atoms and elements

• proton = carries 1 + charge, ~ 1 unit of atomic weight
• neutron = carries no charge, ~ 1 unit of atomic weight
• electron = carries 1 - charge, ~ 0 unit of atomic weight (actually 0.0002)

Atomic weight = number of protons plus neutrons (electrons too small to count)

Molecules = groups of atoms, bonded together.

Molecules held together by chemical bonds of different types

Covalent bonds = sharing of one or more pairs of electrons between two atoms

shapes of the molecules differ (very important)

• CH₄ symmetric. CO₂ symmetric, H₂O asymmetric
• Makes water a polar molecule, methane a non-polar molecule

Other types of bonds: ionic, hydrogen

Shape determines how molecules can fit together, how they can interact

This is a key concept in molecular biology!!!!

Water is a very good solvent for polar molecules and charged ions. A poor

solvent for non-polar molecules.

Acid-Base chemistry

• Some molecules can dissociate and release H ions. called acids
• Some molecules can dissociate and release OH ions (hydroxide ions) called bases

organic molecules are molecules that contain carbon

• carbon, with ability to form 4 covalent bonds, can make very complicated molecules.

structural isomers, different chemical bonds

geometric isomers, same bonds, but different arrangement about double bonds

enantiomers (stereoisomers), some carbon atoms are said to be asymmetric

Functional groups, some combinations occur over and over, get special names

• need to be able to recognize them

Because carbon can form C-C bonds, and make long chains of atoms linked together, some organic molecules can get very large.

• Macromolecules only form in nature by living systems.

Each subunit is called a monomer.

4 important types of macromolecules

• carbohydrates, subunit = sugars
• lipids, subunit = fatty acids
• proteins, subunit = amino acids
• nucleic acids, subunit = nucleotides

• Simple sugars (monosaccharides)
• Disaccharides (two simple sugars linked together by a dehydration reaction)
• Linkage between sugars can differ (alpha or beta)
• different linkage will have different properties..
• Polysaccharides, many subunits (up to 1000’s)

• Most are hydrophobic: fats (and oils), phosholipids, steroids
• Fats = triglycerides
• Phospholipids: molecule has one half polar and one half non-polar
• Steroids: cholesterol -important in cell membrane, and as starting material for steroid hormones like testosterone and estrogen

Large and important group of molecules, polymers of amino acids

Types of proteins:

• enzymes
• structural proteins (hair, silk)
• hormones (insulin)
• transport proteins (hemoglobin)
• receptor proteins (respond to hormones or other signals)
• contractile proteins (muscle)
• defensive proteins (antibodies)

all with same basic structure (learn this from the book)

Some R-groups are charged, some polar, some non-polar. These give each protein a unique set of chemical properties. Learn which AA’s are in which group.

Peptide bond - dehydration (condensation) between amino group of one and carboxylic group of another

Note: each polypeptide has a free amino group at one end (N-terminus) and a free carboxylic acid at the other (C-terminus) --this is important for describing a protein in terms of its amino acid sequence (= primary structure).

Secondary structure: alpha helix, beta-sheet

The same protein can have regions of helix and sheet, as well as regions with no secondary structure (random coil)

Tertiary structure -- interactions between R-groups also can fold up the chain.

Quaternary structure -- some functional proteins are made up of more than one polypeptide

How a protein folds up is largely determined by its primary structure. This then influences the type of secondary, tertiary, or quaternary structure it can have.

Remember, shape of molecule is important.