavities or spaces
  • # of “bad” contacts
  • # of buried charges
  • radius of gyration
  • covalent and noncovalent E
54
Q

T/F: all proteins can be renatured by slowly changing conditions back to favorable

A

F, some but not all

55
Q

Problems w/ protein drugs:

A
  • denaturation
  • aggregation and precipitation
  • protein modification
  • proteolysis
56
Q

Classes of protein drugs:

A
  • vaccines
  • peptides
  • blood products
  • recombinant therapeutic proteins
57
Q

Storage to overcome problems:

A
  • freeze drying
  • maintaining pH
  • balancing ionic strength
  • refrigeration
58
Q

Delivery systems to overcome problems:

A
  • pH sensitive microspheres

- transdermal patches

59
Q

Prion diseases are associated w/…

A

mis-folded proteins

60
Q

Normal form of PrPc:

A
  • transmembrane glycoprotein found at surface of neural cells
  • very soluble
  • easily digested by proteases
  • c stands for cellular
61
Q

Normal PrPc is primarily what shape?

A

alpha helix

62
Q

Abnormal PrPsc:

A
  • sc stands for scrapie
  • identical primary protein structure to PrPc
  • insoluble
  • resistant to digestion by proteases
63
Q

Abnormal PrPsc is primarily what shape?

A

beta sheet

64
Q

Human prion diseases:

A
  • Creutzfeldt-Jakob Diseases (CJD)

- kuru

65
Q

% of Creutzfeldt-Jakob Diseases (CJD) that are in sporadic form?

A

85

66
Q

% of Creutzfeldt-Jakob Diseases (CJD) that are caused by family genetic mutations?

A

14

67
Q

% of Creutzfeldt-Jakob Diseases (CJD) are caused by contamination from brain surgery?

A

1

68
Q

Main symptoms of human prion diseases:

A
  • social withdrawal
  • insomnia
  • dementia
  • muscle paralysis
  • coma
69
Q

Kuru is infectious and comes from…

A

eating brain of deceased humans

70
Q

Effects of disulfide bonds on protein fold:

A

oxidizing and reducing disulfide bonds may affect folding

71
Q

T/F: some proteins require chaperonins to aid in folding

A

T

72
Q

Where are charperonins secreted from?

A

ribosome during translation

73
Q

Most common and understood charperoins:

A

Gro-EL

Biochemistry (9 decks)

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