Honors Biology Ch 2 I. INTRODUCTION A. CHEMISTRY = study of the composition of matter 1. ELEMENT - Fundamental form of matter that has mass and takes up.

Honors Biology Ch 2 Honors Biology Ch 2 I. I. INTRODUCTIONINTRODUCTION

A.A. CHEMISTRY = study of the composition of matter CHEMISTRY = study of the composition of matter 1. ELEMENT - Fundamental form of matter that has mass 1. ELEMENT - Fundamental form of matter that has mass and takes up space and cannot be broken down chemically and takes up space and cannot be broken down chemically apart into another substance with different propertiesapart into another substance with different properties

a. 92 Naturally occurringa. 92 Naturally occurring1.) 4 most common: C, H, O, N, 1.) 4 most common: C, H, O, N,

2.) Other common: P, Ca, S, K Mg, Na, ETC. 2.) Other common: P, Ca, S, K Mg, Na, ETC. (FIG 2.2, P. 21)(FIG 2.2, P. 21)

b. TRACE ELEMENT = one that is less than 0.01% b. TRACE ELEMENT = one that is less than 0.01% of body weight of body weight

1.) EX. I, Cu, ETC.1.) EX. I, Cu, ETC.

B. Structure and function of organism depend on B. Structure and function of organism depend on availability of certain kinds of elementsavailability of certain kinds of elements

1. EX. Mg Deficiency in man = weak sore 1. EX. Mg Deficiency in man = weak sore muscles, poor brain function; Plants= older muscles, poor brain function; Plants= older leaves turn yellow, fall off leaves turn yellow, fall off

C. PHYTOREMEDIATION = use of plants to C. PHYTOREMEDIATION = use of plants to withdraw harmful substances from the withdraw harmful substances from the environmentenvironment

1. EX. Selenium removal from agricultural 1. EX. Selenium removal from agricultural runoff by reeds and grassesrunoff by reeds and grasses

2. EX. Radioactive waste removal by 2. EX. Radioactive waste removal by sunflowers at Chernobylsunflowers at Chernobyl

II. II. REGARDING THE ATOMSREGARDING THE ATOMS (P. (P. 22-23) (2.1)22-23) (2.1)

A. ATOM = The smallest particle that retains the A. ATOM = The smallest particle that retains the properties of an element properties of an element 1. Parts (Subatomic Particles):1. Parts (Subatomic Particles):

a. PROTON – in nucleus, +1 charge a. PROTON – in nucleus, +1 charge (p+)(p+)

b. NEUTRON – in nucleus, 0 charge (n b. NEUTRON – in nucleus, 0 charge (n °)°)

c. ELECTRON – around nucleus, -1 c. ELECTRON – around nucleus, -1 charge (e-)charge (e-)2. Each atoms has same number of protons 2. Each atoms has same number of protons and electrons so overall charge on an atom = and electrons so overall charge on an atom = zero zero 3. CHEMICAL SYMBOL = Abbreviation for an 3. CHEMICAL SYMBOL = Abbreviation for an element, represents 1 atom of that elementelement, represents 1 atom of that element

B. ATOMIC NUMBER = the number of protons in an B. ATOMIC NUMBER = the number of protons in an atom (P.22, TABLE 2.1)atom (P.22, TABLE 2.1)1. EX. H Atomic number = 1, C = 61. EX. H Atomic number = 1, C = 6

C. MASS NUMBER = the number of protons + the C. MASS NUMBER = the number of protons + the number of neutrons number of neutrons 1. EX. C: 6 PROTONS + 6 NEUTRONS = 12 MASS 1. EX. C: 6 PROTONS + 6 NEUTRONS = 12 MASS NUMBERNUMBER

*NOTE: Don’t count electrons b/c mass negligible, D. *NOTE: Don’t count electrons b/c mass negligible, D. **Knowing the atomic number and mass number can **Knowing the atomic number and mass number can help predict how substances might behave in cells, in help predict how substances might behave in cells, in organisms and in environmentorganisms and in environment

