Chemistry Basics

Elements, Molecules and Compounds

matter• any object around us is made of

tiny particles called atoms• atoms are made of protons,

neutrons, and electrons

• every element has its own type of atoms

ex. carbon ex. hydrogen

• isotopes are atoms of the same element that have different number of neutrons, ex.

Pet scans: radioisotopes

• Unstable isotopes are radioactive and are called radioisotopes

• When atoms join together they can form molecules

molecules• combinations of atoms held together by

strong chemical forces of attraction (covalent bonds)

• molecules that contain atoms of the same element are called molecular elements, ex. O2

• molecules that contain atoms of different elements are called compounds, ex. H2O

The elements of life• living things are mostly (98%) made of 6

elements:C – carbonH – hydrogenO – oxygenP – phosphorusN – nitrogenS – sulphur

-each element makes a specific number of bonds with other elements

Carbon: 4 bonds

Hydrogen: 1 bond

Oxygen: 2 bonds

Phosphorus: 3 bonds

Nitrogen: 3 bonds

Sulphur: 2 bonds

Biochemistry

• Field that bridges chemistry and biology• Deals with properties and interactions of

biologically important molecules

• Many of the molecules of life are organic: contain carbon and hydrogen

Life on Earth involves water…

SO WHAT'S SO SPECIAL ABOUT WATER?

1) two-thirds of Earth are covered by it (97% of that is sea water)

2) ours is the only planet in the Solar System where water can exist in its liquid state

3) all life is water-based: we are 75% water!

Structure of Water1) water has a very

slight charge to it, where the O is more negative and the H

is more positive

2) this slight charge difference makes water polar

3) Polar molecules can form hydrogen bonds with other polar molecules

• Intramolecular bonds: bonds within a molecule, ex. covalent, ionic

• Intermolecular interactions: bonds between molecules, ex. hydrogen bonding and hydrophobic/hydrophilic interactions

• Polarity of water:

• Since water is polar it can dissolve other charged or polar substances (ex. salt) but not uncharged or nonpolar substances, ex. Oil

• [remember: like dissolves like]

hydrophilic molecules-like water, can be dissolved in it-are polar

hydrophobic molecules-don’t like water, can’t be dissolved in

it-are non-polar- the natural clumping of non-polar

molecules in water plays a key role in how biologically important molecules are shaped!

Ions in biological systems

• an atom can obtain a stable valence shell by losing or gaining electrons, rather than sharing:

• when an atoms gains/loses an electron it becomes charged, and forms an ion

• cation: a positive ion

• anion: a negative ion

• substances that form ions (ionic compounds) are almost always considered in terms of ions, since they are in an aqueous environment

So…

• In biology STRUCTURE DICTATES FUNCTION

• Since molecules will come together depending on how hydrophobic/hydrophilic hydrogen bonding will determine the function of many large biological molecules: MACROMOLECULES