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Course : Biophysical Chemistry
Code : SY20503
Credit hour : 3
Lectures : 2 hours/week
Lab : 3 hours/week
Lecturer : Dr. Wong Nyet Kui/Cik Hartinie Marbawi
Objectives:
To understand the chemistry build-up of biological molecules
Study the thermodynamics biological systems
Study techniques used in macromolecule studies
Course Organization
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Biophysical Chemistry (SY20503)
-Basic biophysic and physio-chemistry of living biological systems
-Basis phenomenon of thermodynamics in biological systems
including concepts of thermodynamics, characteristic of
biological molecules; such as proteins, DNA, carbohydrates,
determination of molecular weight of macromolecules,
techniques applied in biomolecule studies
-Techniques that are used in structural characterisation ofmacromolecules such as mass spectrometry, x-crystallography
and NMR
Synopsis
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Course Content
Week Lecture Topic Remarks
1-2 The chemistry of life & theory and bondings of molecules
Biological macromoleculesInteraction forces, conformation, denaturation3-D structure of proteins, structural motif
HM
3-4 Hydrodynamic methods and biocalorimetry HM
5-6 Thermodynamics of biological system, Entropy, Free Energy,Equilibrium
HM
MID-TERM BREAK
7-8 Principles of chromatography and electrophoresis HM
9-10 Analytical and spectroscopy methods in molecular structure:Mass spectrometry
WNK
11-12 Analytical and spectroscopy methods in molecular structure:
NMR
WNK
13-14 Analytical and spectroscopy methods in molecular structure:x-ray crystallography
WNK
FINAL EXAMINATION
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Learning outcomes
1. Able to outline, illustrate and interpret the the
chemistry build-up of biological molecules
2. Students will develop and demonstrate the
ability to reason the function ofmacromolecules,
thermodynamics of biological systems
3. Students will be able to design and illustrate various
techniques in macromolecules structural studies suchas chromatography, Mass spectrometry, NMR and
X- ray Crystallography
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ASSESMENT
Practical reports 10%
Mid-semester Examination 30%
Assignment & quizzes 20%
Final Examination 40%
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References
Sheehan, D, (2009) Physical Biochemistry: Principles and Application.
Second Edition. Wiley-Blackwell.
Van Holde KE, Johnson, WC., Ho, PS., (2000). Principles of Physical
Biochemistry. Second Edition. Prentice-Hall
Atkins P. and Paula J. (2006) Physical Chemistry for the Life Sciences. WH
Freeman and Company.
Engel T., Drobny G., and Reid P. (2008) Physical Chemistry for the Life
Science. Prentice Hall.
Cooper, A. Biophysical chemistry(2004) Cambridge : Royal Society of
Chemistry
Bergethon, PR and Simons ER, (1990). Biophysical Chemistry. Molecules
to Membrane. Springer-Verlag
,
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-The chemistry of life
-Theory and bonding of molecules- Biological macromolecules
You should be able to:
- Recall the fundamental knowledge of atoms andmolecules
- Describe the basic chemical structure of polynucleotide,
polypeptide and polysaccharide
- Explain the types of molecules bonding
- Describe the basic structure and function of biological
macromolecules
TOPIC 1
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Atoms
Molecules
Bondings of Molecules
Biological Macromolecules
Cells
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-
-
-
What is Biophysical Chemistry??
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Biophysical Chemistry
The physical study of chemically
isolated substances found in
living organisms.
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The importance of biophysical chemistry
Physical Properties of biological macromolecules:
provide a hierarchical description of molecular
structure:
-Measured by observing their interaction with
electromagnetic radiation:Ultraviolet (UV) spectroscopy.
X-ray crystallography.
Nuclear Magnetic Resonance (NMR), etc.
