basic general, organic and biochemistry

General Chemistry Review

Part I

General Chemistry: Carbon Atom

1. Atomic Theory

2. Covalent Bonding

3. Chemical Formulas

General Chemistry of Carbon

Carbon is a non-metal chemical

element.

A covalent bond is a chemical bond

that involves the sharing of electron

pairs between atoms.

General Chemistry of Carbon

Carbon atomic number = 6 Protons6 Electrons6 Neutrons

Group IV Four valence electrons

Atomic Theory of Carbon

Ground state electronic configuration of

carbon is:

1s22s22p2

[He] 2s22p21S2

Nucleus

Electronic Configuration1

Atomic Theory of Carbon

Carbon atom ground state configuration:1s2 2s2 2Px

1 2Py1 2Pz

Covalent Bonding

Carbon can covalently bond with other elements: Hydrogen

Oxygen

Nitrogen

Sulfur

Halogens

Covalent Bonding

Carbon only forms single, double or triple bonds with other carbon atoms

Covalent Bonding

Carbon only forms single bonds with hydrogen and/or halogens atoms

Covalent Bonding

Carbon may form single bonds with nitrogen, oxygen and sulfur

Covalent Bonding

Carbon may also form double bonds with nitrogen, oxygen and sulfur

Covalent Bonding

Carbon may also form triple bonds with nitrogen, sulfur and oxygen

Chemical Formulas

Three classes are:

1. Molecular

2. Structural

3. Condensed

Molecular Formulas

The types of atoms present

The numbers of each atom present in a

molecule

Molecular Formulas

For example, glucose

Symbols for carbon, hydrogen, and

oxygen are C, H, and O respectively

Molecular formula for glucose is C6H12O6

Structural Formula s

Show arrangement of atoms:

How atoms are bonded,

In which order they are bonded

Whether single, double or triple bonds are

Structural Formulas: Examples

Condensed Formulas

Groups of atoms in a molecule

The sequential relationships of these group of

atoms to each other with or without showing

covalent bonds

Condensed Formulas: Examples

Organic Chemistry Review

Part II

Organic Chemistry: Carbon Atom

1. Structural Classifications

2. Atomic Theory

3. Dipoles &

Resonance

4. Isomers

5. Functional Groups

6. Organic Reactions

Organic Chemistry

The chemistry of compounds which contain carbon.

Carbon forms more compounds than any other element, except hydrogen.

Organic Chemistry Major Concepts

1. Structural Classifications

2. Hybridization

3. Charges of Organic Molecules

4. Dipoles & Dipolar Resonance

5. Isomers

Structural Classification of Carbon Atoms

Three main classifications are:

1. Primary Carbons

2. Secondary Carbons

3. Tertiary Carbons

4. Quaternary Carbons

Primary Carbons

Denoted as 1° carbons.

Also called terminal or end carbon atoms.

Found at the ends of a straight chains or the

branches.

Covalently bonded to one carbon atom.

CH3 – CH2 – CH3

Secondary Carbons

Covalently bonded to two other carbon

atoms.

CH3 – CH2 – CH3

Tertiary Carbons

Covalently bonded to three other carbon

atoms. CH3 – CH – CH3

Quaternary Carbons

Covalently bonded to four other carbon

atoms. CH3 |

CH3 – C – CH3

Definitions

Valence Bond Theory: Electrons in a covalent bond reside in a region

in which there is overlap of individual atomic orbitals.

For example, the covalent bond in molecular methane (CH4) requires the overlap of valence electrons:

Definitions

Types of valence bond theory overlap:

Definitions

Valence Shell Electron Pair Repulsion (VSEPR) Electron pairs arrange themselves around an

atom in order to minimize repulsions between pairs.

Carbon has a valence of four and must have a tetrahedral geometry.

In methane, each carbon atom must have a bond angle of 109.5⁰. This is the largest bond angle that can be attained between all four bonding pairs at once.

Definitions

Hybridization: Atomic orbitals modify themselves to meet

VESPR geometry and valence bond theory. Three types of hybridization for carbon:

Hybridization: Valence Bond Theory

Hybridization: VSEPR Geometry

Hybridizations

In sp3 hybridization, an electron is promoted from a 2s orbital into a p orbital.

The 2s orbital and three 2p orbitals form four hybrid orbitals (sp3).

Ground state: 1s2 2s2 2Px1 2Py

1 2Pz0

Excited state: 1s2 2s1 2Px1 2Py

1 2Pz1

Hybridizations

The overlap of each hybrid orbital with a hydrogen atom results in a sigma bond ( σ bond).

Only one σ bond can exist between two atoms.

Hybridizations

sp3 hybridization of methane:

Hybridizations

sp3 hybridization of ethane:

Hybridizations

In sp2 hybridization, the 2s orbital and two of the 2p orbitals form three hybrid orbitals (sp2).

The Pz orbital of each carbon atom remains unhybridized.

These unhybridized Pz orbitals overlap with one another to form a π-bond.

Hybridizations

sp2 hybridization of ethene:

Hybridizations

sp2 hybridization and bond rotation:

Hybridizations

In sp hybridization, the 2s orbital and one 2p orbital form two hybrid orbitals (sp).

The triple bond is actually one σ bond and two π bonds.

Hybridizations

sp hybridization of ethyne:

No free rotation

Charges in Organic Molecules

Definitions

Dipole: The measure of net molecular polarity. Formula: the magnitude of the charge Q times

the distance r between the charges.

μ = Q × r The larger the difference in electronegativities

of the bonded atoms, the larger the dipole moment.

Definitions

Resonance: Part of the Valence Bond Theory Describes the delocalization of electrons within

molecules. Used when Lewis structures for a single

molecule cannot describe the actual bond lengths between atoms.

Structures are not isomers of the target molecule, since they only differ by the position of delocalized electrons.

Definitions

Resonance Hybrid: The net sum of valid resonance structures. Several structures represent the

overall delocalization of electrons within the molecule.

A molecule that has several resonance structures is more stable than one with fewer.

Definitions

Hyperconjugation: The interaction of the electrons in a sigma

bond (usually C–H or C–C) with an adjacent empty (or partially filled) non-bonding p-orbital, antibonding π orbital, or filled π orbital.

Only electrons in bonds that are β to the positively charged carbon can stabilize a carbocation by hyperconjugation.

Carbon Atom Dipoles

Carbon- Halogen Bonds

Carbon Atom Dipoles

C-O, C-S and C-N Covalent Bonds:

δ+ δ-

Dipolar Resonance

Hyperconjugation

A.K.A "no bond resonance". The delocalization of σ-electrons or lone pair of

electrons into adjacent π-orbital or p-orbital. Overlapping of σ-bonding orbital or the orbital

containing a lone pair with adjacent π-orbital or p-orbital.

An α- carbon next to the π bond, carbocation or free radical should be sp3 hybridized with at least one hydrogen atom bonded to it.

Hyperconjugation

Other hydrogens on the methyl group also participate due to free rotation of the C-C bond.

There is NO bond between an α-carbon and one of the hydrogen atoms.

The hydrogen atom is completely detached from the structure.

The C-C bond acquires some double bond character and C=C acquires some single bond character.

Hyperconjugation

Hyperconjugation: Examples

Isomers

Compounds that have:

The same molecular formula.

Similar or different types of structural

formulas.

Different arrangement of atoms.

Isomers:

Two main classes are:

1. Structural or constitutional

2. Stereoisomers

Structural Isomers

Also known as constitutional isomers

Stereoisomers

a. Configurational

Geometric or Diastereomers

Optical or Enantiomers

b. Conformational or Rotamers

Diastereomers

Geometric Isomers: Examples

Optical Isomers

Definitions

Chiral Molecules - when a molecule and its mirror image cannot completely overlap. They are non-superimposable mirror images of one another.

Dextrorotatory (R, +) - a compound whose solution rotates the plane of polarized light to the right (when looking toward the source of light).

Definitions

Levorotatory (S, -) - a compound whose solution rotates the plane of polarized light to the left (when looking toward the source of light).

Racemic Mixture - a mixture of equal amounts of optical isomers. Because the two isomers rotate the plane of polarized light by the same angle in opposite directions, they cancel each other out and have no net effect.

Determining L (S, -) or D (R, +) configuration

1. Rank the four substituents according to the

atomic numbers of the atoms bonded

directly to the double bonded carbons,

from highest (1) to lowest (4).

2. If two substituents have the same ranking: Look at the next atoms in their substituent

chains. List the atoms that are two bonds away

from the chiral center according to their atomic number, from highest to lowest.

Assign the lower number to the substituent that has the atom with the higher atomic number.

Determining L (S) or D (R) configuration If it is still the same atom for both

substituents, continue down the list until a difference is found and assign a ranking in the same manner.

