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Powerpoint Templates
Chem 88
(Biochemistry)2nd Sem., SY 2010-2011
Melchor CerdaniaSC 124, Dept. Of Chemistry
Silliman University
Grading System
• Lecture (80%)
– Long Exams (50%)
– Quizzes, Problem Sets. Attendance (15%)
– Final Exam (35%)
• Laboratory (20%)
References:•Campbell, Mary and Shawn Farrel. Biochemistry, 4th Ed. Thomson Brooks Cole, 2003.•Timberlake, Karen. General, Organic and Biological Chemistry, 2nd Ed. Prentice Hall, 2008.•Denniston, Katherine, Joseph Topping and Robert Caret. General, Organic and Biochemistry, 5th Ed. McGraw – Hill, 2007.•Garrett, R.H. and C.M. Grisham. Biochemistry, 3rd Ed. Thomson Brooks Cole, 2005.
Note: The above books are the sources of the powerpointpresentations for the course.
•Other Biochemistry books available
Unit 1 Introduction and Water, pH and Buffers
Unit 2 Amino Acids and Proteins
Unit 3 Enzymes
Unit 4 Carbohydrates
Unit 5 Lipids and Membranes
Unit 6 Nucleic Acids
Unit 7 Introduction to Metabolism
Unit 8 Carbohydrate Metabolism 1
Unit 9 Carbohydrate Metabolism 2
Unit 10 Tricarboxylic Acid Cycle, ETC and Oxidative
Phosphorylation
Unit 11 Protein Metabolism
Unit 12 Lipid Metabolism
Topics for Discussions
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Biochemistry
Biochemistry has become the foundation for understanding all biological processes.
It has provided explanations for the causes of many diseases in humans, animals and plants
What is Biochemistry ?
• Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular level.
• It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to investigate the chemistry of living systems by:
A. Studying the structure and behavior of the complex molecules found in biological material and
B. the ways these molecules interact to form cells, tissues and whole organism
• seeks to explain life on a molecular level
• study of the structure, properties and
changes of biomatter
“Chemistry of Life”
Principles of Biochemistry• Cells (basic structural units of living organisms) are highly organized and constant source of energy is required to maintain the ordered state.
• Living processes contain thousands of chemical pathways. Precise regulation and integration of these pathways are required to maintain life
• Certain important pathways e.g. Glycolysis is found in almost all organisms.
• All organisms use the same type of molecules: carbohydrates, proteins, lipids & nucleic acids.
• Instructions for growth, reproduction and developments for each organism is encoded in their DNA
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Cells
• Basic building blocks of life• Smallest living unit of an organism• Grow, reproduce, use energy, adapt, respond to their environment
• Many cannot be seen with the naked eye• A cell may be an entire organism or it may be one of billions of cells that make up the organism
• Types of Cells
Nucleoid region contains the DNA•Cell membrane & cell wall• Contain ribosomes (no membrane) to make proteins intheir cytoplasm
Contain 3 basic cell structures:• Nucleus• Cell Membrane• Cytoplasm with organelles
Two Main Types of Eukaryotic Cells
Biochemistry
Biolog. Nanostructures
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Biochemistry:
Where Chemistry & Biology Meet
• Living things require millions of
chemical reactions just to survive.
• Metabolism = all the chemical reactions
occurring in the body.
• Organic molecules: – usually associated with living things.
– always contain CARBON.
– are “large” molecules, with many atoms
– always have covalent bonds (share electrons)
Elements in Living Organisms
• The most common elements found in living
organisms include:
–Carbon (C)
–Oxygen (O)
–Nitrogen (N)
–Hydrogen (H)
–Phosphorus (P)
–Sulfur (S)
Periodic Table of the Elements
abundant elements are in red
essential ions are in purple
trace elements are in dark blue (more common)
light blue (less common)
Functional groups - specific parts of
molecules involved in biochemical
reactions
Succeeding slides show the general
formulas of:
(a) Organic compounds
(b) Functional groups
(c) Linkages common in
biochemistry
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Bio-molecules
• Just like cells are building blocks of tissues likewise molecules are building blocks of cells.
• Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-molecules)
• Water constitutes 50-95% of cells content by weight.
• Ions like Na+, K+ and Ca+ may account for another 1%
• Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)
• Infinite variety of molecules contain C. • Most bio-molecules considered to be derived from hydrocarbons.
• The chemical properties of organic bio-molecules are determined by their functional groups. Most bio-molecules have more than one.
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Biomolecules – Structure
• Building block
• Simple sugar
• Amino acid
• Nucleotide
• Fatty acid
• Macromolecule
• Polysaccharide
• Protein (peptide)
• RNA or DNA
• Lipid
Amino acids – Proteins
• Amino acids: • Building blocks of proteins.
• R Group (side chains) determines the chemical properties of each amino acids.
• Also determines how the protein folds and its biological function.
• Functions as transport proteins, structural proteins, enzymes, antibodies, cell receptors.
Sugars • Carbohydrates most abundant organic molecule
found in nature.
• Initially synthesized in plants from a complex seriesof reactions involving photosynthesis.
• Basic unit is monosaccharides.
• Monosaccharides can form larger molecules e.g. glycogen, plant starch or cellulose.
Functions• Store energy in the form of starch (photosynthesis in plants) or glycogen (in animals and humans).
• Provide energy through metabolism pathways and cycles.
• Supply carbon for synthesis of other compounds.
• Form structural components in cells and tissues.
• Intercellular communications
Monosaccharides -Polysaccharides
Glycosidic bonds connecting glucose residues are in red
Glucose - Cellulose
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Fatty acids - Lipids
• Are monocarboxylic acid contains even number C atoms
• Two types: saturated (C-C sb) and unsaturated (C-C db)
• Fatty acids are components of several lipid molecules.
• E,g. of lipids are triacylglycerol, steriods (cholestrol, sex hormones), fat soluble vitamins.
Functions
• Storage of energy in the form of fat
• Membrane structures
• Insulation (thermal blanket)
• Synthesis of hormones
Triglyceride
Glycerol Fatty Acid Chains
Nucleic Acids
•Store hereditary information
Contain information for making all the body’s proteins
Two types exist --- DNA & RNA
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Macromolecules
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Macromolecules Molecular Organization of a cell
WATER, pH and
BUFFERS
Water• 70% - human
body
• 95% - tomato
• 80% - apple and
pineapple
• 70% - human
brain
• 82% - human
blood
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• central role in the chemistry of all life
– media for biochemical reactions.
• biomolecules - proteins,
polysaccharides, nucleic acids and
membranes
– all assume their characteristic shapes
in response to water
• related to the functions of biomolecules,
entire cells,and organisms.
Water Water in our body
• Solvent for nutrients and aids in the transport of these nutrients
• Solvent and transporter of waste products
• Essential component of materials made inside the body (synthesize)
• Facilitates the breaking down of nutrients
• Regulates body temperature
• Acts as lubricant
If there is magic on this planet it is contained If there is magic on this planet it is contained If there is magic on this planet it is contained If there is magic on this planet it is contained
in water.in water.in water.in water.
---- Loren Loren Loren Loren EisleyEisleyEisleyEisley from from from from LehningerLehningerLehningerLehninger
Water is simple A.
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but complex
• Structure
• Polarity
• Surface tension
• Ice Floats
• Solvation
Hydrogen bonding is the key to all
these properties.
Water’s Polarity
Hydrogen bonding between
two water molecules
liquid water
solid water
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•Hydrophilic (water-loving)
substances (polar and ionic
(electrolytes)) readily dissolve in
H2O
•Polar water molecules align
themselves around ions or other
polar molecules
Dissolution of ionic and polar
substances in water• A molecule or ion surrounded
by solvent molecules is solvated
• When the solvent is water the molecules or ions are hydrated
Solvated
ions
Dissolution of non-polar solutes in water
• depends on the ratio of polar and non-polar portions of the solute.
