Junhel C. Dalanon, DMD, MAT

What is matter?

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

What do you know about matter?

Solids

Liquids

Gases

Plasma

Solids

• Solids have definite shape and definite volume.

• Solids have mass.• Solids take up space.

Read more!

Particles in Solids:

• Are packed tightly together

• Have very little energy

• Vibrate in place

Liquids

• Liquids take the shape of their container and have definite volume.

• Liquids have mass.• Liquids take up space.

Read more!

Particles in Liquids:

• Are loosely packed

• Have medium energy levels

• Particles flow around each other

Gases

• Gases spread out to fill the entire space given and do not have definite volume.

• Gases have mass.• Gases take up space.

Read more!

Particles in Gases:

• Move freely

• Have LOTS of energy

Plasma

• Lightning is a plasma.• Used in fluorescent light

bulbs and Neon lights.• Plasma is a lot like a gas,

but the particles are electrically charged.

Read more!

Particles in Plasma:

• Are electrically charged

• Have EXTREMELY high energy levels

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STATES of matter?

What would it take for matter to move from one state to another?

Energy determines the state!

Add or Subtract Energy. . .

When energy is added, particles move faster!

When energy is taken away, particles move slower!

What will happen? Why?

Solid + Energy = ?

• When energy is added to solids, they become liquids!

• Examples?

Liquid + Energy = ?

• When energy is added to liquids, they become gases!

• What examples can you think of?

Changing States

• There are several names for matter changing states:

– State change

– Phase change

– Physical change

So, did we get something new?

• Ice cream and melted ice cream?• Chocolate and melted chocolate?• Ice, water, and water vapor?• Steel and molten steel?

Review Questions

1. What state of matter has definite volume and definite shape?

2. Describe the properties of liquids.3. Describe the differences between gases and

plasma.4. What is needed for states of matter to

change phase?

Sect 2.1 The Nature of MatterIdentify the 3 subatomic particles in atoms; differentiate isotopes of elementsExplain what chemical compounds are; describe the 2 types of chemical bonds and other attractive forces

Sect 2.2 Properties of WaterExplain how and why water molecules are polarDifferentiate between solutions and suspensionsExplain acidic and basic solutions

Sect 2.3 Carbon CompoundsDescribe the functions of each group of organic compounds

Sect 2.4 Chemical Reactions and Enzymes Explain how chemical reactions affect chemical bondsDescribe how energy changes affect chemical reactionsExplain the importance of enzymes to living organisms

Sect 2.1 The Nature of Matter• Key Concepts: What 3 sub-

atomic particles make up atoms; how are all of the isotopes of an element similar; what are the 2 main types of chemical bonds?

• Proton, neutron and electron make up an atom

• Isotopes of the same elements have same # of protons

• Ionic and covalent bonds are main chemical bonds

• Terms:-Atom

-Nucleus-Electron/Proton-Element-Isotope-Compound -Molecule-Ion-Ionic bond-Covalent bond-van der Waals forces

Atoms…• 3 main subatomic particles make up

the nucleus of an atom:-Proton, pos

charge -Neutron, neutral-Electron, neg charge

• An element is a substance composed of only 1 type of atom; noted by symbol (O2)

• Isotopes: atoms of the same element, but having different number of neutrons (example- C14). Still has same properties of elementRadioactive Isotopes- emit neutrons at steady rate What element is this?

Chemical Compounds…

• A substance formed by combination of 2 or more elements

• Held together by chemical bonds

• Composition shown by chemical formula:H2O, NaCl

• Very different properties than elements; H and O are gases, H2O is liquid

• A molecule is the smallest unit of most compounds What information is contained in a

chemical formula?

Chemical Bonds…Ionic Bonds: Formed when 1 or more

electrons is transferred from one atom to another

Results in positively or negatively charged atom; referred to as an ion

An example is NaCL; sodium readily gives up its valence electron to chloride, which strongly attracts one electron

Resulting attraction b/w oppositely charged ions is an ionic bond

Covalent Bonds: Results from a sharing of

valence electrons in the orbital of an element

May be single bond(H2O), double (O2) or triple (O3)

The resulting structure is a molecule, the smallest unit of most compounds

Van der Waals Forces…

• Result from attraction of charged molecules to one another

• Molecules attract because charged areas exist (opposites attract)

• Weak when compared to chemical bonds; however they are collectively strong

• An example is a mixture of oil and water Do you feel like this? Ask

questions!

