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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 :-)