E. ISOTOPE = atoms with the same number of protons E. ISOTOPE = atoms with the same number of protons (atomic number) but different numbers of neutrons (atomic number) but different numbers of neutrons 1. EX. C-12, C-13, C-14, all have 6 protons, but 1. EX. C-12, C-13, C-14, all have 6 protons, but different numbers of neutronsdifferent numbers of neutrons

2. Isotopes still react with other atoms in the 2. Isotopes still react with other atoms in the same waysame way

3. RADIOACTIVE ISOTOPE = isotope that has 3. RADIOACTIVE ISOTOPE = isotope that has an unstable nucleus and that stabilizes itself by an unstable nucleus and that stabilizes itself by emitting energy and particlesemitting energy and particles

a. RADIOACTIVE DECAY – results in a. RADIOACTIVE DECAY – results in changing element into a different elementchanging element into a different element

1.) USES: tracers in metabolic pathways 1.) USES: tracers in metabolic pathways (READ P. 23) (2.2)(READ P. 23) (2.2)

2.) carbon dating of fossils2.) carbon dating of fossils

III. III. WHAT HAPPENS WHEN ATOM WHAT HAPPENS WHEN ATOM BONDS WITH ATOM BONDS WITH ATOM (P. 24 - 25) (2.3)(P. 24 - 25) (2.3)

A. ELECTRONS AND ENERGY LEVELSA. ELECTRONS AND ENERGY LEVELS

1. Number and arrangement of electrons 1. Number and arrangement of electrons a. ORBITALS = volumes of space around a. ORBITALS = volumes of space around

the atomic nucleus in which electrons are likely the atomic nucleus in which electrons are likely to be at any minuteto be at any minute

1.) Electrons bounce in and out of these 1.) Electrons bounce in and out of these spaces, avoiding each other (like charges repel), spaces, avoiding each other (like charges repel), but staying as close to the nucleus as they can but staying as close to the nucleus as they can (opposite charges attract) (opposite charges attract)

2.) Each orbital can only hold 2 electrons 2.) Each orbital can only hold 2 electrons max. (FIG. 2.6, P., 24)max. (FIG. 2.6, P., 24)

3.) Orbitals radiate outward from the 3.) Orbitals radiate outward from the nucleus as higher and higher energy nucleus as higher and higher energy levelslevels

4.) Orbitals are contained in “shells” at 4.) Orbitals are contained in “shells” at different distances from the nucleus (FIG. different distances from the nucleus (FIG. 2.8, P. 25)2.8, P. 25)

B. THE NATURE OF CHEMICAL BONDSB. THE NATURE OF CHEMICAL BONDS

1. CHEMICAL BOND = union between 1. CHEMICAL BOND = union between the electron structure of atomsthe electron structure of atoms

a. Atoms react when there are a. Atoms react when there are electron vacancies in the outer most electron vacancies in the outer most energy shell of the atom. energy shell of the atom.

1.) EX. Usually need 8 1.) EX. Usually need 8 electrons (except H or He which need 2)electrons (except H or He which need 2)

2.) EX. C, H, O, & N all 2.) EX. C, H, O, & N all have vacancies, which mean they tend have vacancies, which mean they tend to reactto react

2. CHEMICAL EQUATION = shorthand 2. CHEMICAL EQUATION = shorthand method of showing what happens in a method of showing what happens in a chemical reaction between different chemical reaction between different substances (SEE P. 24, FIG. 2.7)substances (SEE P. 24, FIG. 2.7)

a. REACTANTS = starting a. REACTANTS = starting substancessubstances

b. PRODUCTS = ending substancesb. PRODUCTS = ending substances

c. YIELDS ARROW c. YIELDS ARROW

3. MOLECULE = two or more atoms 3. MOLECULE = two or more atoms bonded togetherbonded together

a. May consists of 1 element (EX. a. May consists of 1 element (EX. MOLECULAR NITROGEN, NMOLECULAR NITROGEN, N22))

b. May consist of 2 or more elements in b. May consist of 2 or more elements in proportions that never vary (Hproportions that never vary (H22O)O)