Sect 2.2 Properties of WaterKey Concepts: Why are water molecules

polar (and just what does polar mean)? What is an acidic/basic solution? Polarity is the property that causes water

molecules to be attracted to one another; polarity is caused by the unequal sharing of electrons in covalent bonds

Acidic solutions are less than pH 7, and have a higher proportion of H+ ions

Basic solutions are greater than 7, and have higher amounts of OH- ions

Terms: Cohesion Adhesion Mixture Solution Solute Solvent Suspension pH Scale Acid Base Buffer

The Water Molecule…• Oxygen, having 8 protons in its nucleus,

has a much stronger attraction for electrons than does Hydrogen (with only one electron)

• At any given time there is a greater likelihood that an electron that is shared between O and H (covalently bonded) will be located nearer the O atom

• This leads to the Oxygen having a slight negative charge (electron is neg. charged) and Hydrogen having a slight positive charge

• This polarity results in hydrogen bonds forming between adjacent water molecules

The Water Molecule, continued…

Why would life on Earth be impossible if water didn’t form hydrogen bonds between molecules?

Cohesion: an attraction between molecules of the same substance -example is the curve of water in a glass

Adhesion: attraction between molecules of different substances -the water at the edge of a glass demonstrates adhesion

Solutions and Suspensions… When 2 or more elements are

mixed together physically but not chemically, a mixture has been produced (example-cake mix before being cooked)

Solutions are mixtures that have a solute totally dissolved in a solvent. An example is salt (NaCl) dissolved in water.

Due to its polarity, water is known as the universal solvent; polarity allows water to dissolve ions and other polar molecules-what happens when Jello Brand gelatin is mixed in hot water?

Suspensions are mixtures that do not have materials completely dissolved in the solute (think of spoiled milk)

Blood plasma, carrying platelets and antibodies, is a suspension (you would not want platelets or antibodies to dissolve)

-what happens when gelatin is mixed in cold water?

Acids, Bases and pH Scale…• Water is very reactive (the

Universal Solvent.) It reacts to form ions, which may be acidic or basic

• H2O H+ + OH-• The reaction is reversible; pure

water is neutral (pH 7)• If the reaction proceeds in the

direction of producing H+ ions, then an acid is formed (by adding HCL for example) and have pH <7

• If the reaction proceeds to produce OH- ions, then a base is formed (adding NaOH) and have pH >7

• Buffers are substances, normally weak acids or bases, that are used to prevent strong acids or bases from reacting and rapidly changing pH, which can damage cells and tissues

• An example is COOH- (acetic acid, or vinegar) which is used to buffer hydrochloric acid (HCL). When COOH- reacts, it releases OH-, a base, making the substance higher in pH (less acidic)

Organic Compounds• It used to be thought that only living

things could synthesize the complicated carbon compounds found in cells

• German chemists in the 1800’s learned how to do this in the lab, showing that “organic” compounds can be created by non-organic means.

• Today, organic compounds are those that contain carbon. (with a few exceptions such as carbon dioxide and diamonds)

Carbon’s Bonding Pattern• Carbon has 4 electrons in its outer shell. To

satisfy the octet rule, it needs to share 4 other electrons. This means that each carbon atom forms 4 bonds.

• The 4 bonds are in the form of a tetrahedron, a triangular pyramid.

• Carbon can form long chains and rings, especially with hydrogens attached.

• Compounds with just carbon and hydrogen are “hydrocarbons”: non-polar compounds like oils and waxes.

Functional Groups

• Most of the useful behavior of organic compounds comes from functional groups attached to the carbons. A functional group is a special cluster of atoms that performs a useful function.

Metabolic Reactions• In cells, compounds are built up and broken down in small steps by

enzymes, which are proteins which cause specific chemical reactions to occur. Each enzyme causes one step in a metabolic pathway to occur.

• An example: condensing 2 sugars together by removing a water (H2O) from two alcohol (-OH) functional groups:

• This reaction can also be reversed by adding water to the bond. This is called hydrolysis, breaking apart a bond by adding water.