3. If a substituent has a double or triple bonds in its chain, it is counted as two or three bonds to the same atom.

4. Determine whether the ranking defines a

clockwise or counterclockwise direction.

If clockwise, the projection is an R

configuration.

If counterclockwise, it is an S configuration.

L (S, -) Configuration

A common optical isomer for amino acids in Biochemistry

Optical Isomers: Examples

Summary of Isomers

Conformational Isomers

Also known as Rotamers Stereoisomers that can be interconverted

by the rotation of atoms about a σ-bond.

Conformational Isomers

Rotamers: Examples

Functional Groups

1. Hydrocarbons

2. Derivatives of Hydrocarbons

Functional Groups

Organic molecules may have functional

groups attached.

A functional group is a group of atoms of a

particular arrangement that gives the entire

molecule certain chemical characteristics.

Functional groups are named according to

the composition of the group.

Functional Groups

Organic chemists use the letter "R" to indicate

an organic molecule.

The "R" can be any organic molecule.

Hydrocarbons

The simplest organic compounds.

Contain only carbon and hydrogen,

Can be straight-chain, branched chain, or cyclic

molecules.

Carbon tends to form four bonds in a tetrahedral

geometry.

Hydrocarbons

Two classifications:

1. Aliphatics

2. Aromatics

Aliphatic - hydrocarbons which do not contain an

aromatic ring.

Hydrocarbons

Aromatic - Aromatic hydrocarbons contain a set

of covalently bound atoms with specific

characteristics:

A delocalized conjugated π system, with the

common arrangement of alternating single and

double bonds

Aliphatics

1. Alkanes

2. Cycloalkanes

3. Alkenes

4. Alkynes

Alkanes

IUPAC ending is …ane

Alkanes

Saturated hydrocarbons. Are hydrocarbons which contain only single

bonds. All alkanes are insoluble in water, but dissolve

in organic solvents. Density, viscosity, melting point & boiling

points increase as the molecular weight/size of the hydrocarbon increases.

Alkanes

Contain single covalent bonds.

Have the same structural formula:

Cn H2n+2

All carbons have single bonds therefore the molecular geometry is tetrahedral.

Alkanes

The names of alkanes start with the name of the alkane but end with the suffix –ane.

Alkanes

Each atom in an alkane uses all its 4 valence electrons in forming single bonds with other atoms.

Alkyl groups may be used as substituents for hydrogens.

Alkanes

Alkyl groups form the branches of straight chain hydrocarbons.

Can have more than one alkyl group for hydrogens. For multiple substituents of the same type, use the

following prefixes: di- tri- tetra- penta- hexa-

Alkanes

Other functional groups can be used as substituents.

More than one substituent requires a prefix. Any hydrogen can be substituted by:

1. Halogens

2. Alcohols

3. Amines

4. Nitriles

5. Thiols

6. Aldehydes

7. Ketones

Alkanes

Any carbon can be substituted by: Carboxylic Acids Esters Amides Thioesters

Addition of other atoms: Ethers Thioethers Disulfides

Cycloalkanes

the prefix cyclo- and the ending …ane

Cycloalkanes

Saturated hydrocarbons. Form one or more rings fused together. A single carbon in a ring may have two hydrogen

atoms. Are insoluble in water, but dissolve in organic

solvents. Have higher boiling points, melting points, and

densities than alkanes.

Cycloalkanes

All have the same general formula:

The carbon atoms in cycloalkanes are sp3

hybridized.

Each atom in a cycloalkane uses all its 4 valence

electrons in forming covalent bonds with other

atoms.

Cycloalkanes

Can have more than one alkyl group to make straight chains.

For multiple alkyl groups of the same type, use prefixes.

Cycloalkanes

Many functional groups can be used as substituents. More than one substituent requires a prefix. Any hydrogen or carbon atom can be substituted by:

Cycloalkanes

The names follow those of the alkanes with the prefix cyclo- .

Cycloalkanes

Alkenes

IUPAC ending is …ene

Alkenes

Also known as olefins. Are unsaturated hydrocarbons and are generally

very reactive. Are insoluble in water, but dissolve in organic

solvents. Ethene, propene and butene are gases at room

temperature. The remaining are liquids. Boiling points increases with molecular mass

(chain length). The higher the molecular mass, the higher the boiling point.

Alkenes

Are hydrocarbons which contain one or more double bonds.

Double bonds are:

Alkenes

The main centers are the carbons of the double bond.

The geometry of each carbon in the center is trigonal planar.

This portion of the molecule is flat, with bond angles of 120 degrees.

Alkenes

All the alkenes with 4 or more carbon atoms in them show structural isomerism.

Alkenes

The carbon-carbon double bond does not rotate.

Substituents groups on the molecule are locked on either one side of the molecule or opposite each other.

Alkenes

The names of alkenes start with the name of the alkane but end with the suffix –ene.

For alkenes above propene, the position of the double bond must be specified in the name.

Alkenes

Can have more than one alkyl group to form branches.

For more than one alkyl group, use prefixes.

Alkenes

Many functional groups can be used as substituents. More than one substituent requires a prefix. Any hydrogen or carbon atom can be substituted by:

Alkenes

For multiple double bonds, use the following prefixes: di- tri- tetra- penta- hexa-

Alkenes

A diene is a hydrocarbon chain that has two double bonds that may or may not be adjacent to each other.

Alkenes: Examples

Alkynes

IUPAC ending is …yne

Alkynes

Also known as acetylenes. Are unsaturated hydrocarbons and are

generally very reactive. Are insoluble in water; but quite soluble in

organic solvents of low polarity (e.g. ligroin, ether, benzene, carbon tetrachloride, etc.).

Alkynes of four or fewer carbon atoms are gases. The rest are liquids.

Their boiling points increase with increasing number of carbons.

Alkynes

Are hydrocarbons which contain one or more triple bonds.

Triple bonds are:

CnH2n-2

Alkynes

The main centers are the carbons of the triple bond.

The geometry of the center is linear. This portion of the molecule is linear, with

bond angles of 180 degrees.

Alkynes

All the alkynes with 4 or more carbon atoms in them show structural isomerism.

Alkynes

The names of alkynes start with the name of the alkane but end with the suffix –yne.

For alkynes above propyne, the position of the triple bond must be specified in the name.

Alkynes

Many functional groups can be used as substituents. Only one substituent is allowed. Any hydrogen or carbon atom can be substituted by:

Alkynes

For multiple double bonds, use the following prefixes: di- tri- tetra- penta- hexa-

Alkynes: Examples

Aromatics

Structures that meet Huckel’s Rule

Aromatics

Coplanar structures, with all the contributing atoms in the same plane.

Are arranged in one or more rings. Benzene rings are not a common motif.

The three general requirements for a compound to be aromatic are: The compound must be cyclic. Each element within the ring must have a p-orbital that

is perpendicular to the ring, hence the molecule is planar.

The compound must follow Hückel's Rule.

Aromatics

The number of π delocalized electrons must follow Hückel's Rule.

number of π electrons = 4n + 2

where n = 0, 1, 2, 3, and so on

The number of π delocalized electrons is an even number, but not a multiple of 4 to be an aromatic compound.

Aromatics

The most common examples of aromatic hydrocarbons are organic compounds, which contain one or more benzene rings.

Benzene

Aromatics

Benzene follows Huckel’s Rule:

Aromatics

Each atom in benzene uses all its 4 valence

electrons in forming covalent bonds with other

atoms.

Other functional groups can be used as

substituents.

More than one substituent requires a prefix.

Aromatics

Any hydrogen or carbon atom can be substituted by:

Aromatics

When two substituents are attached to the benzene ring: Ortho, meta, or para can be used to indicate

where the two substituents are on the benzene ring.

Three classifications:ortho- (o-): position 1, 2- meta- (m): posotion 1, 3- para- (p): position 1, 4-

Aromatics

Aromatics: Examples

o-dihydroxybenzene, m-dihydroxybenzene, p-dihydroxybenzene

Aromatics: Examples

Summary of Hydrocarbon

Derivatives of Hydrocarbons

Are formed when there is a substitution of a functional group at one or more carbon

atoms.

Derivatives of Hydrocarbons

1. Prefixes

2. Haloalkanes

3. Alcohols

4. Ethers

5. Amines

6. Nitriles

7. Thiols

8. Thioethers

9. Disulfides

10. Aldehydes

11. Ketones

12. Carboxylic Acids

13. Esters

14. Amides

15. Thioesters

Prefixes

For multiple substituents of the same

type, use the following prefixes:

tetra-

penta-

Haloalkanes The alkyl halides have the general form

where the R in the general form is typically an alkyl group with a halogen replacing one of the hydrogens.

X is written as: F = fluoro Cl = chloro Br = bromo I = iodo

Haloalkanes

Classify according to the number of carbons

bonded directly to the alkyl halide.

