Introduction to organic & Biochemistry Introduction to organic - - PDF document

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Introduction to Organic Chemistry and Biochemistry Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State) E-mail: upali@chem.latech.edu Office: 311 Carson Taylor Hall ; Phone: 318-257-4941; Office Hours: MTW 9:00 am - 11:00 am; TR 9::00 - !0:00 am & 1:00-2:00 pm.

December 19, Test 1 (Chapters 12-14) January 2 Test 1 (Chapters 15-16) February 6 (Chapters 17-19) February 27, (Chapters 20-22) March 2, 2009, Make Up Exam: Bring Scantron Sheet 882-E

Chemistry 121(01) Winter 2009

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Introduction to Organic and biochemistry Introduction to Organic and biochemistry

Chapter 1 Chapter 1-

• 12

12

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Introduction to organic & Biochemistry Introduction to organic & Biochemistry

Self Study

• 24. Carbohydrate Metabolism
• 25. Lipid Metabolism
• 26. Protein Metabolism

Test 4

• 21. Enzymes and Vitamins
• 22. Nucleic Acids
• 23. Biochemical Energy Production

Test 2

• 15. Aldehydes and Ketones
• 16. Carboxylic Acids, Esters, and

Other Acid Derivatives

• 17. Amines and Amides

Test 3

• 18. Carbohydrates
• 19. Lipids
• 20. Proteins

Test 1

• 12. Saturated Hydrocarbons
• 13. Unsaturated Hydrocarbons
• 14. Alcohols, Phenols, and Ethers

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Introduction to organic & Biochemistry Introduction to organic & Biochemistry

12.1 Organic and Inorganic Compounds 12.2 Bonding Characteristics of the Carbon Atom 12.3 Hydrocarbons and Hydrocarbon Derivatives

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Organic and Inorganic compounds Organic and Inorganic compounds

Ionic Compounds: Ionic Compounds: Have Have cations cations and anions are also called salts made of and anions are also called salts made of metlas metlas and non and non-

• metals

metals Covalent Compounds: Covalent Compounds: Consists of neutral molecules connected by Consists of neutral molecules connected by covalent bonds to non metallic elements. covalent bonds to non metallic elements. Organic Compounds Organic Compounds : : have carbon atoms sharing electrons in covalent bonds. Carbon a have carbon atoms sharing electrons in covalent bonds. Carbon atoms toms form chains, and many atoms can be joined by covalent bonds. form chains, and many atoms can be joined by covalent bonds. Inorganic Compounds: Inorganic Compounds: Consist of ions produced by loss or gain of electrons between a Consist of ions produced by loss or gain of electrons between a metal metal and non metal. and non metal. 1-6

Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Covalent or Ionic Covalent or Ionic

Identify Identify covalent covalent and and ionic ionic compounds: compounds: H H2

2O,

O, NaCl NaCl, C , C2

2H

H5

5OH, CH

OH, CH3

3COOH, Na

COOH, Na2

2CO

CO3

3, CH

, CH3

3OK, KOH

OK, KOH Covalent : Covalent : Ionic: Ionic:

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Organic or Inorganic Organic or Inorganic

Identify Identify organic

• rganic and

and inorganic inorganic compounds: compounds: H H2

2O,

O, NaCl NaCl, C , C2

2H

H5

5OH, CH

OH, CH3

3COOH, Na

COOH, Na2

2CO

CO3

3, C

, C3

3H

H8

8, KOH

, KOH Organic : Organic : Inorganic: Inorganic:

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Introduction Introduction

Organic chemistry Organic chemistry is the study of the compounds is the study of the compounds

• f carbon with H, N, O and S.
• f carbon with H, N, O and S.

Biochemistry Biochemistry is the study of the chemical is the study of the chemical processes in living organisms. It deals with the processes in living organisms. It deals with the structure and function of cellular components. structure and function of cellular components.

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

More details.. Organic vs. Inorganic More details.. Organic vs. Inorganic

Organic compounds Organic compounds are produced by living things. are produced by living things. Inorganic compounds Inorganic compounds are produced by non are produced by non-

• living

living naturalprocesses naturalprocesses or by human intervention in the

• r by human intervention in the

laboratory laboratory.

.

