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Biochem Flashcards

1
Q

Glycine

A

Gly, G, nonpolar

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2
Q

Alanine

A

Ala, A, nonpolar

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3
Q

Valine

A

Val, V, nonpolar

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4
Q

Leucine

A

Leu, L, nonpolar

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5
Q

Isoleucine

A

Ile, I, nonpolar

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6
Q

Phenylalanine

A

Phe, F, nonpolar

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7
Q

Tryptophan

A

Trp, W, nonpolar

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8
Q

Methionine

A

Met, M, Nonpolar

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9
Q

Proline

A

Pro, P, nonpolar

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10
Q

Serine

A

Ser, S (Polar, Neutral)

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11
Q

Threonine

A

Thr, T (Polar, Neutral)

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12
Q

Tyrosine

A

Tyr, Y (Polar, Neutral)

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13
Q

Cysteine

A

Cys, C (Polar, Neutral)

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14
Q

Asparagine

A

Asn, N (Polar, Neutral)

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15
Q

Glutamine

A

Gln, Q (Polar, Neutral)

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16
Q

Aspertate

A

Asp, D (negative)

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17
Q

Glutamate

A

Glu, E, negatively charged

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18
Q

Lysine

A

Lys, K, positive

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19
Q

Arginine

A

Arg, R, positive

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20
Q

Histidine

A

His, H, positive

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21
Q

Characteristics of alpha strands

A

*i and i+4

* all the side chains are projected on the outside

* NH bonds with CO on top

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22
Q

Beta Strand Characteristics

A

*fully extended polypeptide chain

* multiple B strands from B sheet

* parallel and anti parallel

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23
Q

Parallel and anti parallel

A

Parallel - H bond by NH and 2 strands from opp amino acids (turn to my classmate next to me but ignore her and hold out hands to the girl in front of her and person behind her

anti parallel - shake hands with the girl right next to her

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24
Q

Loops/ Turns characteristics

A

* i and i+3

Glycine and proline are the most common

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25
Q

What happens when not glycine in hole of collagen

A

Osteogenesis - bc bigger structures will push away other molecules and nothing will become tightly packed.

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26
Q

Characteristics of tertiary structure

A

Polar chains point out to face aqueous solution, non polar buries to hide from h20

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27
Q

Alpha keratin characteristics

A

* only helices - that wrap around each other

* held together by van der waals, salt bridges and disulfide bonds

*interactions at the every 7 aminos

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28
Q

Characteristics of collagen

A

* bones and cartilages

* 3 helices wrapped around each other

*glycine is every 3rd amino

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29
Q

Can proteins be refolded, why or why not?

A

It can fold but it is not guaranteed that it will return to the same structure that it was - and will most likely be an inert protein

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30
Q

Urea denatures what

A

2nd structures (alpha, beta, turns)

Van der waals, H bonding, salt bridges

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31
Q

guanidinium chloride denatures what

A

2nd structures (alpha, beta, turns)

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32
Q

Beta Mercator ethanol denatures what and how

A

Is a reducing agent that breaks covalent bonds (S-S)

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33
Q

Process of harvesting a protein

A

1) break membrane to bring proteins outside of cell
- can break membrane by lysing, sqessing the cell mechanically (homogenized pressure via air, sonicator - break via sound waves, break chemically
2) place in centrifuge to separate soluble proteins from insoluble cell debris (plasma membrane)

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34
Q

What is the ion exchange column chromatography?

What is the process?

A

* cation and anion exchange

1) choose a buffer that will attract the protein of interest
2) elution from column- flush with high concentration of similarly charged ion to replace the protein of interest and it can flush out

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35
Q

What charge product would you get with cation and anion exchange?

A

Anion - negative charge ( which means the charge on the column is +)

Cation - positiv charge (column is -)

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36
Q

What is size exclusion/ gel filtration chromatography

A

* separate protein based on size

  • basically the larger proteins reach the end the fastes bc its not help up by the beads (too big to go in) and the smaller the beads are…the slower to reach
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37
Q

Affinity chromatography

A

Load the column with a molecule/thing that only the protein of interest would be attracted to

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38
Q

Nickel affinity chromatography

A

1) add a sequence of codes that will translate (make) 6 Histidines at the beginning or end of the sequence. The nitrogen on histidine is the ONLY one that will form a coordination bond with the Nickel - and because there are 6 histidines on this protein… it would have a higher affinity to the nickel than any other protein ( because the histidine is exposed etc)
2) flush with imidazole bc its structure is very similar to histidine and it will replace the histidine and the B protein with His6 will flush down

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39
Q

Salting out

A

The higher concentration of salt ammonium sulfate (NH4SO4) that you add - the more that it will get in between the protein and water. It will bond with the water and the protein will precipitate out (bc its not soluble any more)

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40
Q

What is SDS?

