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Chemistry 4304
Biological Chemistry I
Spring 2013
Dr. Leng
CP--317
CP
What is Biochemistry?
bi·o·chem·is·try
y
P Pronunciation Key
y ((b-km-str)n.
)
1 The study of the chemical substances and vital processes
occurring in living organisms; biological chemistry;
physiological chemistry
chemistry.
2 The chemical composition of a particular living system or
biological substance: viral biochemistry.
Source:
So
ce The
Th American
A
i
Heritage®
H it
® Dictionary
Di ti
off the
th English
E li h Language,
L
Fourth
F th EditionCopyright
Editi C
i ht © 2000
by Houghton Mifflin Company.Published by Houghton Mifflin Company. All rights reserved.
biochemistryn : the organic chemistry of compounds and
processes occuring in organisms; the effort to understand
biology within the context of chemistry
Source: WordNet ® 2.0, © 2003 Princeton University
What is Biochemistry?
•What are we? Are we different from other
organisms such as Bacteria?
•Diseases and tools of diagnosis and treatment.
•Foods.
•Human cloning?
g More
Are they different?
The tree of life: three domains.
What does Life Require?
-Deoxyribonucleic
Deoxyribonucleic Acid (DNA)
-Ribonucleic Acid (RNA)
-Proteins
Proteins (amino acids)
-Carbohydrates (Sugars)
-Lipids
Lipids (Fat)
St t
Structure
andd Function
F ti
We will start off by using DNA to illustrate a few of
the underlying concepts in biochemistry but we could of
choosen other macromolecules.
DNA
genetic material
(a four letter alphabet with no spaces)
AT G C
ATGGCTTACGTTTAAGGCTAAGGCTGG
GCCCTTAAAATTGGCGCCTTAGTGGCG
CCGCGCGTATATAGAGAAGAGGGGCG
CGCAAAATTTT
DNA is a linear polymer, in which each unit of the polymeric
structure is composed of a sugar, a phosphate and a base;
The sequence of base along a DNA strand constitutes the
Genetic information.
DNA is constructed from four
building blocks (bases)
James Watson and Francis Crick’s DNA double helix
structure:
1. Two single strands of DNA combine to form a double helix;
2. Specific base pairing held by hydrogen bonding:
adenine pairs with thymine (A-T); guanine pairs with
cytosine (G-C);
3. Sugar phosphate backbone lies on the outside and the bases
on the inside;
4. The sequence of base along one strand completely
determines the sequence along the other strand: genetic
material (perfect way to store information).
DNA replication
p
Formation of Double Helix
I order
In
d to
t understand
d t d why
h a double
d bl helix
h li forms
f
spontaneously
t
l we
need to take a look at Chemical Bonding
Chemical Bonds in Biochemistry
• Bi
Biochemistry
h i t is
i the
th chemistry
h i t that
th t takes
t k
place within living systems: molecular
i t
interactions;
ti
• Covalent bonds (strong): share a pair of
electrons between adjacent atoms;
• 200-1000 kJ/mol
OH
+
O
O
O
CO2
Chemical Bonds in Biochemistry
Non-covalent bonds,, weaker than covalent bonds
with four fundamental types: i) electrostatic
interactions, ii) hydrogen bonding, iii) van der
Waals interactions, and iv) hydrophobic
interactions.
E =kq1q2/Dr
NH
H N
E-energy
q-charge on atom
D-dielectric
D
dielectric constant
r
r-distance apart
electrostatic
k-proportionality constant
Stronger inside proteins than outside proteins
and non-directional
3
3
Chemical Bonds in Biochemistry
Hydrogen bond are shared between two electronegative atoms such
as oxygen and nitrogen and are directional.
4-20 kJ/mol in energy and similar to electrostatic interactions
Chemical Bonds in Biochemistry
y
van der Waals interactions
-Non-bonded atoms like to be together but not too close
2 to 4 kJ/mol per atom pair but many weak interactions can
be added together
Due to transient electrostatic interactions (non-directional)
Chemical Bonds in Biochemistry
y
• The properties of water affect the bonding
abilities of biomolecules; Water is polar (D
=80, dielectric constant) and interacts with
itself and other molecules via H-bonds.
H bonds.
Water competes for H-bonds
Structure of ice
Chemical Bonds in Biochemistry
y
• Entropy
py
The total entropy of the system and its surrounding always increases
for a spontaneous process
G , Gibbs free energy, must be negative for a process to be favorable
G = H - TS
Chemical Bonds in Biochemistry
y
• How do proteins fold spontaneously since
they create order out of disorder
Water is ordered around non-polar portions of
the pprotein and is released during
g folding.
g
Hydrophobic effect
Chemical Bonds in DNA
Electrostatic Repulsion
between negatively charged
phosphates is unfavorable
Chemical Bonds in DNA
Hydrogen bonding between bases
Hydrogen bonds with water are broken to form
y g bonds so little ggain in energy
gy
these new hydrogen
Important for specificity of base pairing
Chemical Bonds in DNA
Bases pairs stack on top of
each other and interact via
van der
d Waals
W l interactions.
i
i
p
pparts of
Also the non-polar
the base are removed from
water, which is favorable
due to the hydrophobic
effect.
Many weak interactions are important
and surfaces must match
Thermodynamics
First Law: The total energy of a system and its surroundings is
constant. Energy is neither created nor destroyed.
Second Law: The total entropy of a system plus that of its
surroundings
di
always
l
increases.
i
Chaos
h
rules.
l
G , Gibbs free energy,
energy must be negative for a process to be
favorable
G = H - TS
Please review Thermodynamics
Acid-Base Chemistry
The double helix is pH sensitive
Please review buffers and pH