This was the most common definition of "organic" until This was the most common definition of "organic" until Wohler's Wohler's 1828 1828 synthesis of synthesis of urea urea (an (an organic compound

• rganic compound) from

) from ammonium ammonium cyanate cyanate (a (a salt, and therefore? Organic/ salt, and therefore? Organic/inorganic inorganic). But we no longer use this ). But we no longer use this definition, for the simple reason that many compounds that every definition, for the simple reason that many compounds that everyone

• ne

agrees are organic agrees are organic --

• - including "

including "natural products natural products" which are routinely " which are routinely made by living things made by living things --

• - have been synthesized by humans.

have been synthesized by humans.

Organic compounds Organic compounds contain carbon. contain carbon. Inorganic compounds Inorganic compounds don't. don't. Organic compounds contain carbon Organic compounds contain carbon-

• hydrogen bonds.

hydrogen bonds. Inorganic compounds don't. Inorganic compounds don't.

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Bonding Characteristics of the Carbon Atom Bonding Characteristics of the Carbon Atom C is a small atom C is a small atom

• it forms

it forms four bonds four bonds consisting of consisting of single single, , double double, , and and triple triple carbon to carbon carbon to carbon bonds or other atoms bonds or other atoms

• Shows

Shows tetrahedral tetrahedral (all 4 (all 4 -

• ),

), trigonal trigonal planar planar (2 (2 -

• & 1

& 1 =) =) and and linear linear ( 1 ( 1 -

• & 1

& 1 ≡

≡ )

)

• it forms strong bonds with

it forms strong bonds with C, H, O, N C, H, O, N, and some , and some metals metals

• form stable covalent bonds to other carbon

form stable covalent bonds to other carbon atoms atoms – – catenation: catenation: Long Long carbon chains carbon chains can be can be produced. produced.

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Four sp Four sp3

3 hybrids

hybrids Three sp Three sp2

2 hybrids

hybrids Two sp Two sp hybrids hybrids

s and p hybrids s and p hybrids

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Hybrid Atomic Hybrid Atomic Orbitals Orbitals

Hybridization is the mixing up of two or more atomic orbitals There are three types of hybrid atomic There are three types of hybrid atomic orbitals

• rbitals for

for carbon carbon

sp sp3

3 (one s orbital + three p orbitals give four sp3

• rbitals)

sp sp2

2 (one s orbital + two p orbitals give three sp2

• rbitals)

sp sp (one s orbital + one p orbital give two sp orbitals)

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

σ σ and and π π bonds in single and multiple bonds bonds in single and multiple bonds single bond single bond -

• one shared pair of electrons between
• ne shared pair of electrons between

two atoms; a two atoms; a σ σ bond bond double bond double bond -

• two shared pairs of electrons

two shared pairs of electrons between two atoms; one s bond and one between two atoms; one s bond and one π π bond bond triple bond triple bond -

• three shared pairs of electrons

three shared pairs of electrons between two atoms; one s bond and two p bonds between two atoms; one s bond and two p bonds

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

σ σ and and π π bonds bonds

Overlap of hybrid Overlap of hybrid orbitals

• rbitals can form two types

can form two types

• f bonds, depending on the geometry of the
• f bonds, depending on the geometry of the
• verlap
• verlap

σ σ bonds bonds are formed by “direct” overlap π π bonds bonds are formed by “parallel” overlap of unhybrid p prbitlas

s1 s1 p1 p1 s1 p1 1-15

Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Predicting hybridization of atoms in a Lewis Predicting hybridization of atoms in a Lewis structure structure Count sigma bonds and unshared electrons around Count sigma bonds and unshared electrons around the atom the atom

If the total number of pairs: 2 sp hybridization 3 sp2 hybridization 4 sp3 hybridization

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Counting Counting σ σ and and π π bonds in Lewis structure bonds in Lewis structure

H-C-C-H H H H H H C C H H H H-C C-H Hybrid- ization Types of Bonds to Carbon Example sp3 four sigma bonds sp2 three sigma bonds and one pi bond sp two sigma bonds and two pi bonds Ethane Ethylene Acetylene Name

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Draw Lewis structure of molecules Draw Lewis structure of molecules

CHCl CHCl3

3

C C2

2H

H4

4

C C3

3H

H8

8O

O CH CH3

3CH

CH2

2CH

CH2

2OH

OH CH CH3

3CH

CH2

2OCH

OCH3

3

CH CH3

3CO

CO2

2H

H CH CH3

3CHO

CHO

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Resonance Resonance

For many molecules and ions with double For many molecules and ions with double bonds, two or more Lewis structure could be bonds, two or more Lewis structure could be written written

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Curved arrow Electron pushing Curved arrow Electron pushing