Haloalkanes

There can be multiple substitutions of halogens

for hydrogens, and also variations where

alkenes, alkynes or aromatics are involved.

C – O Bonds Organic Compounds

1. Alcohols

2. Ethers

Alcohols

IUPAC ending is …ol

Alcohols

Are organic compounds containing a hydroxyl group, -OH, substituted for a hydrogen atom.

The center of the alcohol functional group is the oxygen.

Have two lone pairs of electrons on the oxygen. This forces the molecular geometry on the

alcohol oxygen to be BENT. This portion of the molecule is flat, with bond angles of 109 degrees.

Alcohols

Are organic compounds containing a hydroxyl group, -OH, substituted for a hydrogen atom.

The names of alcohols start with the name of the alkane but end with the suffix –ol.

Can have more than one hydroxyl group for hydrogens, and also variations where alkenes, alkynes or aromatics are involved.

Use a prefix for multiple hydroxyl groups.

Alcohols

Are classified according to the number of carbon atoms attached directly to the carbon containing the hydroxyl group.

Ethers

… “oxy”….IUPAC ending ….ane

Ethers

Are compounds with the general formula:

The center of the ether functional group is the oxygen.

Have two lone pairs of electrons on the oxygen. This forces the molecular geometry on the ether

oxygen to be BENT. This portion of the molecule is flat, with bond angles of 109 degrees.

Ethers: Examples

Summary of Alcohols & Ethers

C - S Bonds Organic Compounds

1. Thiols

2. Thioethers

3. Disulfides

Thiols

IUPAC ending…thiols

Thiols

Are sometimes called sulfides. Are organic compounds containing a sulfhydryl

group, -SH, substituted for a hydrogen atom. Are the sulfur analogue of alcohols. Sulfur takes

the place of oxygen in the hydroxyl group of an alcohol.

Are stronger acids than alcohols. The –SH functional group itself is referred to as

either a thiol group or a sulfhydryl group.

Thiols

The center of the thiol functional group is the sulfur.

Have two lone pairs of electrons on the sulfur. This forces the molecular geometry on the thiol

sulfur to be BENT. The C–S–H angles approach 90°.

Thiols

Classified according to the number of carbon atoms bonded directly to the carbon containing the thiol group.

The names of thiols start with the name of the alkyl but end with the suffix –thiol.

Thiols

Can have more than one sulfhydryl group, and also variations where alkenes, alkynes or aromatics are involved.

Use a prefix for multiple thiol groups.

Thiols: Examples

Thioethers

IUPAC ending….sulfide

Thioethers

Are sometimes called sulfides. Are compounds with the general formula:

The center of the thioether functional group is the sulfur.

A thioether is similar to an ether except that it contains a sulfur atom in place of the oxygen.

Thioethers

Have two lone pairs of electrons on the sulfur. This forces the molecular geometry on the

thioether sulfur to be BENT. This portion of the molecule is flat, with bond

angles of 90 degrees.

Thioethers: Examples

Disulfides

IUPAC ending…..disulfide

Disulfides

Another class of sulfur containing molecules that have important biological implications.

Have the generic formula:

Are products from the oxidation of two thiols.

Disulfides The center of a disulfide functional group has two

sulfur atoms single bonded to each other and to two different carbon atoms.

Have two lone pairs of electrons on each sulfur. This forces the molecular geometry on the

thioether sulfur to be BENT.

Disulfides

Are named by naming the R groups attached to the sulfur atoms followed by the suffix -disulfide.

Dimethyldisulfide

Disulfides: Examples

Carbon and Nitrogen Organic Compounds

1. Amines

2. Nitriles

Amines

1. IUPAC ending ….amine

2. Prefix is …amino

Amines

Are organic compounds that contain nitrogen and are basic.

The general form of an amine is:

R represents an alkyl group, but either or both of the hydrogens may be replaced by other groups and still retain its class as an amine.

Amines

The center of the amine functional group is the nitrogen.

Have one lone pair of electrons on the nitrogen in addition to the single bonds.

This forces the molecular geometry on the amine nitrogen to be trigonal pyramid.

This portion of the molecule is not flat, with bond angles of 109 degrees.

Amines

The common names for simple aliphatic amines consist of the alkyl group followed by the suffix -amine.

The amino group (-NH2) is named as a substituent in more complicated amines, such as those that incorporate other functional groups or in which the alkyl groups cannot be simply named.

Amines

Are classified according to the number of carbon atoms bonded directly to the nitrogen atom.

Amines: Examples

Nitriles

1. IUPAC ending is …..nitrile

2. Prefix is …..cyano

Nitriles

Are organic compounds that have a

functional group.

Have one lone pair of electrons on the nitrogen

in addition to one triple bond with a carbon atom.

This forces the molecular geometry on the cyano

nitrogen to be linear.

Nitriles

The common names for simple nitriles consist of the alkane/alkyl followed by the suffix -nitrile.

The cyano group (−C≡N) is also used interchangeably.

Nitriles: Examples

Carbonyl Organic Compounds

1. Aldehydes

2. Ketones

Aldehydes (CHO)

IUPAC ending is …al

Aldehydes

Are compounds containing a carbonyl group with a hydrogen attached at end and an organic group of carbons at the other side.

The center of the aldehyde functional group is the carbon double bond oxygen.

Aldehydes

Have two lone pairs of electrons on the oxygen. With three atoms attached to this carbon, the

molecular geometry is trigonal planar. This portion of the molecule is flat, with bond

Aldehydes

IUPAC name includes the prefix from the alkyl groups and the suffix –al.

Aldehydes

IUPAC name for cyclic aldehydes includes the prefix cyclo and the suffix carbaldehyde.

Aldehydes: Examples

Ketones

IUPAC ending is …one

Ketones

Are compounds containing a carbonyl group with two hydrocarbon groups attached to it.

The center of the ketone functional group is the carbon double bond oxygen.

Ketones

Have two lone pairs of electrons on the oxygen. With three atoms attached to this carbon, the

molecular geometry is trigonal planar. This portion of the molecule is flat, with bond

Ketones

IUPAC name includes the prefix from the alkyl group and the suffix -one.

For more than one ketone group, use a prefix.

Ketones: Examples

Summary of Aldehydes & Ketones

Carboxyl Derivatives

1. Carboxylic Acids

2. Esters

3. Amides

4. Thioesters

Are derivatives of carboxylic acids.

Can be distinguished from aldehydes and

ketones by the presence of a group

containing an electronegative heteroatom -

usually oxygen, nitrogen, or sulfur – bonded

directly to the carbonyl carbon.

Have two sides:

1. The carbonyl group attach to an alkyl group. This is called an acyl group.

2. The heteroatom-containing group, refer to as the ‘acyl X' group

Carboxylic Acids

IUPAC ending is …oic acid

Carboxylic Acids

Are important intermediate products for the production of esters and amides.

Are hydrocarbon derivatives for which the functional group is the carboxyl group.

The center of the acid functional group is the carbon double bonded to an oxygen and single bonded to a hydroxyl group.

Carboxylic Acids

Each oxygen atom has a pair of lone electrons. With three atoms attached to this carbon, the

molecular geometry is trigonal planar. This portion of the molecule is flat, with bond angles of 120 degrees.

An additional molecular geometry is centered on the oxygen of the - OH group. This is bent.

Carboxylic Acids

In the IUPAC system, the –e ending in alkane is removed from the name of the parent chain and is replaced -anoic acid for the COOH acidic bond system.

Carboxylic Acids

Cyclic carboxylic acids that are saturated are called cycloalkane carboxylic acids.

Dicarboxylic acids are known as alkanedioic acids.

Carboxylic Acids

Carboxylic Acids: Examples

Esters

IUPAC ending …oate

Esters

Are compounds with the general formula:

The center of the ester functional group is the carbon double bonded to an oxygen and single bonded to an oxygen attached to an alkyl group.

Esters

Each oxygen atom has a pair of lone electrons. With three atoms attached to this carbon, the

molecular geometry is trigonal planar. This portion of the molecule is flat, with bond angles of 120 degrees.

An additional molecular geometry is centered on the oxygen with all single bonds. This is bent.

Esters

Complex esters are more frequently named using the systematic IUPAC name, based on the name for the alkyl group followed by the suffix –oate.

Cyclic esters are called lactones.

Esters: Examples

Amides

IUPAC ending is …amide

Amides

Also known as an acid amide. Are formed when carboxylic acids react with

amines. Are nitrogen-containing organic compounds with

the general formula

Amides

The center of the amide functional group is the carbon double bonded to oxygen and single bonded to nitrogen.

Classified according to the number of carbons attached directly to the nitrogen atom:

Amides

The oxygen atom has two lone pair of electrons. The nitrogen atom has one pair of lone electrons.

