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Introduction to Bioorganic Chemistry. Chemistry of Biomolecules. A biomolecule is a chemical compound that naturally occurs in living organisms. Biomolecules consist primarily of carbon and hydrogen, along with nitrogen, oxygen, phosphorus and sulfur.

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chemistry of biomolecules
Chemistry of Biomolecules
  • A biomolecule is a chemical compound that naturally occurs in living organisms.
  • Biomolecules consist primarily of carbon and hydrogen, along with nitrogen, oxygen, phosphorus and sulfur.
  • Other elements sometimes are incorporated but are much less common.
the six most abundant elements of life
The Six Most Abundant Elements of Life

THIS IS THE LEGAL CHNOPS!! 

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.
organic molecules hydrocarbons

Name and Comments

Space-Filling Model

Molecular Formula

Structural Formula

Ball-and-Stick Model

H

(a) Methane

CH4

C

H

H

H

H

H

(b) Ethane

C

C2H6

H

C

H

H

H

H

H

(c) Ethene (ethylene)

C

C

C2H4

H

H

Organic Molecules: Hydrocarbons

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

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

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

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

isomers1

H

H

H

C

H

H

C

H

H

H

H

H

H

H

H

C

C

C

C

C

H

H

C

H

C

C

H

H

H

H

H

H

H

H

H

X

X

X

C

C

C

C

X

H

H

H

CO2H

CO2H

C

C

H

H

NH2

NH2

CH3

CH3

Isomers

(a) Structural isomers

(b) Geometric isomers

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 d, for "partial" charge.   

the functional groups
The Functional Groups

The 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
hydroxyl group

H

H

C

C

H

OH

H

H

Ethanol

Hydroxyl 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.
carbonyl group

O

C

Carbonyl Group
  • Carbonylgroup 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.
two forms of carbonyl groups aldehydes and ketones

O

C

H

O

C

H

C

H

H

C

H

H

H

H

O

H

C

C

C

H

H

H

Two Forms of Carbonyl Groups: Aldehydes and Ketones

Propanal, an aldehyde

Acetone, a ketone

  • 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.
carboxyl group acids

O

C

OH

H

H

O

O

+ H+

H

C

H

C

C

C

OH

O

H

H

Carboxyl Group (Acids)

Acetic Acid

Acetate

  • 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.
amino group

H

H

N

+N

H

H

N

H

H

H

nonionized

ionized

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
sulfhydryl group
Sulfhydryl Group

SH

  • 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-).
phosphate group acids

O

P

OH

O

OH

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 (–OPO32-) 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).
the functional groups1

OH

CH3

Estradiol

HO

Female lion

OH

CH3

CH3

O

Testosterone

Male lion

The Functional Groups
  • Functional groups are the chemically reactive groups of atoms within an organic molecule.
  • Many are polar
  • Give organic molecules distinctive chemical properties.
  • Most Important in the Chemistry of Life
slide20

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:

synthesis dehydration synthesis
Synthesis = dehydration synthesis

Removal of WATER OH + H forms water, H2O

Leaves bonding sites that join monosaccharide units.

19 Aug. 2009

Chemistry.ppt

21

disassembly hydrolysis
Disassembly = hydrolysis

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

Add WATER OH + H to fill bonding sites.

19 Aug. 2009

Chemistry.ppt

22

slide23

Hydrolysis

Putting together / Taking apart macromolecules:

macromolecules: monomers <--> polymers

fig 4.3

  • Dehydration Synthesis
we will be studying four organic macromolecules
We will be studying four organic macromolecules…
  • Carboyhdrates
  • Lipids
  • Proteins
  • Nucleic Acids