A

1) detergent that denatures the protein completely
2) add lots of sulfate to make the protein charge very negative
3) will break all interactions except S-S bonds (covalent)

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41
Q

SDS - Page (how do the charges move)

A

1) add a positive charge at the end of the terminal so that the negatively charged proteins can migrate towards it . The proteins are separated by size - larger molecules are slower to migrate, smaller ones migrate faster.

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42
Q

BME what test is it found in?

A

SDS Page

It is a reducing agent that breaks S-S bonds

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43
Q

Tracking dye

A

SDS Page - stains blue to see how far things traveled

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44
Q

Glycerol

A

SDS page

Makes the solution heavy so the things stay in the wells and migrate down

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45
Q

What happens if you load something that is a dimer connected by disulfide bond

  • in a reducing gel (with BME)
  • in a non reducing gel (no BME)
A

* there would be 2 lines (right on top of each other) with the size of the monomer)

there would be one line with the monomer size x2

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46
Q

What is Page

A

Gel/ mesh network

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47
Q

What is Isoelectric Focusing

A

* Gel electrophoresis with PI

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48
Q

What is 2D gel

A

Isoelectric focusing with SDS Page

* isoelectric -PI: Pi, left vs right

* SDS page: size, top vs bottom

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49
Q

Define antigen

A

Foreign invaders

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50
Q

Define antibody

A

A protein produced by the body to defend

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51
Q

Define epitope

A

Recognition site that antibodies attach to

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52
Q

Define components of antibodies (what is it made up of)

A

Look at notes

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53
Q

What is monoclonal antibodies and why is it beneficial

A

It is produced by one B cell, so you know what exact properties that you’re getting

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54
Q

What is western blot and describe the process

A

SDS page and antibodies combined and used for detection

55
Q

What is ELISA

A

An INDIRECT diagnostic test - look for antibodies by monitoring the response of the body

56
Q

What is Sandwich ELISA

A

A direct test which tests for antigens ex. COVID test

57
Q

What is Chromatogram

A

Uses gel filtration (size exclusion)

58
Q

What are the 2 models of specificity

A

Lock and key

Induced fit

59
Q

Define initial velocity

A

Velocity at the early stage of reaction

60
Q

Define steady state kinetics

A

Rather of formation of ES complex = rate of dissociation of ES complex and therefore the concentration of ES complex remains steady

61
Q

Equation of rate of formation

A

ES = k1 [E][S]

62
Q

Rate of dissociation of ES complex

A

(K-1, K2)ES or K-1 (ES) & K2 (ES)

63
Q

What is Et

A

Et= E + ES

64
Q

Define theoretical max velocity

A

Max velocity is reached when all free enzymes exist as ES complex

65
Q

Define the relationship of Km and velocity

A

Km is the substrate concentration when the initial velocity equals Vmax/2

*km is the substrate concencetration required to reach half of Vmax

66
Q

What is the equation of y-int

A

Y-int= 1/Vmax & Vm= 1/ y-int

67
Q

What is the equation of slope

A

Slope= Km/Vmax & Km= slope x Vmax

68
Q

What is the Michaeli - Menton Equation

A

Vo = Vmax [S]/ [S] + Km

69
Q

Characteristics of Km

A

* The lower Km, the higher the affinity an enzyme has to substrate

70
Q

Define Activity

A

It is the rate of reaction, amount of product formed over time

71
Q

Define specific activity

A

It is the amount of product formed by 1 mg of the enzyme

72
Q

Define Turnover number

A

It is the amount of times an enzyme turns over, when it is operating in its max velocity

73
Q

What are the characteristics of Turnover

A

Higher the turnover, the faster and more product is being produced

74
Q

Equation for Kcat and the characteristics of it

A

Kcat=Vmax/[Et]