• the larger the portion of nonpolar groups the less soluble the molecule is in water
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• the larger the portion of polar
groups (e.g. hydroxyl groups (-
OH)) the more soluble the
molecule is in water
• solvation occurs
• formation of micelles -
amphipathic molecules
Water is Weakly Ionizable
• autoionization of water
• amphoteric property
• concepts of acids and bases
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Equilibrium Constant - Kw
3
2
[ ][ ]
[ ]
H O OHKeq
H O
+ −
=
since [water] is constant
14
3[ ][ ] 1 10Keq Kw H O OH x
+ − −= = =
[H3O+] = [OH-] = 1 x 10-7
The pH Scale
•pH is defined as the negative
logarithm of the concentration of
H+
•pH range from 1 to 14
•measure of acidity of solutions
•acidic, basic or neutral
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•Added solutes could affect the H+
and OH- concentrations of water
– concentration will change
– could be accounted for using
the Kw expression
1. [OH-] = 1.2 x 10-6
Kw = [H+][OH-] = 1 x 10-14
substitute the value of [OH-]
1 x 10-14 = [H+] 1.2 x 10-6
rearrange the equation to solve for [H+]
[H+] = 1 x 10-14 / 1.2 x 10-6 = 8.3 x 10-9
2. [H+] = 2.45 x 10-5
3. [OH-] = 2.48 x 10-11
• [H+] is use to calculate the pH of the resulting solution
• pH then is use to determine whether the solution is acidic, basic or neutral
From the previous example [H+] = 8.3 x 10-9, the pH of the solution could be calculated.
pH = - log [H+] = -log 8.3 x 10-9 = 8.1
Consequently pH could be used to calculate the [H+] of solution
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• For example
pH = 5.8
[H+] = antilog – pH
[H+] = antilog – 5.8
[H+] = 1.5 x 10-6
[H+] will be use to calculate [OH-] of
the solution.
• a related value to pH is pOH defined
as:
pOH = -log [OH-]
• the Kw expression could now be
expressed in its logarithmic form
Kw = [H+][OH-]
1 x 10-14 = [H+][OH-]
- log 1 x 10-14 = (-log [H+]) + (-log [OH-])
14 = pH + pOH
• pH is determined by calculation or by
experimentation
–Calculation is done if concentration
are known if unknown then
laboratory techniques are used
–Use of indicator or use of the pH
meter
• pH affects the structure and activity
of biological macromolecules like in
the case of enzymes
• pH determination is also important in
medical diagnoses
–Bodily fluids = normal values like
for blood pH = 7.4
–if below this value condition is
called acidosis; if higher condition
is called alkalosis.
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Acid Dissociation Constants
of Weak Acids
• Strong acids and bases dissociate
completely in water
HCl + H2O Cl- + H3O+
• Cl- is the conjugate base of HCl
• H3O+ is the conjugate acid of H2O
Acetic acid is a weak acid
•weak acids and bases do not
dissociate completely in H2O
•solution is made up of weak acid
and the conjugate base
The Henderson-Hasselbalch
Equation
• Defines the pH of a solution in
terms of:
(1) The pKa of the weak acid
(2) Concentrations of the weak acid
(HA) and conjugate base (A-)
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Titration curve of acetic acid
(CH3COOH)
• Titration curves
are used to
determine pKa
values
Titration curve for phosphoric
acid (H3PO4)
Buffered Solutions Resist Changes
in pH
• Buffer capacity is the ability of a solution to
resist changes in pH
• Most effective buffering occurs where:
solution pH = buffer pKa
• At this point: [weak acid] = [conjugate base]
• Effective buffering range is usually at pH
values equal to the pKa ± 1 pH unit
LeChatelier's principle describes how buffers
work.
