Chapter 2: The Nature of Chapter 2: The Nature of Molecules & the Properties of Molecules & the Properties of

WaterWaterOCC Bio-114OCC Bio-114

Created by Dave WernerCreated by Dave Werner

What are you worth? What are you worth?

Compare chemistry of Compare chemistry of the human body to the human body to the earth’s crust and the earth’s crust and seawater.seawater.

Any similarities?Any similarities?

2.1 The Nature of Atoms2.1 The Nature of Atoms

ELEMENTSELEMENTS ARE PURE SUBSTANCES THAT CANNOT ARE PURE SUBSTANCES THAT CANNOT BE BROKEN DOWN CHEMICALLY INTO SIMPLER BE BROKEN DOWN CHEMICALLY INTO SIMPLER KINDS OF MATTER. KINDS OF MATTER. More than 100 elements have been identified, though More than 100 elements have been identified, though fewer than 30 are Important in Living Things.  (The fewer than 30 are Important in Living Things.  (The Periodic Table of Elements, Fig. 2.3) Periodic Table of Elements, Fig. 2.3) All of the Elements are arranged on a Chart known as All of the Elements are arranged on a Chart known as THE PERIODIC TABLETHE PERIODIC TABLE.  Among the information .  Among the information provided in The Periodic Table are the provided in The Periodic Table are the ATOMIC ATOMIC NUMBER, THE CHEMICAL SYMBOL, AND THE NUMBER, THE CHEMICAL SYMBOL, AND THE ATOMIC MASS FOR EACH ELEMENTATOMIC MASS FOR EACH ELEMENT. . Who developed the Periodic Table?Who developed the Periodic Table?– Dmitry MendeleevDmitry Mendeleev

ELEMENTS AND ATOMSELEMENTS AND ATOMS

> 90 Percent of the Mass of living things is > 90 Percent of the Mass of living things is composed of composed of JUST FOUR ELEMENTSJUST FOUR ELEMENTS::   

OXYGEN, O, CARBON, C, HYDROGEN, OXYGEN, O, CARBON, C, HYDROGEN, H, AND NITROGEN, N.H, AND NITROGEN, N.

Each Element has different Each Element has different Chemical Chemical SymbolSymbol which consist of which consist of One or Two One or Two LettersLetters. .

Can you give any examples?Can you give any examples?

ELEMENTS AND ATOMSELEMENTS AND ATOMS

In most cases, the Symbol Derives from In most cases, the Symbol Derives from the First Letter or Other Letters in the the First Letter or Other Letters in the Name of the Element, like - C for Carbon Name of the Element, like - C for Carbon or Cl for Chlorine. or Cl for Chlorine.

Some of the Symbol Names come form Some of the Symbol Names come form their Latin Name - Na for Sodium (natrium) their Latin Name - Na for Sodium (natrium) or K for Potassium (Kalium).or K for Potassium (Kalium).

ATOMSATOMS (fig.2-3)(fig.2-3)The Simplest Particle of an Element that The Simplest Particle of an Element that RETAINS ALL of the PROPERTIES of the RETAINS ALL of the PROPERTIES of the Element is anElement is an ATOMATOM.  Atoms are so small that .  Atoms are so small that their TRUE Structure Cannot be Observe, but their TRUE Structure Cannot be Observe, but scientist have developed Models that describe scientist have developed Models that describe the Structure and Properties of the Atom the Structure and Properties of the Atom (Figure 2.2). (Figure 2.2). An Atom consists of An Atom consists of THREE Kinds of THREE Kinds of ParticlesParticles, , PROTONS AND NEUTRONS PROTONS AND NEUTRONS FOUND IN THE ATOMS NUCLEUS, AND FOUND IN THE ATOMS NUCLEUS, AND ELECTRONS.ELECTRONS. The Central Core of an Atom is called the The Central Core of an Atom is called the NUCLEUSNUCLEUS, Most of the MASS of an Atom is , Most of the MASS of an Atom is concentrated in its Nucleus and consists of concentrated in its Nucleus and consists of Two Kinds of Particles: Two Kinds of Particles: – What are the charges for:What are the charges for:

