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BioChem Exam 1 > L1-2: Properties of Biological Molecules > Flashcards

L1-2: Properties of Biological Molecules Flashcards

1
Q

covalent bonds

A

strong
short
share electrons

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2
Q

noncovalent bonds

A

weak
long
attraction only

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3
Q 
name of bond between monomers:
carbohydrates
lipids
proteins
nucleic acids
A

glycosidic bond
ester
peptide
phosphodiester

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4
Q

strength of a bond is the measure of ?

A

the energy needed to break the bond

strength also depends on distance between atoms

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5
Q

examples of electrostatic interactions and definition

A

an interaction between 2 completely charged ions

ionic bonds NaCl
salt bridges

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6
Q

what is a salt bridge

A

interaction between 2 amino acids in a protein

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7
Q

how do we measure how attractive the 2 ions are to each other? in vacuum

A

in a vacuum we would use coulomb’s law to calculate it

using variables:
force
ion charges
k constant
distance between nuclei
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8
Q

how do we measure how attracted 2 ions are to each other in biological environments?

A

we would use coulomb’s law but add the relative permittivity to it

by using D - dielectric constant – used to account for the other things in the environment that could prevent their interaction

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9
Q

F > 0 means ?

F < 0 means ?

A

F = force between ions

>0 = repulsion
<0 = attraction
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10
Q

define energy of interaction

A

the energy required to separate two ions

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11
Q

dipole

A

means having a partial charge when covalently bonded

can be permanent/polar
or
induced/polarizable

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12
Q

dispersion forces

A

also called van der waals forces

contact distance interactions

ex. stacking of nucleotides

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13
Q

hydrogen bonding

A

sharing a hydrogen bond between two atoms

hydrogen donor and
hydrogen acceptor

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14
Q

distance of hydrogen bonds

A

between donor and acceptor usually around 3 A

range = 2.6 - 3.7

O - H = 2.0A
N - H = 0.9A

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15
Q

H bond breaking and forming

A

take nrg to break

release nrg when formed

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16
Q

explain water’s strange physical properties

A

are explained by it’s ability to form H bonds and create an electric dipole

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17
Q

ice

A

less dense than liquid

H bond distances are greater in solid than in liquid

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18
Q

density

A

a measure of how tightly packed atoms or molecules are

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19
Q

specific heat capacity

A

the amount of heat needed to change the temp of 1g of a given substance by 1 Celsius

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20
Q

heat of vaporization

A

the amount of nrg needed to change 1g of a given substance from liquid to gas

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21
Q

cohesion

A

attraction to self

water molecules attract each other

22
Q

adhesion

A

attraction to other

water and other polar substances attract each other

23
Q

cohesion creates _____.

A

surface tension

24
Q

cohesion and adhesion work together to create ?

A

capillary action

25
Q

water is the universal _____.

A

solvent

26
Q

charged/polar molecules are ______ and will ______ in solution.

A

hydrophilic

dissolve

27
Q

nonpolar molecules are _____ and will _____ in solution.

A

hydrophobic

separate

28
Q

amphipathic molecules

A

have both hydrophilic and hydrophobic parts

29
Q

most rxns are ?

A

reversible

30
Q

chemical rxns = ?

A

making and/or breaking chemical bonds

31
Q

equilibrium does not mean equal ?

A

concentrations

32
Q

Ka is the ____ constant

A

dissociation constant of acids

33
Q

relate the Ka and pKa of strong vs weak acids

A

strong acid = larger Ka

weak acid = larger pKa

same for strong base/weak base pKb’s

34
Q

formula for pKa/pKb

A

pKa = - log Ka

same for pKb

35
Q

Kw and pKw

A

equilibrium constant of water

pKw = -logKw = 14
also
pKw = pH + pOH

36
Q

pH formula

A

pH = -log[H+]

37
Q

buffers

A

are weak acids or weak bases that can stabilize pH

38
Q

Henderson-Hasselbalch Variation conclusions:
pH < pKa
pH > pKa
pH = pKa

A

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

most are deprotonated
[HA] < [A-]

molecules are just as likely to be protonated as deprotonated

39
Q

Gel electrophoresis – direction of migration is based on ?

A

net charge of molecule

40
Q

define isoelectric point

A

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

41
Q

what are the results of the following?
pH < pI
pH > pI
pH = pI

A

the molecule has + charge

the molecule has - charge

then the molecule has no net charge – by definition

42
Q

pI in context of isoelectric focusing

A

the pH changes over the length of the gel

proteins stop moving when they are uncharged
–when pH = pI

43
Q

first law of thermodynamics

A

energy is neither created nor destroyed in a closed system

44
Q

define kinetic energy

A

motion

performing work

45
Q

define potential energy

A

position, potential to do work

chemical energy – the potential nrg w/in chemical bonds

46
Q

closed vs open system

A

ex. universe vs a cell

nrg cannot leave the universe but nrg can leave the cell to matrix and back into the cell

47
Q

which type of metabolic rxns create more disorder? anabolic or catabolic

A

catabolic because nrg is released

anabolic – takes nrg to happen

48
Q

gibbs free nrg equation

A

deltaG = dH - TdS

d = delta

49
Q

deltaG is an example of a _____ function. meaning ?

A

state function

its value depends only on the initial and final values

and not the only pathway to get there

50
Q

delta H values

A

-
nrg is released

+
nrg is added to system

0
closed system

51
Q

delta S values

A 
-
disorder decreases
\+
disorder increases
0
no net change in disorder
52
Q

delta G values

A 
-
free nrg released
\+
free nrg required
0
equilibrium

BioChem Exam 1 (10 decks)

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