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 Structural formula Ball-and-stick model Space-filling model Methane The 4 single bonds of carbon point to the corners of a tetrahedron.

Carbon skeletons vary in length. LE 3-1b Ethane Propane Carbon skeletons vary in length.

Skeletons may be unbranched or branched. LE 3-1c Butane Isobutane Skeletons may be unbranched or branched.

Skeletons may have double bonds, which can vary in location. LE 3-1d 1-Butene 2-Butene Skeletons may have double bonds, which can vary in location.

Skeletons may be arranged in rings. LE 3-1e Cyclohexane Benzene Skeletons may be arranged in rings.

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

figure 02-20b.jpg 2.20 – Part 2 Figure 2.20 – Part 2

LE 4-9 Estradiol Female lion Testosterone Male 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

FUNCTIONAL PROPERTIES LE 4-10aa STRUCTURE (may be written HO—) Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Alcohols (their specific names usually end in -ol) Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).

STRUCTURE EXAMPLE NAME OF COMPOUNDS LE 4-10ab Acetone, the simplest ketone STRUCTURE EXAMPLE Acetone, the simplest ketone Propanal, an aldehyde NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

LE 4-10ac STRUCTURE EXAMPLE Acetic acid, which gives vinegar its sour taste NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Carboxylic acids, or organic acids Has acidic properties because it is a source of hydrogen ions. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group.

LE 4-10ba STRUCTURE EXAMPLE Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Amine Acts as a base; can pick up a proton from the surrounding solution: (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions

STRUCTURE EXAMPLE NAME OF COMPOUNDS LE 4-10bb STRUCTURE EXAMPLE (may be written HS—) Ethanethiol NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Thiols Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20).

STRUCTURE EXAMPLE NAME OF COMPOUNDS LE 4-10bc STRUCTURE EXAMPLE Glycerol phosphate NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Organic phosphates Makes the molecule of which it is a part an anion (negatively charged 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

Made of interchangeable parts 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 03-02bc.jpg Table 3.2 – Part 2 Table 3.2 – Part 2

table 03-02d.jpg Table 3.2 – Part 3 Table 3.2 – Part 3

Proteins: Polymers of Amino Acids Amino acids are covalently bonded together by peptide linkages. Review Figure 3.4

figure 03-04.jpg 3.4 Figure 3.4

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? Alcohol Hydroxyl Carboxyl Amine 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