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Biochem > Chemical Bonding Lecture > Flashcards

Chemical Bonding Lecture Flashcards

1
Q

How much energy required to break covalent bonds?

A

50-100 kcal/mole

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2
Q

Describe the stability of covalent bonds

A

Quite stable under physiological conditions

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3
Q

How much energy required to break non-covalent bonds?

A

5 kcal/mole

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4
Q

Describe stability of non-covalent bonds

A

Break quite easily under physiological conditions but structures held by lots of cooperating non-covalent bonds could be very stable

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5
Q

Non-covalent bonds determine what 2 things?

A
  1. How molecules interact with each other
  2. Shape of large covalently bonded molecules (proteins, nucleic acids)
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6
Q

What does the strength of H bonds depend on?

A

Distance and orientation

e.g. maximum strength when three atoms in a straight line

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7
Q

What does the strength in electrostatic bonds depend on?

A

Distance, not orientation

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8
Q

Non-polar surfaces do not attract each other. They are…

A

Pushed together by the solvent

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9
Q

The strength of a hydrophobic “bond” between 2 non-polar surfaces equals…

A

The strength of additional water-water H bonds that form when nonpolar surfaces are removed from contact with water molecules

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10
Q

List the bonds in descending order of strength

A

Covalent > Hydrogen > Electrostatic > Hydrophobic > Van der Waals (0.5 kcal/mole)

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11
Q

An acid is…

A

A proton donor

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12
Q

A base is…

A

A proton acceptor

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13
Q

Dissociation of an acid always produces what?

A

A conjugate base

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14
Q

Protonation of a base always produces what?

A

A conjugate acid

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15
Q

Strong acids dissociate completely or incompletely?

A

Completely (equilibrium is very far right) e.g. inorganic acids like HCl, H2SO4

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16
Q

Weak acids and bases…

A

Exist in equilibrium with their conjugate species. Carboxylic acids are weak acids, amines are weak bases

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17
Q

[H+] changes __-fold when pH changes by 1 unit

A

10-fold

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18
Q

In the oral cavity, [H+] directly affects what?

A

The balance of mineralization vs. demineralization of the dental enamel

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19
Q

What is Ka a measure of?

A

The position of the equilibrium

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20
Q

What is the Ka eqn?

A

Ka = [H+][A]/[HA]

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21
Q

Ka is the H+ concentration at which exactly _____ of A is protonated

A

Ka is the H+ concentration at which exactly half of A is protonated, i.e. when [H+] = Ka, [A] = [HA]

Ka = [H+][A]/[HA]

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22
Q

What 2 things does the Henderson Hasselbalch Eqn tell you?

A
  1. The fraction of A that is protonated, if you know its pKa and the pH
  2. The pH, if you know pKa and [A]/[HA] ratio of a buffer
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23
Q

How does a buffer work?

A

It reacts with either added H+ or OH- to get rid of some of the added H+/OH- in order to decrease the pH change

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24
Q

What buffering reaction gets rid of added H+?

A

A + H+ –><– AH

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25
Q

What buffering reaction gets rid of added -OH?

A

AH + -OH –><– A + H2O

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26
Q

Because a buffer reaction is an equilibrium reaction, is all of the added H+ or -OH removed?

A

No

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27
Q

Buffers work well when the pH is near what?

A

Their pKa

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28
Q

What is the most important physiological buffer?

A

Bicarbonate (HCO3-)

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29
Q

Where is gaseous CO2 from lungs and tissues dissolved?

A

Blood plasma

CO2 (g) –><– CO2 (d)

CO2 (d) + H2O –><– H2CO3 (catalyzed by carbonic anhydrase)

H2CO3 –><– H+ + HCO3-

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30
Q

Give the eqn and equilibrium constant for the ionization of H2CO3 in equilibrium with dissolved CO2

A

Koverall = [H+][HCO3-]/[CO2(d)]

Koverall = 4.91 x 10^-7, pK = 6.31

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31
Q

IF the pH of blood (7.4) is more than 1 pH unit away from bicarbonate’s pK, why is the bicarbonate system an effective buffer?

A

Even though [CO2(d)] is about 10% of [HCO3-], the bicarbonate buffer system is an OPEN system.