Take for example the acetic acid and sodium
acetate buffer mentioned above. The equation for
the equilibrium that exists in the solution is:
CH3COO - (aq) + H3O
+ (aq) ���� CH3COOH (aq) +
H2O (l)
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• If an acid is added (H3O+) it combines
with CH3COO- to form CH3COOH and water, by the equation above. The pH will not therefore change dramatically.
• If a base is added like potassium hydroxide which is a source of OH- ions, the OH- ions combine with the H3O+ ion in the equilibrium and form water by the equation below. Once more the pH does not change dramatically.
H3O+
(aq) + OH-(aq) ���� 2H2O (l)
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Sodium hypochlorite was dissolved in a solution buffered to pH 6.20. Find the ratio [OCl-] /[HOCl] in this solution. Ka = 3.0 x 10-8
Solution:
pKa = -log Ka = -log 3.0 x 10-8 = 7.52
pH = pKa + log [OCl-]/[HOCl]
6.20 = 7.52 + log [OCl-]/[HOCl]
[OCl-]/[HOCl] = antilog 6.20 – 7.52
[OCl-]/[HOCl] = 0.047
What is the pH of a buffer prepared by dissolving 0.100 mol of weak acid, HA (Ka = 1.0 x 10-5) and 0.050 mol of its conjugate base NaA in 1.00 L?
Solution:
pKa = -log 1.0 x 10-5 = 5
pH = pKa + log [NaA]/[HA]
pH = 5 + log 0.050/0.100
pH = 4.70
Find the pH of the solution prepared by dissolving 12.43 gms of tris (B-), FM = 121.136 gms/mol and 4.67 gms of tris hydrochloride (BH+), FM = 157.597 gms/mol in 1.0 L of water. pKa of BH+ = 8.075
Solution:
moles B- = 12.43 gms/121.136 gms/mol
= 0.10 mol
moles BH+ = 4.67 gms/157.597 gms/mol
= 0.03 mol
pH = pKa + log [B-]/[BH+]
pH = 8.075 + log 0.10/0.03 = 8.60
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How many ml of 0.5 M NaOH should be added to 10.0 g of trisHCl to give a pH of 7.60 in a final volume of 250 ml?
Solution:
moles of trisHCl = 10 g/157.597gms/mol
= 0.063 mol
pH = pKa + log [B-]/[BH+]
Let x = mol of NaOH=[B-]
0.063-x = mol of trisHCl=[BH+]
7.60 = 8.075 + log x/0.063-x
x = 0.0159 mol
Therefore,
volume NaOH = 0.0159 mol/0.5 mol/L = 0.0318L
= 31.8 ml
If we add 12.0 ml of 1.00 M HCl to the solution from the previous slide, what will be the new pH ?
Solution:
moles HCl = 1.00 M x 0.012 L
= 0.012 mole
[B-] = 0.10 mol [BH+] = 0.03 mol
new moles of B- = 0.10 mol – 0.012 mol
= 0.088 mol
new moles of BH+ = 0.03 mol + 0.012 mol
= 0.042 mol
pH = pka + log [B-]/[BH+]
pH = 8.075 + log 0.088/0.04
pH = 8.40 (previous pH = 8.60)
Applications of Buffered
Solutions
• maintain pH of reaction media
• reactions are pH dependent
• regulation of pH of biological fluids
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Regulation of pH in the blood of
animals
• Blood plasma of mammals has a constant pH
which is regulated by a buffer system of:
carbon dioxide /carbonic acid /bicarbonate
• Buffer capacity depends upon equilibria
between:
(1) Gaseous CO2 (air spaces of the lungs)
(2) Aqueous CO2 (dissolved in the blood)
(3) Carbonic acid
(4) Bicarbonate
Carbonate buffering equilibria
Regulation of the pH of blood in mammals