Biochemistry ~ Review of Chemistry

Objectives: 1. Appreciate the basic principles of chemistry which are involved in life processes.

(1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 2.1)

Biology 30 ~Unit 1Mrs. S. Pipke-Painchaud

Terminology Matter ~ anything that has

mass and takes up space.– Living (biotic) and nonliving

(abiotic) things are made up of

atoms.– Examples???

Atoms ~ small particles of matter are composed of smaller subatomic particles: neutrons, protons, and electrons (Nelson 51)

Element ~ a substance of only

one kind of atom (pure substance that cannot be broken down into simpler substances by chemical means.)– Examples:

Compound ~ bond between atoms of 2 or more different elements.

Molecule ~ two or more atoms of the same or different elements bonded together

Sodium: http://www.vanderkrogt.net/elements/images/sodium.jpg

Compound: http://www.webelements.com/webelements/compounds/media/B/B2H6-19287457.jpg

Life . . .

Organic compounds all contain CARBON

99% of all living matter is made up of 4 chemical elements:

carbon hydrogen oxygen nitrogen

Phosphorous and Sulfur are also present to a lesser degree.

Structure of Atoms

All matter inorganic and

organic is made up of atoms.

An atom contains a nucleus (central core) - contains most of the mass

It also contains protons and neutrons

Image from:http://en.wikipedia.org/wiki/Image:Stylised_Lithium_Atom.svg

Protons

Mass of 1 amu– AMU= Atomic Mass Unit (named after the English

Scientist John Dalton, who first studied atoms 2 centuries ago)

– 1 AMU = 1.7 x 10-24g +1 (positive) charge constant for any element atomic number = number of protons Carbon atomic # = 6

– Thus, there are 6 protons

Image from:http://www.chem4kids.com/files/atom_structure.html

C12.011

6

Atomic #

Mass

Mass = 1 AMU no charge

Why the decimal? the number may vary creating isotopes example: Carbon 12 or Carbon 14

Neutrons

C12.011

6

Isotopes

The periodic table is filled with decimals Carbon has 6 protons, 6 neutrons (protons +

neutrons = atomic weight) = 12 but the number is 12.01

protons never change Electrons move between elements (but don’t

have enough weight to make a difference.) Neutrons can change

Image from: http://www.chem4kids.com/files/atom_isotopes.html

Isotopes continued . . . Isotopes

– have the same number of protons but different numbers of neutrons;

– multiple forms of the same element;

– chemical properties are nearly identical Examples:

– Hydrogen1 &2 - Uranium 238 & 235

Image from: http://www.radiation-scott.org/timeline/isotope_definition_LARGE.jpg

Electrons

Surround the nucleus orbit in different energy levels (orbitals) negative charge (-1) No mass

– they have a mass of 9x10-28g but this is not enough to cause a significant weight difference

Balance out the proton charge

May be gained, lost or shared The electron is often considered to be of the most

biological interest because what happens in the cells happens because of the way the electron behaves.

The number of electrons in the atom of a specific element determines how the atom reacts with other atoms.

All chemical reactions are exchanges or changes in the sharing of electrons.

Remember:

The kind of element depends on the number of protons

number of protons = the number of electrons in a neutral atom

Electron Orbitals Electrons orbit the core like the Earth on

its axis. In an electron, however, no more than two electrons can occupy an orbital at the same time. They must also orbit in opposite directions.

Orbitals consist of a series of shells

http://hyperphysics.phy-astr.gsu.edu/hbase/chemical/eleorb.html

The outer shell of electrons determine the atom’s tendency to gain or lose electrons. (I.e. what it can do chemically)

Why are Helium, Neon, Argon, Krypton, Xenon and Radon grouped together?

Noble gases -- chemically inert (less likely to interact) -- have a stable octet

Other elements are reactive depending on the varying degree of electrons in the outer shell. Essentially, atoms are searching for a way

to fill the outer orbit and create a stable octet by joining other atoms

- “the most famous noble gas is Helium, as it is used in balloons. This is because it 'floats' due to the fact it is less dense than air, so rises above it. But the densities increase, so xenon is denser than air, and will fall to the ground.” “As you know, helium is used in balloons and airships because it is less dense than air. But you could just as well use hydrogen. But helium is unreactive (see above) whereas hydrogen is explosive - so helium is much safer.Neon is used inside those bright advertising tubes. When a current is passed through the gas it glows.Argon, krypton and xenon are used in light bulbs of varying sorts and uses, all because they will not react from the heat created by the bulb.”http://www.scienceaid.co.uk/chemistry/periodictable/noblegases.html

Chemical Bonding Chemical Bond: an attractive force that links 2

atoms together– a reaction between atoms

depends on the # of electrons Bond Info

– when bonds form they have potential energy– takes energy to break bonds– bond energy - amount of energy required to break A and B

apart– atoms and molecules don’t exist alone. They react with

each other all of the time.

Bond Information:

General Reaction– Reactants + Energy --> Products + Energy

Endothermic - energy is used up (Delta H+)– Examples: http://ca.youtube.com/watch?

v=C_ylmLirPxM– **http://ca.youtube.com/watch?

v=5RJLvQXce4A&NR=1– Exothermic - energy is released (Delta H-)

• http://ca.youtube.com/watch?v=HjR0mWdIsJ0• Gummy Bear http://ca.youtube.com/watch?

v=LXdYcRI7b_k

Exothermic Reactions:

Heat is give off Examples:

– Freezing and condensing– “Making bonds gives out energy - it is exothermic.