So there is natural presence of CO2 gas at pp 40 mm Hg in lungs and the equilibrium

CO2 (g) –><– CO2 (d)

maintains the CO2 (d) at fairly constant level

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32
Q

Metabolism generates ____ in the body

A

acidity

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33
Q

The bicarbonate buffer system allows the body to convert __ from metabolic acids into a ______ that can be exhaled from the lungs

A

The bicarbonate buffer system allows the body to convert H+ from metabolic acids into a gaseous form (CO2) that can be exhaled from the lungs. Doing so, it evaporates the acidity

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34
Q

List the 6 non-polar aliphatic amino acids

A

Glycine
Alanine
Proline
Valine
Leucine
Isoleucine

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35
Q

List the properties of non-polar amino acids

A

Have methyl/ene side chains that cannot H bond

Avoid water and are found in center of protein structures

Abundant components of protein

Glycine has only H atom side chain

Alanine only has methyl group side chain

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36
Q

List the 4 polar uncharged amino acids

A

Asparagine
Glutamine
Serine
Threonine

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37
Q

List the properties of the polar uncharged amino acids

A

Interact well with water through H bonding

Often found at surface of proteins

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38
Q

List the 3 aromatic amino acids

A

Phenylalanine
Tyrosine
Tryptophan

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39
Q

Lis the properties of the aromatic amino acids

A

Usually hydrophobic

Often buried within protein structures

Their side chains sometimes stack with nucleobases in active sites

Tyr and Trp can H bond and aren’t always buried

Trp is least abundant AA in protein

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40
Q

List the 2 sulfur-containing amino acids

A

Methionine
Cysteine

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41
Q

List the properties of the sulfur-containing amino acids

A

Sulfur in Cys reactive to oxidation and can form disulfide bridges

Extracellular proteins like trypsin, insulin, & blood clotting factors held together in part by disulfides

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42
Q

List the 2 negative acidic charged amino acids

A

Aspartate
Glutamate

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43
Q

List the 3 positive basic charged amino acids

A

Arginine
Lysine
Histidine

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44
Q

The charged AAs have side chains that are _____ or _____

A

acidic; basic

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45
Q

What is Asp and Glu’s pKa roughly at?

A

4

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46
Q

Which positively charged basic AA has a high pKa?

A

Arginine

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47
Q

What is the pKa of Lys?

A

9-10

48
Q

What is the pKa of His?

A

6

49
Q

List the properties of the charged AAs

A

Often protrude at surface of proteins

Often found making electrostatic interactions with other residues

50
Q

What is a Zwitterion?

A

A molecule with a positively charged amino group and a negatively charged carboxyl group

51
Q

What is the isoelectric point (pI)?

A

pH at which a molecule has no net charge. It’s the average of the pK’s of the amino and carboxyl groups.

52
Q

Which amino acids predominate in their protonated form at physiological pH of 7.4?

A

Cysteine
Tyrosine
Lysine
Arginine

53
Q

Which amino acids predominate in their deprotonated form at physiological pH of 7.4?

A

Aspartate
Glutamate
Histidine

54
Q

Due to electronic resonance, peptide bonds have partial double bond character, which makes them…

A

Planar and rigid

55
Q

Insulin is made as a precursor of how many AAs?

A

80

56
Q

Insulin’s precursor is cleaved how many times to make its 2-chain active form?

A

4

57
Q

How many disulfides in insulin?

A

3 (6 original cysteines, now 3 cysteines)

58
Q

What is the most stable protein structure if it needs to be in solution?

A

Secondary

59
Q

What reaction happens in secondary structure?

A

Carboxyl oxygen accepts H from peptide hydrogen 4 residues later in the sequence. This stabilizes the alpha helix in which R groups protrude at regular intervals.

60
Q

Helices can be…

A

amphipathic

61
Q

Beta strands can form which bonds?

A

Regular H bonds with neighbouring beta strands to make beta sheets in which adjacent R groups can also interact. Beta turns can be formed with stabilizing H bonds

62
Q

Which polypeptides can form triple helices?

A

Polypeptides with glycine residues at every 3rd position because H of alpha carbon sticks into middle of triple helix and no other AA R group can fit

63
Q

Why does collagen form a cable-like structure of great strength?

A

Bc collagen chains associate into triple helixes

64
Q

What kind of bonds hold primary structure together?

A

Covalent bonds

65
Q

What kinds of bonds hold together the secondary, tertiary, and quaternary structures of folded proteins inside the cell?

A

Noncovalent bonds

66
Q

Secondary structures are held together by what bonds between C=O and N-H atoms of peptide bonds?

A

H bonds

67
Q

What determines which segments of a polypeptide chain can form stable alpha helix or beta sheet?

A

The side chains of the amino acids

68
Q

Hemoglobin is composed of…

A

2 alpha and 2 beta subunits

69
Q

LDH has…

A

4 copies of a single subunit type

70
Q

Globins are largely what?

A

Alpha-helical

71
Q

Why are globins a bit unusual?

A

They have all helix connected by turns

72
Q

What don’t globins have?

A

beta structure

73
Q

What structures does myoglobin not have?

A

Quaternary

74
Q

What structure does hemoglobin not have?

