What is Biochemistry?
• A science that integrates life with chemistry
• A science that attempts to determine how
lifeless molecules combine to give the
attributes of life
• A science that operates by the principle that
life’s molecules are selected for the functions
they perform.
• A science that delves into the world of the
unseen for answers to life’s mysteries.
What are the Challenges of Biochemistry?
To understand the chemical complexity of a cell
To determine how cells are able to extract and transform
energy from their surroundings
To learn how cells are capable of self-replication
To determine how cells sense and respond to changes
in their environment
To understand the structural logic behind the selection
of specific molecules for specific tasks
How does Biochemistry Differ from
Organic Chemistry?
See Tutorial
“Getting Started”
• Organic chemistry is the chemistry of
carbon compounds. Biochemistry is the
study of carbon compounds that crawl
-Mike Adam
A Biochemist is a person who can’t tell the difference between a
plant or an animal
-E Harris
What are the Objectives of
Biochemistry 410
• To introduce students to the properties of
molecules found in living cells.
• To compare and contrast the properties of
molecules in the different categories.
• To demonstrate the structure-function
principle of biochemistry.
• To threaten, cajole, or otherwise persuade
students that a knowledge of biochemistry
is essential to understanding the properties
of life.
Chemical Perspective
The Elements
and
Molecules of Life
Peptide bond
Glycosidic bond
Ionic bond
H-bond
Hydrophobic bond
Phosphodiester bond
Disulfide bond
Take Home: Weak and strong forces hold biomolecules
together.
Important Functional Groups in Biomolecules
CH3-
Methyl
CH3CH2-
Ethyl
CH3CO
Acetyl
CH3(CH2)nC-
Acyl
O
Phenyl
R-SH
Sulfhydryl
R-S-S-R
Disulfide
Important Functional Groups (Continued)
R-OH
Hydroxyl (alcohol)
R-NH3
Amino (amine)
NH2
Guanidinium
C
NH-
H2N
O
O-P-O
O
Phosphate
Carboxyl
CH2OH
H
CH3-C-COO
Methyl
Hydroxyl
O OH
+ NH3
HO
Amino
HO
OH
Phenyl
Hydroxyl
H
CH2-C-COO
H
HO-CH2-C-COO
+ NH3
+ NH3
Acyl
O
CH3(CH2)nCH2-C-O-CH2
Sulfhydryl
H
HS- CH2-C-COO
+ NH3
Trimethylamine
CH3(CH2)nCH2-C-O-CH2
O
+
O
CH2 O-P-O CH2-CH2-N(CH3)3
Phospho
O
Biomolecules
CH2COO
HO-C-COO
CH2COO
O=C=O
Citrate
COO
C=O Pyruvate
CH3
COO
HO-C H
CH3
L-lactate
CH2OH
DHAP
C=O
CH2OPO3
COO
C=O
CH2 a-Keto
CH2 glutarate
COO
COO
CH2
CH2
COO
Succinate
Biomolecules (cont.)
H
OOC
C
C
COO
Fumarate
H
HS-CoA
Acetyl-CoA
Fatty Acyl-CoA
BIOENERGY
Electrical
Mechanical
Sound
Light
Osmotic
Heat?
Light to electrical
Chemical to mechanical
Sound to electrical
CHEMICAL
(Sight)
(Muscle contraction)
(Hearing)
Basic Thermodynamics
Q: How do we know when a given reaction or process will
occur spontaneously or in a favored direction?
A: Berthelot (1860) All spontaneous reactions occur with
the liberation of heat. Therefore, spontaneous reactions
are exothermic.
A: Gibbs (1870). Heat is not the only index of spontaneity.
Many spontaneous processes occur without liberating heat.
The order or entropy must also be considered.
Q: Is it possible for a reaction to actually absorb heat or
remain isothermal and still be favored in one direction?
A: Yes
Q: Can you give an example?
A: When ice melts or salt dissolves in water or when a gas
confined to one chamber diffuses to occupy two chambers,
these are spontaneous reactions that absorb heat.
Q: So, knowing the favored direction must account for
both energy release and order.
A: Yes, energy as heat is called enthalpy. Enthalpy change
or H measures energy released at constant pressure. In a
favored reaction H is less than 0, i.e., H is negative.
Entropy is a probability function. The probability that the
system will exist in any form other than perfect order. In a
favored reaction entropy change or S is positive.
The combination gives rise to a state function called the
free energy. A reaction will always be favored in the direction
that free energy change is negative or less than 0.
Q: Can you give me a equation that helps me see this
A:
Maximal (– G)
Entropy
G = H - TS
occurs when H
change
Enthalpy
Free energy
is negative and
change
change
S is positive
Enthalpy: H
Energy Change at constant pressure
Energy locked in chemical bonds
Bomb Calorimeter
Glucose + 6O2
Initial State
Final State
6CO2 + 6H2O
H = heat evolved
Take Home: Because energy differential is independent
of path taken, energy from combustion in a bomb
calorimeter is the same as in the body
Oxidation of Palmitic Acid (C16H32O2)
H2 O
H2 O
H2 O
O2
CO2
H2O
Initial
State
Reaction
Final
State
H =
q
p = heat evolved at constant
H
pressure
At constant pressure and volume, no work has been
done against or by the surroundings.
1 atm
H2 O
1 atm
H2 O
q
Initial
State
1 atm
H2 O
O2
At constant P, if
the surroundings
can do work on
the system… more
heat can be evolved
w
CO2
H2O
q
1 atm
q=E + w
H2 O
CO2
w = PV
w = nRT
Final State
CH3(CH2)14COOH + 23O2
16CO2 + 16H2O
ENTROPY S
Relates to molecular order
Energy unavailable during a chemical transition
“A spontaneous reaction is one that favors movement
from order to disorder…occurs with a positive change
in entropy”
“To go from disorder back to order requires input
of energy”
Take Home: Living system take chemicals from their
disordered environment and assemble them into ordered
arrays of structural molecules. Hence, living systems live
on NEGATIVE entropy.