With three atoms attached to this carbon, the molecular geometry is trigonal planar. This portion of the molecule is flat, with bond angles of 120 degrees.

Amides

The molecular geometry centered on the nitrogen is bent and also flat as an extension of the trigonal planar geometry.

Amides

In the IUPAC system: For primary amides, the –e is removed from the

alkane name and the suffix -amide is added.

Amides

For 2⁰ and 3⁰ amides, alkyl groups attached to the nitrogen are named as substituents.

The letter N is used to indicate they are attached to the nitrogen.

For more than one of the same substituent groups, use a prefix.

Amides

Amides: Example

Thioesters

1. IUPAC ending….-thioate or -carbothioate

2. Prefix….thio & ending….-ate or -carboxylate

Thioesters

Are the product of esterification between a carboxylic acid and a thiol.

Are compounds with the functional group:

The center of the thioester functional group is the carbon double bonded to an oxygen and single bonded to sulfur attached to an alkyl group or hydrogen.

Thioesters

The oxygen and sulfur atoms, each, have two sets of lone pairs electrons.

With three atoms attached to this carbon, the molecular geometry is trigonal planar. This portion of the molecule is flat, with bond angles of 120 degrees.

Thioesters

The molecular geometry centered on the sulfur is bent and also flat as an extension of the trigonal planar geometry.

Thioesters

In the IUPAC system, the name consist of the alkyl group followed by the alkane with the suffix –thioate or –carbothioate

Alkyl groups attached to the sulfur are named as substituents. The letter S is used to indicate they are attached to the sulfur.

S-Methyl ethanethioate (IUPAC)

Thioesters

For common names, the name consist of the alkyl group followed by the prefix “thio” before the common name with the suffix –ate or -carboxylate.

Alkyl groups attached to the sulfur are named as substituents. The letter S is used to indicate they are attached to the sulfur.

S-PENTACHLOROPHENYL PENTACHLORO-1,3-BUTADIENE-1-THIOCARBOXYLATE

Thioesters: Examples

Summary of Carboxyl Derivatives

Summary of Functional Groups

Organic Reactions

1. Chemical Bonds2. Non-polar Reactions

3. Polar Reactions4. Classifications

Chemical Bonds in Reactions

1. Bond Breaking

2. Bond Forming

Chemical Bond Breaking

Polar reactions involve heterolytic bond cleavage

Radical reactions involve homolytic bond cleavage

Chemical Bond Making

Non-polar Reactions

Free Radicals Formation

Free Radicals

Are neutral and electron-deficient. They do not meet the octet rule. Examples:

Free Radicals

Stability of free radicals:

Free Radicals

React to complete its valence shell.

General Form:

Non-polar Reactions

Termination step:

Polar Reactions

1. Nucleophiles

2. Electrophiles

Lewis acid-base definition: transfer of electron pair from a base to an acid

Definitions

Nucleophiles

Are attracted to a positively charged cations or atoms with partially positive dipole.

Share or transfer its electrons with an electrophile during a reaction.

Nucleophiles

Can be negatively charged anions, neutral ions, molecules with a lone pair of electrons or at least one π bond.

Because nucleophiles donate electrons, they are by definition Lewis bases.

Nucleophiles: Examples

Electrophiles

Atoms that are positively charged, carry a partially positive dipole, or does not have an octet of electrons.

Attracted to electrons of nucleophiles in a chemical reaction.

Because electrophiles accept electrons, they are Lewis acids.

Electrophiles

H+ NO+

HCl Alkyl halides Acyl halides Cl2

Organic peracids Carbenes Radicals BH3

Carbonyl compounds Diisobutylaluminium

hydride (DIBAL)

The most common in organic syntheses are:

Polar Reactions

Nucleophiles – transfers electrons to an electrophilic atom

Electrophiles - accept electrons from a nucleophilic atom

Polar Reactions

General Form:

Products never exceed the octet rule.

Polar Reactions

The nucleophilic site can be neutral or negatively charged.

Polar Reactions

The electrophilic site can be neutral or positively charged.

Organic Reactions

1. Addition2. Elimination 3. Substitution

4. Rearrangement5. Condensation

6. Esterification7. Hydrolysis

8. Oxidation & Reductions

9. Combustion

Addition Reactions

The components of an organic molecule A–B are added to the carbon atoms in a C=C bonds.

Involve the conversion of a π bond into 2 σ bonds.

General form: A + B → C

Addition Reactions

Symmetrical alkenes produce one product.

Unsymmetrical alkenes produce racemic mixtures.

Addition Reactions

Alcohols are often produced by addition reactions.

Initial attack by the π bond of an alkene on a Hδ+ of H3O+ produces a carbocation.

The carbocation then undergoes nucleophilic attack by a lone pair of electrons from H2O.

This is followed by elimination of H+ to form the alcohol.

Addition Reactions

With symmetrical alkenes, addition of hydroxyl group produces one type of alcohol.

Addition Reactions

With unsymmetrical alkenes, addition of

hydroxyl group produces different types of

alcohols depending on the location of the

double bond

Addition Reactions

Formation of hemiketals & hemiacetals: Reactions between an acohol and either a

ketone or aldehyde.

Elimination Reactions

The removal or “elimination” of adjacent atoms from a molecule.

Two σ bonds are lost, replaced by a new π bond.

The dehydration reaction of alcohols to generate alkene proceeds by heating the alcohols in the presence of a strong acid, such as sulfuric or phosphoric acid, at high temperatures.

The required range of reaction temperature

decreases with increasing substitution of the

hydroxyl carbon:

1° alcohols: 170° - 180°C

2° alcohols: 100°– 140 °C

3° alcohols: 25°– 80°C

If the reaction is not sufficiently heated, the alcohols do not produce alkenes, but they react with one another to form ethers (Williamson Ether Synthesis).

General form: A → B + C

1⁰ Alcohols

2⁰ Alcohols

In dehydration reactions of alcohols, hydride

or alkyl shifts relocate the carbocation to a

more stable position.

The dehydrated products are a mixture of

alkenes, with and without carbocation

rearrangement.

Hydride or alkyl shifts are the result of

hyperconjugation. The interaction between the

filled orbitals of neighboring carbons and the singly

occupied p orbital in the carbocation stabilizes the

positive charge in carbocation.

The tertiary cation is more stable than a secondary

cation, which is more stable than a primary cation.

Hydride shift:

Alkyl shift:

Substitution Reactions

Nucleophilic substitution reactions. An electronegative atom is replaced by

another more electronegative atom, called a stronger nucleophile.

The stronger nucleophile must possess a pair of electrons and have a greater affinity for the electropositive carbon atom than the original electronegative atom.

A σ bond is replaced by another σ bond .

General form: A + B → C + D

Non-polar reactions:

Polar reactions:

Rearrangement Reactions

Are isomerisation reactions. An organic molecule changes structure. Constitutional change in carbon skeleton. Reaction may involve changes in bond type.

General form: A → B

Condensation Reactions

Two molecules combine to form one single

molecule with the loss of a small molecule.

When this small molecule is water, it is known

as a dehydration reaction.

Other possible small molecules lost include

hydrogen chloride, methanol, or acetic acid.

When two separate molecules react, their condensation is termed intermolecular.

The condensation of two amino acids to form a peptide bond (red) with expulsion of water (blue).

When a condensation is performed between

different parts of the same molecule, the

reaction is termed intramolecular

condensation.

In some cases this leads to ring formation.

Esterification Reactions

Esters are obtained by refluxing a carboxylic acid with an alcohol in the presence of an acid catalyst.

The reaction is driven to completion by using an excess of either the alcohol or the carboxylic acid, or by removing the water as it forms.

Alcohol reactivity order : CH3OH > 1o > 2o > 3o (steric effects).

A carboxylic acid and an alcohol react together under acidic conditions to form an ester and lose water.

Esters can also be made from other carboxylic acid derivatives, especially acyl halides and anhydrides, by reacting them with the appropriate alcohol in the presence of a weak base.

If a compound contains both hydroxy- and carboxylic acid groups, then cyclic esters or lactones can form via an intramolecular reaction. Reactions that form 5- or 6-membered rings are particularly favorable.

Pericyclic esters

Hydrolysis

A reaction in which water is a reactant, and

becomes part of the reaction product.

A number of organic compounds undergo

hydrolysis with water, such as amides, esters,

halogenoalkanes and acyl halides.

Hydrolysis

Reactions require a catalyst.

The catalyst is either an acid (H+ ions) or alkali

(OH- ions).

Hydrolysis might involve refluxing in the

presence of dilute hydrochloric acid or sodium

hydroxide solution.

Hydrolysis

In the overall reaction, a bond in an organic molecule is broken.

A water molecule also breaks into ions. The -OH group from water is added to one

end of the organic molecule and the remaining H atom is added to the other.

