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Biochemistry > Chapter 2 > Flashcards

Chapter 2 Flashcards

1
Q

what does energy conversion in a biological system have to obey?

A

the laws of thermodynamics

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2
Q

describe oxidation (3)

A
  1. loss of electrons
  2. decrease in the number of hydrogens
  3. increase in the number of bonds to oxygen
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3
Q

describe reduction (3)

A
  1. gain of electrons
  2. increase in the number of hydrogens
  3. decrease in the number of bonds to oxygen
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4
Q

what happens to the molecule being oxidized?

A

it loses electrons, is a reductant, results in an oxidized product and free electrons; oxidized number increases

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5
Q

what happens to the molecule being reduced?

A

gains electrons, is an oxidant, results in a reduced product with more electrons; oxidation number decreases

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6
Q

give the general format for a redox reaction

A

oxidant + reductant yields oxidized product + reduced product

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7
Q

what are the 3 types of work?

A
  1. osmotic work: done to overcome osmosis
  2. chemical work: costs energy, make ATP
  3. mechanical work: ex is muscle contraction
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8
Q

what are redox reactions? (2)

A
  1. a series of linked reactions
  2. transfer of electrons from one compound to another in sequential form
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9
Q

when are redox reactions used?

A

in processes in which chemical work is performed and energy is made

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10
Q

what is the system?

A

what you are studying in a box

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11
Q

what are the surroundings?

A

everything outside the box you are studying

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12
Q

what are the 3 types of systems?

A
  1. open
  2. closed
  3. isolated
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13
Q

describe an open system; give an example

A

matter and energy are freely exchanged with the surroundings and example is biological systems

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14
Q

describe a closed system

A

only energy is exchanged with the surroundings; NOT matter

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15
Q

describe an isolated system

A

neither matter nor energy is exchanged with the surroundings

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16
Q

what is the first law of thermodynamics

A

energy can neither be created nore destroyed; energy is only converted from one form to another

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17
Q

what is q? when is it positive and negative?

A

q is heat
+q: heat is transferred into the system
-q: energy leaves the system

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18
Q

what is enthalpy?

A

enthalpy = energy = heat

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19
Q

is there any work done by the system on the surroundings in biological conditions? why or why not?

A

no; cell not trying to change volume, wanting to achieve homeostasis so pressure x change in volume = 0 and since work = -pressure x change in volume so work equals 0

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20
Q

compare and contrast exothermic versus endothermic reactions

A
  1. exothermic rxns release heat and enthalpy is negative; example is combustion of gas (heat has left the system)
  2. endothermic rxns absorb heat and enthalpy is positive; heating coffee (heat has entered the system)
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21
Q

what is the second law of thermodynamics? give an analogy

A

all spontaneous processes in the universe tend toward disorder (entropy, S) and dispersal of energy in the absence of energy; your room will tend toward disorder if you don’t put effort in to keep it clean

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22
Q

describe the entropy of the universe

A

always increasing

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23
Q

describe the states of water and their entropy

A

solid phase has least, liquid water is more, gas is most entropy

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24
Q

compare homeostasis to equilibrium based on definition

A
  1. homeostasis is maintaining the perfect state
  2. equilibrium is allowing for the natural state
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25
Q

describe homeostasis (4)

A
  1. highly ordered steady state in terms of temp, pressure, biomolecular concetration, etc.
  2. low entropy, high enthalpy (low disorder, requires high energy input)
  3. requires energy and delays equilibrium
  4. maintained by living organisms
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26
Q

describe equilibrium (4)

A
  1. less ordered state, system tends toward disorder
  2. high entropy, low enthalpy (high disorder, low energy input to maintain)
  3. homeostasis is not maintained
  4. macromolecules tend to equilibrate to their surroundings (ex. is DNA denaturing in acidic surroundings)
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27
Q

what is Gibbs free energy? (G)

A

the different between enthalpy and entropy of a system at a given temperature (in units of Kelvin)

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28
Q

can absolute values of Gibbs free energy be found? what do we do instead?

A

no; measure the difference in the two states

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29
Q

when delta G (different in Gibbs free energy of two states) is 0 what does this mean

A

the rate of formation of products and reactants in equal

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30
Q

what does Gibbs free energy tell you?

