Atoms Molecules and Compounds

• Matter is anything that takes up space and has mass.

• Matter can come in four physical forms or phases; solid, liquid gas and plasma.

• Matter is composed of Quarks, Leptons, neutrinos

• Organic means it contains a carbon and usually found in living organisms. Inorganic is matter without a C.

• Atoms are the smallest units of an element that still have its characteristics.

• Atoms are composed of 3 types of particles, proton, neutron, electron

• Ions are atoms that have lost or gained electrons, charged atoms– Cation + charge– Anion -charge

• Atomic number is the number of protons• Atomic mass is the number of protons and

neutrons• Isotope-atoms of the same element with a

different number of neutrons.

Atomic particles

Particle Mass Charge Location

Proton

P1 +1 Nucleus

Neutron

N1 0 Nucleus

Electron

e-0 -1 Cloud

Electron Orbital filling

• 1s2

• 2s2 2p6

• 3s2 3p6 3d10

• 4s2 4p6 4d10 4f14

• 5s2 5p6 5d10 5f14

• 6s2 6p6 6d10

• 7s2 7p6

Chemistry• Law of Conservation of Matter- matter cannot be created or

destroyed but may be transformed from one form into another form.

• States of Matter-Solid, liquid, gas, and plasma• Mixture is when elements keep there own identity ex solution• Type, single and double replacement (substitution), synthesis,

decomposition• Chemical energy is stored in the bonds.• Catalyst-speeds up a chemical reaction with out being used

up• Chemical reaction where two materials are combined and

energy is exchanged and new material/s are formed.– Reactants are what are originally combined– Products are what is formed– Yield sign tells you which way the reaction will normally

proceed. Lowest energy and highest enthalpy

Bonding • Covalent Bond-Sharing bond to complete the outer

shell, usually resulting in a molecule• Ionic Bond-is a bond that actually has a transfer of

electrons from one atom to another Making ions with a specific crystalline lattice, is the compound.

• Metallic Bond-the ability of a metallic compound to bend, Sea of Electrons, that roll.

• Hydrogen bond- a bond that contains hydrogen,

• Van der waals Forces attractive forces between atoms

Laboratory made Bismuth

Fluorite

Garnet

Beryl

Bauxite

Aluminum Aluminum Can

Chem Quiz

• 1.How many protons, neutrons and electrons does Ca45/20 have?

• 2.What is I 127/53, and I 126/53?

• 3.If a Na atom becomes an ion with a +1 charge explain what happened.

• 4.What is a sharing bond called?

• 5.Organic means…….

Chem Quiz1.How many protons, neutrons and electrons does Ca45/20 have?20Protons, 25 Neutrons, and 20 electrons2.What is I 127/53, and I 126/53? Isotopes of Iodine3.If a Na atom becomes an ion with a +1 charge explain what happened. The Na atom has lost 1 electron (-1) and is now a positive ion(cation)4.What is a sharing bond called? Covalent5.Organic means living or containing a carbon

Acid and Base• pH is the reciprocal log of the hydronium ion

concentration. Alkaline (7-14), acidic(1-7), 7 is neutral• Alkalinity is how basic something is, Acidity is how acid

some thing is.• Usually acid have a H3O+, or H+ (Hydronium) in the cation

and bases usually have an OH- (Hydroxide) in the anion.

• Acids may be vinegar, Acetic acid, Sulfuric Acid (H2SO4), Hydrochloric acid (HCl), Nitric Acid (HNO3)

• Bases are Sodium Hydroxide (NaOH) Lye, drain cleaner, Magnesium hydroxide MgOH, Calcium hydroxide CaOH, antacids

Chemical Energy

• Energy is the ability to do work• Energy can be divided into two types.• Kinetic energy-1/2 mv2 is the energy of motion.• Potential Energy-mgh is the energy of position.• Activation Energy-Energy needed to start a

chemical reaction• Law of Conservation of energy- Energy cannot

be created or destroyed but transformed.

