Goldfarb D. Biophysics DeMYSTiFied
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342 Biophysics DemystifieD
chapter 9
1. A
2. C
3. C
4. C
5. C
6. A
7. A
8. D
9. B
10. D
chapter 10
1. C
2. D
3. A
4. D
5. A
6. B
7. C
8. D
9. F
10. C
chapter 11
1. B
2. A
3. D
4. A
5. B
6. D
7. B
8. D
9. A
10. C
chapter 12
1. A
2. D
3. B
4. B
5. A
6. C
7. D
8. C
9. D
10. A
Final Exam
1. C
2. A
3. A
4. E
5. B
6. C
7. C
8. D
9. D
10. E
11. C
12. E
13. D
14. D
15. D
16. C
17. B
18. A
19. E
20. A
21. A
22. A
23. D
24. B
25. D
26. D
27. A
28. D
29. C
30. E
31. C
32. E
33. B
34. D
35. C
36. D
37. D
38. A
39. D
40. C
41. A
42. C
43. B
44. C
45. E
46. A
47. D
48. C
49. D
50. C
51. C
52. C
53. D
54. D
55. B
56. A
57. B
58. C
59. E
60. E
61. D
62. C
63. B
64. D
65. C
66. D
67. E
68. A
69. E
70. A
71. C
72. B
73. B
74. D
75. D
76. A
77. C
78. D
79. A
80. B
81. D
82. D
83. E
84. D
85. C
86. C
87. D
88.
D
89. A
90. D
91. E
92. D
93. C
94. A
95. C
96. D
97. D
98. A
99. D
100. E
343
Quar
k
w
B
E
De Broglie’s photon
sin
sin
S
D
ec
ec
2
B
B
Electr yclosity
E
lec
ty closit
y
Relativist
Ong
in
ca
a
a
e
a
e
ev
m
m
k
e
appendix
Units, Conversions,
and Constants
Common Prefixes
Prefix Symbol Factor
Femto f 10
15
Pico p 10
12
Nano n 10
9
Micro µ 10
6
Milli m 10
3
Centi c 10
2
Kilo k 10
3
Mega M 10
6
Giga G 10
9
Tera T 10
12
344 BIOPHYSICS DeMYSTiFieD
Standard Units
Quantity Unit Symbol Equivalent to
Length Meter m
Velocity, speed Meter per second m/s
Acceleration Meter per second
squared
m/s
2
Meter per second per
second
Mass Kilogram kg
Time Second s
Temperature Kelvin K
Amount Mole mol 6.022 10
23
Current Ampere A
Force Newton N kg
•
m/s
2
Pressure Pascal Pa N/m
2
m
1
•
kg
•
s
2
Energy, work Joule J N
•
m kg
•
m
2
/s
2
Power Watt W J/s
Current Ampere A C/s
Electric charge Coulomb C A
•
s
Electromotive force
(electrical potential)
Volt V J/C
Electrical resistance Ohm Ω V/A
Volume Liter L 10
3
m
3
Concentration Molarity M mol/L
Some Conversions for Nonstandard Units
Quantity Standard Unit Nonstandard Unit Conversion
Energy Joule Calorie 1 cal 4.184 J
Force Newton Pound 1 lb 4.4482 N
Length Meter Inch 1 in 0.0254 m
Length Meter Angstrom 1 Å 10
10
m
Pressure Pascal Torr (mm Hg) 1 torr 133.322 Pa
Temperature Kelvin Centigrade °C K 273.15
Volume Meter
3
Liter 1 L 10
3
m
3
Appendix UNITS, CONVERSIONS, AND CONSTANTS 345
Some Useful Constants
Constant Symbol Value
Boltzmannʼs constant
k
B
1.3806 10
23
J/K
Planckʼs constant
h
6.626068 10
34
J
•
s
Coulombʼs constant
k
e
8.98755 10
9
N
•
m
2
/ C
2
Speed of light
c
2.9979 10
8
m/s
Avagadroʼs number mol 6.022 10
23
Acceleration due to gravity
g
9.807 m/s
2
Some Useful Formulas
Formula Meaning Equation
F m a
Force mass times acceleration, Newtonʼs second
law of motion
1-1
E h
Energy of electromagnetic radiation is equal to
Planckʼs constant times the frequency of the
radiation
3-2
H U PV
Enthalpy internal energy pressure times
volume
4-3
S Q/T
Entropy change heat flow divided by
temperature
4-11
G H – T S
Gibbs energy change 4-14
W
N
nn nn
12 3L
MAX
!
!!!!
⋅⋅
Number of ways to arrange N objects into L
MAX
groups with n
i
items in group i
5-1a
W
N
n
i
i
L
!
(!)