A

the energy that is available in a system

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31
Q

what are the standards under which Gibbs free energy is compared in chemical reactions? (3)

A
  1. constant pressure (1 atm)
  2. room temperature (298K)
  3. concentration of reactants and products is equal to 1M at the beginning of the reaction
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32
Q

what are the conditions under which Gibbs free energy is compared for biological reactions? (6)

A
  1. constant pressure (1 atm)
  2. room temperature (298K)
  3. concentration of reactants and products is equal to 1M at the beginning of the reaction
  4. pH = 7
  5. concentration of H2O is 55.5 M
  6. if needed in the reaction, concentration of Mg2+ is 1mM
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33
Q

compare exergonic versus endergonic reactions based on what happens with energy

A

exergonic releases energy and endergonic absorbs energy

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34
Q

describe exergonic reactions (3)

A
  1. delta G is negative
  2. seen in forward reactions
  3. reaction is favorable and spontaneous
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35
Q

describe endergonic reactions (3)

A
  1. delta G is negative
  2. seen in reverse reactions
  3. reaction is unfavorable and nonspontaneous
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36
Q

what sign of H (enthalpy) is favorable and why?

A

want negative delta H; want to be releasing heat since that is favorable and costs nothing

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37
Q

what sign of entropy (S) is favorable and why?

A

want positive delta S; want entropy to be increasing because decreasing disorder is favorable

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38
Q

what does Gibbs free energy depend on?

A

the equilibrium constant (Keq)

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39
Q

how is the Keq determined?

A

by using equilibrium concentrations

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40
Q

what does Keq show?

A

shows directionality of the reaction under standard conditions

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41
Q

describe what the signs of Keq indicate

A

Keq >1: reactions favors formation of products
Keq <1: reaction favors formation of reactants
Keq =1: neither reactants nor products are favored at equilibrium

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42
Q

does Keq = 1 indicate that a reaction is at equilibrium

A

NO; Keq is already calculated at equilibrium

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43
Q

what is Q?

A

the mass-action ratio; the ratio of inital/actual ratio of concentration of products over reactants

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44
Q

describe the steps for calculating the actual delta G

A
  1. covert all units to M
  2. find Q value (see formula)
  3. dinf delta G, see formula
45
Q

what are coupled reactions?

A

reactions that contain something on either side of the arrow that is the same; can be coupled

46
Q

how to you find the overall free energy of a coupled reaction?

A

cross out common intermediates and add individual free energies to find the overall free energy

47
Q

relate endergonic and exergonic reactions to couple reactions

A

endergonic and exergonic reactions can be coupled to give a favorable overall net reaction

48
Q

give an example of a coupled reaction and its favorable overall net outcome

A

ATP hydrolysis; provides energy

49
Q

what is the energyc charge?

A

the measure of the energy state of a cell

50
Q

what is the body’s high energy molecule?

A

ATP

51
Q

describe catabolic pathways (3)

A

CUTS; overall goal is generate ATP
1. generate ATP and reduced coenzymes, NADH, NADPH, and FADH2 using stored fuels
2. occurs when energy charge (EC) is low (we need ATP then)
3. convert energy-rich compounds into energy-depleted compounds

52
Q

describe anabolic pathways (3)

A

ADDS
1. USE ATP to replenish stored fuels
2. occurs when EC is high (have excess ATP and want to use it)
3. produce larger biomolecules from smaller molecules

53
Q

how does water life live through the winter?

A

water is less dense as a solid than as a liquid which makes ice float and then ice insulates the water below

54
Q

why is water the biological solvent?

A

due to its hydrogen bonding capabilities

55
Q

what in the structure of water accounts for its polarity?

A

its bent structure induces a dipole

56
Q

when does hydrogen bonding occur?

A

when a hydrogen atom is covalently bonded to an electronegative atom and in close proximity to another electronegative atom (either O or N) whose free lone pairs allows for the interaction

57
Q

what happens to the hydrogen atom in a hydrogen bond?

A

it is shared between two electronegative atoms

58
Q

is the hydrogen bonding of water permanent?

A

no; it is temporary, molecules of water exchange partners as time passes

59
Q

how many hydrogen bonds can one molecule of water form?

A

4

60
Q

what is solubility?

A

the ability of a solute to dissolve to homogeneity in a solvent

61
Q

what happens to ionic compounds in water that explains water’s role in biomolecule solubility?

A

ionic compounds form a lattice, while the water creates a hydration layer around each ion, preventing the ions from rejoining the crystal

62
Q

what do weak noncovalent interactions allow for?give an example

A

allow unstable structures to exist for a short period of time; enzyme subunits and substrates temporarily bind to each other stronger than they bind to water to fulfil their function, then dissociate (multi-subunit enzymes that catalyze biochemical reactions allow for assembly and disassembly of protein monomers)

63
Q

what is the strongest type of intermolecular interaction?

A

ionic interactions

64
Q

what are ionic interactions? what kind of interactions are these?

A

bonds between oppositely charged atoms; electrostatic interactions

65
Q

what does the strength of an ionic interaction depend on?

A
  1. the distance between the ions
  2. the environment between the ions
66
Q

give an example of ionic interactions

A

salt birdges in proteins

67
Q

what is the strongest covalent intermolecular interaction?