ProtonsProtonsNeutronsNeutronsElectronsElectrons

Atoms ContinuedAtoms ContinuedA. A. PROTONSPROTONS:  A POSITIVE CHARGED :  A POSITIVE CHARGED PARTICLE.  All Atoms of a given Element PARTICLE.  All Atoms of a given Element have the SAME Number of Protons.  The have the SAME Number of Protons.  The Number of Protons in an Atom is called the Number of Protons in an Atom is called the ATOMIC NUMBER which appears Above the ATOMIC NUMBER which appears Above the Chemical Symbol. Chemical Symbol. B.B. NEUTRONS NEUTRONS - NEUTRONS HAVE NO - NEUTRONS HAVE NO ELECTRICAL CHARGE.  The number of ELECTRICAL CHARGE.  The number of Neutrons in an Atom is derived by the Neutrons in an Atom is derived by the ATOMIC MASS MINUS THE ATOMIC ATOMIC MASS MINUS THE ATOMIC NUMBER.  OR THE NUMBER OF NUMBER.  OR THE NUMBER OF PROTONS PLUS THE NUMBER OF PROTONS PLUS THE NUMBER OF NEUTRONS EQUAL THE ATOMIC MASS. NEUTRONS EQUAL THE ATOMIC MASS. C. The number of Positively Charged Protons C. The number of Positively Charged Protons is Balanced by an Equal Number of small,  is Balanced by an Equal Number of small,  NEGATIVELY CHARGED PARTICLES called NEGATIVELY CHARGED PARTICLES called ELECTRONS (e-)ELECTRONS (e-). .

Putting Radioisotopes To UsePutting Radioisotopes To Use

All atoms of an element have the same All atoms of an element have the same number of protons. However, all atoms of number of protons. However, all atoms of an element do not necessarily have the an element do not necessarily have the same number of neutrons. same number of neutrons. Atoms of the same element that have Atoms of the same element that have different number of Neutrons are called different number of Neutrons are called ISOTOPESISOTOPES. Additional neutrons change . Additional neutrons change the mass of an elementthe mass of an elementCan you name any isotopes?Can you name any isotopes?

IsotopesIsotopes

Carbon has 3 natural isotopes (Fig. 2-4)Carbon has 3 natural isotopes (Fig. 2-4)

RadioisotopeRadioisotope

An unstable, or radioactive isotope.An unstable, or radioactive isotope.

Radioactive DecayRadioactive Decay = Natural process by = Natural process by which an atom emits energy as subatomic which an atom emits energy as subatomic particles and x-rays as its unstable particles and x-rays as its unstable nucleus spontaneously breaks apart; nucleus spontaneously breaks apart; transforms one element into another in a transforms one element into another in a predictable time span.predictable time span.

Ex: Carbon DatingEx: Carbon Dating

RadioCarbon DatingRadioCarbon Dating

2.3 What Happens when Atom 2.3 What Happens when Atom Bonds With Atom?Bonds With Atom?

Each Orbital or Energy Level (shell) can Each Orbital or Energy Level (shell) can hold only a certain number of electrons. hold only a certain number of electrons. The The First Level,First Level, Nearest the Nucleus, Nearest the Nucleus, can only hold can only hold TWO ElectronsTWO Electrons.  The .  The Second and other Second and other OUTER LevelsOUTER Levels can can hold up to hold up to EIGHT ElectronsEIGHT Electrons each. each. A STABLE ATOM IS AN ATOM THAT A STABLE ATOM IS AN ATOM THAT HAS A FULL OUTER LEVEL.HAS A FULL OUTER LEVEL.

Atoms ContinuedAtoms Continued

The Electrical Charges of the Electrons OFFSET those The Electrical Charges of the Electrons OFFSET those of the Protons, making the NET Electrical Charge of an of the Protons, making the NET Electrical Charge of an Atom Atom ZEROZERO. . Electrons are high-energy particles with very little mass.  Electrons are high-energy particles with very little mass.  They MOVE About the Nucleus at very High Speeds in They MOVE About the Nucleus at very High Speeds in one of seven different one of seven different ORBITALSORBITALS OR OR ENERGY ENERGY LEVELSLEVELS. An orbitals is a three-dimentional region . An orbitals is a three-dimentional region around a nucleus that indicates the probable location of around a nucleus that indicates the probable location of an electron. (fig.) an electron. (fig.) Electrons in orbitals that are farther away form the Electrons in orbitals that are farther away form the nucleus have Greater Energy than electrons that are in nucleus have Greater Energy than electrons that are in orbitals closer to the nucleus.orbitals closer to the nucleus.

