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Introduction to Bioorganic Introduction to Bioorganic ChemistryChemistry

222

Chemistry of BiomoleculesChemistry of Biomolecules

A A biomoleculebiomolecule is a chemical compound th is a chemical compound that naturally occurs in living organisms.at naturally occurs in living organisms.

Biomolecules consist primarily of carbon aBiomolecules consist primarily of carbon and hydrogen, along with nitrogen, oxygen, nd hydrogen, along with nitrogen, oxygen, phosphorus and sulfur.phosphorus and sulfur.

Other elements sometimes are incorporateOther elements sometimes are incorporated but are much less common.d but are much less common.

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The Six Most Abundant The Six Most Abundant Elements of LifeElements of Life

THIS IS THE LEGAL CHNOPS!!

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Valence Valence

Each element has a characteristic valence that determines the number of covalent bonds it can form.A shared electron pair is called a covalent bond.

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Organic Molecules: HydrocarbonsOrganic Molecules: Hydrocarbons

Hydrocarbons the simplest organic molecules, contain only carbon and hydrogen atoms.

(a) Methane

(b) Ethane

(c) Ethene (ethylene)

Molecular Formula

Structural Formula

Ball-and-Stick Model

Space-Filling Model

H

H

H

H

H

H

H

H

H

H

H H

HH

C

C C

C C

CH4

C2H6

C2H4

Name and Comments

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IsomersIsomers

Organic molecules exist in three-dimensional Organic molecules exist in three-dimensional space, and the same set of atoms can be put space, and the same set of atoms can be put together in many recognizably different together in many recognizably different ways, resulting in molecules called isomers.ways, resulting in molecules called isomers.

1. Structural isomers: Variations in the position at which 1. Structural isomers: Variations in the position at which different atoms are joined together.different atoms are joined together.

2. Geometric isomers: Variations in the placement of 2. Geometric isomers: Variations in the placement of atoms around carbon atoms joined by double covalent atoms around carbon atoms joined by double covalent bonds.bonds.

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IsomersIsomers

(a) Structural isomers

(b) Geometric isomers

H H H H H

H

H H H H H

H

H

HH

H

H

H

H

H

H

H

HH

H

H

H

H

CO2H

CH3

NH2

C

CO2H

H

CH3

NH2

X X

X

X

C C C C C

C

C

C C C

C C C C

C

H

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Polarity (review)Polarity (review)

As we already know…Many combinations of different elements result in unequal electron sharing, called polar bonding.

As a result, the electron distribution is asymmetric, or polar, and the oxygen atom is said to be electronegative. This asymmetry results in regions of slight negative and positive charge in different regions of the molecule, denoted by the Greek symbol , for "partial" charge.                                                    

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The Functional GroupsThe Functional GroupsThe properties of different biological molecules depend on certain characteristic groupings of atoms called functional groups.The names of the six most important functional groups are:

– Hydroxyl– Carbonyl

–Aldehydes – Ketones

– Carboxyl– Amino– Sulfhydryl– Phosphate

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Hydroxyl GroupHydroxyl Group

OH

In a hydroxyl group (–OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–).Hydroxyl groups are not highly reactive, but they readily form hydrogen bonds and contribute to making molecules soluble in water.Alcohols and sugars are "loaded" with hydroxyl groups.

Ethanol

H

H

H

H H

C C OH

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Carbonyl GroupCarbonyl Group

Carbonyl group consists of a carbon atom joined to an oxygen atom by a double bond (symbolized as C=O).Like hydroxyl groups, carbonyl groups contribute to making molecules water-soluble. All sugar molecules have one carbonyl group, in addition to hydroxyl groups on the other carbon atoms.

C

O

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Two Forms of Carbonyl Groups: Aldehydes Two Forms of Carbonyl Groups: Aldehydes and Ketones and Ketones

Aldehyde groups, where the C=O group is at the end of an organic molecule. A hydrogen atom is also located on the same carbon atom.Keto groups, where the C=O group is located within an organic molecule. All sugars have either a keto or an aldehyde group. An aldehyde and a ketone may be structural isomers with different properties, as is the case for acetone and propanal.

C

O

C C C

H

H

H H

H O

H

H

H

HH

H

H

C C

C

O

Propanal, an aldehydeAcetone, a ketone

131313

Carboxyl Group (Acids)Carboxyl Group (Acids)

The carboxyl group (symbolized as COOH) has both a carbonyl and a hydroxyl group attached to the same carbon atom, resulting in new properties.

Carboxyl groups are weak acids, dissociating partially to release hydrogen ions.

O

C

OH

Acetic Acid

H C

H

H

C

O

OH

H

H

H

C

O

C

O

+ H+

Acetate

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Amino Group Amino Group

The amino group (–NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton.

Found in amino acids

nonionized ionized

N

H

H H

+N H

H

N

H

H

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Sulfhydryl GroupSulfhydryl Group

The sulfhydryl group (–SH) consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape.

Two sulfhydryl groups can interact to help stabilize protein structure called disulfide bond (symbolized as -S-S-).

SH

161616

Phosphate Group (Acids)Phosphate Group (Acids)

In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (–OPO3

2-) is an ionized form of a phosphoric acid group (–OPO3H2; note the two hydrogens).

Makes the molecule of which is a part an anion (negatively charged ion).

Can transfer energy between organic molecules (e.g., ATP).

O P

O

OH

OH

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ATP

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The Functional GroupsThe Functional Groups

Functional groups are Functional groups are the chemically the chemically reactive groups of reactive groups of atoms within an atoms within an organic molecule.organic molecule.

Many are polarMany are polar

Give organic Give organic molecules distinctive molecules distinctive chemical properties. chemical properties.

Most Important in the Most Important in the Chemistry of LifeChemistry of Life

CH3

OH

HO

O

CH3

CH3

OH

Estradiol

Testosterone

Female lion

Male lion

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Putting things Putting things together…let’s together…let’s

make some make some MACROMOLECULESMACROMOLECULES

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Monomers & Polymers:

• monomers• smaller building blocks of the polymers (macromolecules)

• amino acids build proteins:

•Nucleotides build nucleic acids:

• monosaccharides build carbohydrates:

• fatty acids & glycerol build lipids:

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19 Aug. 2009 Chemistry.ppt 21

Synthesis = dehydration synthesisSynthesis = dehydration synthesis

Removal of WATERRemoval of WATER OH + H forms water, OH + H forms water, HH22OO

Leaves bonding sites that join Leaves bonding sites that join monosaccharide units.monosaccharide units.

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19 Aug. 2009 Chemistry.ppt 22

Disassembly = hydrolysisDisassembly = hydrolysis

Break bond between monosaccharide Break bond between monosaccharide units (“lysis” means “to break”)units (“lysis” means “to break”)

Add WATERAdd WATER OH + H to fill bonding sites. OH + H to fill bonding sites.

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Putting together / Taking apart macromolecules:

macromolecules: monomers <--> polymers

Dehydration Synthesis

•

•

Hydrolysis

•

•

fig 4.3

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We will be studying four organic We will be studying four organic macromolecules…macromolecules…

CarboyhdratesCarboyhdrates

LipidsLipids

Proteins Proteins

Nucleic AcidsNucleic Acids