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AtomsAtoms
Atom = smallest particle a substance can beAtom = smallest particle a substance can be
divided into that can retain its propertiesdivided into that can retain its properties
All atoms have the same structureAll atoms have the same structure protonsprotons (positively charged)(positively charged)
neutronsneutrons (no associated charge)(no associated charge)
electronselectrons (negatively charged)(negatively charged)
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AtomsAtoms
An atom can be characterized by:An atom can be characterized by:
Atomic NumberAtomic Number
the number of protons in the nucleusthe number of protons in the nucleus
atoms with the same atomic number exhibit the sameatoms with the same atomic number exhibit the same
chemical properties and are considered to belong to thechemical properties and are considered to belong to the
samesame elementelement
e.g. Carbon = C: atomic number = 6e.g. Carbon = C: atomic number = 6
Atomic Mass (mass number)Atomic Mass (mass number)
the number of protons plus neutrons in the nucleusthe number of protons plus neutrons in the nucleus
electrons have negligible mass (1/1840 dalton)electrons have negligible mass (1/1840 dalton)
e.g. C: atomic mass = 12.011e.g. C: atomic mass = 12.011
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Atomic SymbolAtomic Symbol
Atomic Mass = Number of Protons +Atomic Mass = Number of Protons +
Number of NeutronsNumber of Neutrons
Atomic Number = The Number of ProtonsAtomic Number = The Number of Protons
in the Nucleusin the Nucleus
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AtomsAtoms
Electrons are associated with energyElectrons are associated with energy
Potential energyPotential energy:: energy of positionenergy of position
e.g. Rollercoaster at top of peake.g. Rollercoaster at top of peak
e.g. As electrons move away from core, theye.g. As electrons move away from core, theyincrease potential energyincrease potential energy
The field of energy around an atom isThe field of energy around an atom is
arranged as levels calledarranged as levels called electron shellselectron shells
OrbitalsOrbitals are the location electrons are mostare the location electrons are most
likely to be found within this volume of spacelikely to be found within this volume of space
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Electron Arrangement ofAtoms
1 electron 6 electrons 7 electrons 8 electrons
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6 elements make up most of the body
weight of organisms
-Carbon
-Hydrogen
-Oxygen
-Nitrogen
-Phosphorus
-Sulphur
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ElementsBasic building block of matter 92 naturally occurring elements
Only 6 elements make up most of thebody weight of organisms
C Carbon
H Hydrogen
N Nitrogen O Oxygen
P Phosphorus
S Sulfur
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Elements
About 25 elements are essential for life
Four elements make up 96% of living matter:
carbon (C) hydrogen (H)
oxygen (O) nitrogen (N)
Four elements make up most of remaining 4%:
phosphorus (P) calcium (Ca)
sulfur (S) potassium (K)
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Ions
Ions atoms that have gained or lost one or
more electronsGaining an electron makes gives a negative
charge
Losing an electron gives a positive charge
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Sodium Ion
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Isotopes
Isotopes atoms that have the same
number of protons but different numbers of
neutrons Some isotopes are unstable and break up
into particles with lower atomic numbers
this process is known as radioactive decay
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Molecules
A molecule is a group of atoms held together by
energy
e.g. water (H2O), sodium chloride (NaCl), oxygen (O2)
The energy holding two atoms together is called achemical bond
There are 3 principal types of chemical bonds
1. Ionic2. Covalent
3. Hydrogen
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BONDINGS OF MOLECULES
1) Covalent Bond
2) Noncovalent interaction
- Electrostatic Interaction- Van der Waals Interaction
- Hydrogen Bond
- Steric Repulsion
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COVALENT BONDS
Covalent bonds form between two atoms
when they share electrons
strong bond
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COVALENT BONDING
A covalent bond Each Hydrogen has 1
electron in shell
Sharing 2 electrons fills the
shell, increasing stability
A double covalent bond Sharing 2 pairs of electrons
Oxygen has total of 8
electrons (2 in inner shell, 6in outer shell)
Sharing 2 more fills its outershell, increasing stability
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Electrostatic interaction
Vis directly proportional to the product of the
two changes
Proportional constant (e = 1.602 1019 C).
Vis also inversely proportional to the,
D= dielectric constant
of the homogeneous medium (D = ~80 for water)
rij= the distance separating thetwo charged species
Coulomb's law,
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Van der Waals interaction
The attractive or repulsive force between molecules (or
between parts of the same molecule) other than thosedue to covalent bonds or to the electrostatic interactionof ions with one another or with neutral molecules.
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HYDROGEN BONDS
A hydrogen bond occurs when two
electronegative atoms share the same
hydrogen atom.
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Hydrogen bonding of Water
Molecules
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Water molecules contain two covalent bonds
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HYDROGEN BONDS
Hydrogen bonds form in association with polar
molecules
Figure 3.10 Hydrogen bonding water molecules
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Hydrogen Bonds Give Water Unique
Properties
Water is essential for life
The chemistry of life is water chemistry!
