Chapter 2

The chapter that defines all that follow after…

Section 1: The Nature of Matter

• Atoms: the smallest particle of an element that has the properties of that element

– Parts of an atom:• Protons – positively

charged, found in core

• Neutrons – no charge, found in core

• Electrons – negatively charged, found in a cloud around the core

electron

neutron

proton

Atoms bond together …• Elements

– consists of only one kind of atom, – cannot be broken down into a simpler type of matter by either physical

or chemical means, and – can exist as either atoms (e.g. argon) or molecules (e.g., nitrogen).

NOTE: A molecule consists of two or more atoms of the same element, or different elements, that are chemically bound together. Note that the two nitrogen atoms which comprise a nitrogen molecule move as a unit.

• Compounds– consists of atoms of two or more different elements bound together, – can be broken down into a simpler type of matter (elements) by

chemical means (but not by physical means), – has properties that are different from its component elements, and – always contains the same ratio of its component atoms.

• Ions– Charged (positive/negative) atoms due to loss or gain of an electron– Cations - have more protons than electrons and are positively charged– Anions - have more electrons than protons and are negatively charged

Three Types of Bonds

Covalent Bonds – (electron sharing) – formed when electrons are shared between two elements – strongest type of bond Ex. H + Cl = HCl

Ionic Bonds – (electron donating) – electrons from one atom are donated to another creating an ion (atoms that are positively charged due to the loss of electrons or negatively charged due to addition of electrons) - positive and negative atoms are attracted to each other creating the bond Ex. Na + Cl = Na+Cl-

Hydrogen Bonds – (weak electrical attractions) – larger Oxygen molecules pull smaller Hydrogen molecules closer – “almost” share an electron Ex. 2H + O = H2O

Section 2: Water and Solutions

• Properties of Water– Water is polar – it has a positive and negative side

• Solutions – substances dissolved in water (Ex. Salt water)– Polar molecules can dissolve in water creating a solution– Non-polar molecules (like oil) can not dissolve in water and do not

create a solution

– Water is cohesive – water molecules stick together– Water is adhesive – Water molecules stick to other

substances– Water stores heat efficiently (High Specific Heat, High Heat

of Vaporization)– Water is less dense as a solid

6

Water is polar … Water is a good solvent.

- Water dissolves polar molecules

and ions.

-hydrophilic: “water-loving”

7

Water is polar …

• Water organizes non-polar molecules.

• hydrophobic: “water-fearing”

- Water causes hydrophobic molecules to aggregate or assume specific shapes.

http://www.realeyz.com/photo/macro/photos/leaf_drops.jpg

CohesionCohesion is the property of water that causes it to be attracted to itself.

•Surface tension measures the strength of water molecules attracting to one another.

•This property allows insects to walk on the surface of water and the creation of waves.

Surface Tension

Capillarity Water molecules will “tow”

each other along when in a thin glass tube.

AdhesionAttraction between molecules of different substances

Ex: glass and waterOr a visit to the doc

http://staff.um.edu.mt/rlib1/sm/wpe32.jpg

Cohesion-Adhesion Theory

(aka Transpiration)-As water evaporates from leaves, it tugs on the water molecules below-Cohesion and adhesion pull water up and replace missing water molecules-Water enters the roots by osmosis

www.emc.maricopa.edu/.../BioBookPLANTHORM.html

Did you ever wonder: How does water move from roots to leaves when a tree doesn’t have a heart to pump the water?

High Specific Heat

•Water resists temperature change, both for heating and cooling.

•Water can absorb or release large amounts of heat energy with little change in actual temperature.

High Heat of Vaporization

• In order for water to evaporate, hydrogen bonds must be broken. As water evaporates, it removes a lot of heat with it.

•Thus, the heat of vaporization refers to the amount of energy required to convert water from a liquid to a gas.

Water is Less Dense as a Solid

•Which is ice and which is water?

Density of Ice•Most solids are more dense than their liquids

•This makes solids sink

•Ice is less dense than liquid water

•Due to H-Bonds•Important to life because bodies of water freeze top down•Allows life to survive below

http://shiftingbaselines.org/blog/images/Iceberg.jpg

Acids & BasespH ScaleMeasurement of the concentration of hydrogen ionsAcid: forms H+ when dissolved in waterHigh concentration of [H+](or hydronium ion);low conc. of [OH-]

Base: reduces H+ when dissolved in waterHigh [OH-](a.k.a. hydroxide ion);low [H+]

Stomach Acid = pH 2

Section 3: Chemistry of CellsOrganic Compounds

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

• There are four major types– Carbohydrates– Lipids– Proteins– Nucleic Acids

Carbohydrates

• Carbohydrates – Made of carbon, hydrogen, and oxygen in the proportion of 1:2:1– 1 carbon:2 hydrogen:1 oxygen

