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173 Terms

1
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with gel electrophoresis, which side has the anode, and which side has the cathode

anode is to the right, cathode is to the left

2
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hydrophobic effects drives what level of protein structure formation?

tertiary structure

3
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if pH>pI, does the protein gain (-) or lose (-) electrons?

loses protons, becomes deprotonated

4
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if pH<pI, does the protein gain (-) or lose (-) electrons?

gains protons, becomes protonated

5
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what is pI?

pH when protein’s charge is neutral

6
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are integrated membrane proteins hydrophobic or hydrophilic?

hydrophobic

7
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does phosphorylation cause a molecule to become more positive or negative?

more negative

8
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does dephosphorylation cause a molecule to become more positive or negative?

more positive

9
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are D- or L- amino acids more uncommon in nature?

D-amino acids

10
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are D- or L- amino acids more recognized by proteases?

L-amino acids

11
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do enantiomers have the same charge?

yes

12
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amino acids with thiols (-SH) and hydroxyls (-OH) act as _____ in biological reactions

nucleophiles

13
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when amino acids with thiols and hydroxyls are deprotonated, it _______ their nucleophilicity

betters

14
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what is salt bridging?

when elements of H-bonding and ionic bonding are combined (occurs between oppositely charged molecules); leads to electrostatic interactions

15
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between which amino acids does salt bridging occur?

aspartic acid or glutamic acid, and lysine or arginine

16
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what are proteases?

enzyme that catalyzes hydrolysis of peptide bonds in polypeptide chains

17
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why are proteases’ movement limited?

since the double bond can switch positions (between O and N)

18
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what are G proteins?

signaling proteins in cells that are switched “on” a when they bind to GTP, and “off” after GTP is hydrolyzed (GTP—>GDP, where bonds are broken)

19
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is glycine chiral or achiral?

achiral

20
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is cysteine chiral or achiral?

chiral

21
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does cysteine have (S)- or (R)- configuration?

(R)-configuration

22
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is cysteine a D- or L- amino acid?

L-amino acid

23
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when pH>pka, _____ form decreases, and _____ form increases

protonated, deprotonated

24
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when pH<pka, _____ form decreases, and _____ form increases

deprotonated, protonated

25
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why does tryptophan like fluorescence?

because of its conjugation

26
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why is proline unique?

because it possesses a secondary amino (imine) group, which can help position neighboring atoms

27
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which two amino acids are exclusively found at beta turns?

proline and glycine (other a.a’s are found at a-helices)

28
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if it’s a hydrophilic molecule (i.e. peptide hormones), does it require a second messenger?

yes

29
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if it’s a hydrophobic molecule (i.e. steroids), does it require a second messenger?

no

30
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what does in vivo mean?

conducted in a living organism

31
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what does in vitro mean?

conducted in a lab

32
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what is a voltage-gated ion channel?

a channel that activates upon a change in membrane potential; usually caused by another ion channel

33
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(forming) peptide bonds are thermodynamically _____ and kinetically _____

unstable (because it requires GTP hydrolysis/energy input), stable (because it has a high activation energy, meaning it’ a slow reaction)

34
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which proteins migrate the fastest/slowest in SDS-PAGE?

smaller proteins migrate fastest, larger proteins migrate slowest

35
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which proteins migrate the fastest/slowest in size exclusion chromatography?

larger proteins migrate fastest, smaller proteins migrate slowest

36
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what do reducing agents do in SDS-PAGE/size exclusion chromatography?

break the bonds in between dimers, etc.

37
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what is Western blot?

a protein separation and identification technique by using antibodies to detect specific proteins

38
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what are the steps of Western blot?

  1. protein electrophoresis: separates proteins based on size

  2. protein transfer: transferred from gel —> membrane (blotting)

  3. addition of blocking protein from milk/BSA: prevents non-specific binding of antibodies to membrane

  4. addition of primary antibodies: specifically binds to protein of interest

  5. addition of secondary antibodies: binds to primary antibody and is labeled with a marker for visualization

  6. visualization: using fluorescence/chemiluminescence/autoradiography to visualize; shows up as a band on membrane

39
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antibodies participate in _____ interactions

noncovalent protein-protein interactions

40
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alpha helices are stabilized by _____

hydrogen bonds (like secondary structures)

41
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what is affinity chromatography?

it allows protein to bind while other contaminants are wiped away; takes of advantages of specific protein-ligand interactions

42
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how do you elite proteins gently in affinity chromatography?

use a structure found in the “tag” attached to the protein (basically one that is similar)

43
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how do you gently elude proteins in an ion-exchange chromatography?

use a sodium chloride gradient

44
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what does SDS do?

acts as a denaturing, disrupting protein interactions (like some organic solvents)

