• Biology - the scientific study of life

There is no biology without chemistry

• Covalent bond - the sharing of a pair of the outermost shell valence electrons by two atoms

• Molecules - two or more atoms held together by covalent bonds

• Electronegativity - an atomś attraction for the electrons of a covalent bond (like gravity)

In a nonpolar covalent bond, the atoms share the electrons equally (H2).

In a polar covalent bond, one atom is more electronegative, and the atoms don’t share the electrons equally. This leads to partial charges (H2O).

• Ionic bonds - result from the taking or losing of an electron which creates two oppositely charged ions that are attracted to each other.

  • Cation - positively charged ion.

  • Anion - negatively charged ion

• Hydrogen bonds - form when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom. A hydrogen bond is considered a weak bond.

Properties of Water

The four emergent properties of water that contribute to Earth’s suitability for life:

1. cohesive behavior (stickiness)

2. ability to moderate temperature

3. expansion upon freezing

4. versatility as a solvent

Water molecules are linked by multiple hydrogen bonds.

• Cohesion - molecules staying close together because of hydrogen bonds. This is self-to-self stickiness.

• Adhesion - one substance clinging to a different substance (like tape).

• Capillary Action - the ability of a liquid to flow in narrow spaces without the assistance of, or even in opposition to, external forces like gravity.

• Specific heat - the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1 degree Celcius.

  • The specific heat of water is 1 calorie/(gram x degree Celcius) this is a high specific heat. Water is very resistant to changes in temperature.

• Heat of vaporization - the heat a liquid must absorb for 1 gram to be converted to a gas.

• As a liquid evaporates, its remaining surface cools, a process called evaporative cooling.

Ice floats in liquid water because hydrogen bonds in ice are more ‘ordered’ making ice less dense. Water is the most dense at 4 degrees Celcius.

Organic Chemistry

All of life is built on carbon. We are ~72% water. We are ~25% carbon compounds:

• Carbohydrates

• Lipids

• Proteins

• Nucleic Acids (not covered until Genetics)

Organic chemistry: the study of carbon compounds (carbon chemistry).

Carbon atoms are versatile building blocks. They can make 4 stable covalent bonds.

Hydrocarbons: organic molecules consisting of only carbon and hydrogen.

• Many organic molecules, such as fats, have hydrocarbon components

• Hydrocarbons can undergo reactions that release a large amount of energy

Isomers: compounds that have the same number of atoms of the same elements but different structures and properties

1. Structural isomers: differ in the covalent arrangement of their atoms

2. Cis-trans isomers: carbons have covalent bonds to the same atoms, but the atoms differ in their spatial arrangement

• This is due to the inflexibility of double bonds

• the subtle differences in shape between such isomers can greatly affect the activities of organic molecules

3. Enantiomers: isomers that are mirror images of one another

• They differ in shape due to the presence of an asymmetric carbon

• Enantiomers are left-handed and right-handed versions of the same molecule

• Usually, only one isomer is biologically active

Functional groups: chemical groups that affect molecular function by being directly involved in chemical reactions

Polymer: a long molecule consisting of many similar building blocks.

These small building-block molecules are called monomers.

Dehydration reaction (synthesis): when two monomers bond together through the loss of a water molecule

Polymers are disassembled into monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction.

Carbohydrates

Carbohydrates: include sugars and the polymers of sugars

• the simplest carbohydrates are monosaccharides or simple sugars

Uses of Carbohydrates

• Fuel source in the cell

• Structural (cell walls in plants)

• Cell communication (blood types)

Monosaccharides: have molecular formulas that are usually multiples of CH2O

• Glucose is the most common (C6 H12 O6)

• Monosaccharides = monomers of carbs

A disaccharide is formed when a dehydration reaction joins two monosaccharides.

Polysaccharides: the polymers of sugars have storage and structural roles (stop being sugar)

Starch: a storage polysaccharide of plants, consists entirely of glucose monomers. (store energy in things like potatoes so they can live underground and sprout)

Glycogen: a storage polysaccharide in animals (stored in muscles or livers)

The polysaccharide cellulose is a major component of the tough wall of plant cells - structure and support

• Cellulose is a polymer of glucose but the glycosidic linkages in cellulose differ

• A rope of cellulose is fiber - we can’t digest it so we use it to improve gut health

Chitin: another structural polysaccharide, is found in the exoskeleton of arthropods (crabs, insects eg.)

• Chitin also provides structural support for the cell walls of many fungi

Lipids

Lipids do not form true polymers (not made from uniform monomers).

The unifying feature of lipids is having little or no affinity for water

Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds.

Examples of important lipids are fats, phospholipids, and steroids.

Used for energy storage and part of the cell membrane. They are also hormones

Fats: constructed from two types of smaller molecules: glycerol and fatty acids

Glycerol: three-carbon alcohol with a hydroxyl group attached to each carbon

Fatty acid: consists of a carboxyl group attached to a long carbon skeleton

Saturated fatty acids: have the maximum number of hydrogen atoms possible and no double bonds (solid at room temperature)

Unsaturated fatty acids: have one or more double bonds (liquid at room temperature)

The major function of fats is energy storage

In a phospholipid, two fatty acids and a phosphate group are attached to glycerol

• the two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head

Phospholipids are major constituents of cell membranes

Steroids: lipids characterized by a carbon skeleton consisting of four fused rings

Cholesterol: is an important steroid and is a component in animal cell membranes (adds flexible rigidity to cell walls) (type of steroid)

Proteins

• Most structurally and functionally diverse group

• Function: involved in almost everything

  • enzymes (pepsin, DNA polymerase)

  • structure (keratine, collagen)

  • carriers and transport (hemoglobin, aquaporin)

  • cell communication

    • signals (insulin and other hormones)

    • receptors

  • defense (antibodies)

  • movement/motor (actin and myosin)

  • storage (bean seed proteins)

• Structure

  • monomer = amino acids

    • 20 kinds of different amino acids

  • polymer = polypeptide

    • protein can be one or more polypeptide chains folded and bonded together

    • large and complex molecules

    • complex 3-D shape

Amino Acids

Peptide bonds:

• covalent bond between NH2 (amine) of one amino acid & COOH (carboxyl) of another (dehydration synthesis)

Primary Structure:

• amino acids in a chain

• amino acid sequence determined by gene (DNA)Secondary structure:

• ‘Local folding’

  • folding along short sections of polypeptide

  • interactions between adjacent amino acids

    • H bonds

      • weak bonds between R groups

  • forms sections of the 3-D structure

    • α - helix

    • β - pleated sheet

Tertiary structure:

• “Whole molecule folding”

  • interactions between distant amino acids

    • hydrophobic interactions

      • cytoplasm is water-based

      • nonpolar amino acids cluster away from water

    • H bonds and ionic bonds

    • disulfide bridges

Quaternary structure:

• more than one polypeptide chain bonded together

  • only then does polypeptide become a functional protein

    • hydrophobic interactions

Protein denaturation:

• the unfolding or destruction of a protein

  • conditions that disrupt H bonds, ionic bonds, disulfide bridges

  • caused by:

    • temperature

    • pH

    • salinity

  • alters secondary and tertiary structure

  • destroys functionality

    • some proteins can return to their functional shape after denaturation, many cannot

Nucleic Acids

There are two types of nucleic acids:

• Deoxyribonucleic acid (DNA)

• Ribonucleic acid (RNA)

Monomer: nucleotide (sugar, phosphate, nitrogenous base)