Hydrolysis of an Ester:

The addition of a strong acid, such as dilute hydrochloric acid, is required to free the carboxylic acid molecule.

In the base-catalyzed, the carboxylic acid molecule loses a proton to a hydroxide ion.

Hydrolysis of Amides & Nitriles:

Amide acid catalyzed - HCl

Nitrile acid catalyzed – HCl or H2SO4

Hydrolysis of Halogenalkanes:

Hydrolysis of Aromatics

Summary of Hydrolysis Reactions

1. The hydrolysis of a primary amide:

RCONH2 + H2O → RCOOH + NH3

2. The hydrolysis of a secondary amide:

RCONHR' + H2O → RCOOH + R'NH2

Summary of Hydrolysis Reactions

3. The hydrolysis of an ester:

RCOOR' + H2O → RCOOH + R'OH

4. The hydrolysis of a halogenoalkane:

RBr + H2O → ROH + H+ + Br-

Reduction & Oxidation (REDOX) Reactions

1. Oxidation States

2. Oxidations

3. Reductions

Definitions

Oxidation-Reduction reactions: Involve changes in oxidation state at one or more

atoms. Can often be identified by changes in the number

of oxygen atoms at a particular position in the hydrocarbon skeleton or in the number of bonds between carbon and oxygen at that position.

It is not consider an oxidation or reduction reaction: Addition or loss of H+, H2O, HX.

Definitions

Oxidation: The oxidation state increases Loss of H2 Loss of a C-H bond Addition of O or O2

Formation of a C-O bond or equivalent (C-Cl, CΞN, C-S)

Addition of X2 (halogens)

Definitions

Reduction: The oxidation state decreases Addition of H2 or H-

Formation of a C-H bond Loss of O or O2

Loss of a C-O bond or equivalent Loss of X2.

An increase in the number of hydrogen atoms in a hydrocarbon is often an indication of a reduction.

Oxidation States

Carbon oxidation states are assigned on the basis of the electronegativity of attached atoms. For each bond to a more electronegative atom

give +1. For each bond to a less electronegative atom

(even H) give –1. For each bond to carbon give 0.

Oxidation States

In nitrogen-containing compounds, the number of carbon–nitrogen bonds changes with the oxidation state of carbon.

Oxidation States

Assign oxidation states to all atoms in the following structure:

C+1 HO +3

H+1H+1+1

1) Identify if the following reactions are oxidation-reduction reactions.

2) For any that are, identify the atoms that are oxidized and reduced.

Br I+ NaI +NaBr

O+ KMnO4 + MnO2 + H2O

Problem

No, both Br and I are more electronegative than C

Yes, the carbon atoms are reduced, the H2 molecule is oxidized

Problem

Summary of Oxidation States

REDOX Reactions of Alcohols

Alcohols can undergo either oxidation or

reduction type reactions.

Oxidation is a loss of electrons.

Reduction is a gain of electrons.

Oxidation of Alcohols

1⁰ and 2⁰ alcohols are easily oxidized by a variety

of reagents.

The most common reagents used:

Pyridinium chlorochromate (PCC)

Potassium permanganate

Thermal dehydrogenation

Oxidation of Alcohols

The most common reagent used for oxidation of 2⁰

alcohols to ketones is chromic acid, H2CrO4.

3⁰ alcohols are resistant to oxidation because they

have no hydrogen atoms attached to the oxygen

bearing carbon (carbinol carbon).

Oxidation of 1 ⁰ Alcohols

1⁰ alcohols are easily oxidized just like 2⁰ alcohols. The product of oxidation is an aldehyde. The aldehyde is easily oxidized to an acid as a result

of “over-oxidation”.

A reagent that selectively oxidizes a 1⁰ alcohol to an aldehyde is pyridinium chlorochromate, PCC.

Oxidation of 2 ⁰ Alcohols

The alcohol and chromic acid produce a chromate ester, which then reductively eliminates the Cr species.

The Cr is reduced (VI IV), the alcohol is oxidized to a ketone.

Summary of Oxidation of Alcohols

Reduction of Alcohols

Normally an alcohol cannot be directly reduced to

an alkane in one step.

The –OH group is a poor leaving group and

hydride displacement cannot happen.

Instead, the hydroxyl group is easily converted into

other groups that are better leaving groups, and

allow reaction to move forward.

Commons reagents are tosyl chloride and lithium aluminum hydride (LiAlH4).

The reaction involves the formation of a tosylate. The tosylates can undergo either substitution or

elimination reactions.

The tosylate reduces to cyclohexane very easily with lithium aluminum hydride.

Reduction of Carboxylic Acids

Carboxylic acids are reduced to 1⁰ alcohols.

Reduction of Esters

Esters are reduced to 1⁰ alcohols.

Reduction of Amides

Amides are reduced to 1⁰, 2⁰, or 3⁰ amines.

Reduction of Aldehydes

Aldehydes and ketones are reduced to 1⁰ and 2⁰ alcohols respectively.

Summary REDOX Reactions

Combustion Reactions

The reaction of an organic molecule with

oxygen to form carbon dioxide, heat/energy

and water.

Combustion Reactions

Alkanes:

Alkenes:

Alcohols

Introduction to Biochemistry

Part III – Foundations of Organic Chemistry in Biochemistry

Biochemistry

1. Macromolecules

4. Carbohydrates

Definitions

Biochemistry is the study of chemical compounds and reactions which occur in living organisms.

It overlaps extensively with organic chemistry since most compounds in living cells contain carbon.

Biochemistry involves the study of carbohydrates, lipids, proteins and nucleic acids, which are the types of molecules involved in the chemistry of living organisms.

Definitions

Hydrogen bonds – ionic and hydrophilic interactions between a polar or ionic molecules and water.

Definitions

Hydrophobic interactions - tendency of nonpolar substances to aggregate in aqueous solution and exclude water molecules.

Macromolecules

All living things contain these organic molecules: carbohydrates, lipids, proteins, and nucleic acids.

These organic molecules are often called macromolecules.

They may be very large, containing thousands of carbon and hydrogen atoms and bonded to other smaller molecules.

They are classified as polar, ionic or non-polar molecules.

Macromolecules

Polar and ionic molecules have either full or

partially (dipole) positive or negative charges.

They are attracted to water molecules.

They are said to be hydrophilic because

they interact with (dissolve in) water by

forming hydrogen bonds.

Macromolecules

Nonpolar molecules are neutral (NO dipole).

They are NOT attracted to water or polar

molecules.

They are hydrophobic because they DO

NOT dissolve in water or form hydrogen

bonds.

Macromolecules

Nonpolar molecules are hydrophobic.

Polar and ionic molecules are hydrophilic.

Macromolecules

Portions of macromolecules may be hydrophobic and other portions of the same molecule may be hydrophilic.

The chains may be branched or form rings.

Functional Groups in Biochemistry

1. Hydrocarbons

2. Aromatics

3. Common Functional Groups

Functional Groups

Some functional groups are polar and others can ionize.

For example, if the hydrogen ion is removed from the COOH group, the oxygen will retain both of the electrons and will have a negative charge.

The hydrogen that is removed leaves behind its electron and is now a hydrogen ion (proton, cation, H+).

Functional Groups

If polar or ionizing functional groups are attached

to hydrophobic molecules, the molecule may

become hydrophilic due to the functional group.

Some ionizing functional groups are: -CO2H, -OH,

R2-C=O, and -NH2.

Hydrocarbons

Cycloalkanes

Aromatic Compounds

Common Functional Groups

Summary of Functional Groups

Important bond linkages in Biochemistry:

Organic Reactions Classes:

1. Group Transfer

2. REDOX

3. Eliminations, Isomerizations,

Rearrangements

4. C-C Bond Making & Breaking

5. Hydrolysis

Group Transfer Reactions

Nucleophilic Substitution Transfer an electrophile from one nucleophile

to another. Commonly transferred groups:

1. Acyl

2. Phosphoryl

3. Glycosyl

4. Amino

Group Transfer Reactions: Acyl GroupAcylation Reactions

Group Transfer Reactions: Phosphoryl GroupPhsophorylation Reaction

Group Transfer Reactions: Glycosyl Group

Glycosylation Reactions

Group Transfer Reactions: Amino Group

Transamination Reactions

REDOX Reactions

Involve the loss or gain of electrons. C-H bond cleavage with the loss of electrons. Use of electron acceptors:

Coenzyme Q Fe centers in Cytochrome C

REDOX Reactions

Electrons are highly reactive and do not exist

on their own in cells.

If oxidation occurs to one molecule in the cell,

reduction must immediately to another

molecule.

