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CHE 541 > 1 - Size, Energy, and Time > Flashcards

1 - Size, Energy, and Time Flashcards

1
Q

What are the three basic ideas of biochemistry?

A

Size, energy, and time

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2
Q

What is size?

A

How big or small an item is

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3
Q

What are some examples of size?

A

Length of bonds, diameters of molecules, volumes of complexes, etc.

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4
Q

How big is 1 angstrom?

A

0.1 nm

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5
Q

What is the length of a C-C bond?

A

1.5 angstroms

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6
Q

What item is 1.5 angstroms?

A

C-C bond

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7
Q

What is the length of a C-H bond?

A

1.1 angstroms

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8
Q

What item is 1.1 angstroms?

A

C-H bond

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9
Q

What is the length of a C-O bond?

A

1.0 angstroms

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10
Q

What item is 1.0 angstroms?

A

C-O bond

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11
Q

What is the diameter of an alpha helix (backbone to backbone plus side chains)?

A

10 angstroms (1 nm)

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12
Q

What item is 1 nm?

A

Diameter of an alpha helix

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13
Q

What is the diameter of a large protein?

A

100 angstroms (10 nm)

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14
Q

What item is 10 nm?

A

Diameter of a very large protein

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15
Q

What is the size (diameter) of an average protein?

A

30-40 angstroms (3-4 alpha helixes stacked together)

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16
Q

What is the diameter of a ribosome?

A

200 angstroms (20 nm)

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17
Q

What is the diameter of a clathrin coated vesicle?

A

1000 angstroms (100 nm)

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18
Q

What item is 100 nm?

A

Diameter of a clathrin coated vesicle

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19
Q

What is the length of an E. coli cell?

A

1000 nm (1 um)

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20
Q

What is the diameter of a cell nucleus?

A

5-6 microns

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21
Q

What is the diameter of an “average” cell?

A

15 microns

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22
Q

How many proteins can be fit inside a ribosome?

A

About 100

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23
Q

What math is done to calculate how many proteins can fit inside a ribosome?

A
  1. V = 4/3 * pi * r^3
  2. Radius of protein ~20 A (diameter ~40 A)
  3. Radius of ribosome ~100 A (diameter ~200 A)
  4. (100 A / 20 A)^3 ~ 100 proteins
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24
Q

True or false: there is a lot of free water in the cell

A

False: there is very little free water in the cell (tightly packed)

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25
Q

What is the distance of a synapse?

A

~200 A

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26
Q

What is the size of a receptor in a synapse?

A

~100 A

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27
Q

If drawn to scale, what can be said about vesicles being released into a synapse?

A

Vesicles are released directly on synapse (synapse ~ 200A, receptor ~100 A)

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28
Q

What did the study with trafficking organelles look at?

A

The size and copy number of various proteins

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29
Q

What did the study with trafficking organelles find?

A

Lots of proteins stuck to the surface, membrane packed with proteins, extend to different heights

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30
Q

Where is energy seen in biochemistry?

A

Reaction rates, binding mechanisms, and thermodynamics

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31
Q

What are some examples of energy considerations?

A

Thermal energy (RT), free energy, enthalpy and entropy, electrostatics

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32
Q

What quantity represents thermal energy?

A

RT (gas constant * temperature)

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33
Q

What is the significance of PV=nRT?

A

It describes how chemists could easily manipulate the environment (PV) to alter energy (nRT)

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34
Q

What is thermal energy?

A

Available energy to catalyze a reaction (jiggling molecules)

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35
Q

What does HEW stand for?

A

Hen egg white (lysozyme)

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36
Q

What does HEW lysozyme do?

A

Catalyzes breakdown of sugar

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37
Q

What does the cavity of HEW lysozyme have?

A

Strong negative charge

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38
Q

What is the significance of clefts and grooves in a protein?

A

This is where enzymes catalyze reactions

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39
Q

True or false: most enzymes catalyze reactions at the surface

A

False: most enzymes catalyze reactions in clefts and grooves

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40
Q

Why do enzymes catalyze reactions in the clefts and grooves?

A

They can bring reaction groups out of the solution and make them more reactive

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41
Q

Why does bringing reaction groups out of solution make them more reactive?

A

They are stripped from water

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42
Q

What is a typical value of RT at room temperature?

A

~600 cal/mol (~1 kcal)

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43
Q

What is the conversion rate between kcal and J?

A

1 kcal/mol = 4.2 J/mol

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44
Q

What is the difference between RT and kT?

A

RT is the thermal energy in one mole, while kT is the thermal energy in one molecule

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45
Q

What is the typical strength of an H-bond?

A

~5 kcal/mol

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46
Q

What is the typical energy released from hydrolysis of ATP?

A

~10 kcal/mol

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47
Q

What is the energy of a photon (500 nm)?

A

~50 kcal/mol

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48
Q

What is the typical energy of a covalent bond?

A

~50-100 kcal/bond

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49
Q

How much does energy “span” in biochemistry?

A

~2 orders of magnitude

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50
Q

Where is time seen in biochemistry?