Shell Model (Fig. 2.8)Shell Model (Fig. 2.8)

From Atoms to MoleculesFrom Atoms to Molecules1. Under Natural Conditions, 1. Under Natural Conditions, MOST Elements MOST Elements DO NOTDO NOT Exist by themselves; Most Exist by themselves; Most elements COMBINE with elements COMBINE with other Elements. other Elements. 2. A 2. A PURE SUBSTANCEPURE SUBSTANCE that that is made up of Atoms of TWO is made up of Atoms of TWO or MORE Elements is called or MORE Elements is called a a COMPOUNDCOMPOUND. . 3. The Proportion of each 3. The Proportion of each kind of Atom is FIXED,  A kind of Atom is FIXED,  A CHEMICAL FORMULACHEMICAL FORMULA Shows the KIND and Shows the KIND and PROPORTION of Atoms PROPORTION of Atoms each Element that forms a each Element that forms a particular Compound - particular Compound - WATER = HWATER = H220 - indicates 0 - indicates TWO HYDROGEN Atoms to TWO HYDROGEN Atoms to ONE OXYGEN Atom. ONE OXYGEN Atom.

From Atoms to MoleculesFrom Atoms to Molecules

Is a Is a Mixture Mixture different than a different than a CompoundCompound??

2.3 The Nature of Chemical Bonds2.3 The Nature of Chemical Bonds

The Tendency of elements to combine and form The Tendency of elements to combine and form Compounds depends on the Number and Arrangement Compounds depends on the Number and Arrangement of Electrons in their Atoms. of Electrons in their Atoms. An Atom is Chemically Stable when its Outermost An Atom is Chemically Stable when its Outermost Energy Level is Filled (8 E-) Energy Level is Filled (8 E-) Most Atoms are NOT Stable in their Natural State, so Most Atoms are NOT Stable in their Natural State, so they tend to React, or Combine with other Atoms they tend to React, or Combine with other Atoms (CHEMICAL REACTIONS), in ways that make the (CHEMICAL REACTIONS), in ways that make the Atoms More Stable. Atoms More Stable. Most Atoms tend to undergo Most Atoms tend to undergo CHEMICAL REACTIONSCHEMICAL REACTIONS,  ,  Combining in ways that Cause their Atoms to Become Combining in ways that Cause their Atoms to Become Stable.  In Chemical Reactions, Stable.  In Chemical Reactions, CHEMICAL BONDSCHEMICAL BONDS are are broken, Atoms are Rearranged, and New Chemical broken, Atoms are Rearranged, and New Chemical Bonds, or Attachments, are formed.Bonds, or Attachments, are formed.

BondingBonding

Ionic and Covalent Bonding – Youtube

Ionic and covalent bonding example

IONIC BONDING - TRANSFER OF IONIC BONDING - TRANSFER OF ELECTRONSELECTRONS (Fig.2.9)(Fig.2.9)

1.1. IONIC BOND IONIC BOND IS A BOND IS A BOND FORMED BY ELECTRICAL FORMED BY ELECTRICAL ATTRACTION BETWEEN ATTRACTION BETWEEN TWO OPPOSITLY CHARGED TWO OPPOSITLY CHARGED IONS. IONS. 2. AN ATOM OR MOLECULE 2. AN ATOM OR MOLECULE WITH AN ELECTRICAL WITH AN ELECTRICAL CHARGE IS CALLED AN CHARGE IS CALLED AN IONION. . 3. 3. If an Atom has More If an Atom has More Protons than Electrons it is Protons than Electrons it is POSITIVELY CHARGED (+).POSITIVELY CHARGED (+). 4. 4. If an Atom has More If an Atom has More Electrons than Protons it is Electrons than Protons it is NEGATIVELY CHARGED (-)NEGATIVELY CHARGED (-)   The formation of Table Salt The formation of Table Salt (NaCl) is an example of an (NaCl) is an example of an IONIC BOND:IONIC BOND:

COVALENT BONDS - SHARING COVALENT BONDS - SHARING OF ELECTRONSOF ELECTRONS

1. A 1. A COVALENT BONDCOVALENT BOND forms forms when TWO Atoms SHARE One or when TWO Atoms SHARE One or MORE Pairs of Electrons. (Figure) MORE Pairs of Electrons. (Figure) 2. Water is made up by Atoms Held 2. Water is made up by Atoms Held together by a Covalent Bonds.  In together by a Covalent Bonds.  In the Presence of one another, the Presence of one another, hydrogen atoms and oxygen atoms hydrogen atoms and oxygen atoms can achieve stability by sharing can achieve stability by sharing pairs of electrons in a ration of TWO pairs of electrons in a ration of TWO Atoms of Hydrogen to ONE Atom of Atoms of Hydrogen to ONE Atom of Oxygen. Oxygen. 3. Covalent Bonding Results in the 3. Covalent Bonding Results in the Formation of Formation of MOLECULESMOLECULES. . 4. A 4. A MOLECULEMOLECULE is the Simplest is the Simplest Part of a Substance that Retains all Part of a Substance that Retains all the Properties of the Substance and the Properties of the Substance and that can Exist in a Free State. that can Exist in a Free State. 5.   Water formation is an example 5.   Water formation is an example of a Molecule of Water.of a Molecule of Water.

