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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