Four Basic Types of Organic Molecule

• Most organic molecules in the cell are: carbohydrates (sugars and starches), lipids (fats), proteins, and nucleic acids (DNA and RNA).

• These molecules are usually in the form of polymers, long chains of similar subunits. Because they are large, these molecules are called macromolecules. The subunits are called monomers.

• The cell also contains water, inorganic salts and ions, and other small organic molecules.

Carbohydrates• Sugars and starches: “saccharides”.• The name “carbohydrate” comes from

the approximate composition: a ratio of 1 carbon to 2 hydrogens to one oxygen (CH2O). For instance the sugar glucose is C6H12O6.

• Carbohydrates are composed of rings of 5 or 6 carbons, with alcohol (-OH) groups attached. This makes most carbohydrates water-soluble.

• Carbohydrates are used for energy production and storage, and for structure.

Sugars• Simple sugars, like glucose and fructose, are composed of a

single ring. • Glucose is the main food molecule used by most living things:

other molecules are converted to glucose before being used to generate energy. Glucose can also be assembled into starch and cellulose.

• Fructose is a simple sugar found in corn that is used to sweeten soda pop and other food products.

• Ribose and deoxyribose are part of RNA and DNA: they are 5 carbon sugars.

• Vitamin C is derived from a simple sugar.• Disaccharides are two simple sugars joined together. Most of

the sweet things we eat are disaccharides: table sugar is sucrose, glucose joined to fructose. Plants use photosynthesis to make glucose, but convert it to sucrose for ease of transport and storage. Lactose, milk sugar, is a glucose joined to another simple sugar called galactose. Maltose, malt sugar, is what yeast converts to ethanol when beer is brewed.

Complex Carbohydrates• = polysaccharides (many sugars linked

together).• Can be linear chains or branched.• Some is structural: the cellulose of plant cell

walls and fibers is a polysaccharide composed of many glucose molecules. The chitin that covers insects and crustaceans is another glucose polymer (with a bit of modification). We don’t have enzymes that can digest these polymers. Cows and termites depend on bacteria in their guts to digest cellulose, producing methane as a byproduct.

• Some is food storage: starch and its animal form glycogen. Also glucose polymers, but linked differently: we have enzymes that can digest starch. We animals store glycogen in the liver as a ready source of glucose, the basic food molecule needed by all cells.

Lipids• Lipids are the main non-

polar component of cells. Mostly hydrocarbons—carbon and hydrogen.

• They are used primarily as energy storage and cell membranes.

• 4 main types: fats (energy storage), phospholipids (cell membranes), waxes (waterproofing), and steroids (hormones).

Fats• Triglycerides are the main type of fat. A

triglyceride is composed of 3 fatty acids attached to a molecule of glycerol.

• Fatty acids are long hydrocarbon chains with an acid group at one end. The chains pack together to make a solid fat. In liquid fats, like vegetable oils, double bonds kink the hydrocarbon chain, which prevents the chains from packing together nicely. This lowers the melting temperature, making them liquids.

• Glycerol is a 3 carbon carbohydrate. It has 3 alcohol (-OH) groups, which link up with the acid groups in the fatty acids.

• Fats store about twice as much energy per weight as carbohydrates like starch.

Trans fats• Hydrocarbon chains with all single bonds (solid fats)

are called saturated; fats with double bonds (liquid oils) are called unsaturated.

• Margarine is made by “hydrogenation”: reducing the double bonds back to single bonds and adding in hydrogens, which raises the melting temperature, giving solid margarine instead of liquid vegetable oil.

• Most animal fats are saturated. Lard is purified animal fat, and it used to be used for deep frying. However, saturated fat increases blood cholesterol levels and leads to clogged arteries and heart disease.

• Several years ago, most companies replaced lard with partially hydrogenated vegetable oil, which was thought to be much healthier than lard.

• Unfortunately, partial hydrogenation leads to trans-fatty acids instead of the cis-fatty acids that occur naturally. And trans fatty acids proved to be even worse for your health than lard. Oops!

Phospholipids• Phospholipids are the main

component of cell membranes.• Phospholipids are very similar to

triglycerides: they have a glycerol with 2 fatty acids attached, plus a phosphate-containing “head” group instead of a third fatty acid.