A

Rates, reaction mechanisms (how enzymes change conformation over time)

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51
Q

What are some examples of time?

A

Neuronal signaling, water molecules vibrating, kinesin transport via ATP hydrolysis

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52
Q

How do proteins that hydrolyze ATP usually work?

A

They usually bend proteins (similar to Pacman) (clamping)

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53
Q

How do kinesin “feet” work?

A

They open and close through ATP hydrolysis clamps

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54
Q

How long is the vibrational period of a C-C stretch?

A

~30 fs

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55
Q

How long does it take to break a bond?

A

One period

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56
Q

How long does rotation of a side chain take?

A

~1 ns

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57
Q

How long does rotation of a protein domain take?

A

~1 us

58
Q

How long does it take a small protein to diffuse 100 nm?

A

~1 ms

59
Q

How long does it take a small protein to diffuse 10 nm?

A

~1 us

60
Q

How fast does unmyelinated neuronal conduction take?

A

~2 mph

61
Q

How fast does myelinated neuronal conduction take?

A

~200 mph

62
Q

How long does it take a signal to travel from the brain to the arm?

A

~20 ms

63
Q

What is the speed of a kinesin molecule?

A

~1.6 um/s (160 um per step)

64
Q

How many steps does a kinesin molecule take per second?

A

100 steps per second (1 step in 10 ms)

65
Q

True or false: one sec is a short time in a biochemical scale

A

False: one sec is a long time for a cell time scale

66
Q

What are some examples of organic reactions catalyzed by enzymes?

A

Group transfer reactions, oxidation-reduction reactions, isomerization and rearrangement, breaking and making bonds

67
Q

What are some group transfer reactions?

A

Methyl, hydroxyl, carboxyl, formyl, acyl, glycosyl transferases, transfer of N-containing, S-containing, P-containing groups

68
Q

What are some oxidation-reduction reactions?

A

Involves OH, C=O, CH-CH, SH, metal ions

69
Q

What are some isomerization and rearrangement reactions?

A

Racemases, epimerases

70
Q

What are some bond forming and breaking reactions?

A

Ligases forming C-O, C-S, C-N, and C-C bonds, hydrolases, carboxylases

71
Q

What are the three basic types of reaction mechanisms?

A

Nucleophilic catalysis, electrophilic catalysis, and acid-base

72
Q

What is a nucleophilic attack?

A

An electron rich reagent attacks an electron poor site in a reaction

73
Q

What is an example of a nucleophilic attack?

A

Catalytic triad in serine proteases

74
Q

How do serine proteases work?

A
  1. His serves as a base to take up proton from Ser -PH

2. Ser serves as a nucleophile to attack carbonyl carbon on protein backbone

75
Q

How can the reaction rate of a serine protease be increases?

A

By placing a positive charge near the oxygen of the carbonyl group

76
Q

How does placing a positive charge near the oxygen of a carbonyl group increase the rate of a serine protease reaction?

A

Electron density is pulled towards the oxygen, making the carbon more partial positive (more electron poor). This makes it more reactive to a nucleophilic attack

77
Q

Which is more common in biochemistry and why: nucleophiles, or electrophiles?

A

Nucleophiles, because proteins are electron rich

78
Q

What is electrophile catalysis?

A

An electron “sink” to catalyze the reaction

79
Q

What are good electrophiles in biochemistry?

A

Coenzymes, vitamins, and minerals (metal ions)

80
Q

How do electrophiles catalyze reactions?

A

They guide reaction mechanisms of proteins, and pull electrons to catalyze cleavage

81
Q

What is an example of a electrophile catalysis reaction?

A

Decarboxylation (through vitamin B6)

82
Q

How does a groove interact with a substrate?

A

The groove is complementary to the substrate based on shape and electrostatics

83
Q

How does excluding water increase reactivity?

A

By strengthening the effect of charge and other polar groups

84
Q

What amino acids are found in the groove of HEW lysozyme?

A

Glu and Asp

85
Q

Why are Glu and Asp found in the groove of HEW lysozyme?

A

The reactivate intermediate is a positively charged oxycarbenium substrate, so the negatively charged amino acids help stabilize this structure

86
Q

What is pKa?

A

The disassociation constant for an acid

87
Q

What is the formula for Kd for an enzyme and substrate?

A

Kd = [ES] / [E][S]

88
Q

What reactions are needed to calculate Kd for an enzyme and substrate?

A

Association: E + S -> ES
Disassociation: ES -> E + S

89
Q

What formulas involve delta G?

A

delta G = delta H - T delta S = -RTln(Kd)

90
Q

What is enthalpy?

A

Energetics

91
Q

What is entropy?

A

Order/disorder

92
Q

What is a positive delta G?

A

Unfavorable reaction

93
Q

What is a negative delta G?

A

Favorable reaction

94
Q

When is free energy most negative in an enzyme/substrate reaction?

A

In the association (ES)

95
Q

How come the delta G becomes more positive if E and S get too close together?

A

There are steric conflicts

96
Q

What is the energy of two interacting charges in a vaccuum?

A

500 kJ/mol

97
Q

What is the energy of two interacting charges in water?

