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Biochemistry > Conceptual Exam 1 > Flashcards

Conceptual Exam 1 Flashcards

1
Q

Polar AA’s?

A

STCNQY

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2
Q

Positively charged AA’s @ 7?

A

RK

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3
Q

What forms disulfide bonds?

A

C

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4
Q

Peptide bonds flow in what order?

A

N —–> C terminus

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4
Q

Negatively charged AA’s @ 7?

A

ED

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5
Q

What is the free energy equation?

A

_____________

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5
Q

What is change in G?

A

Free energy

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6
Q

What is change in H?

A

enthalpy

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7
Q

What is change in S?

A

Entropy

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8
Q

Is higher or lower entropy favorable? Enthalpy?

A

Higher; Lower

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9
Q

Is a negative or positive free energy more favorable? Negative or positive spontaneous?

A

Negative; negative

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10
Q

Describe the hydrophobic effect.

A

Polar regions interact with H_2O. Nonpolar cluster to form hydrophobic core.

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11
Q

Write out the Henderson-Hasselbach equation.

A

________________________

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12
Q

What are the AA’s with titratable side chains? pKa’s?

A

HERCKDY; 6, 4,12, 8, 10, 4,10

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13
Q

Draw out a titration graph for histidine.

A

___________________________

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14
Q

What does it mean when pka=pH?

A

50% of AA is deprotonated/protonated

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15
Q

What is the pI?

A

Isoelectric point where net charge = 0

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16
Q

What is the equivalence point?

A

pH=pI

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17
Q

How can proteins be separated?

A
  1. Size
  2. Function
  3. Charge
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18
Q

What does a low pI tell us?

A

There are negative side chains.

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18
Q

What AAs absorb UV light in order of lowest absorbance to highest absorbance?

A

F, Y, W

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19
Q

What is the elution order of cation exchange? What is the gel? Resin charge?

A
  1. Negative
  2. Neutral
  3. Positive

CM

Negative

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20
Q

What is the elution order of anion exchange? What is the gel? Resin charge?

A
  1. Positive
  2. Neutral
  3. Negative

DEAE

Positive

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21
Q

What are the steps of affinity chromatography?

A
  1. Loading
  2. Separation
  3. Elution
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22
Q

What is size exclusion chromatography? Elution order?

A

Separates based on size, large to small

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23
Q

What is affinity chromatography?

A

Separates based on binding affinity

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24
Q

What do you use in the elution step of AC?

A

ATP or salt

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25
Q

What is recombinant DNA? Example?

A

Artificial DNA with unnatural sequence combinations, tagged histidines that help anchor proteins

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26
Q

Most effective type of separation technique?

A

Affinity chromatography

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27
Q

How do you find the most effective purification system in a table?

A

How much specific activity increases

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28
Q

Two types of PAGE?

A

SDS and native page

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29
Q

What does denatures mean?

A

removes 2, 3, and 4 degree structure

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30
Q

What does SDS do and how?

A

Denatures proteins by giving them uniform charge which separates by size

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31
Q

What does BME do? What is it used for?

A

Reduces disulfide bonds on cysteine residues, finding disulfide bonds

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32
Q

Reducing SDS? Non-reducing?

A

SDS + BME; SDS only

33
Q

What does native page do? Allows for determination of?

A

Separates proteins without denaturation; mass, size, and charge

34
Q

Where are larger/smaller proteins on PAGE?

A

Larger top; smaller bottom

35
Q

Homo vs hetero oligomers?

A

Hetero have different molecules and homo have the same molecules

36
Q

Without BME can you determine whether something is a hetero or homo oligimer?

A

NO

37
Q

What does IEF PAGE do?

A

Separates proteins based on their isoelectric point (where PH charge = 0).

38
Q

How many levels of protein structure?

A

4

39
Q

What is primary structure?

A

Amino acid sequence joined together by peptide bonds

39
Q

What is secondary structure?

A

Helix, beta sheets, turns, coils with hydrogen bonds

40
Q

What is tertiary structure?