• The head group is hydrophilic, while the fatty acids are hydrophobic. Cell membranes are 2 layers, with the head groups facing out and the fatty acids forming the interior of the membrane.

• Phospholipid membranes allow only a few molecules to pass through them: water, some gases. They are what keeps the inside of cells separated from the outside.

Steroids and Waxes• Steroids are hydrocarbons with the carbon atoms

arranged in a set of 4 linked rings.• Cholesterol is an essential component of cell

membranes (along with the phospholipids). However, too much of it in the blood can cause “plaques” to form in the blood vessels, leading to atherosclerosis (hardening of the arteries in the heart).

• Steroid hormones are made from cholesterol. These hormones include estrogen, testosterone, vitamin D, cortisone, and many others.

• Waxes: waterproof coating on plants and animals. Composed of fatty acids attached to long chain alcohols.

Proteins• The most important type of

macromolecule.• Roles: • Structure: collagen in skin, keratin

in hair, crystallin in eye.• Enzymes: all metabolic

transformations, building up, rearranging, and breaking down of organic compounds, are done by enzymes, which are proteins.

• Transport: oxygen in the blood is carried by hemoglobin, everything that goes in or out of a cell (except water and a few gasses) is carried by proteins.

• Also: nutrition (egg yolk), hormones, defense, movement

Amino Acids• Amino Acids are the subunits of

proteins. • Each amino acid contains an amino

group (which is basic) and an acid group. Proteins consist of long chains of amino acids, with the acid group of one bonded to the amino group of the next.

• There are 20 different kinds of amino acids in proteins. Each one has a functional group (the “R group”) attached to it.

• Different R groups give the 20 amino acids different properties, such as charged (+ or -), polar, hydrophobic, etc.

• The different properties of a protein come from the arrangement of the amino acids.

Protein Structure• A polypeptide is one linear chain of amino acids. A

protein may contain one or more polypeptides. Proteins also sometimes contain small helper molecules such as heme.

• After the polypeptides are synthesized by the cell, they spontaneously fold up into a characteristic conformation which allows them to be active. The proper shape is essential for active proteins. For most proteins, the amino acids sequence itself is all that is needed to get proper folding.

• Proteins fold up because they form hydrogen bonds between amino acids. The need for hydrophobic amino acids to be away from water also plays a big role. Similarly, the charged and polar amino acids need to be near each other.

• The joining of polypeptide subunits into a single protein also happens spontaneously, for the same reasons.

• Enzymes are usually roughly globular, while structural proteins are usually fiber-shaped. Proteins that transport materials across membranes have a long segment of hydrophobic amino acids that sits in the hydrophobic interior of the membrane.

• Denaturation is the destruction of the 3-dimensional shape of the protein. Denaturation inactivates the protein, and makes it easier to destroy. This is the effect of cooking foods.

Nucleic Acids• Nucleotides are the subunits of nucleic acids.• Nucleic acids store genetic information in the

cell. They are also involved in energy and electron movements.

• The two types of nucleic acid are RNA (ribonucleic acid) and DNA (deoxyribonucleic acid).

• Each nucleotide has 3 parts: a sugar, a phosphate, and a base.

• The sugar, ribose in RNA and deoxyribose in DNA, contain 5 carbons. They differ only in that an –OH group in ribose is replaced by a –H in DNA.

• The main energy-carrying molecule in the cell is ATP. ATP is an RNA nucleotide with 3 phosphate groups attached to it in a chain. The energy is stored because the phosphates each have a negative charge. These charges repel each other, but they are forced to stay together by the covalent bonds.

DNA and RNA• DNA uses 4 different bases: adenine,

guanine, thymine, and cytosine. The order of these bases in a chain of DNA determines the genetic information.

• DNA consists of 2 complementary chains twisted into a double helix and held together by hydrogen bonds. DNA is a stable molecule which can survive thousands of years under proper conditions

• RNA consists of a single chain that also uses 4 bases: however, the thymine in DNA is replaced by uracil in RNA. RNA is much less stable than DNA, but it can act as an enzyme to promote chemical reactions in some situations.