Reactions

• Most reactions are reversible, but tend toward lowest energy and greatest enthalpy (disorder).

• Reactants are the materials that are put together • Products are the results of mixing chemically

active elements• Reactants -> Products. Reactions can be

reversed, depending on conditions. If one of the reactants is in limited supply that limits how much or many of the product/s will be produced.

• To satisfy the Law of Conservation of Matter what ever you put into a reaction you will get out.

Type of Reactions

• A. C6H12O6 -> 6H2O + 6CO2

• B. 6H2O + 6CO2 -> C6H12O6

• C. 2NaOH + Ca(C2H3O2) -> 2NaC2H3O2 + Ca(OH)2

• ZnSO4 + Cu -> Zn + CuSO4

Organic Compounds

• Organisms use some elements in large amounts some in trace amounts

• Organic compounds are composed of chains or circles or elemental C. Organic compounds form the materials that living organisms are composed of

• The four major groups of organic compounds are carbohydrates, protein, lipids, and nucleic acids

Organic Compounds

• Lipids-Oil,fat: stored or reserve energy and taste

• Carbohydrates-sugars, breads, cereals: Energy everyday or immediate

• Protein-”Meat”, beans, nuts: repair, maintenance, growth:

• Nucleic Acids-DNA,RNA, all cells has nucleic acids: Heredity, codes for the proper proteins to be produced.

Organic Compounds-containing C or come from living things.

• C electron configuration is 1s2 2sp3, forms 4 covalent bonds. Carbon can form single, double or triple bonds.

• Structural formula- rings, chains or combinations can be formed. So many different ways carbon can combine, stereoscopic isomers (mitten)

• Biosynthesis or Condensation-build up of organic compounds. Making of Polymers, or one large molecule from several smaller molecules. Monomers form polymers

• Hydrolysis-splitting of molecules with water. Converting polymers to monomers.

Biosynthesis and Condensation

• What elements are present in the compounds?

• What are the building blocks or molecules that make up the compounds?

• What compounds or molecules make up the building blocks?

Proteins

• Examples are beef, pork, chicken, and fish muscle• Composed of Amino Acids(19), CHOSPN and Fe

– Amine NH2– Alkyl group R which is in the middle and is a variable– Organic Acid –COOH

• Condensation• Hydrolysis• Sequence of AA shape thus determines the protein

characteristics• Proteins are very species specific. Antibodies per

person varies as an example.

Protein, Enzymes(organic catalysts)

• Control specific reactions, controlling all of the chemical reactions in our bodies

• How an enzyme works– Substrates-substance that enzyme causes to react.– Active site is the area on an enzyme that fits a certain

substrate– Once reaction is finished, enzyme moves on

• Enzyme system-team of enzymes • Coenzyme nonprotein enzyme

Fats and Lipids

• More energy per mass, More bonds• Examples are oils, fats, waxes, butter • Composed of C,H, and O, insoluble in water• Formation- Condensation, Dehydration Synthesis

– 3 fatty acids– glycerol

• Decomposition-Hydrolysis (3 water + Fat -> 1 glycerol + 3 fatty acids)

• Saturated all single bonds, Unsaturated double bonds

Trans Fats• Trans fat is the common name for unsaturated fat with trans-isomer (E-isomer) fatty acid(s).

Because the term refers to the configuration of a double carbon-carbon bond, trans fats are sometimes monounsaturated or polyunsaturated, but never saturated.