Curved arrow Curved arrow: : a symbol used to show the a symbol used to show the redistribution of valence electrons redistribution of valence electrons In using curved arrows, there are only two In using curved arrows, there are only two allowed types of electron redistribution: allowed types of electron redistribution:

• from a bond to an adjacent atom
• from an atom to an adjacent bond

Electron pushing by the use of curved arrows is Electron pushing by the use of curved arrows is also used in explaining reaction mechanisms also used in explaining reaction mechanisms

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Drawing Curved Arrows Drawing Curved Arrows

To show the movement of electrons in breaking and forming To show the movement of electrons in breaking and forming

• bonds. The
• bonds. The tail

tail of the arrow is started at the site of electron

• f the arrow is started at the site of electron

density (negative character such as a pi bond or density (negative character such as a pi bond or lone pair lone pair of

• f

electrons) and proceeds to the arrowhead which is drawn to electrons) and proceeds to the arrowhead which is drawn to the site of electron deficiency (positive character). the site of electron deficiency (positive character). NEGATIVE TO POSITIVE! NEGATIVE TO POSITIVE!

Arrows can be drawn from: 1) lone pair bond 2) bond lone pair 3) bond bond

tail head

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Bond Properties Bond Properties

Bond strength Bond strength: : strongest strongest weakest weakest Bond length Bond length: : longest shortest longest shortest C C C C C C > > C C C C C C > >

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Formula Formula

Molecular formula Molecular formula

• kind and number of each type of atoms

Structural formula Structural formula

• each atom and bond in a molecule

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Condensed formula Condensed formula

Condensed formula Condensed formula

• Shorthand way of writing a formula.
• Lists all atoms in order and tells how they are

bound together.

• Example.

Example. Propane Propane C

C3

3H

H8

8

CH CH3

3CH

CH2

2CH

CH3

3

This is a convenient format for describing a This is a convenient format for describing a molecule using text. molecule using text.

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Structural Formula of hydrocarbons Structural Formula of hydrocarbons

One simple class of compound is the One simple class of compound is the alkane alkane which which has only C, H and single bonds. has only C, H and single bonds.

methane ethane propane butane

CH CH4

4

CH CH3

3CH

CH3

3

CH CH3

3CH

CH2

2CH

CH3

3

CH CH3

3CH

CH2

2CH

CH2

2CH

CH3

3 H C H H H H C H C H H H H H C H C H C H H H H H H C H C H C H H H H C H H H

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Line Formula of hydrocarbons Line Formula of hydrocarbons

One simple class of compound is the One simple class of compound is the alkane alkane which which has only C, H and single bonds. has only C, H and single bonds.

methane ethane propane butane

CH CH4

4

CH CH3

3CH

CH3

3

CH CH3

3CH

CH2

2CH

CH3

3

CH CH3

3CH

CH2

2CH

CH2

2CH

CH3

3

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Line formula Line formula

Similar to structural formula. Similar to structural formula. Each line represents a bond. Each line represents a bond. Carbons are assumed to be present at the end Carbons are assumed to be present at the end

• f each line segment.
• f each line segment.

Hydrogen is not shown when bound to carbon. Hydrogen is not shown when bound to carbon.

N OH OH H H 2C C H 2 C H 2 CH CH 2 H 2 C H 2 C H 2 C C H 2 C H 2 H 2C H 2 C H 2 C H 2C C H 2 C H 2 N H 2 C H 2 C H 2C C H 2 C H 2 H 2C H 2 C H 2 C O H H H 2 C CH CH 3

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Models Models

Three dimensional representations Three dimensional representations

Ball and Stick Ball and Stick Space Filling Space Filling

Both are mod Both are models ls of

• f prop
• pane

ane.

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Base names of organic compounds Base names of organic compounds

Prefix Carbons Prefix Carbons Meth Meth-

• 1

1 Eth Eth-

• 2

2 Prop Prop-

• 3

3 But But-

• 4

4 Pent Pent-

• 5

5 Hex Hex-

• 6

6 Hept Hept-

• 7

7 Oct Oct-

• 8

8 Non Non-

• 9

9 Dec Dec-

• 10

10

I s I see much ee much memorization in memorization in your future!

• ur future!

