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BCH 369 > Week 2: Thermo, IMF, Acids & Bases, and Amino Acids > Flashcards

Week 2: Thermo, IMF, Acids & Bases, and Amino Acids Flashcards

1
Q

All cells require _______ to carry out life processes. _________ is the ultimate source of energy on the Earth.

A

energy
The Sun

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2
Q

Oxidation is _______
Reduction is ________

A

loss of electrons
gain of electrons

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3
Q

Many cellular process include the _________ of electrons

A

movement

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4
Q

Many biochemical reactions involve __________

A

oxidations and reductions (redox chemistry)

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5
Q

Thermodynamics is the study of ______ and ________

A

transformations
transfer of energy

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6
Q

Changes in energy are calculated as:

A

final minus the initial state

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7
Q

If change in free energy is negative (free energy decreases), reaction is:
energy ______

A

spontaneous (reaction or process takes place without outside intervention)
energy released to environment

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8
Q

If change in free energy is positive (free energy increases), reaction:

A

will not occur unless energy supplied

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9
Q

Processes that __________ are favored.

A

release energy (spontaneous reactions)

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10
Q

The term spontaneous means….

A

energetically favored. It does not necessarily mean fast.

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11
Q

First law of thermodynamics:

A

energy can neither be created nor destroyed
“you cant win” (no such thing as > 100%)

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12
Q

Second law of thermodynamics:

A

total entropy of system must increase over time
“you cant break even” (energy transfer < 100%)

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13
Q

The _______ and the ________ are examples of spontaneous processes because they represent an ________ in disorder and entropy of the Universe and have a negative _______ at constant temperature and pressure

A

the hydrolysis of ATP to ADP and Pi
the oxidation of glucose to CO2 and H2O by an organism

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14
Q

Spontaneous processes are the ones plants or animals use to ________ to the organism

A

provide energy
(often involving a break down or loss)

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15
Q

Nonspontaneous processes are the ones used to…

A

build up the compounds needed so we can later use the reactions that provide energy

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16
Q

the ________ and the _______ are examples of nonspontaneous processes

A

The phosphorylation of ADP to ATP (attachment of phosphate group_

production of glucose and O2 from CO2 and H2O in photosynthesis

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17
Q

An increase in entropy occurs when the final state has ________ than the initial state

A

more possible random arrangements

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18
Q

Assuming the value of ∆S is positive, an increase in temperature increases the _________ component to the overall energy change.

A

-∆G contribution of the entropy

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19
Q

Urea dissolves very readily in water, but the solution becomes very cold as the urea dissolves. How is this possible? It appears that the solution is absorbing energy.

A

The heat exchange, getting colder, reflects only the enthalpy or ∆H component of the total energy change. The entropy change must be high enough to offset the enthalpy component and to add up to an overall -∆G.

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20
Q

When a reaction feels cold, it means energy is being _______ and ________

A

absorbed, used to power some change

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21
Q

Photosynthesis is _________, requiring light energy from the Sun. The complete aerobic oxidation of glucose is _______ and is a source of energy for many organisms, including humans. It would be reasonable to expect the two processes to take place _______ in order to ________ for the endergonic one.

A

endergonic
exergonic
differently
provide energy

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22
Q

Gibbs free energy (G, J/mol) is energy…

A

relevant to biochemical systems

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23
Q

Enthalpy (H, J/mol) is the…

A

heat content of a system

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24
Q

How does enthalpy relate to G?

A

Negative change in enthalpy contributes to a negative change in Gibbs free energy or a spontaneous reaction

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25
Q

equation of ∆G?