• Trans fats are not essential fatty acids; indeed, the consumption of trans fats increases the risk of coronary heart disease12 by raising levels of "bad" LDL cholesterol and lowering levels of "good" HDL cholesterol.3 Health authorities worldwide recommend that consumption of trans fat be reduced to trace amounts. Trans fats from partially hydrogenated oils are more harmful than naturally occurring oils.4 Some studies have shown natural trans fats in beef and dairy products can have the opposite health effect and can actually be beneficial, e.g. lowering total and LDL cholesterol and triglyceride levels.567

• Unsaturated fat is a fat molecule containing one or more double bonds between the carbon atoms. Since the carbons are double-bonded to each other, there are fewer bonds connected to hydrogen, so there are fewer hydrogen atoms, hence the name, 'unsaturated'. Cis and trans are terms that refer to the arrangement of the two hydrogen atoms bonded to the carbon atoms involved in a double bond. In the cis arrangement, the hydrogens are on the same side of the double bond. In the trans arrangement, the hydrogens are on opposite sides of the double bond.

• The process of hydrogenation adds hydrogen atoms to unsaturated fats, eliminating double bonds and making them into partially or completely saturated fats. However, partial hydrogenation, if it is chemical rather than enzymatic, converts a part of cis-isomers into trans-unsaturated fats instead of hydrogenating them completely. Trans fats also occur naturally in a limited number of cases: Vaccenyl and conjugated linoleyl (CLA) containing trans fats occur naturally in trace amounts in meat and dairy products from ruminants, although the latter also constitutes a cis fat.

Carbohydrates

• Make up most of your diet, composed of CHO, examples are sugar, starches, cellulose.

• Sugars are organized in plants as food– Monosaccharide-simple sugar– Disaccharides-double sugar – Polysaccharides- starches – Dehydration synthesis– Hydrolysis

• Carbohydrates if not used are converted to fats by the liver.

Nucleic Acids• Gives instructions to the cell to make

proteins, heredity, these instructions are passed on from generation to generation

• Composition Nucleotides– 5 carbon sugar

• Deoxyribose (Ribose minus an Oxygen)• Ribose

– Phosphoric acid– Nitrogen base

• Pyrimadine- this is the single ring structure• Purines- this is the double ring structure

• Types– Ribonucleic Acid (RNA)– Deoxyribonucleic Acid (DNA)

DNA, RNA

• DNA• Linear, Double helix, • Thymine,

Deoxyribose sugar• 3 forms heredity,

Biologically the Master Molecule of Life

• Nucleus, or rings

• RNA• Linear, Single side

ladder • Urasil, Ribose sugar• 4 forms involved in

making proteins• Found in all parts of

the cell

Groups, Names

• Organic Acid(COOH)

• Amine NH2

• Alkyl R

• Alcohol (COH)

• Alkanes

• Alkenes

• Alkynes

Protein

Protein

Amino AcidPeptide Bond

Alkyl Organic Acid Amine

Lipids

Lipids

Glycerol

Fatty Acid

Fatty Acid

Fatty Acid

Carbohydrates

MonosaccharideGlucose

MonosaccharideFructose

MonosaccharideGalactose

Disaccharide Sucrose

PolysaccharideStarches

Nucleic Acid

RNA, DNA

NucleotideHydrogen Bonding

Phosphoric Acid

5 Carbon Sugar Ribose, Deoxyribose

N- BasePurine

Pyrimadeines

Organic CompoundsCompound Elements Building

BlocksUnits that Form Blocks

Nucleic Acid

Fats, Lipids

Carbohydrates

Protein

Organic Compounds

Compound Elements Building Blocks

Units that Form Blocks

Nucleic Acid CHO-N P Nucleotides 5-C Sugar

Phosphoric A

N-base

Fats, Lipids COH Glycerol

3 Fatty Acids

Carbohydrates COH Monosaccharide

Protein COH, P, S, Fe Amino Acid Amine, Alkyl, Organic Acid

Reactions

• Dehydration Synthesis, Condensation

• Building up of large molecule with the release of water as a product.

• Hydrolysis• Breaking apart of

large molecules, with water as a reactant.

Chemistry Review

Organic Chemistry

Homeostasis

• Homeostasis is that constant state of balance where everything in the body is in equilibrium.