This is why freezing and condensing are exothermic. In a chemical reaction you need to put energy in to break bonds in the reactants,you get energy out when new bonds are formed to make the products. If you get out more energy than you have to put in, then overall the reaction is exothermic. This is what normally occurs” (gcsescience.com).

Endothermic Reactions

Heat is taken in Examples:

– Melting and boiling– “Breaking bonds (overcoming the force of

attraction) requires energy, you have to put heat in - it is endothermic. This is why melting and boiling are endothermic if you have to put in more energy than you get out, then the reaction is endothermic,but except in rare circumstances, the reaction doesn't happen” (gcsescience.com).

Examples:

http://antoine.frostburg.edu/chem/senese/101/thermo/faq/exothermic-endothermic-examples.shtml

You Tube Exothermic Reaction Video:

http://www.youtube.com/watch?v=80Q3GgeeIVM

1. Covalent Bonding

two atoms share a pair of electrons– No Charge

– example: Hydrogen (H2), Oxygen (02)and Nitrogen (N2)

H-HO-O N N

Structural, Ball and Stick, Space filling Models

http://jchemed.chem.wisc.edu/JCESoft/CCA/CCA5/MAIN/1ORGANIC/ORG02/TRAM02/1MODELSMETHANE/0060807/MOVIE.HTM

Bonding Patterns

H = 1 O = 2 N = 3 C = 4 Remember the element will always have X

number of lines leading to another element.

Ex.HCN2 H2O

NOTE: as the number of orbitals increases the stability of the covalent bond decreases because the electrons are more shielded from the other atom’s nucleus by more orbitals.

2. Ionic Bonds

Ions: electrically charged atoms– have a positive or negative charge

depending on the number of electrons that they have.

Cations: + – ex/ Ca2+, Mg2+, Na+

Anions: -– Cl-, O2-

Ionic Bond: is the transfer of electrons form one element to the other.– One of the atoms in the bond pair has the

shared pair of electrons all of the time– 1 atom give up e- to another and each one

becomes a charged ion. When in solution ions will separate

– NaCl --> (in solution) Na+(gained) + Cl- (lost)

RED-OX Reactions

Reduction:– gaining of electrons– most reducing reactions lead to the storage

of energy– sugars and fats are highly reduced

compounds– material reduced is called the oxidizing

agent

Oxidation:– loss of electrons– most oxidation reactions involve the

release of energy– material oxidized is called the reducing

agent OIL RIG

3. Hydrogen Bonding

Arises from attraction from slight “+” charge of H atom and a slight “-“ charge from a nearby F, O or N atom.– Example: H2O

Polar Molecules sharing of electrons in a covalent bond

may not be equal. Overall charge of the molecule is

neutral but 1 region is “+” and the other is “-“

http://web.mit.edu/esgbio/www/chem/review.html

Water - is a polar molecule

It boils at 100 degrees (Energy is added to break H bonds so that the molecules can escape.)

Has very unique properties- covers ¾ of the earth’s surface- between 45-95% of any living organism consists of water- is necessary for life- it is the most effective solvent on earth- as water cools it shrinks until it reaches 4 C (max density

(min. vol))- at 4 C the polarity causes the molecule to join together

in hexagonal lattices- creates a space which causes water to expand when it

freezes Why does this matter??

It Floats when frozen!- If it didn’t it would sink and all of the oceans would

freeze solid- Would kill all life- The sun never shines down to the bottom of a deep

lake so it would never thaw out- more gas dissolves in water when it’s cool as compared

to warm

in the fall the top layer of water cools off first cold water dissolves more gases (O2) as it cools the water begins to sink (Because more dense) long periods of cool water replenish the oxygen in a lake warm water moves to the surface process is called turnover if it freezes really fast and the ice is covered by snow soon

after you will get winter kill

**Hydrogen bonding is what allows insects to walk on water, a bubble to exist and you to overfill your glass.

http://www.wonderquest.com/waterwalk-blueice-magneticpoles.htm

Supercooling of water . . . Watch it freeze.

http://www.youtube.com/watch?v=YLeL8XFBB_0

Types of Reactions

Synthesis Reaction:– build compounds– requires energy– ex. Photosynthesis

Decomposition Reaction:- break down compounds- release energy- ex. Digestion processes

Ionization:– convert non-ionic compounds into ions

• ex. HCl --> H+ + Cl-

pH -- Potential Hydrogen

Measure of Acids and Bases Acid:

– any solution that has more H+ than OH-• ex// HCl = [H+] >[OH-]

Base:– any solution that has more OH- than H+

• ex// NaOH = [OH-] > [H+]

Logarithmic scale moves by 10

http://www.ec.gc.ca/acidrain/kids.html

Complete DEMO

What is an Acid Anhydride? An acid without water RXN from DEMO

– H20 + CO2 --> H2CO3 (carbonic acid) + H+ + HCO3-

Our blood has a pH of 7.35 - 7.45

So what happens if we drink a can of coke with a pH of 5 or less? Buffers

– neutralize excess acids and bases which prevent changes in pH

– found in all living cells because each reaction needs to maintain a common pH

– only absorbs the excess acid or base – it keeps the reaction in a specific range– the more reactions occurring the more

buffers needed

Why does a child pass out when he/she holds his/her breath for a long time? Change in blood pH (7.35-7.45) CO2 in blood forms carbonic acid pH sensors in the carotid arteries detect

a change in pH and send a message to the brain

the brain causes us to pass out therefore you have to take a breath

(unconscious)

Metabolism– the sum of all chemical reactions in a cell

or organism

Any last questions??

Complete the review crossword puzzle Set a quiz date

THE END :-)