A

∆G = ∆H - T∆S

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26
Q

Entropy is the measure of the _______ and measure of ________

A

dispersion of the energy of the system
disorder or randomness

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27
Q

Conditions where ∆G will always be a negative value:

A

reaction is exothermic (∆H < 0)
entropy increases (∆S > 0)
the temp. is such that T∆S contributes significantly to making ∆G negative

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28
Q

_______ influences entropy changes

A

Temperature (T, units of K)
absolute temperature in Kelvin

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29
Q

∆G > 0, _______

A

nonspontaneous or endergonic

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30
Q

∆G < 0, ________

A

spontaneous or exergonic

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31
Q

energy absorbing

A

endergonic

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32
Q

energy releasing

A

exergonic

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33
Q

∆G = 0 indicates

A

equilibrium

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34
Q

Dynamic equilibrium is when movement and reactions…

A

proceed in the forward and reverse directions at the same rate

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35
Q

∆G is the change in free energy, indicates _____ and measure of ____ NOT ______

A

likelihood of reaction
equilibrium
NOT speed

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36
Q

Molecules are always…

A

in motion

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37
Q

exothermic:

A

heat released (-)

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38
Q

endothermic:

A

heat absorbed (+)

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39
Q

When two atoms with the same electronegativity form a bond, the electrons are shared _______ between the two atoms.

A

equally

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40
Q

The polar nature of ______ largely determines its _______ properties.

A

water
solvent

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41
Q

The unique fitness of water for ___________ determines the properties of many important biomolecules. Water can also act as ________, giving it great versatility in biochemical reactions.

A

an acid and as a base

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42
Q

Under what circumstance is a molecule that has a dipole not a polar molecule?

A

If the dipole is cancelled out by another of equal and opposite orientation. The classic example is CO2. Each carbon-oxygen bond is a dipole, but the two cancel each other out and the molecule is nonpolar.

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43
Q

Which would you think would be a stronger interaction and why: an interaction between a sodium ion and the partial negative charge on the oxygen in ethanol, or the interaction between two ethanol molecules?

A

The sodium ion is a fully charged cation. Therefore, its interaction with the partial negative charge on the oxygen of ethanol would be stronger than the interaction of the same oxygen with a partially positive charge from the hydrogen of another ethanol molecule.

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44
Q

Which of the standard 20 amino acids can form disulfide bridges in protein structures?

A

Cysteine because it contains a thiol group in its side chain. A disulfide bridge is formed when a sulfur atom from one cysteine forms a single covalent bond with a sulfur atom from a second cysteine in a different part of the protein.

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45
Q

Isoleucine has _____.

Lysine has ______.

Aspartate has _____.

Leucine has _______.

A

a chiral center.

an amino group

a carboxylic acid

a branched hydrocarbon

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46
Q

Identify the polar amino acids, the basic amino acids, and the sulfur-containing amino acids in the peptide with the following amino acid sequence:

Arg-Gln-Tyr-Cys-Thr-Lys-Met-Ser

A

Polar amino acids include Asn, Gln, Ser, Thr, Cys, and Tyr.

Basic amino acids include Arg, His, and Lys.

The two sulfur-containing amino acids are Cys and Met.

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47
Q

Identify the nonpolar amino acids, the acidic amino acids, and the aromatic-group-containing amino acids in the peptide with the following amino acid sequence:

Asp-Gly-Met-Ala-Pro-Trp-Tyr-Ile

A

Nonpolar amino acids include Met, Trp, Ile, Phe, Leu, Val, Pro, Ala, and Gly.

Acidic amino acids include Asp and Glu.

The three aromatic-containing amino acids are Tyr, Phe, and Trp.

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48
Q

Any process that results in a _______ from the system is favored.

A

release of energy

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49
Q

adding energy to the system from its surroundings will result in an_______ of the system, which is ________.

A

increase in the energy

unfavorable

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50
Q

Biochemical reactions that are not favored are coupled with ________ in order for the overall process to occur.

A

favored reactions

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51
Q

The value for ΔG for the oxidation of glucose to CO2 and H2O by an organism is _______, due to the _______. Therefore, this is a _______.

A

negative

increase in disorder

spontaneous process

52
Q

For the separation of a disaccharide into two monosaccharides, one would expect the entropy change in the reaction to be
______.

