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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