75
Q

A

Alanine, Ala, A, Nonpolar

76
Q
A

Glycine, Gly, G, Non polar

77
Q
A

Valine, Val, V, Nonpolar

78
Q
A

Leucine, Leu, L, Nonpolar

79
Q
A

Isoleucine, Ile, I, Nonpolar

80
Q

Structure

A

Phenylalanine, Phe, F, Nonpolar

81
Q
A

Tryptophan, Trp, W, Nonpolar

82
Q
A

Methionine, Met, M, Nonpolar

83
Q
A

Proline, Pro, P, Nonpolar

84
Q
A

Serine, Ser, S, Polar neutral

85
Q
A

Threonine, Thr, T, Nonpolar

86
Q
A

Tyrosine, Tyr, Y, Polar neutral

87
Q
A

Asparagine, Asp, N, Polar neutral

88
Q
A

Cysteine, Cys, C, polar netural

89
Q
A

Glutamine, Gln, Q, Polar neutral

90
Q
A

Aspertate, Asp, D, negative

91
Q
A

Glutamate, Glu, E, negative

92
Q
A

Lysine, Lys, K, positive

93
Q
A

Histidine, His, H, positive

94
Q
A

Arginine, Arg, R, Positive

95
Q

Competitive

A
96
Q

Uncompetitive

A
97
Q

Non competitive

A
98
Q

What happens to Vmax, Km, and Y-int with competitive, NC, and UC

A
99
Q

What is the y=mx +b for Vmax etc,

what is the formula for Vmax

what is the formula for km

what is the formula for x-int

A
100
Q

What are the 2 types of bisubstrate reaction?

A

Sequentia and Ping Pong

101
Q

What is sequential?

A

It can be ordered or random

102
Q

What is ping pong

A
103
Q

What is the free energy change equation for reaction

A
104
Q

What to do if Et is given in mass

A

Convert mass to moles using the MW of the protein

105
Q

What are the characteristics of Km and Kcat?

A

Higher Kcat is better

lower km is better

106
Q

Velocity of reaction when [S] = 10% of km

A
107
Q

Acids catalysts make…..

A

Better leaving groups and it increases the electrophicity of the carbonyl (electrophile)

108
Q

Basic catalyst makes….

A

Better nuclephiles by increasing the nucleophility of the nucleophile

109
Q

What is the mode of recognition for cymotripsin

A
110
Q

What is the mode of recognition for trypsin

A
111
Q

What is the mode of recognition for elastase

A

Small side chains

112
Q

What is the mechanism of Chymotrypsin

A
113
Q

What are the modes of recognition for chymotripsin, trypsin, and elastase

A
114
Q

What is the mechanism for cysteine protease

A
115
Q

What is the mechanism for aspartyl protease

A
116
Q

Why are amide bonds stable in protease reaction

A

Amide bonds are very unreactive towards any nucleophile

117
Q

What is the role of the catalytic triad

A

Bodies way of providing basic and acidic conditions

* Serine forms the catalytic bond

* Histidine provides the proton to make serine more nucleophilic

*Aspertates COO- makes the positive charge on Histidine more stable

118
Q

Site Directed Mutagenesis

A
119
Q

Process of Elisa Sandwich

A
120
Q

Describe the process of ELISA

A
121
Q
A
122
Q

What is the equation that shows the process from enzyme to product

A
123
Q

What are the reaction rates of the equations

A
124
Q

In the M. M equation, which are constants and which are variables

A
125
Q

Equation for Vo in terms of Km

A
126
Q

Equation for Kcat and the characteristics of it

A

Kcat = Vmax/ Et

127
Q

Carbon dioxide combines with water to make what?

A

Carbonic acid –> which disassociates into bicarbonate acid

128
Q

What is the mechanism from CO2 and H20 –> carbonic acid

A
129
Q

How can you make the mechanism of making carbonic acid faster?

A

By making water more acidic (and this is done by Zn)

130
Q

What is the goal of metalloprotease and what is the mechanism?

A
131
Q

Explain this graph

A
132
Q

What is regulation?

A

Factors that helps the enzyme function at the right place and time.

133
Q

What are the 5 ways that enzymes are regulated

A
  1. ATCase
  2. Proteolytic cleavage
  3. Multiple forms of the same enzyme
  4. Control by covalent modification (phosphate hat makes enzyme active)
  5. Control by gene expression
134
Q
A

Biochem (2 decks)

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