Sect. 2.3 Carbon CompoundsKey Concept:o What are the functions of each

group of organic compounds?

o Organic compounds are those substances made up of carbon atoms with side chains of other molecules

o Macromolecules:Carbohydrates

LipidsNucleic

Acids Proteins

Terms:o Monomero Polymer o Carbohydrateo Polysaccharideo Lipido Nucleic Acido Nucleotideo Ribonucleic Acid (RNA)o Deoxribonucleic Acid (DNA)o Proteino Amino Acid

The Chemistry of CarbonCarbon is so vital to life, an entire branch of chemistry is devoted to its study: organic chemistry Carbon (C) has 4 valence electrons; this means that there are 4 electrons in the outer shell (valence shell) that can bond with other elementsCH4, methane, is very common because hydrogen seeks one additional electron, and carbon needs 4 to fill its outer shellCarbon can also single, double or triple bond with other carbon atoms

C: 6 electrons (2 in inner orbital, 4 in valence orbital)

Macromolecules…• Molecules formed by a process

known as polymerization

• Large molecules built from smaller ones called monomers; this process makes polymers

• These polymers make up the four groups of macromolecules found in living organisms: -carbohydrates -lipids

-nucleic acids (DNA/RNA) -proteins

Carbohydrates… • Carbs are compounds typically made of C, H and O in the ratio of 1:2:1

• Used as energy source and as structural component

• When broken down, the release of stored energy in chemical bonds provides energy to run cell functions

• Simple sugars (ie, glucose): monosaccharides

• Complex sugars (glycogen, cellulose): polysaccahrides

Glucose: C6H12O6 The formula for

photosynthesis2 common carbohydrates

Lipids…

Lipid group is very large; varies in structure

Non-soluble in water

Constructed mostly from C and H atoms; frequently combine a carb group and fatty acid chain

Used to store energy and are a very important part of biological membranes

Lipids that form when a glycerol molecule and a fatty acid group form are called saturated or unsaturated fats

Unsaturated fats contain single C-C bonds, and are in a bent shape; they are less likely to stick and clog arteries

Saturated fats have a double carbon bond, are straight, and more sticky, causing clogs

Nucleic Acids…• Nucleic acids are macro-molecules

that are made up of individual monomers called nucleotides

• Constructed from C, H, O, N, P • Nucleotides contain 3 parts:

-5 carbon sugar-phosphate group (PO3)-nitrogenous base

• Nucleic acids store and transmit hereditary information; 2 types exist: -RNA (sugar: ribose) -DNA (sugar: deoxyribose)

What are the 3 parts of a nucleotide?

Proteins…Proteins are macromolecules that are made up of amino acid monomers; there are more than 20 amino acid groups present in living things

There are literally hundreds of thousands of proteins; this is possible because the bonding regions on amino acids are identical and can join with any R group (R group is also known as a side chain)

Depending on the side chain, the protein may be:

-structural-regulatory-enzymatic-hormonal-transport or many other functions

It is not necessary to know what each side chain is; know that an amino group always pairs with a carboxyl group (COOH) and an R group

Proteins, con’t….

Proteins have layers (levels), just like ogres and onions 4 levels of organization:

Primary- sequence of amino acidsSecondary- twisting or folding of amino acids in chainTertiary- chain itself is foldedQuarternary- 2 or more protein chains combined (hemoglobin)

Hydrogen Bonds and van der Waals forces hold proteins together

Sect 2.4 Chemical Reactions and Enzymes

Key Concepts: What happens to chemical bonds during a reaction; how does energy change affect occurrence of reactions; and, why are enzymes important to living things?

• Bonds break or form during reactions• Put in energy, reactions are more

likely to occur• Enzymes make reactions easier and

more likely to occur

Terms: Chemical reaction Reactant Product Activation energy Catalyst Enzyme Substrate

Chemical Reactions and enzymes…Chemical reactions involve reactants and products -Reactants break bonds and release energy inc. ΔS; catabolic/exothermic reaction frequently spontaneous

-Products form bonds and store energydec. ΔS; anabolic/endothermic reaction

REQUIRE energy inputActivation energy is the energy required to get a reaction startedEnzymes are used to lower the activation energy, or speed up a chemical reactionEnzymes provide a site (active site) where molecules can come together to make a reaction occur, reducing the energy needed to start the reaction. The reactants are known as substrates