1.) COMPOUND = substance that 1.) COMPOUND = substance that results from combining 2 or more results from combining 2 or more different kinds of elements, has different kinds of elements, has different properties than either different properties than either element didelement did

a.) EX. Ha.) EX. H220, NaCl0, NaCl

4. MIXTURE = 2 or more 4. MIXTURE = 2 or more substances intermingle, but each substances intermingle, but each keeps its own propertieskeeps its own properties

IV. IV. IMPORTANT BONDS IN BIOLOGICAL IMPORTANT BONDS IN BIOLOGICAL MOLECULESMOLECULES (P. 26 - 27) (2.4) (P. 26 - 27) (2.4)

A. ION FORMATION AND IONIC BONDINGA. ION FORMATION AND IONIC BONDING1. ION = atom that lost or gained 1 or more electrons 1. ION = atom that lost or gained 1 or more electrons

a. Now has a positive charge (if lost electrons)a. Now has a positive charge (if lost electrons)1.) EX. Na loses 1 electron; now Na+1.) EX. Na loses 1 electron; now Na+

b. OR now has a negative charge (if gained b. OR now has a negative charge (if gained electron(s)) electron(s))

1.) EX. Cl gains 1 electron, now Cl1.) EX. Cl gains 1 electron, now Cl--

SEE P. 26, FIG. 2.9SEE P. 26, FIG. 2.92. IONIC BOND = an association of 2 ions that have 2. IONIC BOND = an association of 2 ions that have opposing charges (opposites attract) opposing charges (opposites attract)

a. EX. TABLE SALT, NaCla. EX. TABLE SALT, NaCl

B. COVALENT BOND = sharing 1 or more electron pairs B. COVALENT BOND = sharing 1 or more electron pairs with another atomwith another atom

1. EX. MOLECULAR HYDROGEN, OXYGEN, 1. EX. MOLECULAR HYDROGEN, OXYGEN, NITROGEN, ETC.NITROGEN, ETC.

2. EX. SUGAR, FAT, PROTEIN, ETC.2. EX. SUGAR, FAT, PROTEIN, ETC.3. MAY BE POLAR OR NONPOLAR3. MAY BE POLAR OR NONPOLAR

a. NONPOLAR COVALENT BOND = a. NONPOLAR COVALENT BOND = atoms have same pull on the electrons; share them atoms have same pull on the electrons; share them equally equally

1.) EX. H1.) EX. H22

b. POLAR COVALENT BOND = atoms b. POLAR COVALENT BOND = atoms of different elements have unequal pull on the of different elements have unequal pull on the electrons, more attractive atom ends up with a slight electrons, more attractive atom ends up with a slight negative charge, less attractive ends up with a slight negative charge, less attractive ends up with a slight positive charge= charge is unevenly distributed over positive charge= charge is unevenly distributed over the molecule the molecule

1.) EX. H1.) EX. H22OO

C.C. HYDROGEN BOND = weak HYDROGEN BOND = weak attraction between an electronegative attraction between an electronegative atom (such as O or N in a polar covalent atom (such as O or N in a polar covalent bond) and an electropositive atom (such as H) bond) and an electropositive atom (such as H)

1. May form between 2 different 1. May form between 2 different molecules Ex Hmolecules Ex H22O O

2. May form between different parts of 2. May form between different parts of the same parts of the same molecule as it the same parts of the same molecule as it twists and folds back on itselftwists and folds back on itself

a. EX. DNA molecule (FIG. 2.11, a. EX. DNA molecule (FIG. 2.11, P. 27); helps some proteins hold their shapeP. 27); helps some proteins hold their shape

3. Easier to break than a covalent bond, 3. Easier to break than a covalent bond, but stablebut stable

Examples of H-Bonding Examples of H-Bonding

V. V. PROPERTIES OF WATERPROPERTIES OF WATER (P.28 -29) (P.28 -29) (2.5)(2.5)

A. Life needs water: Live in it, or cart it around A. Life needs water: Live in it, or cart it around with us, reactions occur in it, cell shape and with us, reactions occur in it, cell shape and internal structure may depend on itinternal structure may depend on it