This entropy change is expected because…

A

positive

one disaccharide molecule can be randomized in fewer ways than two monosaccharides

53
Q

The three van der Waals forces in order of decreasing strength are:

A

Dipole-dipole > Dipole-induced dipole > Induced dipole-induced dipole

54
Q

_____ and ______ employ H-bonds within their internal structures to control and maintain their molecular shapes.

A

Proteins
nucleic acids

Ex. chromosomal DNA, transfer RNA, and hemoglobin

55
Q

Most _____, like _______, do not require H-bonds to control their structures. They are good H-bond formers, though.

A

mono- and disaccharides

glucose and sucrose

56
Q

________, do not form many H-bonds and thus do not employ H-bonds to control their structures.

A

Lipids, like triacylglycerols and cholesterol

57
Q

Which of the following molecules can serve as both a hydrogen bond donor and acceptor?

CO2, (CH3CH2)2O, CH3OPO3^2-, CH3OH, H2O

A

CH3OH and H2O

The formation of a H-bond requires a pair of polarized bonds, one of which contains an electropositive H atom (the donor) and the other of which contains an electronegative atom with a free lone pair of electrons (the acceptor). Nitrogen and oxygen are often found to be acceptors in H-bonds, and these two atoms are often bound to the donor hydrogens.

C-H bonds are not polar and thus will not form H-bonds. Hydrocarbons contain only these sorts of bonds and thus are hydrophobic.

58
Q

A conjugate acid will be identical to its conjugate base except for the presence of _______ on the conjugate acid at its acid dissociation site.

A

an extra hydrogen

59
Q

Pregabalin is an acid with a pKa of 4.2; its structure includes a carboxyl group. To be absorbed into the bloodstream, it must pass through the membrane lining the stomach and the small intestine. Electrically neutral molecules can pass through a membrane more easily than can charged molecules.

Would you expect more pregabalin to be absorbed in the stomach, where the pH of gastric juice is about 1, or in the small intestine, where the pH is about 6?

A

More pregabalin will be absorbed in the stomach because pregabalin molecules will have a less negative average charge there than in the small intestine.

At pH ~ 1 pregabalin’s carboxylic acid will be dominantly protonated, meaning that the charge on pregabalin in the stomach will be less negative than the charge on pregabalin in the small intestine. Thus, pregabalin in the stomach will more easily cross the stomach membrane than it will be able to cross the small intestine membrane.

60
Q

The key to selecting a good buffer for biochemical reactions is twofold:

A
  1. the pH of the chosen buffer should be close to the optimal pH for the biochemical reaction
  2. the buffer should not interact with the components of the biochemical reaction.

The details of the makeup of the buffer are irrelevant. Only the pKa value and the degree of interaction with the reaction of interest are important.

61
Q

Calculate the pH of a buffer solution prepared by mixing 50.0 mL of 1.25 M lactic acid and 25.0 mL of 0.75 M sodium lactate.

(The pKa for lactic acid is 3.86. The molar mass for lactic acid is 90.1 g/mol and the molar mass for sodium lactate is 112.1 g/mol.)

A

3.34

62
Q

buffers works best when the _______ equals the _______

A

pH of the solution
pKa of the buffer

63
Q

Electronegativity is the measure of force of an atom’s __________ in a chemical bond

A

attraction for shared electrons

64
Q

Oxygen and nitrogen are more electronegative than ___

A

carbon and hydrogen

65
Q

Electronegativity often relates to ______ as ___________

A

reactivity
nucleophiles/electrophiles

66
Q

Electrons are _______ in polar bonds

A

unequally shared

67
Q

Polar bonds:
more _____ found closer to one atom
______ generated
Due to difference in __________ of atoms

A

negative charge
partial dipole
electronegativity

68
Q

Dipole is a measure of __________
Arrow points to ________

A

polarity of chemical bond
center of electronegativity

69
Q

van der Waals radius is the distance between ______ and ________

A

nucleus of atom
its effective electronic surface

70
Q

CO2 has ____ but is _____ overall due to ______

A

polar bonds
nonpolar
linear geometry

71
Q

In a nonpolar bond, two atoms share electrons ______

A

evenly

72
Q

Ionic bonds is the attraction of ________, held together by ________

Ex?