Water is a polar molecule
The partial charges of hydrogen bondscreates polarity
Water can form hydrogen bonds Hydrogen bonding confers on water many
different special properties
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Hydrophobic interaction
- The preference of nonpolar groups or
molecules for nonaqueous environments
Nonpolar molecules have difficulty fitting
into aqueous solutions
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Steric repulsion
When two atoms or two molecules
approach each other, repulsion between
them will eventually take place
Steric repulsion arise from the fact that
each atom within a molecule occupies a
certain amount of space.
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Biological macromolecules
-Starch
-Nucleic acid
-Carbohydrate -Protein
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Biological
macromolecules
Biological macromolecules are large moleculesformed from many smaller units, and are (usually)
polymers of precise length and specific sequence.
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Monomers of
Polynucleotide- nucleotide
Polypeptide - peptide
Polysaccaharide- saccharide
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Source: Tsai, 2007
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Polynucleotide
long polymers,
made up of linear arrays of monomers called
nucleotides, consisting of nitrogen bases (pyrimidines
and purines) linked to sugar phosphate
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Polypeptide
Polypeptides are linear polymers of -aminoacids, connected by amide bonds (peptide
bonds) between the amino group- carboxyl
group forming a head-to-tail condensation.
,
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Polysaccharide
composed of many monosaccharide
(glycose) units joined together by an acetal linkage
(glycosidic linkage) hydroxyl group of one unit with an
alcohol of another unit
size of polysaccharide (glycan) molecules 100 - 100 000
monosaccharide units,
Mw- 1616000kDa.
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Source: Tsai, 2007
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Functional group
name
Functional group
structure Examples
Biological
molecules
Amino
Amines Proteins
Carbonyl
Ketones &
aldehydes
Lipids
Carboxyl Carboxylic acids Proteins
Hydroxyl Alcohols Carbohydrates
Phosphate Phosphates Nucleic acids
Sulfhydryl Thiols Proteins
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Biological macromolecules, structure and the forces
that stabilize them
Protein
The amine functional group is NH2
and the
carboxylic acid functional group is COOH.
The ends of the amino acid monomer are
essential in the formation of bonds between
amino acids. The bond that links amino
acids together is called the peptide bond,
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Enzymes
Enzymes are referred to as catalysts.
A catalyst is a substance that assistsother chemical reactions to occur
without being chemically changed
itself.
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Proteins Can Be Separated and Purified
Column Chromatography
Ion exchange Chromatography
Electrophoresis
N l i id
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sugar
Nitrogen base
phosphate
Nucleotide Molecule
Nucleic acidDeoxyribonucleic Acid - DNA
DNA- large molecule (macromolecule) which stores
hereditary information that controls the activities of everycell of the body.
.
covalently bonded together
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Nucleic acidsStructure of the DNA Double Helix
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C b h d t
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Carbohydrates
Containing the elements carbon, hydrogen and oxygen in which
the ratio of hydrogen to oxygen is the same as in water twohydrogen's to one oxygen.
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Lipids
Lipids -organic compounds containing carbon, hydrogen
and oxygen.
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TriglyceridesTriglycerides are lipid
molecules formed from
two building blocks,
glycerol and three
fatty acids.
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PhospholipidsThe phospholipid molecule is similar to a triglyceride except that thethird fatty acid is replaced by a phosphate group.
phosphate
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Phospholipid bilayer
When phospholipid molecules aremixed in water, they will form a
stable bilayerstructure with the
phosphate heads facing the water
and the water fearing fatty acid tails
facing each other.
Hydrophobic tails
Hydrophilic heads
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Cholesterol
Cholesterol - unusual type of lipid.
It is made up of four rings (1, 2, 3, 4) of carbon atoms joined
together by covalent bonds.
Cholesterol is needed for:- the structure of the plasma membranes of cells
- manufacture a class of hormones called the steroids.
Cholesterol molecule1 2
3 4
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The chemistry of life
Life made of cells
Each cell is a bag made of lipids and sugars, some proteins
etc.
It is semi permeable and can be affected by the environment
Contains macromolecules which are essential for life
proteins, nucleic acids,lipids, sugars, etc.(water and ions)
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The sizes of cells relative to other molecules
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The Biological Cell
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Animal Cell
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Plant cell
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Atom
Molecules
Bondings of Molecules
Biological Macromolecules
Cells