B. Polarity of water molecule B. Polarity of water molecule

1. SEE FIG. 2.12, P. 281. SEE FIG. 2.12, P. 28

2. Causes attraction to other polar 2. Causes attraction to other polar moleculesmolecules

a. H-Bonds with itself a. H-Bonds with itself b. H- Bonds with other polar b. H- Bonds with other polar

moleculesmolecules

1.) HYDROPHILIC MOLECULES = 1.) HYDROPHILIC MOLECULES = loves water, attracted to it (Ex. Sugar)loves water, attracted to it (Ex. Sugar)

c. Non-polar molecules repelledc. Non-polar molecules repelled1.) HYDROPHOBIC MOLECULES = 1.) HYDROPHOBIC MOLECULES =

Fears water, repelled by it (Ex. Oil)Fears water, repelled by it (Ex. Oil)2.) USE: Life reactions- cell membrane2.) USE: Life reactions- cell membrane

HydrophilicHydrophilic HydrophobicHydrophobic

C. Water’s Temperature- stabilizing effectsC. Water’s Temperature- stabilizing effects

1. TEMPERATURE = Measure of the 1. TEMPERATURE = Measure of the molecular motion of a given substance. molecular motion of a given substance.

a. More molecular motion= greater Ta. More molecular motion= greater T

b. Water - can absorb much more b. Water - can absorb much more heat energy without great increase in T. heat energy without great increase in T.

1. ) WHY? - Heat energy goes to 1. ) WHY? - Heat energy goes to breaking H bonds rather than to vibrationbreaking H bonds rather than to vibration

c. RESULT: Water can buffer great T c. RESULT: Water can buffer great T swings w/o harm to the organism (helps swings w/o harm to the organism (helps prevent over heating and freezing in cells prevent over heating and freezing in cells and tissues)and tissues)

d.d. EVAPORATION – breaking of H EVAPORATION – breaking of H bonds near surface; water vapor bonds near surface; water vapor escapes, taking heat energy with it escapes, taking heat energy with it

1.) USE – Cooling 1.) USE – Cooling during perspirationduring perspiration

e.e. FREEZING WATER – H- bonds FREEZING WATER – H- bonds lock water in lattice pattern lock water in lattice pattern

1.) Allows ice to be less 1.) Allows ice to be less dense than waterdense than water

2.) Ice sheets on surface of 2.) Ice sheets on surface of ponds insulate water belowponds insulate water below

a. ) Fish, etc. can live a. ) Fish, etc. can live beneath ice w/o freezingbeneath ice w/o freezing

D. WATER’S COHESIOND. WATER’S COHESION1. COHESION = 1. COHESION =

water sticks to itself (H-Bond) water sticks to itself (H-Bond) a. Capacity to resist rupturing a. Capacity to resist rupturing

when placed under tensionwhen placed under tension1.) Ex. Water strider 1.) Ex. Water strider

on top; water holds up bugon top; water holds up bugb. ADHESION (water sticks b. ADHESION (water sticks

to something else) with Cohesion to something else) with Cohesion (ADHESION NOT IN TEXT!!!)(ADHESION NOT IN TEXT!!!)

1.) EX. Movement of 1.) EX. Movement of water up a plant root/stem against gravitywater up a plant root/stem against gravity

E. WATER’S SOLVENT E. WATER’S SOLVENT PROPERTIESPROPERTIES

1. Water’s polarity allows it to 1. Water’s polarity allows it to dissolve ions and other polar dissolve ions and other polar moleculesmolecules

a. SOLVENT = substance a. SOLVENT = substance doing the dissolving doing the dissolving

b. SOLUTE = any dissolved b. SOLUTE = any dissolved substance substance

1.) Water dissolves 1.) Water dissolves substances using substances using Spheres of Spheres of hydrationhydration (SEE P. 29 FIG. 2.15) (SEE P. 29 FIG. 2.15)

VIVI. ACIDS, BASES AND BUFFERS. ACIDS, BASES AND BUFFERS (P. (P. 30 -31) (2.6)30 -31) (2.6)

A. Hydrogen ions (HA. Hydrogen ions (H++): act as free protons; are ): act as free protons; are chemically activechemically active