A

opposite charges
(+) and (-) ions

Ex. salt crystals

73
Q

Salt bridge (_______)
attraction of _______
_______ attraction
_______ in biomolecules

A

charged functional groups
opposite charges
electrostatic attraction
Ionic bond in biomolecules

74
Q

Bond between negatively charged carboxyl group and positively charged amine group is an example of ______

A

salt bridge

75
Q

Ion-dipole interactions is when ions ____ interact with ____

A

in solution
molecules that have dipoles

76
Q

-KCl dissolved in H2O is an example of?

_______ potassium ions interact with _______ and _______ chloride ions interact with _______

A

Ion-dipole interaction

Positively charged potassium ions
negative dipoles on oxygen
negatively charged chloride ions
positive dipoles on the hydrogens

77
Q

Bonding occurs with the _____ of radii

A

overlap

78
Q

the ______ the overlap, the ______ the bond distance, the ______ the bond

A

greater
shorter
stronger

79
Q

3 types of van der Waals interactions:

A

Dipole-dipole
Dipole-induced dipole
Induced dipole-induced dipole (London dispersion forces)

80
Q

van der Waals forces:
______ associations
______ attraction of ______
NOT ________

A

noncovalent
weak, dipoles
NOT electrostatic interactions of charged ions (NO NET CHARGE)

81
Q

strengths of bonds found in biochem:

______ play vital role in biological systems and structures

A

Covalent (O-H)
Covalent (C-H)
Ionic interactions
Ion-dipole, Hydrogen bonds (equal)
van der Waals interaction

weaker forces

82
Q

Hydrophilic (_______)
* Tending ______ in water
* Examples - ________

A

water-loving
to dissolve
Ionic and polar substances

83
Q

Hydrophobic (______)
* Tending ______ in water
* Hydrophobic interactions: _____
* Examples: ________

A

water-hating
not to dissolve
Attractions between nonpolar molecules
hexane or other alkanes

84
Q

Amphipathic (amphi = ______)
* Molecule that contains…

A

“both”
both hydrophobic and hydrophilic regions

85
Q

Micelle formation by amphipathic molecules:
______ in water:
______ buried inside
_______ on surface
Formation depends on…

A

spherical arrangement
hydrophobic parts buried inside
hydrophilic parts on surface
attraction between temporary induced dipoles

86
Q

Water has unique properties for a molecule its size, such as….

This is due to the ______ possible between water molecules.

A

a very high boiling point and melting point.

extensive hydrogen bonding

87
Q

Stronger hydrogen bond =
Weaker hydrogen bond =

A

linear
non-linear

88
Q

What are some macromolecules that have hydrogen bonds as a part of their structures?

A

Proteins and nucleic acids

89
Q

hydrogen bonding has not been observed between ______ molecules because the ______ bond is not sufficiently _______ for greatly unequal distribution of electrons at its two ends. Also, there are no __________ to serve as _______.

A

CH4
C—H
polar
unshared pairs of electrons
hydrogen bond acceptors

90
Q

For a bond to be called a hydrogen bond, it must have a hydrogen covalently bonded to…. This hydrogen then forms a hydrogen bond with another…

A

oxygen, nitrogen, or fluorine

91
Q

________ bind to nucleic acids as a result of ________ to the negatively charged phosphate groups.

A

Positively charged ions
electrostatic attraction

92
Q

Acids are compounds that _________ when dissolved in aqueous solution. In other words, they are ________.

A

release hydrogen ions (protons)
proton donors

93
Q

Bases are compounds that are ________.

A

proton acceptors

94
Q

pH is a measure of the ______ of the solution. The _____ the pH, the ________ the solution

A

acidity
lower
more acidic

95
Q

pH = ?

