8/22/2011
1
Biochemistry is…“… the study of the
chemical processes/reactions that occur within living organisms.”
“…a summation of the molecular interactions occurring in all forms of life…”
Biochemistry of Proteins class, 2004“… the study of the chemistry done in the human body.”
Biochemistry
“Biochemistry asks how the remarkable properties of living organisms arise from the thousands of different lifeless biomolecules”
“The study of biochemistry shows how the collection of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by the physical and chemical laws that govern the nonliving universe”
Nelson and Cox, 2004
8/22/2011
2
Biochemistry“The essence of biological processes – the basis of
the uniformity of living system – is in its most fundamental sense molecular interactions; in other words, the chemistry that takes place between molecules.”
“Biochemistry is the chemistry that takes place within living systems”
Berg, Tymoczko, and Stryer, 2003
Name: Tube worms
Location: First discovered on the Galapagos Rift off the coast of Ecuador
Description: In 1977, scientists first discovered entire communities of
organisms flourishing miles below the surface of the ocean, around
openings in the ocean floor out of which hot, mineral-rich water erupts.
The openingshost a variety of strange and amazing organisms that have
adapted to immense pressure, total darkness, and proximity to super-
heated water that reaches 662 degrees F.
Biochemistry is the chemistry of life.
Name: Methane Ice Worms
Location: Gulf of Mexico, 80 miles off
the coast of Louisiana
Description: In 1997, vast colonies of
strange, rosy-pink worms 1-2 inches in
length were found burrowing in mounds
of methane-rich ice erupting from the sea
floor in the Gulf of Mexico.
8/22/2011
3
1. A high degree of chemical complexity and microscopic organization.
2. Systems for extracting, transforming and using energy from the environment. Life is opposing entropy.
3. Mechanisms for sensing and responding to alterations in their surroundings.
4. Diverse living organisms share common chemical features.
Three domains of Life
8/22/2011
4
Three domains of Life
Three domains of Life
8/22/2011
5
Source of energy and source of carbon
Autotrophs - which can utilize, inorganic nutrients or light as a source of energy.
Heterotrophs - which require organic compounds as a source of energy.
Photoautotrophs - which use light as an energy source and CO2 as the carbon source.
Photoheterotrophs- which use light as the energy source and reduced organic compounds as a carbon source.
Source of energy and source of carbon
Chemoautorophs - which use inorganic chemicals as an energy source and CO2 as a principal carbon source.
Chemoheterotrophs - which use organic compounds as an energy source as well as a principal carbon source.
8/22/2011
6
Bacterial Cells
Gram-negative cell has an additional layer and the outside of the cell appears convoluted.
Gram-positive wall is much thicker and its external appearance is smoother.
Gram-positive and gram-negative cells do share one thing in common that is unique to bacteria - peptidoglycan.
streptococci E. coli
Animal cells
8/22/2011
7
8/22/2011
8
Cellular organization and hierarchy.
1A 8 A
1
H
1.01
2A 3 A 4 A 5 A 6 A 7 A
2
He
4.00
3
Li
6.94
4
Be
9.01
5
B
10.81
6
C
12.01
7
N
14.01
8
O
16.00
9
F
19.00
10
Ne
20.18
11
Na
22.99
12
Mg
24.31
3 B 4 B 5 B 6 B 7B 8B 1 B 2 B
13
Al
26.98
14
Si
28.09
15
P
30.97
16
S
32.07
17
Cl
35.45
18
Ar
39.95
19
K
39.10
20
Ca
40.08
21
Sc
44.96
22
Ti
47.88
23
V
50.94
24
Cr
52.00
25
Mn
54.94
26
Fe
55.85
27
Co
58.93
28
Ni
58.71
29
Cu
63.55
30
Zn
65.38
31
Ga
69.72
32
Ge
72.59
33
As
74.92
34
Se
78.96
35
Br
79.90
36
Kr
83.80
37
Rb
85.47
38
Sr
87.62
39
Y
88.91
40
Zr
91.22
41
Nb
92.91
42
Mo
95.94
43
Tc
(98)
44
Ru
101.1
45
Rh
102.9
46
Pd
106.4
47
Ag
107.9
48
Cd
112.4
49
In
114.8
50
Sn
118.7
51
Sb
121.8
52
Te
127.6
53
I
126.9
54
Xe
131.3
55
Cs
132.9
56
Ba
137.3
57
La*
138.9
72
Hf
178.5
73
Ta
180.9
74
W
183.9
75
Re
186.2
76
Os
190.2
77
Ir
192.2
78
Pt
195.1
79
Au
197.0
80
Hg
200.6
81
Tl
204.4
82
Pb
207.2
83
Bi
209.0
84
Po
(209)
85
At
(210)
86
Rn
(222)
87
Fr
(223)
88
Ra
226.0
89
Acª
227.0
104
Rf
(261)
105
Db
(262)
106
Sg
(263)
107
Bh
(262)
108
Hs
(265)
109
Mt
(266)
110
(269)
111
(272)
Only about 30 elements are essential to organisms.
