L1-2: Properties of Biological Molecules

Question 1

covalent bonds

Answer 1

strong
short
share electrons

Question 2

noncovalent bonds

Answer 2

weak
long
attraction only

Question 3

name of bond between monomers:
carbohydrates
lipids
proteins
nucleic acids

Answer 3

glycosidic bond
ester
peptide
phosphodiester

Question 4

strength of a bond is the measure of ?

Answer 4

the energy needed to break the bond

strength also depends on distance between atoms

Question 5

examples of electrostatic interactions and definition

Answer 5

an interaction between 2 completely charged ions

ionic bonds NaCl
salt bridges

Question 6

what is a salt bridge

Answer 6

interaction between 2 amino acids in a protein

Question 7

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

Answer 7

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

using variables:
force
ion charges
k constant
distance between nuclei

Question 8

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

Answer 8

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

Question 9

F > 0 means ?

F < 0 means ?

Answer 9

F = force between ions

>0 = repulsion
<0 = attraction

Question 10

define energy of interaction

Answer 10

the energy required to separate two ions

Question 11

dipole

Answer 11

means having a partial charge when covalently bonded

can be permanent/polar
or
induced/polarizable

Question 12

dispersion forces

Answer 12

also called van der waals forces

contact distance interactions

ex. stacking of nucleotides

Question 13

hydrogen bonding

Answer 13

sharing a hydrogen bond between two atoms

hydrogen donor and
hydrogen acceptor

Question 14

distance of hydrogen bonds

Answer 14

between donor and acceptor usually around 3 A

range = 2.6 - 3.7

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

Question 15

H bond breaking and forming

Answer 15

take nrg to break

release nrg when formed

Question 16

explain water’s strange physical properties

Answer 16

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

Question 17

ice

Answer 17

less dense than liquid

H bond distances are greater in solid than in liquid

Question 18

density

Answer 18

a measure of how tightly packed atoms or molecules are

Question 19

specific heat capacity

Answer 19

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

Question 20

heat of vaporization

Answer 20

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

Question 21

cohesion

Answer 21

attraction to self

water molecules attract each other

Question 22

adhesion

Answer 22

attraction to other

water and other polar substances attract each other

Question 23

cohesion creates _____.

Answer 23

surface tension

Question 24

cohesion and adhesion work together to create ?

Answer 24

capillary action

Question 25

water is the universal _____.

Answer 25

solvent

Question 26

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

Answer 26

hydrophilic dissolve

Question 27

nonpolar molecules are _____ and will _____ in solution.

Answer 27

hydrophobic separate

Question 28

amphipathic molecules

Answer 28

have both hydrophilic and hydrophobic parts

Question 29

most rxns are ?

Answer 29

reversible

Question 30

chemical rxns = ?

Answer 30

making and/or breaking chemical bonds

Question 31

equilibrium does not mean equal ?

Answer 31

concentrations

Question 32

Ka is the ____ constant

Answer 32

dissociation constant of acids

Question 33

relate the Ka and pKa of strong vs weak acids

Answer 33

strong acid = larger Ka weak acid = larger pKa same for strong base/weak base pKb's

Question 34

formula for pKa/pKb

Answer 34

pKa = - log Ka same for pKb

Question 35

Kw and pKw

Answer 35

equilibrium constant of water pKw = -logKw = 14 also pKw = pH + pOH

Question 36

pH formula

Answer 36

pH = -log[H+]

Question 37

buffers

Answer 37

are weak acids or weak bases that can stabilize pH

Question 38

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

Answer 38

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

Question 39

Gel electrophoresis -- direction of migration is based on ?

Answer 39

net charge of molecule

Question 40

define isoelectric point

Answer 40

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

Question 41

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

Answer 41

the molecule has + charge the molecule has - charge then the molecule has no net charge -- by definition

Question 42

pI in context of isoelectric focusing

Answer 42

the pH changes over the length of the gel proteins stop moving when they are uncharged --when pH = pI

Question 43

first law of thermodynamics

Answer 43

energy is neither created nor destroyed in a closed system

Question 44

define kinetic energy

Answer 44

motion | performing work

Question 45

define potential energy

Answer 45

position, potential to do work | chemical energy -- the potential nrg w/in chemical bonds

Question 46

closed vs open system

Answer 46

ex. universe vs a cell nrg cannot leave the universe but nrg can leave the cell to matrix and back into the cell

Question 47

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

Answer 47

catabolic because nrg is released anabolic -- takes nrg to happen

Question 48

gibbs free nrg equation

Answer 48

deltaG = dH - TdS d = delta

Question 49

deltaG is an example of a _____ function. meaning ?

Answer 49

state function its value depends only on the initial and final values and not the only pathway to get there

Question 50

delta H values

Answer 50

- nrg is released + nrg is added to system 0 closed system

Question 51

delta S values

Answer 51

``` - disorder decreases + disorder increases 0 no net change in disorder ```

Question 52

delta G values

Answer 52

``` - free nrg released + free nrg required 0 equilibrium ```