chemistry basics. elements, molecules and compounds

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