45
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what is positive cooperativity?

when subsequent ligands bind with stronger affinity than the 1st; seen with sigmodial curves

46
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what does ion-exchange chromatography do?

separates molecule by charge

47
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what does a cation-exchange column do?

binds cations (+, pH<7)

48
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what does an anion-exchange column do?

binds anions (-, pH>7)

49
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what is an epitope?

a specific region within a protein where an antibody binds; can have amino acids that are close or far apart in primary structures

50
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where are the most common phosphorylation sites?

serine, threonine, and tyrosine (usually at hydroxyls groups)

51
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what is a common site for glycosylation?

asparagine

52
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what is a common site for ubiquitination?

lysine

53
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what type of structure only exist for multimetric proteins (where there are multiple polypeptide chains)?

quaternary structures

54
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what amino acid groups are oxidized to form disulfide bonds and stabilize the protein?

cysteine thiol groups

55
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protein bind hydrolysis is _____ and doesn’t need _____

spontaneous, GTP

56
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quaternary structure proteins binds DNA at a _____ temperature, and blocks _____

lower, transcription

57
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does tertiary structure proteins bind at a lower temperature or higher temperature?

also at a lower temperature, but transcription can still occur

58
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how are tertiary structures stabilized?

by noncovalent interactions between side chains

59
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ternary structures (3-part proteins) can form two ways:

a specific order or randomly

60
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with native PAGE, protein structure is ______ and binding interactions _____ occur

preserved, can

61
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with SDS-PAGE, protein structure is ______ and binding interactions _____ occur

denatured, can’t

62
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what are cofactors?

non-amino acid groups used by proteins. they can be organic (coenzyme)/inorganic, and can bind tightly/loosely

63
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what are prosthetic groups?

tightly bound cofactors

64
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the function of a protein is determined by its _____

3D form

65
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side chains interact through _____

electrostatic interactions; similar charges repel, different charges attract

66
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disulfide bond formation is an _____ reaction

oxidation

67
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the more disulfide bonds formed, the more _____ that occurs

dimerization

68
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with high Gibbs free energy, a _____ is applied on the membrane

saturating agonist

69
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with low Gibbs free energy, a _____ is applied on the membrane

spontaneous closing

70
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what is a heterotetramer?

consists of 4 polypeptide subunits whose quaternary structure is mostly held together by noncovalent interactions; subunits are usually different sizes

71
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what is a homotetramer?

same as a heterotetramer, but with subunits of the same sizes

72
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_____, _____, and _____ usually act as nucleophiles

hydroxyls, thiols, amines

73
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how do you find the number of possible combos for a peptide?

using a factorial (i.e. 3!)

74
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what is precision?

same results multiple times

75
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what is accuracy?

how close you are to a recorded/expected value

76
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the right side of a NMR graph is _____

shielded

77
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the left side of a NMR graph is _____

deshielded

78
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Hill coefficient > 1 means…

positive cooperativity (sigmodial graph)

79
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Hill coefficient < 1 means…

negative cooperativity (sigmodial graph)

80
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Hill coefficient = 1 means…

noncooperativity (hyperbolic graph)

81
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the urea cycle is powered by _____ and _____

deamination, deamidation

82
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what is deamination?

where the nitrogen removed from amino acid backbone

83
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what is deamidation?

where ammonia is released from amides, found in glutamine and asparagine

84
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what is a haloprotein?

correctly folded protein that contains all cofactors

85
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what is an apoprotein?

correctly folded protein that doesn’t contain all cofactors

86
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describe a heme structure

a porphyrin ring with a central iron atom

87
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hydrophobic interactions play a big role in _____

protein folding

88
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when it’s a -deltaG, kd is _____ than 1

greater

89
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when it’s a +deltaG, kd is _____ than 1

less than 1, but greater than 0

90
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what is an allosteric effector?

they bind to proteins at one site and cause a conformation change at another

91
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chiral amino acids rotate _____

plane-polarized light (every a.a. but glycine)

92
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what are the amino acids with alkyl side chain groups?

alanine, proline, leucine, isoleucine, and valine

93
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which amino acids have branched alkyl side chain groups?

leucine, isoleucine, and valine

94
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nucleophiles are an electron _____ species and _____ an electron pair to form a chemical bond

rich, donates

95
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electrophiles are an electron _____ species and _____ an electron pair to form a chemical bond

deficient, accepts

96
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in the RHR, your thumb is the

magnetic force (F)

97
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in the RHR, the index finger is

the moving charge (v)

98
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in the RHR, your middle finger is

the magnetic field line (B)

99
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if the magnetic field points into the page, z is

negative, and exerts an opposite force on the protons

100
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if the magnetic field points out of the page, z is

positive, and exerts an opposite force on the protons