Molecular Modeling of Biological Molecules

Goals

• Review chemical bonding (ionic and covalent), periodic table

• Describe the properties of carbon that make it important to living things

• Become familiar with the major functional groups found in biological molecules

• Assemble subunits of 3 biological molecules– carbohydrates, proteins, and lipids

Basic atomic structure- protons, neutrons, and electrons

The periodic table logically arranges and describes all matter

Valence electrons determine bonding

Atoms seek complete valence electron shells (the octet rule)

In Ionic bonding, atoms strip valence electrons from partners, forming ions

In covalent bonding, electron pairs are shared, and molecules are formed

In neutral molecules, carbon always forms 4 bonds

Structuralformula

Ball-and-stickmodel

Space-fillingmodel

Methane

The 4 single bonds of carbon point to the corners of a tetrahedron.

LE 3-1b

Ethane Propane

Carbon skeletons vary in length.

LE 3-1c

Butane Isobutane

Skeletons may be unbranched or branched.

LE 3-1d

1-Butene 2-Butene

Skeletons may have double bonds, which can vary in location.

LE 3-1e

Skeletons may be arranged in rings.

Cyclohexane Benzene

Organic Chemistry

• The chemistry of carbon• Hydrocarbons are the

most basic example– Combustible– Can form rings

The variety of carbon compounds is limitless

The physical/chemical properties of carbon skeletons can be modified by functional groups

2.20 – Part 2

Figure 2.20 – Part 2

figure 02-20b.jpg

LE 4-9

Estradiol

Testosterone

Male lion

Female lion

• The six functional groups that are most important in the chemistry of life:– Hydroxyl group– Carbonyl group– Carboxyl group– Amino group– Sulfhydryl group– Phosphate group– Methyl group

LE 4-10aa

STRUCTURE

(may be written HO—)

NAME OF COMPOUNDS

Alcohols (their specific namesusually end in -ol)

Ethanol, the alcohol present inalcoholic beverages

FUNCTIONAL PROPERTIES

Is polar as a result of theelectronegative oxygen atomdrawing electrons toward itself.

Attracts water molecules, helpingdissolve organic compounds suchas sugars (see Figure 5.3).

LE 4-10ab

STRUCTURE

NAME OF COMPOUNDS

Ketones if the carbonyl group iswithin a carbon skeleton

EXAMPLE

Acetone, the simplest ketone

A ketone and an aldehyde maybe structural isomers withdifferent properties, as is the casefor acetone and propanal.

Aldehydes if the carbonyl group isat the end of the carbon skeleton

Acetone, the simplest ketone

Propanal, an aldehyde

FUNCTIONAL PROPERTIES

LE 4-10ac

STRUCTURE

NAME OF COMPOUNDS

Carboxylic acids, or organic acids

EXAMPLE

Has acidic properties because it isa source of hydrogen ions.

Acetic acid, which gives vinegarits sour taste

FUNCTIONAL PROPERTIES

The covalent bond betweenoxygen and hydrogen is so polarthat hydrogen ions (H+) tend todissociate reversibly; for example,

Acetic acid Acetate ion

In cells, found in the ionic form,which is called a carboxylate group.

LE 4-10ba

STRUCTURE

NAME OF COMPOUNDS

Amine

EXAMPLE

Because it also has a carboxylgroup, glycine is both an amine anda carboxylic acid; compounds withboth groups are called amino acids.

FUNCTIONAL PROPERTIES

Acts as a base; can pick up aproton from the surroundingsolution:

(nonionized)

Ionized, with a charge of 1+,under cellular conditions

Glycine

(ionized)

LE 4-10bb

STRUCTURE

(may be written HS—)

NAME OF COMPOUNDS

Thiols

EXAMPLE

Ethanethiol

FUNCTIONAL PROPERTIES

Two sulfhydryl groups caninteract to help stabilize proteinstructure (see Figure 5.20).

LE 4-10bc

STRUCTURE

NAME OF COMPOUNDS

Organic phosphates

EXAMPLE

Glycerol phosphate

FUNCTIONAL PROPERTIES

Makes the molecule of which itis a part an anion (negativelycharged ion).

Can transfer energy between organic molecules.

Organic molecules are good energy sources

Energy is required to form covalent bonds; energy is released when bonds are broken

Most molecules in living things fall into four categories

• Carbohydrates• Lipids• Proteins• Nucleic acids

These all exhibit modular construction

Modular housing

Made of interchangeable parts

Freight trains have modular assembly

Most biopolymers of life are formed by dehydration synthesis

Hydrolysis is the reverse

reaction (Catabolic)

Carbohydrates• “Carbon” + “Hydro”• Formula (CH2O)n

• Different from hydrocarbons

• Soluble in water• Includes: table

sugar, honey, starch, glycogen, cellulose, high fructose corn syrup

• Glucose is the monomer

Glucose can cyclize to form a ring structure

Atoms in bonds are free to rotate around the bonds

Glucose + Glucose = Maltose (A Sugar dimer)

Chain can be extended to thousands

Proteins are polymers made of 20 different kinds of amino acid monomers

Table 3.2 – Part 2

Table 3.2 – Part 2

table 03-02bc.jpg

Table 3.2 – Part 3

Table 3.2 – Part 3

table 03-02d.jpg

Proteins: Polymers of Amino Acids

• Amino acids are covalently bonded together by peptide linkages. Review Figure 3.4

3.4

Figure 3.4

figure 03-04.jpg

Lipids

• Non-polar• High-energy molecules• For energy storage• Forms cell membranes• Hormones• Members of family

include oils, fats, waxes, and cholesterol (steroids)

Triglycerides are a primary lipid structure

Dehydration synthesis links fatty acids to glycerol

Fatty acids can be saturated and unsaturated (cis and “trans”)

Review

• Atomic structure- protons, neutrons electrons• Valence electrons• Carbon • Functional groups• Carbohydrate structure• Protein structure• Lipid structure

An –NH2 group represents which of the following?

A. AlcoholB. HydroxylC. CarboxylD. AmineE. Phosphoryl

Things left unsaid• Isotopes of all elements exist (some of these are

radioactive)• Electronegativity determines polarity of covalent

bonds, and thus solubility• Water has important physical properties essential

to life on earth• Isomers have the same molecular formula but

not the same shape in space• Nucleic acids are comprised of nucleotide

monomers