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Biochemistry > Properties of Biological Molecules > Flashcards

Properties of Biological Molecules Flashcards

1
Q

Properties of Covalent Bonds

A

strong, short, share electrons

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2
Q

properties of Noncovalent Interactions

A

weak, long, attraction only (charge-to-charge attraction)

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3
Q

strengths of bonds measured by

A

energy needed to break the bond and distance between atoms

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4
Q

noncovalent interactions

A
  • charge-charge interactions
  • charge-diple
  • dipole-dipole
  • charge-induced dipole
  • dipole-induced dipole
  • dispersion (van der Waals or hydrophobic interactions)
  • hydrogen bond
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5
Q

charge-charge interactions

A

an interaction between 2 completely charged ions

ex. ionic bonds (NaCl) and salt bridge (interaction between 2 amino acids in a protein)

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6
Q

Force = positive

A

repulsion

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7
Q

force = negative

A

attraction

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8
Q

Dielectric constant

A

effect of medium that could prevent ions from interacting with each other

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9
Q

energy of interaction =

A

(kq1q2) / D*r

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10
Q

dipoles involve ____ charges

A

partial

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11
Q

polar

A

permanent dipoles

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12
Q

polarizable

A

induced dipoles

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13
Q

dispersion (van der Waals or hydrophobic interaction)

A

taking a nonpolar molecule and inducing a dipole so there is something attractive to hold together

highly dependent on distance

ex. benzene ring stacking

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14
Q

hydrogen bonds

A

sharing proton (hydrogen atom)

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15
Q

hydrogen bond donor

A

atom that is covalently bonded to hydrogen atom

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16
Q

hydrogen bond acceptor

A

atom that is accepting the hydrogen

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17
Q

water’s H-bonds in:

solid

liquid

gas

A

optimal H-bonds

suboptimal H-bonds

No H-bonds

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18
Q

density is measure of

A

how tightly packed atoms or molecules are

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19
Q

hydrogen bond distances in waters are greater in ____ than in ____

A

solid

liquid

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20
Q

specific heat capacity

A

amount of heat needed to change the temperature of 1 gram of a given substance by +/- 1 degree C

(why oceans do not freeze)

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21
Q

heat of vaporization

A

amount of energy needed to change 1 gram of a given substance from liquid to gas

(why sweating removes body heat)

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22
Q

hydrogen bonds ____ energy to break and ____ energy when they form

A

use

release

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23
Q

cohesion

A

attraction to self

water molecules attract each other

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24
Q

adhesion

A

attraction to other

water and other polar substance attract each other

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25
Q

cohesion creates

A

surface tension

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26
Q

cohesion and adhesion work together to create

A

capillary action

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27
Q

charged/polar molecules are hydrophilic and _____ in water

A

dissolve

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28
Q

nonpolar molecules are hydrophobic and _____ in water

A

no not dissolve

but rather separate

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29
Q

amphipathic molecules (such as lipids and fatty acids) have both

A

hydrophilic and hydrophobic parts

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30
Q

noncovalent interactions ____ energy to break and ____ energy when formed

A

use

release

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31
Q

covalent bonds ____ energy when broken and ____ energy to form

A

release

use

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32
Q

dynamic equilibrium

A

same amount being made as destroyed

rate of reactant formed = rate of products formed

no NET formation or destruction

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33
Q

Ka =

A

[H+] [A-] / [HA]

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34
Q

pKa =

A
  • log Ka
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35
Q

Strong acid:

Ka
pKa
Energy of Interaction

A

Ka = Larger

pKa= Smaller

Energy of Interaction = Smaller

36
Q

Weak acid:

Ka
pKa
Energy of Interaction

A

Ka = Smaller

pKa = Larger

Energy of Interaction = Larger

37
Q

Water equilibrium =

A

H2O OH- + H+

38
Q

Kw = 10^-14 M

A

[H+] [OH-] / [H2O]

39
Q

pH =

A
  • log [H+]
40
Q

pKw =

A

pH + pOH

41
Q

pKw = 14

A
  • log Kw
42
Q

buffer

A

weak acid or base that can stabilize pH

absorbs change in [H+]

43
Q

Henderson-Hasselbalch

A

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

or

[A-]/[HA] = 10^pH-pKa

44
Q

if pH < pKa

A

then most of the molecules are protonated since [HA] > .[A-]

45
Q

if pH > pKa

A

then most of the molecules are deprotonated since [HA] < [A-]