1
MAX
∏
Number of ways to arrange N objects into L
MAX
groups with n
i
items in group i
5-1b
Z
e
E
i
L
i
1
MAX
∑
Partition function 5-4
F
n
N
e
Z
i
i
Ei
kT
Fraction of molecules in state i
5-6
(Continued )
346 BIOPHYSICS DeMYSTiFieD
Formula Meaning Equation
EEFE
e
Z
ii
i1
L
i
Ei
kT
⋅⋅
MAX
∑∑
Average energy 5-8
Fk
qq
r
e
12
2
Force between two electrostatic charges 6-1
U
qq
r
12
ε
Potential energy between two electrostatic charges 6-2b
p
d
E
Polarizability 6-10
H
RT
S
R
Z e1
Partition function for a two-state transition 10-2
rNL
2
⋅
RMS (root-mean-square) end-to-end distance in a
freely jointed chain
10-4
Wr Lk – Tw
Writhe = linking number twist 10-5
a (v
2
- v
1
)/t
Acceleration 12-2
v
2
2
v
1
2
2 a d
Final velocity in terms of initial velocity, accelera-
tion, and distance traveled
12-9
P g h (1/2)
v
2
constant
Bernoulliʼs equation for a frictionless fluid 12-12
d (1/2) a t
2
Distance traveled under a constant acceleration if
the initial velocity is zero
12-24
Quar
k
w
B
E
De Broglie’s photon
sin
sin
S
D
ec
ec
2
B
B
Electr yclosity
E
lec
ty closit
y
Relativist
Ong
in
ca
a
a
e
a
e
ev
m
m
k
e
347
Absorbance A measure of how much light does not pass through a sample. Com-
monly reported in terms of molar extinction coefficient, or how much light is ab-
sorbed per concentration per length of sample that the light passes through.
Absorption spectroscopy A form of EM spectroscopy in which we shine light of
known wavelengths through a sample and measure the intensity of the light
that comes out the other side.
Acid A molecule or functional group that increases the concentration of
hydrogen ions (protons) in solution.
Active site The part of a molecule or complex that is involved in carrying out
its function. A molecule or complex can sometimes have more than one
active site, depending on the function of the molecule.
Active transport Transport in which the cell expends energy to move a mole-
cule or ion across a membrane. See also primary active transport and secondary
active transport.
Adiabatic system A closed system that is thermally isolated from its surround-
ings; there is no exchange of heat or matter, but it is possible for the system
to exchange nonheat energy with its surroundings. For example, the system
can do work on its surroundings (or have work done on it).
Aldehyde A carbonyl carbon that is also directly covalently bonded to at least
one hydrogen atom.
Allosteric protein A protein that exhibits the property of allostery.
Allosteric regulation Regulation of a biochemical process via the allosteric site
on a molecule.
Glossary
348 Biophysics DemystifieD
Allosteric site The part of a molecule or complex, other than the active site,
that influences the active site of the molecule.
Allostery
A property of a molecule, usually of a protein, whereby the biological
activity of one part of the molecule (the active site) is affected by some action
or intermolecular binding at another part of the molecule (the allosteric site).
The ability of the molecule’s active site to carry out its function is dependent
on binding or activity at some other site (the allosteric site) on the molecule.
Alpha carbon
In an amino acid, the carbon atom that has the amine group and
carboxyl group attached to it.
Alpha helix
A common secondary structure in proteins in which the polypep-
tide chain forms a right-handed helical shape. The backbone of the chain is on
the inside of the helix with the various amino acid side chains on the outside.
Amine group
A nitrogen atom bonded in such a way as to have a pair of non-
bonded valence electrons. An amine nitrogen atom has three single covalent
bonds to three other atoms.
Amino acid
Any of a class of biochemical compounds that contain both an
amine group and a carboxylic acid group (carboxyl group) attached to a
single carbon atom. This carbon atom (called the alpha carbon) also has a side
chain (some other group of atoms) attached to it. There are 20 or so different
amino acids found in living things, and each is named according to its side
chain.
Amphipathic
Having both hydrophobic and hydrophilic properties in the same
molecule; sometimes also called amphiphilic.
Amphiphilic
Same as amphipathic
Analytical techniques A technique used to measure physical aspects of a bio-
logical system.
Analytical ultracentrifuge
An ultracentrifuge that contains special optical de-
vices and sensors that can track the movement of molecules as they are being
centrifuged.
Anion
A negative ion; an atom or molecule that has negative charge due to
having one or more extra electrons.
Antibody Also called immunoglobulin, any of a class of proteins that can recog-
nize and bind to foreign objects (i.e. antigens, such as viruses and bacteria).
Antiport
Cotransport where at least some of the different types of transported
molecules or ions are being transported in opposite directions across a bio-
logical membrane.
Glossary 349
Aromatic A molecular ring structure having (1) all of the atoms making up
the ring lying within a plane and (2) all of the ring atoms contributing elec-
trons from their pi orbital to make up the covalent bonds that hold the ring
together. In an aromatic structure, the pi electrons (electrons from the pi
orbital) are delocalized; that is, they are shared among all of the atoms in
the ring.
Atomic force microscopy (AFM)
A technique to provide highly magnified im-
ages similar to those of SEM (i.e., images of the surface of a specimen) but
with resolution similar to that of TEM (about 10 times better than SEM).