HYDROGEN BONDINGHYDROGEN BONDING 1. The Polar Nature of Water also 1. The Polar Nature of Water also causes Water Molecules to be causes Water Molecules to be attracted to one another or stick attracted to one another or stick together. together.

2. The Type of ATTRACTION that 2. The Type of ATTRACTION that Holds TWO Water Molecules Holds TWO Water Molecules Together is called HYDROGEN Together is called HYDROGEN BONDING. (Fig. 2.8c) BONDING. (Fig. 2.8c)

3. A POSITIVE REGION OF ONE 3. A POSITIVE REGION OF ONE MOLECULE IS ATRACTED TO MOLECULE IS ATRACTED TO THE NEGATIVE REGION OF THE NEGATIVE REGION OF ANOTHER MOLECULE. ANOTHER MOLECULE.

4. A Hydrogen Bond is a WEAK 4. A Hydrogen Bond is a WEAK Bond that can be easily broken. Bond that can be easily broken.

2.4-2.5 Water: A Vital Compound2.4-2.5 Water: A Vital CompoundPolarity of the Water MoleculePolarity of the Water Molecule

Many of Water's Biological Functions stem from its Chemical Structure. Many of Water's Biological Functions stem from its Chemical Structure.

In the Water Molecule, H2O, the Hydrogen and Oxygen Atoms SHARE In the Water Molecule, H2O, the Hydrogen and Oxygen Atoms SHARE Electrons to form a Covalent Bond, but these atoms DO NOT Share the Electrons to form a Covalent Bond, but these atoms DO NOT Share the electrons Equally. electrons Equally.

The Oxygen Atom, because of it 8 Protons versus Hydrogen's 1 Proton, The Oxygen Atom, because of it 8 Protons versus Hydrogen's 1 Proton, PULLS the Shared Electrons towards its Nucleus and AWAY from the PULLS the Shared Electrons towards its Nucleus and AWAY from the Hydrogen Atom.  As a result, the Electrical Charge is UNEVENLY Hydrogen Atom.  As a result, the Electrical Charge is UNEVENLY Distributed in the Water molecule. (Fig. 2.9) Distributed in the Water molecule. (Fig. 2.9)

Although the TOTAL Electrical Charge on a Water Molecule is Although the TOTAL Electrical Charge on a Water Molecule is NEUTRAL, the region of the molecule where the Oxygen Atom is NEUTRAL, the region of the molecule where the Oxygen Atom is located has a Slightly NEGATIVE Charge, while the regions of the located has a Slightly NEGATIVE Charge, while the regions of the molecule where each of the Two Hydrogen Atoms are located have a molecule where each of the Two Hydrogen Atoms are located have a Slightly POSITIVE Charge. Slightly POSITIVE Charge.

Water’s Solvent Properties Water’s Solvent Properties

Because of this UNEVEN PATTERN of CHARGE, Water Because of this UNEVEN PATTERN of CHARGE, Water is called a is called a POLAR MOLECULEPOLAR MOLECULE.  Molecules with a .  Molecules with a Slightly Negative End and a Slightly Positive are called Slightly Negative End and a Slightly Positive are called Polar Molecules. Polar Molecules. It is this Polar Nature that makes Water VERY It is this Polar Nature that makes Water VERY EFFECTIVE in EFFECTIVE in DissolvingDissolving many other substances. many other substances. Water Dissolves Other Polar Substances including, Water Dissolves Other Polar Substances including, Sugars, some Proteins, and Ionic Compounds such as Sugars, some Proteins, and Ionic Compounds such as Sodium Chloride, NaCl. Sodium Chloride, NaCl. An Ionic Compound mixed in water trends to An Ionic Compound mixed in water trends to DISSOCIATEDISSOCIATE (Break Apart) into Ions.  This breaking up (Break Apart) into Ions.  This breaking up of an Ionic Compound FREES Ions to participate in of an Ionic Compound FREES Ions to participate in many Biological Reactions. many Biological Reactions. Demonstration – Salt in waterDemonstration – Salt in water