1. Bulk elements H, Na, K, Ca, C, N, O, P, S, and Cl
2. Trace elements Mg, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, Se, and I
3. Most abundant H, O, N and C (99% of the cellular mass)Form the strongest bonds.
Trace elements
Bulk elements
8/22/2011
9
Representatives of the organic compounds cellular materials are constructed from
1. Amino acids
2. Nucleic Acids
glycine phenylalanine
adenine cytosine
3. Fatty acids/Lipids
4. Carbohydrates/Sugars
Phosphatidylcholine
Tetradecanoic acid, myristic acid
Glucose
8/22/2011
10
Chemical Bonds in Biochemistry
1. Covalent bonds
2. Electrostatic interactions
3. van der Waals interactions
4. Hydrogen bonds
5. Hydophobic interactions (will be discussed later)
1. Covalent bonds
Formed by the sharing of a pair of e- between adjacent atoms.bond length = 1.54Ǻ bond energy = 348 kJ mol-1
Energy must be expended to break covalent bonds.
Bond energy of a triple bond > double bond > single bond
bond length = 1.34Ǻ bond energy = 614 kJ mol-1
bond length = 1.20Ǻ bond energy = 839 kJ mol-
Chemical reactions are the breaking and/or forming of covalent bonds.
8/22/2011
11
bond length = 1.47Ǻ bond energy = 293 kJ mol-1
bond length = 1.43Ǻ bond energy = 358 kJ mol-1
bond length = 1.82Ǻ bond energy = 272 kJ mol-1
bond length = 1.84Ǻ bond energy = 264 kJ mol-1
bond length = 1.10Ǻ bond energy = 413 kJ mol-1
bond length = 1.54Ǻ bond energy = 348 kJ mol-1
bond length = 1.34Ǻ bond energy = 614 kJ mol-1
bond length = 1.60Ǻ bond energy = 573 kJ mol-1
bond length = 1.20Ǻ bond energy = 799 kJ mol-1
bond length = 1.29Ǻ bond energy = 615 kJ mol-1
8/22/2011
12
2. Electrostatic Interactions (ion-ion)Depends on the electric charge on atoms.
Energy = kq1q2/Dr Coulomb’s law
where q1 and q2 = charges of atomsr = distance between atomsD = dielectric constant of the mediumk = proportionality constant = 332
Na+1 Cl-1r
q1 q2
Electrostatic interaction between 2 atoms each bearing -1 or +1 charges, at a distance of 3Ǻ in water (D = 80).
Long-range effect because the energy falls off as 1/r.
mol
kcalE 4.1
380
1)1)(332(
3. Hydrogen bonds – fundamentaly electrostatic interactionsRelatively weak interactions that are responsible for many of the properties of water.
H-atom is partially shared between two electonegative atoms (N or O).
H-bond donor – the atom the hydrogen is most tightly associated withH-bond acceptor – less tightly linked to the hydrogen
The electonegative atom to which the H is covalently bonded pulls e-
away from the H-atom giving the H-atom a partial positive charge (δ+). The H-atom can then interact with an atom having a partial negative charge (δ-).
These interactions are much weaker than covalent bondsE = 1-3 kcal mol-1
bond distance = 1.5-2.6 Ǻ
8/22/2011
13
0.9 Å 2.0 Å
180˚
Hydrogen
bond donor
Hydrogen
bond acceptor
4. van der Waals interactionsBasis of the interaction is the distribution of electronic charge around an atom changes with time.
Charge distribution is transiently asymmetric and acts via electrostatic interactions to induce asymmetry on neighboring atoms.
8/22/2011
14
The attraction between two atoms increases as they come closer to each other until they are separated by the van der Waals contact distance at shorter distances repulsion dominates.
Energies are quite small 0.5 – 1.0 kcal mol-1 per atom pair.
But can be substantial when summed over a large of atoms at the surface of two large molecules.