46
Q

if pH = pKa

A

then the molecules are just as likely to be protonated as deprotonated

47
Q

gel electrophoresis

A

direction of migration based on net charge of molecule

(concerned with pKa of phosphate backbone in DNA- 2 phosphates that are accessible)

at physiological pH –> at least 1 neg charge on every single phosphate

48
Q

isoelectric point (pI)

A

the pH where all molecules of a given species in solution have an overall charge of 0

pI = pKa (+1) + pKa (-1) / 2

49
Q

if pH < pI,

if pH > pI,

if pH = pI,

A

then the molecule has a positive charge

then the molecule has a negative charge

then (by definition) the molecule has no net charge

50
Q

pI in context: isoelectric focusing

A

the pH changes over the length of the gel

proteins stop moving when they are uncharged (pH = pI)

51
Q

pI in context: protein solubility

if pH > pI or pH < pI then

if pH = pI then

A

proteins have net charge –> all have same net charge (repulsive to each other but attracted to H2O)

overall net neutral charge, but have local areas that are charged, so proteins are now more attracted to each other than water

52
Q

first law of thermodynamics

A

energy is neither created nor destroyed in a closed system

53
Q

chemical energy

A

type of potential energy

the potential energy within chemical bonds

54
Q

when considering something at the atomic level, we see that

A

atoms are always in motion

the electric charges of protons and electrons in atoms constantly pull and push at each other (potential energy)

55
Q

closed system

A

energy cannot leave the system

ex. the universe

56
Q

open system

A

energy exchanged between system and surrounds

ex. a cell

universe is considered the surroundings

57
Q

second law of thermodyanics

A

disorder is increasing

-increased number of molecules moving around –> increased heat

58
Q

anabolic reactions

A

small molecules are assembled into large ones

energy is required

59
Q

catabolic reactions

A

large molecules are broken down into small ones

energy is released

results in more disorder

60
Q

gibbs free energy equation

A

deltaG = deltaH - TdeltaS

61
Q

deltaG

A

change in available/usable energy (gibbs free energy)

62
Q

deltaH

A

change in total energy (enthalpy) in the system

63
Q

T

A

temperature in Kelvin (degreesC + 273)

64
Q

deltaS

A

change in disorder (entropy)

65
Q

what drives the sign of deltaG

A

TdeltaS

66
Q

negative deltaH

A

energy is released from the system

67
Q

positive deltaH

A

energy is added to the system

68
Q

deltaH = 0

A

likely to be in closed system

69
Q

negative deltaS

A

disorder decreases

70
Q

positive deltaS

A

disorder increases

disorder increases in order to create energy for work

71
Q

deltaS = 0

A

no net change in disorder

72
Q

negative deltaG

A

free energy is released

exergonic rxn

favorable rxn

spontaneous rxn

products favored over reactants

energy is available to do work in system

73
Q

positive deltaG

A

free energy required

endergonic rxn

unfavorable rxn

driven rxn

free energy is required to drive reaction forward

reactants favored over products

74
Q

deltaG = 0

A

equilibrium

no net forward or reverse rxn

products are made at same rate that reactants are made

75
Q

what kind of rxn has energy released

A

exergonic rxn

spontaneous

energy of products is less than energy of reactants

76
Q

what kind of rxn requires energy

A

endergonic rxn

not spontaneous

energy of reactants is less than energy of products

77
Q

state function

A

value depends only on the initial and final values, not the pathway to get there

ex. deltaG, deltaH, and deltaS

78
Q

transition state

A

a high, energy, unstable form of the reactant(s) that is ready to form product(s)

top of curve in rxn diagram

79
Q

activation energy (Ea or deltaG++)

A

an energy barrier that must be overcome for the rxn to proceed

80
Q

enzmes

A

catalyze rxns by lowering the activation energy

81
Q

the activation energy is lowered by stabilizing the transition state:

A

substrate orientation

straining substrate bonds

favorable microenvironment

covalent bonding with substrate

82
Q

Q

A

equilibrium constant (when we are not at equilibrium)

83
Q

Q = K

A

we are at equilibrium and the rxn proceeds in neither direction

84
Q

Q < K

A

the rxn proceeds towards the products

85
Q

Q > K

A

rxn proceeds towards reactants

86
Q

biochemical strategies to drive an unfavorable rxn

A
  1. maintain Q < K (create a pathway by using up the products)
  2. couple it to a highly favorable rxn (e.g. ATP hydrolysis) (couple to exergonic rxn)
87
Q

chemistry standard state ______ biology standard state

A

does not equal

Biochemistry (32 decks)

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