REDOX Reactions

Formation of alkenes Products are:

Trans (anti) – Major Cis (syn)

Elimination of: Water Ammonia 1⁰ Amines Alcohols

Types of Mechanisms:1. Concerted

2. Carbocation Formation: C-O bond breakage

3. Carbanion Formation: C-H bond breakage

Two Types of Reactions:1. Dehydrations

2. Deaminations

Elimination Reactions: Concerted & Carbocation

Elimination Reactions: Carbanion

Elimination Reactions: Dehydration

Enzyme catalyzed reactions.

Two Types of Enzyme-Catalysis:

1. Acid: Protonation of OH group

2. Base: Abstraction of a proton

Elimination Reactions: Dehydradation

Other Dehydration Reactions

Condensation reactions. Involved in the assembly of all four types of

macromolecules. An H atom is removed from a functional

group on one molecule, and an OH group is removed from another molecule.

Products: a larger molecule + water

Condensation of Amino Acids

Condensation of Saccharides

Condensation of Fatty Acids

Elimination Reactions: Deaminations

Isomerization Reactions

Relocation of a = bond.

Intramolecular shift of a proton.

Most common are base catalyzed reactions.

Isomerization Reactions

Breaking and reforming C-C bonds to

rearrange carbon atoms in the backbone of a

molecule.

Useful in oxidation of odd number of carbon

atoms fatty acids and several amino acids.

C-C bond Breaking & Making Reactions Addition of a nucleophilic carbanion to an

electrophilic carbon atom. Most common electrophilic carbon atoms are

sp2 hybridized carbonyl carbon atoms:

1. Aldehydes

2. Ketones

3. Esters

4. Carbon Dioxide

C-C bond Breaking & Making Reactions1. Condensation

Aldol Claisen Ester Other Condensations Reactions:

o Amino Acids o Saccharides o Fatty Acids

2. Decarboxylations

Condensation Reactions: Aldol

Condensation Reactions: Claisen Esters

Decarboxylation Reactions

Removes a carboxyl group Releases carbon dioxide.

Decarboxylation Reactions

Decarboxylation Reactions: Citric Cycle

Decarboxylation Reactions: Precursors of the Citric Cycle

Hydrolysis

Involved in the breakdown of macromolecules into their monomers.

Water is added to break the bonds between monomers.

H from the water is added to one molecule, and the OH group is added to the adjacent monomer.

Covalent bond between monomers breaks to form two smaller molecules.

Hydrolysis of Proteins

Hydrolysis of Polysaccharides

Hydrolysis of Fats

Synthesis of Common Functional Groups

Biochemistry: The Chemistry of the Human Body

Part IV - Macromolecules

Macromolecules

Many of the common macromolecules are synthesized from monomers.

Carbohydrates

1. Monosaccharides

2. Disaccharides

3. Polysaccharides

Carbohydrates

Compounds which provide energy to living cells.

Made up of carbon, hydrogen and oxygen with a ratio of two hydrogens for every oxygen atom.

The name carbohydrate means "watered carbon" or carbon with attached water molecules.

Are used directly to supply energy to living organisms.

Carbohydrates

Many carbohydrates have empirical formuli which would imply about equal numbers of carbon and water molecules.

The general formula for carbohydrates is (CH2O)n.

The names of most sugars end with the letters -ose.

The pentose sugars ribose and deoxyribose are important in the structure of nucleic acids like DNA and RNA.

Carbohydrates

Three key classification schemes for sugars are:

1. Monosaccharides

2. Disaccharides

3. Polysaccharides

Monosaccharides

Simple sugars, having 3 to 7 carbon atoms. Are linear molecules but in aqueous solution they

form a ring form structure. In aqueous solution, monosaccharides with

five or more C atoms form cyclic ring structures.

These 6-membered ring compounds are called pyranoses.

These rings form due to a general reaction that occurs between alcohols and aldehydes or ketones to form derivatives called hemiacetals or hemiketals.

Monosaccharides

May form several types of stereoisomers since

they share the same molecular formula.

Four Classes of Stereoisomers:

1. Diastereomers

2. Enantiomers

3. Epimers

4. Anomers

Monosaccharides: Isomers

Monosaccharides: Diastereomers

Stereoisomers that are not mirror images of each other.

Diastereomers for the molecular formula C5H10O5:

Monosaccharides: Diastereomers

Diastereomers for the molecular formula C6H12O6:

Monosaccharides: Enantiomers

Stereoisomers that are mirror images of each other. Two types: D or L

Monosaccharides: Epimers

Two diastereomers that differ around one chiral center.

Monosaccharides: Anomers

Stereoisomers that differ in the configuration around the anomeric carbon.

Two types of anomers are: α or β. In hemiacetals, the anomeric carbon is at position 1.

Monosaccharides: Anomers

In hemiketals, the anomeric carbon is at position 2.

Disaccharides

Glycosides

Formed from two monosaccharides.

The -OH of one monosaccharide condenses with

the intramolecular hemiacetal of another

monosaccharide, forming a glycosidic bond.

Glycosidic bonds can be: α or β.

Disaccharides

Common disaccharides are:

1. Sucrose

2. Lactose

3. Maltose

4. Trehalose

Disaccharides

Sucrose

Prevalent in sugar cane and sugar beets

Sucrose

Lactose

Found exclusively in milk.

Lactose

Maltose

Major degradation product of starch.

Maltose

Trehalose

Found in bacteria, yeast, invertebrates, mushrooms and seaweed.

Glycosidic Linkages:

Protects organisms from extreme temperatures and drying out.

Trehalose

Is used: As a preservative for foods and to minimize

harsh flavors and odors. As a moisturizer in cosmetics. As an natural sweetener for diabetics. Antioxidant to stabilize proteins and lipids in

neurodegenerative diseases like Alzheimer's and Huntington's Disease.

To protect organs for transplants.

Trehalose

Is: Involved in the regulation of developmental

and metabolic processes in plants. The major transport sugar in shrimp, insects

and plants. The major carbohydrate energy storage

molecule used by insects for flight.

Trehalose

In plants, synthesis is carried out by trehalose phosphate synthase and trehalose phosphatase:

Trehalose

Degradation:

Trehalase

Polyssacharides

Ten or more monosaccharides bonded together to form long chains.

The chains are typically contain hundreds of monosaccharaides.

Can have one, two or many different types of monosaccharides.

1. Homopolysaccharides

2. Heteropolysaccharides

Polyssacharides

Are classified as:

1. Cellulose

2. Chitin

3. Glycogen

4. Starches

Cellulose & Chitin

Are polysaccharides with 1500 glucose rings chain together.

Function is support and protection. The monomers of cellulose and chitin are

bonded together in such a way that the molecule is straight and unbranched.

The molecule remains straight because every other glucose is twisted to an upside-down position compared to the two monomers on each side.

Cellulose & Chitin

Humans and most animals do not have the necessary enzymes needed to break the linkages of cellulose or chitin.

Some bacteria and some fungi produce enzymes that digest cellulose.

Some animals have microorganisms in their gut that digest cellulose for them.

Fiber is cellulose, an important component of the human diet.

Cellulose

Is composed of beta-glucose monomers. Cellulose fibers are composed of long parallel

chains of these molecules. The chains are attached to each other by

hydrogen bonds between the hydroxyl groups of adjacent molecules.

The cell walls of plants are composed of cellulose.

Cellulose

Chitin

The cell walls of fungi and the exoskeleton of arthropods are composed of chitin.

The glucose monomers of chitin have a side chain containing nitrogen.

Chitin

Glycogen

Animals and some bacteria store extra carbohydrates as glycogen.

In animals, glycogen is stored in the liver and muscle cells.

Between meals, the liver breaks down glycogen to glucose in order to keep the concentration of glucoses in the blood stable.

After meals, as glucose levels in the blood rise, glucose is removed from the blood and stored as glycogen.

Glycogen

Homopolymer of glucose. Two types of glycosidic linkage: α–(1, 4) for straight chains α–(1, 6) for branched chains, occurring every

8-10 residues.

Glycogen

Glycogen is a very compact structure that

results from the coiling of the polymer chains.

This compactness allows large amounts of

carbon energy to be stored in a small volume,

with little effect on cellular osmolarity.

Starches

Starch and glycogen are composed of 300 –

1000 alpha-glucose units join together.

It is a polysaccharide which plants use to

store energy for later use.

Starches are smaller than cellulose units, and

can be more readily used for energy.

Starches

Foods such as potatoes, rice, corn and wheat

contain starch granules which are important energy

sources for humans.

The human digestive process breaks down the

starches into glucose units with the aid of enzymes,

and those glucose molecules can circulate in the

blood stream as an energy source.

Starches

Amylopectin is:

1. A form of starch that is very similar to

glycogen.

2. Branched but have less branches than

glycogen.

Amylose is:

A form of starch that is unbranched.

Starches

Starches & Glycogen

The bond orientation between the glucose subunits of starch and glycogen allows the polymers to form compact spirals.

