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Biochemistry > Proteins > Flashcards

Proteins Flashcards

(73 cards)

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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
Alpha helix has _____ residues per turn
3.6
26
The H bonds between C'=O in the alpha helix have residue of...
n
27
N-H in alpha helix have residue of...
n+4 | - fewer residues per turn compared to H bonds
28
Alpha helix have a dipole moment w/...
negative at C terminus and positive at N terminus
29
What makes alpha helix and beta sheet very stable and energetically favorable?
- H bonds | - max separation of amino acid (residue) side chains
30
beta-pleated sheets are arranged either:
- parallel | - antiparallel
31
beta-pleated sheets are usually up to _____ residues long w/ psi and phi angles in the _______ quadrant of Ramachandran plot
5-10, upper left
32
T/F: For beta-pleated sheets, H bonds that form between C'=O groups and the N-H groups are on the same strand
F, each are on their own strand
33
T/F: beta-pleated sheets are pleated w/ alpha C above and below plane
T
34
Loop regions (turns) usually connect...
two adjacent antiparallel beta strands | - proline is often found here
35
Random coil is a term given to...
secondary structure which is neither helical or beta sheet
36
Globular proteins have a defined...
inside and outside
37
Beta sheets of globular proteins are...
usually twisted/wrapped into barrel structures
38
Polypeptide chain of globular proteins can...
turn in a # of ways
39
Helix-loop-helix motif is called...
EF HAND
40
Protein stability is affected by:
- pH - temp - chemicals
41
T/F: electrostatic interaction that contributes to enthalpy stabilizes protein and reduces entropy
T
42
pH can cause a change in _______ and alter _______
protonation state, H bonds
43
pH will eventually cause ______
protein to denature
44
Proteins are soluble at _____ pH, but insoluble near their ____
high and low, pl
45
Proteins can denature due to change in:
- temp (thermal denaturation) - chem (guanadinium hydrochloride/urea) - ionic strength - solvent nature (hydrophobic effect)
46
Thermal denaturation:
increase in temp = increases unfolding
47
Protein folding is driven by...
enthalpy
48
An increase in [urea] leads to...
denaturization of proteins
49
Ionic strength changes include:
- salting in | - salting out
50
Salting in:
soluble proteins by increasing ionic strength w/ type of ion that tends to result in solubilizing of proteins
51
Salting out:
precipitate proteins by increasing ionic strength w/ type of on that tends to form protective ion shells - repels protein molecules and decreases solubility
52
Folding proteins will maximize:
- # of H bonds | - buried nonpolar groups
53
Folding proteins will minimize:
- interstitial cavities or spaces - # of "bad" contacts - # of buried charges - radius of gyration - covalent and noncovalent E
54
T/F: all proteins can be renatured by slowly changing conditions back to favorable
F, some but not all
55
Problems w/ protein drugs:
- denaturation - aggregation and precipitation - protein modification - proteolysis
56
Classes of protein drugs:
- vaccines - peptides - blood products - recombinant therapeutic proteins
57
Storage to overcome problems:
- freeze drying - maintaining pH - balancing ionic strength - refrigeration
58
Delivery systems to overcome problems:
- pH sensitive microspheres | - transdermal patches
59
Prion diseases are associated w/...
mis-folded proteins
60
Normal form of PrPc:
- transmembrane glycoprotein found at surface of neural cells - very soluble - easily digested by proteases - c stands for cellular
61
Normal PrPc is primarily what shape?
alpha helix
62
Abnormal PrPsc:
- sc stands for scrapie - identical primary protein structure to PrPc - insoluble - resistant to digestion by proteases
63
Abnormal PrPsc is primarily what shape?
beta sheet
64
Human prion diseases:
- Creutzfeldt-Jakob Diseases (CJD) | - kuru
65
% of Creutzfeldt-Jakob Diseases (CJD) that are in sporadic form?
85
66
% of Creutzfeldt-Jakob Diseases (CJD) that are caused by family genetic mutations?
14
67
% of Creutzfeldt-Jakob Diseases (CJD) are caused by contamination from brain surgery?
1
68
Main symptoms of human prion diseases:
- social withdrawal - insomnia - dementia - muscle paralysis - coma
69
Kuru is infectious and comes from...
eating brain of deceased humans
70
Effects of disulfide bonds on protein fold:
oxidizing and reducing disulfide bonds may affect folding
71
T/F: some proteins require chaperonins to aid in folding
T
72
Where are charperonins secreted from?
ribosome during translation
73
Most common and understood charperoins:
Gro-EL

Biochemistry (9 decks)

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