ATPase
Any enzyme that couples a process or reaction to hydrolysis of ATP
and utilizes the energy from the hydrolysis of ATP to drive the process or
reaction.
Available energy
Energy that can be transformed into work, where work equals
force times distance. Available energy is also called free energy, and Gibbs en-
ergy.
Base pairing
Hydrogen bonding between nucleotide bases in nucleic acids
such that adenine and thymine (or adenine and uracil, in the case of ribo-
nucleic acids) always pair together, and guanine and cytosine always pair
together.
Base stacking
Stacking interaction among nucleotide bases.
Base A molecule or functional group that decreases the concentration of
hydrogen ions (protons) in solution. Bases often decrease the concentration
of hydrogen ions by increasing the concentration of hydroxyl (OH
2
) ions in
solution. The hydroxyl ions then combine with the hydrogen ions to form
water.
Beta sheet
A common secondary structure in proteins in which two polypep-
tide strands are hydrogen-bonded to one another. Also called beta pleated
sheet.
Binding site
A particular location on a molecule that binds to another molecule
or ligand.
Biochemical physics See Molecular and Subcellular Biophysics.
Biophysical chemistry
See Molecular and Subcellular Biophysics.
Biomechanics The branch of biophysics that deals with the application of
forces to biological objects.
Biopolymer
A biomolecule that is a polymer.
350 Biophysics DemystifieD
Boltzmann distribution A particular distribution derived by Ludwig Boltz-
mann and containing the maximum the number of permutations.
Budding
Extrusion, or pushing out, of a portion of a membrane until it pinches
off to form a new liposome.
Calorimeter An instrument designed to measure heat energy and other thermody-
namic properties.
Calorimetry
Any of a series of techniques using instruments designed to di-
rectly measure thermodynamic properties such as heat.
Carbohydrate A molecule made of carbon, hydrogen, and oxygen, in the ratio
C
n
H
2n
O
n
. See also dexyocarbohydrate.
Carbonyl group A carbon atom with a double covalent bond to an oxygen
atom.
Carboxyl group
A carbonyl carbon that is also covalently connected to a
hydroxyl group.
Carboxylic acid A substance whose molecules contain a carboxyl functional
group.
Catalyst
A substance that modifies the rate of a chemical reaction, without
actually being consumed by the reaction.
Cation
A positive ion; an atom or molecule that is missing one or more electrons.
Cation-pi interaction An attractive interaction between a cation (positive ion)
and the partial negative change of the pi electrons of an aromatic molecule.
Cell A pouch or sack of biomolecules where the entire pouch is (or was) alive.
Cell cycle
The phases of cell growth and cell division. The two main phases of
the cell cycle are interphase and cell division. A third phase, called quiescent,
means that the cell has essentially left the cycle and has stopped growing and
dividing, but continues to utilize energy to do work.
Cell division
The process whereby cells come from preexisting cells, by repli-
cating their DNA and then dividing in two.
Cell theory
The two tenets of cell theory are: (1) All living things are made of
one or more cells, and (2) all cells come from preexisting cells.
Cell wall A relatively stiff protective layer on the outside surface of the cell
membrane of some cells. Commonly found on plant cells and many prokary-
otic cells, but rarely on animal cells.
Centrifuge
A machine used to spin a sample of material around in a circular
motion in order to apply force to the sample.
Glossary 351
Chaperone A protein that acts as a folding moderator.
Chlorophyll A class of molecules that absorb light for photosynthesis.
Chloroplasts
Organelles that carry out photosynthesis; found in plant cells and
a few other eukaryotes.
CHNOPS An acronym for the elements most commonly found in living cells:
carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.
Chromatin
All of the DNA molecules in a cell together, in their tertiary or
quaternary structures, but not in their condensed state appearing as individual
chromosomes (as they are sometimes), but rather in a state where they are
more spread out, like a plate of spaghetti, and it is difficult to detect one
DNA molecule from another.
Chromosome
A DNA molecule as it exists in the cell in its organized and
compact tertiary or quaternary structure (which may also include associated
proteins).
Circular DNA
A DNA molecule in which then ends of the DNA strand are
covalently bonded together, forming a circle.
Closed duplex DNA (cdDNA) A circular, double-stranded, double-helical
DNA in which the two ends of the double helix are covalently bonded
together forming a double-helical circle,
Closed system A system that can exchange only energy (not matter) with its
surroundings.
Command voltage The value of the voltage that is held constant by a voltage
clamp.
Complementary A property of two nucleic acid sequences such that the se-
quence of nucleotides in one nucleic acid sequence can perfectly base-pair
with the nucleotides in another nucleic acid sequence.
Complex A quaternary structure. The term complex usually implies that the at
least two different molecules make up the complex; however, the term may
sometimes be used for a quaternary structure in which all of the component
molecules are identical.
Conformational transition
A change in the shape (conformation) of a
molecule.
Constructive interference The interference of two or more waves, specifically
in a way that results in a larger or more intense wave (the peaks become
higher and the troughs become lower).