Summary of Carbohydrates CHO Monosaccharides:

simple sugars Functional group(s):

Carboxyl Hydroxyl

Disaccharides Polysaccharides

Summary of Carbohydrates

Proteins

Definitions

Peptide - a short chain of amino acids bonded together.

Oligopeptide- a short chain of at least 2 amino acids and up to 20 amino acids long.

Polypeptide - a longer chain of many amino acids, typically 50 or more.

Proteins - consist of one or more polypeptides, subunits, chains or domains.

Proteins

Are the building materials for living cells, appearing in

the structures inside the cell and within the cell

membrane. About 75% of the dry weight of our bodies.

They contain carbon, hydrogen, oxygen, nitrogen,

sulfur and phosphorus.

Protein molecules are often very large and are made

up of hundreds to thousands of amino acid units.

Proteins

Functions:

Transport oxygen (Hb)

Build tissue (Muscle)

Copy DNA for cell replication

Support the body as structural proteins

Components of cell membranes (receptors, membrane

transport, antigens)

Control metabolic reactions as regulatory proteins called

enzymes

Proteins

Functions:

Hormones

Storage (egg whites of birds, reptiles; seeds)

Protection (antibodies)

Toxins (botulism, diphtheria) Some proteins are in solution in the blood and other body

fluids. Others are solids that make up the framework of tissue,

bone and hair.

Proteins

Proteins can be characterized as extremely long-

chain polyamides. The amides contain nitrogen,

and nitrogen composes about 16% of the protein

atomic content.

In the cell, the DNA directs or provides the

master blueprint for creating proteins, using

transcription of information to mRNA and then

translation to actually create proteins.

Proteins

Proteins are synthesized via condensation of amino

acids under the influence of enzyme catalysts.

The 20 amino acids are combined in different ways to

make up the 100,000 or so different proteins in the

human body.

The amino acid units in a protein molecule are held

together by peptide bonds, and form chains called

polypeptide chains.

Proteins

During translation, the protein goes through several different structural stages:1. Primary

2. Secondary

3. Tertiary

4. Quaternary Final structures may undergo post-

translational modifications based on their determined function.

Proteins

Subunit or domain

Proteins: Primary Structure

The sequence of amino acids in the polypeptide chain.

The sequence of the R groups determines the folding of the protein.

A change of a single amino acid can alter the function of the protein.

Sickle cell anemia - caused by a change of one amino acid from glutamine to valine.

Proteins: Primary Structure

Proteins: Secondary Structure

Folding and coiling due to H bond formation between carboxyl and amino groups of non-adjacent amino acid.

R groups are NOT involved. This bonding produces two common kinds of shapes

seen in protein molecules- coils, called alpha helices, and beta sheets.

A single polypeptide may contain many of these helices and sheets.

Proteins: Secondary Structures

AlphaBeta

Proteins: Tertiary Structure

The overall 3-dimensional shape of the polypeptide chain.

Hydrophobic interactions with water molecules are important in creating and stabilizing the structure of proteins.

Hydrophobic (nonpolar) amino acids aggregate to produce areas of the protein that are out of contact with water molecules.

Hydrophilic (polar and ionized) amino acids form hydrogen bonds with water molecules.

Hydrogen bonds and ionic bonds form between R groups to help shape the polypeptide chain.

Disulfide bonds are covalent bonds between sulfur atoms in the R groups of two different amino acids. These bonds are very important in maintaining the tertiary structure of some proteins.

The shape of a protein is typically described as

being globular or fibrous.

Globular proteins contain both coils and sheets.

Fibrous proteins are elongated molecules in

which either α-helices or β-pleated sheets are

the dominant structures.

Proteins: Quaternary Structure

Relationship among multiple polypeptide chains forming one protein structure.

Contain two or more tertiary structures that associate to form a single protein.

The overall 3-D structure is due to interactions between polypeptide chains after synthesis:

1. Hydrophobic & hydrophilic interactions

2. H- bonds

3. Ionic interactions

4. Disulfide bonds

Proteins: Quaternary Structure

Proteins: Enzymes

Some proteins are structural, but some are control proteins called enzymes.

These enzymes can be used in the synthesis of proteins, including their own synthesis.

Each protein, including enzymes, is made according to a pattern of nucleotides along a segment of the DNA called a "gene".

A single living cell contains thousands of enzymes.

Proteins: Enzymes

Speed up the rate of chemical reactions.

Proteins are able to function as enzymes due

to their shape.

Enzyme molecules are shaped like the

reactants, allowing the reactants to bind closely

with the enzyme.

Proteins: Enzymes

Have a small a pocket located on the 3-D surface of the folded protein.

This is the binding site, where the substrate binds and chemical reactions take place .

The binding site matches the shape of the

substrate molecules.

The enzyme is then able to hold the substrate

molecules in the correct orientation for the

chemical reaction to proceed.

The enzyme itself does not participate in the

reaction and is not changed by the reaction.

Proteins: Enzymes

Other Kinds of Proteins

Simple proteins contain only amino acids.

Conjugated proteins contain other kinds of

molecules.

Three key classes of conjugated proteins:

1. Glycoproteins (carbohydrates)

2. Nucleoproteins (nucleic acids)

3. Lipoproteins (lipids)

Conjugated Proteins

Amino Acids

Are organic compounds. Each has a carboxyl group and an amino group

attached to the same carbon atom, called the alpha carbon.

Amino acids have the general form:

Amino Acids

There are 20 amino acids which make up the proteins, distinguished by the R-group.

The structure of the R-group determines the chemical properties of the amino acid.

Types of chemical properties:

1. Polar Charged

2. Nonpolar

3. Electrically Charged

Amino Acids: Polar Uncharged

Are hydrophilic and can form hydrogen bonds.

1. Serine

2. Threonine

3. Glutamine

4. Asparagine

5. Tyrosine

6. Cysteine

Amino Acids: Nonpolar

Are hydrophobic and are usually found in the center of the protein.

Also found in proteins which are associated with cell membranes.

1. Glycine2. Alanine3. Valine4. Leucine

5. Isoleucine6. Methionine7. Phenylalanine8. Tryptophan9. Proline

Amino Acids: Electrically Charged

Have electrical charges that can change depending on the pH.

1. Aspartic Acid

2. Glutamic Acid

3. Lysine

4. Arginine

5. Histidine

Amino Acids: Chemical Properties

The simplest amino acid is glycine. It fits in

tight spaces in the 3-D structure of proteins. It

contain hydrogen as an R group.

Cysteine can form covalent disulfide bonds in

3 and 4 structures.⁰ ⁰

Proline has a unique structure and causes

kinks in the protein chains.

Amino Acids

Amino acids are the structural elements from which proteins are built.

When amino acids bond to each other, it makes an amide bond.

This bond is formed as a result of a condensation reaction between the amino group of one amino acid and the carboxyl group of another.

Amino Acids

Amino acids can have either left-handed or right-handed molecular symmetry.

The most common are left-handed amino acids. These are the building blocks of proteins.

Amino Acids

The human body can synthesize all of the amino acids necessary to build proteins, except for the ten called the “essential amino acids”.

An adequate diet must contain these essential amino acids.

Typically, they are supplied by meat and dairy products, but if those are not consumed, some care must be applied to ensuring an adequate supply.

Amino Acids: Non-essential

The 10 amino acids that we can produce are:

alanine, asparagine, aspartic acid, cysteine,

glutamic acid, glutamine, glycine, proline,

serine and tyrosine.

Tyrosine is produced from phenylalanine, so

if the diet is deficient in phenylalanine,

tyrosine will be required as well.

Amino Acids: Essential

The essential amino acids are: arginine (required

for growing children), histidine, isoleucine, leucine,

lysine, methionine, phenylalanine, threonine,

tryptophan, and valine.

Humans do not have all the enzymes required for

the biosynthesis of essential amino acids.

Amino Acids

The failure to obtain enough of any of the 10 essential amino acids has serious health implications and can result in degradation of the body's proteins.

Muscle and other protein structures may be degraded to obtain the one amino acid that is needed.

The human body does not store excess amino acids for later use. The amino acids must be obtained from food daily.

Amino Acids

Summary of Proteins & Amino Acids

Monomer: amino acids 20 total, 9 or 10 essential

Functional group(s): Carboxyl Amino

Polymer Polypeptide Protein

Summary of Amino Acids

Nucleic Acids

Control the processes of heredity:

Transcription

Translation

Cell Replication

The key nucleic acids are:

DNA (deoxyribonucleic acid)

RNA (ribonucleic acid)

Nucleic Acids

Nuclei acid consist of a long chain of units

called nucleotides.

Nucleotides are the basic structural units of

nucleic acids

The nucleotides are made up of a phosphate

group, a pentose sugar, and a nitrogen base.

Nucleic Acids

The sugar ribose is characteristic of RNA.