A

6 kJ/mol

98
Q

How does water decrease interaction energy?

A

By shielding charges, reducing reactivity (higher dielectric constant)

99
Q

How can enzymes increase the rate through oritentation?

A

By constraining the reactants and reactive groups

100
Q

How can enzymes constrain reactive groups?

A

Bonds, rings, etc. (less rotation)

101
Q

What coenzymes are used in DHFR?

A

NADP+ and tetrahydrofolate

102
Q

How do the two coenzymes in DHFR interact?

A

The reactive end of one is next to the reactive end of another (through tight groove binding)

103
Q

What is chymotrypsin and what does it do?

A

A member of the serine proteases that cleaves aromatic amino acids

104
Q

What is the role of the specificity pocket?

A

To determine the type of amino acid to be cleaved

105
Q

What is the specificity pocket in chymotrypsin?

A

Hydrophobic (aromatic)

106
Q

What is the catalytic triad in serine proteases?

A

Asp, His, and Ser

107
Q

True or false: Asp changes protonation state during serine protease catalysis

A

False: it does not change protonation

108
Q

What is the purpose of the NH in chymotrypsin?

A

It orients the carbonyl with the positive charge, and polarizes it (better attack from Ser nucleophile)

109
Q

What does the Asp do in the catalytic triad?

A

It orients His properly (so His can act as a base to charge Ser)

110
Q

What is the specificity pocket in trypsin?

A

Negatively charged (cleave positive residues)

111
Q

What does trypsin do?

A

Cleaves positive amino acids

112
Q

What do 30% of most proteins have?

A

Bound metal ions

113
Q

What are most metal ions in biochemistry?

A

Cations

114
Q

What is the significance of metal ions in biochemistry?

A

They have huge electrostatic components, making them reactive when water is excluded

115
Q

What are some examples of metal ions seen in biochemistry?

A

Fe2+, Fe3+, Cu2+, Zn2+, Mn2+, Co3+, Mo3+, Mo6+

116
Q

What are some examples of iron-containing proteins?

A

Hemoglobin and mitochondrial electron transport, heme proteins (porphyrin ring complex to carry O2), cytochromes, and iron-sulfur proteins

117
Q

What are some examples of copper containing proteins?

A

One electron transfer agents (Cu+ -> Cu2+)

118
Q

What are some examples of zinc containing proteins?

A

Carbonic anhydrase, and alcohol dehydrogenase

119
Q

What are some examples of manganese containing proteins?

A

Arginase

120
Q

What are some examples of molybdenum containing proteins?

A

Nitrate reductase

121
Q

What does carbonic anhydrase do?

A

It uses water to hydrate CO2 and form bicarbonate

122
Q

How does carbonic anhydrase work?

A
  1. It uses 3 His to coordinate Zn2+
  2. Zn2+ is used to pull H from H2O
  3. OH- attacks CO2 to form HCO3 (bicarbonate)
123
Q

What is the purpose of zinc in carbonic anhydrase?

A

It pulls H from H2O to make a strong nucleophile (polarized)

124
Q

What is the rate limiting step for carbonic anhydrase?

A

Diffusion of CO2 into the binding site (fast reaction rate)

125
Q

What is the HEW lysozyme mechanism?

A
  1. Acid catalysis by Glu to form intermediate (electrostatic stabilization)
  2. Nucleophilic attack by water (Glu mediated)
126
Q

True or false: pKa can be changed by burying groups?

A

True: burying groups can lead to more direct reactions, changing pKa

127
Q

How do aspartic acid proteases work?

A

Two Asp polarize water, which is used as a nucleophile

128
Q

What is an example of an aspartic acid protease?

A

HIV protease

129
Q

How does enolase work?

A
  1. An unprot Lys attacks H, Mg2+ stabilizes charge

2. Prot Glu acts as an acid to drive the reaction

130
Q

What is the significance of Mg2+ in enolase?

A

It stabilizes the highly negative intermediate

131
Q

What is significant about Lys and Glu in enolase?

A

Lys is unprot, and Glu is prot, which would not occur in solution. This is needed for the reaction to occur

132
Q

What would happen if there was free water in enolase?

A

The amino acids would have different charges, and the Mg2+ would not be as effective

133
Q

How do ribonucleases work?

A

One His acts as a base (unprot), and another His acts as an acid (prot)

134
Q

How does the pyruvate dehydrogenase complex work?

A

It uses many subunits, coenzymes, and reactive groups to sequester reactive intermediates

135
Q

How does carbamoyl phosphate synthetase II work?

A

It has an internal tunnel to sequester reactive intermediates

136
Q

What is the Arrhenius equation?

A

k = Aexp(-Ea/RT)

137
Q

What is the diffusion equation?

A

x^2 = 2Dt

138
Q

What is the equation for the diffusion coefficient?

A

D = kT/f (f = frictional coefficient)

139
Q

What does the diffusion equation relate?

A

Relates the time for diffusion to the temperature and shape of the molecule

140
Q

What is the HH equation?

A

pH = pKa + log(A-/HA)

CHE 541 (20 decks)

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