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Biochemistry > Properties of Biological Molecules > Flashcards

Properties of Biological Molecules Flashcards

(87 cards)

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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
cohesion creates
surface tension
26
cohesion and adhesion work together to create
capillary action
27
charged/polar molecules are hydrophilic and _____ in water
dissolve
28
nonpolar molecules are hydrophobic and _____ in water
no not dissolve but rather separate
29
amphipathic molecules (such as lipids and fatty acids) have both
hydrophilic and hydrophobic parts
30
noncovalent interactions ____ energy to break and ____ energy when formed
use release
31
covalent bonds ____ energy when broken and ____ energy to form
release use
32
dynamic equilibrium
same amount being made as destroyed rate of reactant formed = rate of products formed no NET formation or destruction
33
Ka =
[H+] [A-] / [HA]
34
pKa =
- log Ka
35
Strong acid: Ka pKa Energy of Interaction
Ka = Larger pKa= Smaller Energy of Interaction = Smaller
36
Weak acid: Ka pKa Energy of Interaction
Ka = Smaller pKa = Larger Energy of Interaction = Larger
37
Water equilibrium =
H2O OH- + H+
38
Kw = 10^-14 M
[H+] [OH-] / [H2O]
39
pH =
- log [H+]
40
pKw =
pH + pOH
41
pKw = 14
- log Kw
42
buffer
weak acid or base that can stabilize pH | absorbs change in [H+]
43
Henderson-Hasselbalch
pH = pKa + log ([A-]/[HA]) or [A-]/[HA] = 10^pH-pKa
44
if pH < pKa
then most of the molecules are protonated since [HA] > .[A-]
45
if pH > pKa
then most of the molecules are deprotonated since [HA] < [A-]
46
if pH = pKa
then the molecules are just as likely to be protonated as deprotonated
47
gel electrophoresis
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
isoelectric point (pI)
the pH where all molecules of a given species in solution have an overall charge of 0 pI = pKa (+1) + pKa (-1) / 2
49
if pH < pI, if pH > pI, if pH = pI,
then the molecule has a positive charge then the molecule has a negative charge then (by definition) the molecule has no net charge
50
pI in context: isoelectric focusing
the pH changes over the length of the gel proteins stop moving when they are uncharged (pH = pI)
51
pI in context: protein solubility if pH > pI or pH < pI then if pH = pI then
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
first law of thermodynamics
energy is neither created nor destroyed in a closed system
53
chemical energy
type of potential energy the potential energy within chemical bonds
54
when considering something at the atomic level, we see that
atoms are always in motion the electric charges of protons and electrons in atoms constantly pull and push at each other (potential energy)
55
closed system
energy cannot leave the system ex. the universe
56
open system
energy exchanged between system and surrounds ex. a cell universe is considered the surroundings
57
second law of thermodyanics
disorder is increasing -increased number of molecules moving around --> increased heat
58
anabolic reactions
small molecules are assembled into large ones energy is required
59
catabolic reactions
large molecules are broken down into small ones energy is released results in more disorder
60
gibbs free energy equation
deltaG = deltaH - TdeltaS
61
deltaG
change in available/usable energy (gibbs free energy)
62
deltaH
change in total energy (enthalpy) in the system
63
T
temperature in Kelvin (degreesC + 273)
64
deltaS
change in disorder (entropy)
65
what drives the sign of deltaG
TdeltaS
66
negative deltaH
energy is released from the system
67
positive deltaH
energy is added to the system
68
deltaH = 0
likely to be in closed system
69
negative deltaS
disorder decreases
70
positive deltaS
disorder increases | disorder increases in order to create energy for work
71
deltaS = 0
no net change in disorder
72
negative deltaG
free energy is released exergonic rxn favorable rxn spontaneous rxn products favored over reactants energy is available to do work in system
73
positive deltaG
free energy required endergonic rxn unfavorable rxn driven rxn free energy is required to drive reaction forward reactants favored over products
74
deltaG = 0
equilibrium no net forward or reverse rxn products are made at same rate that reactants are made
75
what kind of rxn has energy released
exergonic rxn spontaneous energy of products is less than energy of reactants
76
what kind of rxn requires energy
endergonic rxn not spontaneous energy of reactants is less than energy of products
77
state function
value depends only on the initial and final values, not the pathway to get there ex. deltaG, deltaH, and deltaS
78
transition state
a high, energy, unstable form of the reactant(s) that is ready to form product(s) top of curve in rxn diagram
79
activation energy (Ea or deltaG++)
an energy barrier that must be overcome for the rxn to proceed
80
enzmes
catalyze rxns by lowering the activation energy
81
the activation energy is lowered by stabilizing the transition state:
substrate orientation straining substrate bonds favorable microenvironment covalent bonding with substrate
82
Q
equilibrium constant (when we are not at equilibrium)
83
Q = K
we are at equilibrium and the rxn proceeds in neither direction
84
Q < K
the rxn proceeds towards the products
85
Q > K
rxn proceeds towards reactants
86
biochemical strategies to drive an unfavorable rxn
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
chemistry standard state ______ biology standard state
does not equal

Biochemistry (32 decks)

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