A

3-D folds with hydrophobic interaction, disulfide bonds, H-bonds, and ionic bonds

41
Q

What is quaternary structure?

A

Interaction of many polypeptide subunits

42
Q

What does entropy pertain to? Enthalpy?

A

Hydrophobic; aqueous

43
Q

What drives folding (2)?

A
  1. Negative free energy
  2. Entropy
44
Q

What is the hydrophobic effect and why does entropy increase?

A

Clusters of lipids cause H_2O molecules to be disordered

45
Q

What are Van der Waal interactions?

A

Very weak interactions between two atoms

46
Q

Draw graph of van der Waal interaction.

A

__________________________

47
Q

Draw the graph of the Leonard Jones potential.

A

____________________________

47
Q

What is the Leonard Jones potential?

A

2 interacting atoms repel when too close, attract at moderate distance, and DO NOT interact when too far away

48
Q

Write out Coulomb’s Law.

A

_____________________________________

49
Q

What is Coulomb’s Law?

A

Electrostatic interactions affect energy of system

50
Q

What is E in Coulomb’s Law? Example in H_2O and core of protein?

A

Dielectric constant; 80 and 2

51
Q

Draw out the Ramachandran Plot and where alpha helices and betas live.

A

______________________________________

52
Q

What two AA are not favored in alpha helices? Why?

A

Gly and Pro; steric hindrance

53
Q

For every turn, how many residues and length in alpha helices? Beta?

A

3.6; 5.4
2; 7

54
Q

What is the hydrogen bonding pattern of alpha helices?

A

i to i+4

55
Q

Intramolecular or intermolecular bonding in alpha helices?

A

Intra

56
Q

When are proteins exposed? Buried?

A

Polar; nonpolar

57
Q

Two types of B-sheets? Describe differences.

A

Antiparallel has alternating NC terminus pattern, colinear H bonding so favorable and parallel same NC pattern

58
Q

Which two AA involved in B-turns?

A

Gly and Pro

59
Q

What type of AA do B-sheets favor?

A

Room for bulky so F, W, Y

60
Q

What are B-turns?

A

connect two segments of B-sheets

61
Q

What is a domain? Importance?

A

Independent folding unit that could undergo movement at a single entity
Important because a single protein can have multiple functions.

62
Q

What is an active site?

A

Where substance binds

63
Q

Is folding spontaneous?

A

YES

63
Q

What is usually lost after protein denatured?

A

Function

63
Q

Once denaturation happens, is it always reversible?

A

NO

64
Q

What is critical for the function of RNase?

A

disulfide bonds

64
Q

Draw out the energy funnel? Label entropy, energy, native percent, and three stages of protein.

A

_________________________________________

65
Q

What did Anfinsen discover? Order of experiment?

A

He discovered that RNase is 100% recoverable after denaturation.
Steps: Urea, reducing agent (BME), removes urea, adds oxygen

66
Q

What is urea, BME, oxygen?

A

strong denaturant; reducing agent; oxidant (reforms disulfide bonds)

67
Q

Two ways to determine charge in protein structure?

A

Tryptophan fluorescence and circular dichroism

68
Q

What does tryptophan fluorescence do? Draw graph.

A

Wavelength shifts when denatured

69
Q

What does circular dichroism do? Draw graph.

A

Polarized light bends based on 2/3 structure

70
Q

What is aggregation?

A

Process in which oxidized, misfolded, or damaged proteins bind together forming large mass without original function

71
Q

What are chaperones?

A

Proteins that assist folding of other proteins and prevent misfolding

72
Q

Equation of ligand and protein interaction.

A

____________________

73
Q

What is Kd?

A

Dissociation constant, ligand concentration @ which 50% of binding sites are occupied

74
Q

Draw out protein and ligand interaction graph.

A

__________________________

75
Q

Write Fraction bound equation and change in G equation.

A

_____________________

76
Q

What does a low KD tell us?

A

High affinity so more spontaneous

77
Q

What does a high KD tell us?

A

Low affinity so less spontaneous

78
Q

Write out Beer’s Law.

A

_______________________

Biochemistry (8 decks)

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