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Functional Groups in Organic Compounds Functional Groups in Organic Compounds

Functional group Functional group: : an atom or group of atoms within a an atom or group of atoms within a molecule that shows a characteristic set of physical and molecule that shows a characteristic set of physical and chemical properties chemical properties Functional group Functional group

• divide organic compounds into classes
• the sites of characteristic chemical reactions
• the basis for naming organic compounds

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Alcohol Alcohol(carbon (carbon, hydrogen and , hydrogen and

• xygen)
• xygen)

CH CH3

3-

• CH

CH2

2-

• OH

OH Thiol Thiol ( (thioalcohol thioalcohol) ) thio thio means means sulfur sulfur CH CH3

3-

• CH

CH2

2-

• SH

SH Amine Amine CH CH3

3-

• CH

CH2

2-

• NH

NH2

2

Ether Ether CH CH3

3-

• CH

CH2

2-

• O

O-

• CH

CH2

2-

• CH

CH3

3

An alcohol (Ethanol) H- C-C- O- H H H H H

CH3 N H H CH3 N H CH3 CH3 N CH3 CH3 (a 1° amine) (a 2° amine) (a 3° amine)

Common Functional Groups Common Functional Groups

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Carbonyl group Carbonyl group

• r unit
• r unit

Aldehyde Aldehyde ketones ketones Carboxylic acids Carboxylic acids

O CH3-C-O-H CH3COOH CH3CO2H

• r
• r

Acetic acid

Common Functional Groups (continued) Common Functional Groups (continued)

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Class Functional group Example

Classification of organic compounds Classification of organic compounds

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

IUPAC IUPAC -

• a general system: Examples

a general system: Examples

prop-en en-e e = propene eth-an an-ol

• l = ethanol

but-an an-one

• ne = butanone

but-an an-al al = butanal pent-an an-oic

• ic acid

acid = pentanoic acid cyclohex-an an-ol

• l = cyclohexanol

eth-yn yn-e e = ethyne eth-an an-amine amine = ethanamine cyclo-pent-en en-

• e

e CH3CH=CH

2

OH HC CH

CH3 CH2 NH 2

CH3CH2OH

H O OH O O 1-34

Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

The IUPAC system: Naming Organic Compounds The IUPAC system: Naming Organic Compounds

As a general system of nomenclature As a general system of nomenclature

prefix prefix-

• infix

infix-

• suffix

suffix

• prefix

prefix tells the number of carbon atoms in the parent

• infix

infix tells the nature of the carbon-carbon bonds

• suffix

suffix tells the class of compound

• ne or more triple bonds
• ne or more double bonds

all single bonds

• yn-
• en-
• an-

Nature of Carbon-Carbon Bonds in the Parent Chain Infix Suffix Class

• e
• ol
• al
• one
• oic acid

hydrocarbon alcohol aldehyde ketone carboxylic acid

• amine

amine

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Hydrocarbons Hydrocarbons

Composed of only carbon and hydrogen; in petroleum Composed of only carbon and hydrogen; in petroleum and coal and coal Saturated Saturated -

• hydrocarbons with all

hydrocarbons with all C C-

• C single bonds

C single bonds Unsaturated Unsaturated -

• hydrocarbons with at

hydrocarbons with at least one least one C C-

• C double

C double bond bond or

• r triple bonds

triple bonds

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Classification of Hydrocarbons Classification of Hydrocarbons

H-C C-H H-C-C-H H H H H H C C H H H Hydrocarbons Alkanes (Chapter 3) Alkenes (Chapters 4-5) Alkynes (Chapter 4) Arenes (Chapter 9) Only carbon- carbon single bonds One or more carbon-carbon double bonds One or more carbon-carbon triple bonds One or more benzenelike rings Class Example Carbon- carbon bonding Name Ethane Ethylene Acetylene Benzene Saturated Unsaturated

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Examples of Examples of Alkanes Alkanes, Alkenes, Alkynes and , Alkenes, Alkynes and Arenes Arenes:

:

C C H H H H H H C C H H H H C C H H

ethane ethene ethyne benzene C2H6 C2H4 C2H2 C6H6 CnH2n+2 CnH2n CnH2n−2 CnHn saturated unsaturated unsaturated Aromatic alk alkan ane e alkene alkene alk alkyn yne e Ar Aren ene e

C C C C C C H H H H H H

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Chemistry 121, Winter 2008, LA Tech Chemistry 121, Winter 2008, LA Tech

Biochemical Principles

Structures of Monomers and Polymers found in living systems

• Carbohydrates (glucose, starch, cellulose)
• Proteins (amino acids, proteins)
• Nucleic acids (Nucleotides-A,T,G,C and RNA & DNA)

Functions of Biological molecules

• Enzymes and Vitamins
• Nucleic Acids and hereditary

Biochemical Energy Production

• Carbohydrate Metabolism
• Lipid Metabolism
• Protein Metabolism