The sugar deoxyribose is characteristic of

Nucleic Acids

For RNA, the bases are adenine, guanine,

cytosine and uracil.

For DNA, the bases may be adenine, guanine,

cytosine or thymine.

Nucleic Acids

The larger bases adenine and guanine are purines which differ in the kinds of atoms that are attached to their double ring.

The other bases (cytosine, uracil, and thymine) are pyrimidines, which differ in the atoms attached to their single ring.

The resulting DNA (deoxyribonucleic acid) contains no uracil, and RNA(ribonucleic acid) does not contain any thymine.

Stores information regarding the sequence of amino acids in each of the body’s proteins.

Is the master blueprint for the production of proteins and cell replication.

In protein synthesis, serves as a pattern for mRNA synthesis, in a process called transcription.

mRNA contains all the DNA information to manufacture a protein, in a process called translation.

DNA Structure

Is a double helix. The bases may be attached in any order. This

gives the vast number of possibilities of arrangements, making the genetic code diverse.

The bases are only attached by hydrogen bonds to their complementary base. This arrangement makes possible the separation of the strands and the replication of the DNA double helix.

DNA Structure

Antiparallel

1. The end of a single strand that has the

phosphate group is called the 5’ end. The

other end is the 3’ end.

2. The two strands of a DNA molecule run in

opposite directions.

DNA Structure

Complimentary base pairing

Two hydrogen bonds hold adenine to thymine.

Three hydrogen bonds hold cytosine to

guanine.

DNA Base Pairing

Is directly involved in the synthesis of proteins in a process called "translation".

mRNA itself is directed synthesized from DNA in a process called transcription.

mRNA is the template for the synthesis of all proteins.

RNA has many forms, but the three most important are messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA).

RNA Structure

RNA Base Pairing

The anti-sense strand is used as a template to

produce a single strand of mRNA.

The sequence of bases on a segment of DNA called

a gene is copied to a strand of mRNA with the

assistance of RNA polymerase.

The bases in the mRNA strand are complimentary to

the bases in DNA.

The mRNA contains three-letter codes, called a codon. It is the code for one amino acid.

The sequence of codes in DNA therefore determines the sequence of amino acids in the protein.

The mRNA has regions called introns and exons. Introns are not a part of the pattern for the protein

to be synthesized, so those segments are excised from the mRNA.

Exons are the only segments present before the mRNA's are released from the nucleus.

These pattern for protein synthesis is then read and translated into the language of amino acids for protein synthesis with the help of tRNA.

Is directly involved in the translation of the sequence of nucleotides in mRNA with rRNA.

The synthesis of tRNA itself is directed by the DNA in the cell that provides a pattern for the production of mRNA by "transcription".

When mRNA reaches rRNA to be translated, tRNA molecules with all the required amino acids must be present for the process to proceed.

Since most proteins use all twenty amino acids, all must be available, attached to appropriate tRNA molecules.

Is commonly called a cloverleaf form.

Binds an amino acid at one end opposite to

the anticodon on the other end.

This anticodon will bind to a codon consisting

of three nitrogenous bases which specify an

amino acid according to the genetic code.

The many types of tRNA have roughly the

same size and shape, varying from about 73

to 93 nucleotides.

Besides the usual bases A, U, G, and C, all

have a significant number of modified bases,

which are formed by modification after the

transcription.

Letter Code Modified Bases

I Inocine

mI methylinosine

mG methylguanosine

m2G dimethylguanosine

Psi Pseudouridine

D Dihydrouridine

All tRNAs have sequences of nucleotides that

are complementary to other parts of the

molecule and base-pair to form the five arms

of the tRNA.

Four of the arms are fairly consistent, but the

variable arm can range from 4 to 21

nucleotides.

Associates with a set of proteins to form ribosomes.

Physically moves an mRNA molecule and catalyze the assembly of amino acids into protein chains.

Binds tRNAs and various accessory molecules necessary for protein synthesis.

Ribosomes are composed of a large and small subunit, each of which contains its own rRNA molecule or molecules.

Translation

Translation is the whole process by which the

base sequence of an mRNA is used to bring and

join amino acids in a polypeptide.

The three types of RNA participate in this

essential protein-synthesizing pathway in all

cells.

Translation

Adenosine triphosphate is a nucleotide that is

used in energetic reactions for temporary energy

storage.

Energy is stored in the phosphate bonds of ATP.

The cells use the energy stored in ATP by

breaking one of the phosphate bonds, producing

Summary of Nucleic Acids

Monomer: nucleotide A, T (or U), C, G

Functional group(s): Phosphate Amino Hydroxyl

Polymer: DNA and RNA

Basic Nucleotide Structure

Summary of Nucleic Acids

Lipids

Fats, oils, waxes, and sterols are collectively known as lipids.

Fats contain only carbon, hydrogen, and oxygen.

Lipids

Are insoluble in water but soluble in nonpolar solvents.

Are also an important component of cell membranes.

Used for long-term energy storage. One gram of fat stores more than twice as

much energy as one gram of carbohydrate.

Lipids

Important classes of lipids:

1. Phospholipids

2. Steroids

3. Glycerides

4. Waxes

Phospholipids

Contain: Phosphate group on third -OH group of

glycerol. Two fatty acids.

Have a polar head, which increases hydrophilicity.

Phospholipids

Arrange themselves into double-layered membranes with the water-soluble phosphate ends on the outside and the fatty acid facing the inside.

Cell membranes are not rigid or stiff since phospholipids are in constant motion as they move with the surrounding water molecules and slide past one another.

Phospholipids

They also form spheroid structures called micelles.

Steroids

Have no fatty acid component. Contains a backbone of 4 carbon rings in 6-

6/6-5 arrangement. Examples:

Hormones Cholesterol Cell membrane components

Steroids

Steroids: Cholesterol

Cholesterol is a vital component of the cell membranes and used by cells to synthesize other steroids.

High cholesterol levels are associated with heart disease and the formation of plaques which obstruct blood vessels.

High blood levels of cholesterol bound to a carrier molecule called a low-density lipoprotein (LDL) are associated with the formation of the plaques in arteries.

Steroids: Cholesterol

Cholesterol bound to high-density lipoproteins tends to be metabolized or excreted and is often referred to as "good cholesterol".

Glycerides

Fats and oils are composed of fatty acids and glycerol.

Fatty acids have a long hydrocarbon chain with a carboxyl group.

The chains of fatty acids usually contain 16 to 18 carbons.

Fats are nonpolar and therefore they do not dissolve in water.

Glycerides

Fats are generally classified as esters of fatty acids and glycerol.

There can be one to three ester linkages of fatty acid chains to the glycerol, leading to the classification as:

1. Monoglycerides

2. Diglycerides

3. Triglycerides

Glycerides: Nomenclature

Fatty Acids

Structure:

Two classes:

1. Saturated

2. Unsaturated

Saturated Fatty Acids

Have no double bonds between the carbons in

its fatty acid chains.

Animal fats are more highly saturated than

vegetable fats.

Highly saturated fats are usually solid at room

temperature.

Unsaturated Fatty Acids

Also called “polyunsaturated fat”.

Contain at least one to several double bonds

between the carbons in its fatty acid chains.

Each double bonds produces a "bend" in the

molecule.

Molecules with many bends cannot be packed

as closely together, so these fats are less dense.

Usually these fatty acid are oils.

Most oils are of vegetable origin.

Triglycerides composed of unsaturated fatty

acids melt at lower temperatures than those with

saturated fatty acids.

Trans fat is the common name for a type of

unsaturated fat with trans-isomer fatty acids.

Most trans fats consumed today are created

industrially by partial hydrogenation of plant oils.

The goal of partial hydrogenation is to add hydrogen

atoms to cis-unsaturated fats, making them more

saturated.

These saturated fats have a higher melting point,

which makes them attractive for baking and extends

their shelf-life.

Trans fats are not essential in the diet and have

been linked with rises in levels of "bad" LDL

cholesterol and lowering levels of "good" HDL

cholesterol.

Saturated & Unsaturated Fatty Acids

Triglycerides

Are made up of a glycerol molecule with three fatty acid molecules attached to it.

Glycerol contains 3 carbons and 3 hydroxyl groups.

It reacts with 3 fatty acids to form a triglyceride or fat molecule.

The naturally occurring fatty acids always have an even number of carbon atoms.

Triglycerides

Are composed of a long-chain fatty acid bonded to a long-chain alcohol

They form protective coverings for plants and animals (plant surface, animal ears).

Summary of Lipids

Monomer: Fatty acid Functional group(s):

Carboxyl Cholesterol Fused Rings Ester

Polymers: many – depending on the type of lipid Phospholipid, Steroid, Triglycerides, Waxes

Summary of Lipids

Summary of Biochemistry

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