A

It has all structures

75
Q

We could say that the folded structure of protein is encoded in the ____ _____ ______

A

amino acid sequence

76
Q

Why is the quaternary structure important?

A

It facilitates more complex protein behaviour

It is the basis of many important anatomical structures

77
Q

The single subunit of myoglobin binds oxygen ____ _____, in a simple ______ ______ reaction that depends on the _____ _____ ______

A

The single subunit of myoglobin binds oxygen fairly strongly, in a simple reversible equilibrium reaction that depends on the free oxygen concentration

78
Q

How does hemoglobin’s quaternary structure benefit it?

A

4 subunits bind and release O2 in a concerted fashion, giving a sigmoid binding curve with a threshhold of binding

79
Q

When Keq is very large, a _____ amount of reactant is present at equilibrium

A

tiny

Sometimes say reaction is “irreversible”

80
Q

What 2 things do Keq and G tell us?

A
  1. Relative proportion of reactants and products that will be present at equilibrium
  2. How much useful work can be obtained from a reaction, under standard conditions when [products] = [reactants] = 1 M
81
Q

If Keq > 1 (G < 0), equilibrium favors ______, and the reaction will ______ energy

A

products; yield

82
Q

G = 0 means that…

A

The reaction is at equilibrium

83
Q

If Keq <1 (G > 0), equilibrium favors _______, and the reaction will _____ energy

A

reactants; absorb

84
Q

Keq and G tell us nothing about what?

A

How fast a reaction will occur

85
Q

Kinetically favoured means…

A

it forms the fastest in a reaction

86
Q

Thermodynamically favoured means…

A

it is the most stable

87
Q

ATP is thermodynamically ______

A

unstable

88
Q

ATP is kinetically ______

A

Stable

89
Q

Catalysts…

A

lower energy of activation and increase the rate at which reaction goes to equilibrium

90
Q

Keq and G depend on what?

A

Initial and final states

91
Q

Are Keq and G altered by presence of a catalyst?

A

No

92
Q

An enzyme increases the rates of the forward and reverse reactions….

A

by exactly the same factor

93
Q

Enzyme kinetics are…

A

a quantitative description of enzyme activity as a function of substrate conc

94
Q

In uncatalyzed reactions, the reaction rate depends on what?

A

The conc of reactants in a simple linear fashion (law of mass action)

95
Q

In catalyzed rxns, the reaction rate levels out when?

A

At high substrate conc

96
Q

Vmax is a measure of what?

A

The max capacity of the enzyme

97
Q

What does Vmax depend on?

A

How much of enzyme is present

98
Q

Km is a measure of what?

A

The affinity of the enzyme for the substrate. It tells us how a given amount of that enzyme will respond to changes in substrate conc

99
Q

What is Km independent of?

A

Amount of enzyme present

100
Q

Km is the substrate conc at which the activity of the enzyme is ___ ___ ___

A

half of Vmax (half-maximal)

101
Q

Removal of the inhibitor results in ____ ____ of enzyme activity

A

rapid recovery

101
Q

Enzyme inhibition usually refers to what?

A

Reversible inhibition

102
Q

Give 2 examples of reversible enzyme inhibitors

A

Physiological enzyme inhibitors; many drugs

103
Q

Enzyme inactivation refers to what?

A

Irreversible effects

104
Q

Give 2 examples of irreversible inactivators

A

Some drugs like aspirin and many toxic substances (esp toxic metals)

105
Q

Name 2 reversible inhibitors

A

Competitive and non-competitive inhibitors

106
Q

With competitive inhibitors, inhibition can be overcome with what?

A

High [S]

107
Q

What are an important class of competitive inhibitors?

A

Enzymatic reaction products

108
Q

Can non-competitive inhibitors be overcome with high [S]?

A

No

109
Q

What happens to the Vmax and Km with competitive inhibition?

A

Vmax stays the same
Km increases

110
Q

What happens to the Vmax and Km with non-competitive inhibition?

A

Vmax decreases
Km stays the same

111
Q

Aspirin is a suicide substrate for…

A

Cyclooxygenase

112
Q

Acetoaminophen and ibuprofen are _____ inhibitors of cyclooxygenase

A

Reversible

Bind but don’t react at active site

113
Q

Lead and mercury react with which groups?

A

-SH groups

114
Q

Lead and mercury act as _____ ____ of many enzymes

A

irreversible inactivators

115
Q

Mercury is a controversial component of _____ ____

A

dental amalgam

116
Q

Mercury is extremely ___ ___ in ____. The rate of release is _____ ____.

A

Mercury is extremely tightly bound in amalgam. The rate of release is extremely slow.

Biochem (6 decks)

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