A

hydrogen bonding

68
Q

what does a hydrogen bond involve?

A
  1. h-bond donor: O-H, N-H, S-H
  2. h-bond acceptor: O, N, S, with lone pair of electrons, sometimes F
69
Q

what is key in h-bonding?

A

electronegativity!

70
Q

why are hydrogen bonds not as strong as ionic bonds?

A

the atoms in a hydrogen bond don’t have a formal charge, only a dipole

71
Q

what is the 2nd strongest covalent bond?

A

Van der Waals interactions

72
Q

describe Van der Waals interactions

A

temporarily occur between the dipoles of nearby electronically neutral molecules (dipole is made when molecules are close)

73
Q

what do Van der Waals interactions depend strongly on?

A

the distance between the two atoms

74
Q

what is the weakest of the covalent interactions?

A

hydrophobic effects

75
Q

what do hydrophobic effects occur between?

A

nonpolar molecules

76
Q

describe hydrophobic interactions (4)

A
  1. form between molecules that DO NOT form bonds with water
  2. play an important role in protein folding
  3. hydrophobic regions cluster together away from water
  4. occur between nonpolar amino acid residues, lipids
77
Q

describe water osmosis

A

water osmosis as a solvent moves to dissolve solutes; moves from low solute concentration to high solute concentration

78
Q

what is osmotic pressure?

A

the amount of pressure needed to counteract osmosis

79
Q

describe how red blood cells relate to osmosis

A

red blood cells can change shape depending on their cellular environment as a result of osmosis

80
Q

describe what happens to a red blood cell in a hypotonic solution

A

ruptures as water rushes in from low solute concentration to high solute concentration

81
Q

what happens to a red blood cell in an isotonic solution?

A

nothing, she vibin

82
Q

what happens to a red blood cell in a hypertonic solution

A

cell shrinks as water rushes out from low solute concentration to high solute concentration

83
Q

what is the water ionization constant (Kw)?

A

1.0x10^-14 M^2 = [H+][OH-]

84
Q

what is the equilibrium constant for the autoionization of water?

A

Keq = [H+][OH-]

85
Q

what do strong acids/bases do in water?

A

ionize completely in water

86
Q

what do weak acids do in water? also give formula

A

only partially ionize; HA (double arrow) H+ + A-

87
Q

what is acid strength determined by?

A

the acid dissociation constant (Ka)

88
Q

give the formula of ionization of strong acids

A

HA —> H+ + A-

89
Q

describe strong acids (6)

A
  1. ionize completely
  2. higher Ka
  3. lower pKa
  4. lower [HA]
  5. higher [H+]
  6. higher [A-]
90
Q

describe weak acids (6)

A
  1. only partially ionize
  2. lower Ka
  3. higher pKa
  4. higher [HA]
  5. lower [H+]
  6. lower [A-]
91
Q

relate pH to pKa involving protons

A

if pH higher than pKa, proton goes away

92
Q

what is given by pH = -log[H+]

A

the point at which the solution gives/accepts a proton to/from solute

93
Q

what is given by pKa = -logKa

A

the point at which a solute gives/accepts a proton to/from the solution

94
Q

what is [HA]?

A

protonated form of an acid

95
Q

what is [A-]?

A

the unprotonated form of an acid

96
Q

if pH > pKa?

A

solute is deprotonated (gives a proton to solution)

97
Q

if pH < pKa?

A

solute is protonated (accepts a proton from solution)

98
Q

if pH = pKa?

A

equilibrium

99
Q

describe monoprotic acids; give examples

A

have one dissociable proton and the pKa is the point at which protonation/deprotonation occurs; HCl, CH3, CO2H

100
Q

describe polyprotic acids; give examples

A

have more than one dissociable proton and each dissociable proton has its own pKa; H2SO4, H3PO4

101
Q

what is a buffer?

A

a solution which resists changes in pH (sucks up or spits protons)

102
Q

what composes a buffer?

A

a weak acid/base pair

103
Q

when is a buffer most effective?

A

at a pH near the pKa of the buffer

104
Q

what is the buffering range?

A

1 pH unit above and below the pKa

105
Q

give an example of a biological buffer; describe how works

A

carbonic acid-bicarbonate buffering system;
1. bicarbonate picks up a proton to become carbonic acid
2. carbonic acid dissociates to form CO2 and water, both of which are eliminated from the body by respiration or through the kidneys

106
Q

what are membranes made of?

A

amphipathic lipid molecules that self-assemble into a bilayer

107
Q

what does membrane fluidity depend on?

A

composition: which lipids are present

108
Q

what do membranes do. generally?

A

put up big hydrophobic barriers between aqueous environments

Biochemistry (20 decks)

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