• main source of energy; • provide structure in plants

3 Types of Carbohydrates

Monosaccharide (simple sugars) – the building blocks of carbohydrates Ex. Glucose and Fructose (fruit sugars)

Disaccharides (double sugars) – 2 or more monosaccharides put together Ex. Sucrose (table sugar) and Lactose (milk sugar)

Polysaccharides (many sugars) – 3 or more monosaccharides put together Ex. Rice, potatoes, beans, corn, pasta, bread

Monosaccarides (simple sugars) the building blocks of carbohydrates

• EXAMPLES:

• Glucose (product of photosynthesis, used in cellular respiration)

• Fructose (fruit sugar)

Disaccharides (double sugars) 2 or more monosaccharides put

together • EXAMPLES

• Sucrose (table sugar)

• Lactose (milk sugar)

Polysaccharides (many sugars) 3 or more monosaccharides put

together Examples of polysaccharide groupsStarches: plants store energy (extra glucose)

in this form (rice, potatoes, beans, corn)

Glycogen: animals store energy (extra glucose) in this form in two areas, the muscles and liver, when these are full the remaining energy is stored in fats.

Cellulose – used in the structure of the cell wall of plants. Cannot be digested by humans but is essential for digestive health.

Lipids

• insoluble organic compounds (do not dissolve in water);

• made of fatty acids and glycerol in the proportion of 1:3;

– 1 glycerol : 3 fatty acids• held together by hydrogen bonds; • store a lot of energy

– Contain almost 2x the energy found in carbohydrates (9 calories VS 4 calories)

• 4 Types of Lipids– Fats/Oils– Waxes– Phospholipids– Steroids

Fats and oils provide long term energy storage and act

as insulation to keep animals warm

• Fat is solid at room Temp, oils are liquid

• Saturated fats – stick butter, lard, that whitish waxy looking stuff that forms on a steak or hamburger in the refrigerator; unhealthy fats, effect heart/liver functions, weight gain, and cholesterol levels

• Unsaturated fats – olive oil, fish oil, etc are much better for you and can even raise your level of “good” cholesterol.

Waxes & Phospholipids

• Waxes – provide protection by repelling water (Ex. Cuticle of plants); naturally occur on fruits and vegetables to prevent dehydration

• Phospholipids – make up the cell membrane

Steroids

• Serve structural and control functions in the body

• Examples – Hormones such as Estrogen and

Testosterone– Cholesterol that is produced by the body

Proteins Large complex molecules made of amino acids

(20 amino acids are used to make a variety of protein combinations)

How the amino acids are arranged is key to biodiversity.

• 6 Major Protein Functions:– Movement – actin and myocin are proteins needed for contraction and relaxation of muscle fibers

and therefore muscle movement

– Structure – collagen is the most abundant protein in the human body, it gives elasticity and firmness to skin; forms bones, tendons, ligaments, and cartilage.

– Defense – antibodies are proteins that help animals fight off invasion by viruses and bacteria

– Transport – hemoglobin is the protein in red blood cells that carries oxygen through the bloodstream; a lack of red blood cells is called anemia

– Nutrition – casein is a protein in breast milk that stores amino acids for use by newborn mammals; many proteins are used to build muscles and repair injuries

– Regulation – enzymes catalyze (speed up) chemical reactions in the cells; we get them from eating raw vegetables (note the verb catalyze is from the non catalyst – a chemical that speeds a chemical reaction without being altered itself)

– MSDTNR

Nucleic AcidsLarge complex molecules that contain

hereditary or genetic information

• 2 Types of nucleic acids– DNA (deoxyribonucleic acid) – caries

instructions that control the activities of the cell

– RNA (ribonucleic acid) – responsible for protein synthesis

One more important biological molecule

ATP

• adenosine triphosphate

• energy currency of the cell; contains 2 extra energy storing phosphate groups

• cells need a steady supply of ATP to function

Section 4:

Energy and Chemical Reactions • Energy – the ability to move or change matter; many types including

chemical, light, heat, mechanical, and electrical

• Energy can be stored or released in a chemical reaction » Chemical reactions are processes in which chemical

bonds between atoms are broken and new ones formed producing one or more new substances;

» summarized as … reactants → products

• Metabolism – all the chemical reactions that occur within an organism

• Activation Energy – energy needed to start a reaction (like the first push to get a large object rolling downhill)

• Enzymes – act as a catalyst to speed up reactions once started– Enzymes affect specific substances (ex. Amylase affects starch &

glucose) and are affected by factors like temperature and pH

Steps in the Enzyme Reaction

• Coordinating enzyme and substrate are available• Substrate binds to enzyme’s active site• Chemical bonds in substrate break; substrate is

converted into its products• Products are released; enzyme is unchanged