Higher _____ means more acidic and means ______ value

A

-log[H +].

[H +]

lower pH

96
Q

Higher Ka value…

A

stronger acid, more dissociation

97
Q

effects of adding weak acid or base to water

A

only partial dissociation

98
Q

pH at which group is 1/2 ionized?

A

when pH value equals pKa

99
Q

[H +] =

A

10^-pH

100
Q

[OH-] [H3O+] =

A

1 x 10^-14

101
Q

Buffers work based on the nature of ________ that compose the buffer.

A

weak acids and their conjugate bases

102
Q

If a source of extra hydrogen or hydroxide ion is added to a buffer solution, it reacts with buffer components and is neutralized.__________.

A

neutralized

103
Q

H-H equation –>

A

pH = pKa + log ( [A-] / [HA] )

104
Q

equal amounts of the acid and conjugate base pH =

A

pKa

105
Q

Buffering capacity is the ability of a substance to _______ when ________ are added

A

resist changes in pH
acids or bases

106
Q

______ buffer within cells
_______ buffer in blood

A

phosphate
carbonate

107
Q

Since a __________ has both a positive and negative charge, it is able to act as both a base or an acid depending on the situation.

A

zwitterion

108
Q

all amino acids are _______ molecules

A

polar

109
Q

_______ is technically not an amino acid. _______ contains no chiral carbon atoms.

A

Proline
Glycine

110
Q

Peptides are formed by reacting the ________ of one amino acid with the ________ of another amino acid in a ____________

A

carboxyl group
amino group
covalent (amide) bond.

111
Q

Proteins consist of ________; the number of amino acids in a protein is usually _______.

A

polypeptide chains
100 or more

112
Q

Peptides are molecules formed by linking _______ by ______

A

two to few dozen amino acids
amide bonds

113
Q

The pKa of acetic acid is 4.76. Which statement is true at pH 4.0?

A

[A-] < [HA]

114
Q

Which of the following molecules will not form hydrogen bonds?

HF
H2CO3
HCOOH
H2O
NH3

A

All of these can form hydrogen bonds.

115
Q

Breaking bonds

A

Endothermic

116
Q

Forming bonds

A

Exothermic

117
Q

What are two characteristics of a molecule that can be a hydrogen bond acceptor?

A

1) Available non-bonding lone pair of electrons. Note that if this lone pair is involved in resonance, it will NOT
be available for hydrogen bonding.
2) Electronegative atom: The lone pair of electrons needs to be on one of Nitrogen, Oxygen, or Fluorine.

118
Q

Hydrogen bonds are an _______ force, therefore…

A

intermolecular force
bond BETWEEN molecules not within a molecule

119
Q

Hydrogen bonds can be accepted by a _______ of an ______

A

free lone pair
O, N, or F atom

120
Q

When phospholipids are placed in water, is the process of bilayer formation spontaneous?

A

Yes – the entropy of the surroundings increases.

121
Q

________ and _________ drives the spontaneous folding of proteins

A

Hydrophobic interaction, hydrogen bonding that increase surrounding entropy

122
Q

Glycine is the most simple amino acid – its R group is just a hydrogen. Therefore, the only way it could
ever have a positive charge is…

A

if the pH is very low AND it is by itself.

123
Q

ou work in a lab and your partner has just informed you that in his peptide chain (DRGRADNER), the
amine group of his Glycine has just been protonated and now has a positive charge. You become
confused. Why?

A

It is impossible due to the amine nitrogen being involved in a peptide bond.

124
Q

Water is capable of forming ________ hydrogen bonds

A

4

125
Q

A buffer solution is present when a ______ is in combination with ________.

Adding NaF and HCl in a beaker together would create a _______

A

weak acid, its conjugate base

For A, we are combining F- and HF – the weak acid HF is with its conjugate base F-, so this is considered a buffer
solution.

buffer solution

BCH 369 (12 decks)

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