B. The pH ScaleB. The pH Scale1. Some water molecules split into hydroxide 1. Some water molecules split into hydroxide (OH(OH--) and hydrogen ions (H) and hydrogen ions (H++) )

HH22O O H H+ + + OH+ OH--

a. They balance each other out, so water a. They balance each other out, so water is neutral in charge (pH) is neutral in charge (pH)

b. Compare other substances to pure b. Compare other substances to pure water, to determine Hwater, to determine H++ ion concentration ion concentration

2. EXAMPLE SCALE 2. EXAMPLE SCALE P. 30, FIG. 2.16P. 30, FIG. 2.16

a. One a. One increment on pH increment on pH scale corresponds to scale corresponds to a tenfold increase or a tenfold increase or decrease in the Hdecrease in the H++ ion concentration ion concentration

b. Ranges b. Ranges from 0 to 14from 0 to 14

B. HOW DO ACIDS DIFFER FROM BASES?B. HOW DO ACIDS DIFFER FROM BASES?1. ACID = substance that when dissolved in water donates 1. ACID = substance that when dissolved in water donates protons (Hprotons (H++ ions) to other solutes ions) to other solutes

a. pH less than 7a. pH less than 7b. EX. Vinegar, citric acid, stomach acid, battery acidb. EX. Vinegar, citric acid, stomach acid, battery acid

2. BASE = substance that when dissolved in water donates 2. BASE = substance that when dissolved in water donates hydroxide ions (OHhydroxide ions (OH--) (“alkaline”)) (“alkaline”)

a. pH greater than 7a. pH greater than 7b. EX. Sea water, baking soda, egg whiteb. EX. Sea water, baking soda, egg white

3. IMPORTANCE OF pH 3. IMPORTANCE OF pH a. Chemical reactions in a. Chemical reactions in

body depend of enzymesbody depend of enzymes1.) Certain enzymes 1.) Certain enzymes

only work in certain pHs EX. only work in certain pHs EX. Stomach acid & enzymesStomach acid & enzymes

b. Use of household b. Use of household products - pH can be dangerous products - pH can be dangerous EX. Drain cleaner , ammonia, EX. Drain cleaner , ammonia, chemical burnschemical burns

c. Environmental hazards c. Environmental hazards

1.) EX. Acid Rain1.) EX. Acid Rain

C. BUFFERS AGAINST SHIFTS IN pH C. BUFFERS AGAINST SHIFTS IN pH 1. BUFFER SYSTEM = partnership 1. BUFFER SYSTEM = partnership between a weak acid and the base that between a weak acid and the base that forms when the acid dissolves in waterforms when the acid dissolves in water

a. Helps counter slight pH shiftsa. Helps counter slight pH shiftsb. EX. Blood pH and carbonic b. EX. Blood pH and carbonic

acid/bicarbonate ion Read P. 31acid/bicarbonate ion Read P. 31

1.) Blood pH = 7.3 -7.51.) Blood pH = 7.3 -7.5a.) If falls to 7, can a.) If falls to 7, can

cause coma!! (acidosis) cause coma!! (acidosis)

b.) Of too high, 7.8, b.) Of too high, 7.8, can cause tetany (alkalosis) can cause tetany (alkalosis)

D. SALTSD. SALTS

1. SALT = compounds that 1. SALT = compounds that

release ions other than Hrelease ions other than H++

or OHor OH-- when dissolved in when dissolved in

water water

a. Can result from a a. Can result from a

reaction between a strong acid and reaction between a strong acid and a strong base, plus water formsa strong base, plus water forms

b. EX. HCl + NaOH b. EX. HCl + NaOH NaCl+H NaCl+H22O O

c. Salt ions that play a role in c. Salt ions that play a role in metabolism (EX. Nametabolism (EX. Na++, K, K++, Ca, Ca2+2+))

Calcium metabolism regulator

Na +/ K+ pump controls Some protein channels in the cell membrane