• The cells are in a constant state of flux Or change to maintain a balance.

• Everything increases in size and number. Everything decreases in size and number.

Homeostasis

Cell transport

Passive transport Active transport

Concentration Gradient

Osmosis

Carrier Protein

Endocytosis ExocytosisDiffusion

Facilitated Diffusion

Sodium-Potassiumpump

is added by

which includes

such as of substances down their such asOf substances

against their

Which uses a

Cell Membrane

• Why some things are not passed through a membrane.– Particle size– Solubility– Conditions inside and outside of the cell– Charge, ions

Conditions Environment Cell Water movement

Solute conc in the Hypo Hyper Into cell environment is lower

than in the cell

Solute conc in the Hyper Hypo Out of cell

the environment higher

than in cell

Solute and environment is Isotonic Isotonic Balanced

equal

Diffusion • Diffusion is the gradual spreading out of molecules.• Law of Diffusion substances diffuse form an area of

high concentration to areas of lower concentration. • Diffusion through a membrane

– Nature of membrane– Permeable membrane

• Solute-what you want dissolved• Solvent-Universal solvent is water-what it is dissolved in

– Equilibrium diffusion pressure is zero

• Factors that affect the rate of diffusion– Temperature– Mechanical agitation– Greater concentration gradient– Pressure-from high to low

Osmosis- A Type of Diffusion• Osmosis is the passage of water through a

selectively permeable membrane from an area of high concentration to an are of lower concentration

• A type of passive transport no cell energy is expended– Concentration gradient is a difference in

concentrations of a material across a space(Percal)

• Osmosis and plant cells (osmotic system 2 solutions between a membrane)– Hypotonic-more water on the inside than on the

outside. Greater concentration of water molecules inside than outside the cell, water moves outside the cell. Cell crenate.

– Turgor pressure water in the cytoplasm pushes against the cell wall of the plant. This allows soft delicate tissue to become stiff. Ex. Primrose, bindweeds

Animal Water Problems• Animal cells have no cell wall to contain an

increase in water molecules, they simply split or go through cytolysis.

• One celled organisms have real problems, keeping up with the the constant influx of water. Contractile vacuole constantly pumps out the water.

• Fish, and other aquatic organisms remove excess water in the gills, and urine.

• Kidney, Lungs and sweat glands remove excess water.

• Nature-H2O contains impurities, minerals – Lowers the concentration of H2O molecules– One celled animals burst in distilled H2O(100 % H2O), Contractile

vacuole cannot keep up with H2O diffusing in– Blood Same-Hemolysis in Distilled H2O, Crenate in salt water

Plasmolysis

• Plasmolysis is when the cell splits and loses turgor pressure

Isotonic, Hyertonic

• Isotonic is when the passage of water is in equilibrium

• Hypertonic higher water molecule concentration outside than inside of the cell. Water moves into the cell, lyses

Diffusion of Ions• Acid, mineral, salt, base ionic solution is

formed

• Ions do not pass, membrane may be charged– Hydrophilic-water loving, water attracting

from the surface of the cell membrane– Hydrophobic-water scared. Water is

repelled from the surface of the material

Active Transport (carrier molecules)

• Cell energy is used, so the cell membrane becomes more or less permeable depending on the situation.

• Root cells absorb mineral ions from the soil solution with a lower ion concentration

• Algae, Iodine conc 1000x greater than saltwater• Grated channel-Protein controlled passage that allows

the cell to be permeated as needed. Material cell to cell

• Sodium Potassium pump. Sodium is moved out and Potassium is moved in. Works against a gradient

• Carrier molecule that transports material through the membrane

Large Molecules

• Pinocytosis-cell drinking, water vacuoles

• Amino acids and fats

• Exocytosis-Large molecules exiting the cell

• Endocytosis-large molecules entering the cell– Phagocytosis-engulfing– Vesicle forms as a result