SOLUTIONSSOLUTIONS

SOLUTIONSOLUTION is a Mixture in which One or More is a Mixture in which One or More Substances are Substances are UNIFORMLY DistributedUNIFORMLY Distributed in Another in Another Substance.  Solutions can be mixtures of liquids, solids, Substance.  Solutions can be mixtures of liquids, solids, or gases. or gases. Think of Sugar Water (The Solution) - the Sugar is Think of Sugar Water (The Solution) - the Sugar is dissolved in the Water and is Uniformly Distributed. dissolved in the Water and is Uniformly Distributed. The The SOLUTESOLUTE (Sugar) is the Substance Dissolved in the (Sugar) is the Substance Dissolved in the Solution (Sugar Water).  The particles that compose the Solution (Sugar Water).  The particles that compose the Solute may be Ions, Atoms, or Molecules. Solute may be Ions, Atoms, or Molecules. The The SOLVENTSOLVENT (Water) is the Substance in which the (Water) is the Substance in which the Solute is dissolved. Solute is dissolved. When Sugar, a Solute, and Water, a Solvent, are mixed, When Sugar, a Solute, and Water, a Solvent, are mixed, a Solution of Sugar Water Results. a Solution of Sugar Water Results.

Water’s CohesionWater’s Cohesion

The Hydrogen Bonds in Water exert a significant The Hydrogen Bonds in Water exert a significant Attractive Force, causing Water to Cling to Itself Attractive Force, causing Water to Cling to Itself (Cohesion) and to other Surfaces (Adhesion). (Cohesion) and to other Surfaces (Adhesion). An Attractive Force BETWEEN PARTICLES OF An Attractive Force BETWEEN PARTICLES OF THE SAME KIND is known as COHESION. THE SAME KIND is known as COHESION. An Attractive Force BETWEEN PARTICLES OF An Attractive Force BETWEEN PARTICLES OF THE different KIND is known as ADHESION.  THE different KIND is known as ADHESION.  Adhesion causes Water to look like it is Climbing Adhesion causes Water to look like it is Climbing up the side of a Glass. up the side of a Glass.

Water’s AdhesionWater’s Adhesion

ADHESION is the Attractive Force BETWEEN UNLIKE ADHESION is the Attractive Force BETWEEN UNLIKE SUBSTANCES. SUBSTANCES. Together, Adhesion and Cohesion enable Water Together, Adhesion and Cohesion enable Water Molecules to MOVE UPWARD through narrow tubes Molecules to MOVE UPWARD through narrow tubes Against the PULL OF GRAVITY.  This Property of Water Against the PULL OF GRAVITY.  This Property of Water is known as CAPILLARITY.  This is what allows Plants to is known as CAPILLARITY.  This is what allows Plants to move Water from their Roots to their Leaves. move Water from their Roots to their Leaves. Water MUST GAIN or LOSE a LARGE Amount of Water MUST GAIN or LOSE a LARGE Amount of ENERGY for its Temperature to Change = High Specific ENERGY for its Temperature to Change = High Specific Heat.  This makes Water a VERY STABLE Molecule. Heat.  This makes Water a VERY STABLE Molecule. Water's ability to Absorb Large amounts of Energy Water's ability to Absorb Large amounts of Energy HELPS keep cells at an EVEN Temperature despite HELPS keep cells at an EVEN Temperature despite Temperature changes in the Environment.Temperature changes in the Environment.

2.6 ACIDS AND BASES 2.6 ACIDS AND BASES (Fig. 2.16)(Fig. 2.16)

One molecule of water One molecule of water dissociatesdissociates to form TWO Ions, H+ and OH- to form TWO Ions, H+ and OH-The OH- is known as the The OH- is known as the HYDROXIDE IONHYDROXIDE ION.  The free H+ ion can .  The free H+ ion can react with another water molecule:            react with another water molecule:            The H3O+ ion is known as the The H3O+ ion is known as the HYDRONIUM ION.HYDRONIUM ION. ACIDITY or ALKALINITYACIDITY or ALKALINITY is a measure of the relative amounts of is a measure of the relative amounts of Hydronium Ions and Hydroxide Ions dissolved in a Solution. Hydronium Ions and Hydroxide Ions dissolved in a Solution. NEUTRAL SOLUTION NEUTRAL SOLUTION - If the number of Hydronium Ions in a - If the number of Hydronium Ions in a solution EQUALS the number of Hydroxide Ions, the Solution is said solution EQUALS the number of Hydroxide Ions, the Solution is said to be Neutral. to be Neutral. ACIDACID - If the number of Hydronium Ions (H - If the number of Hydronium Ions (H33O+) in a Solution is O+) in a Solution is GREATER than the number of Hydoxide Ions (OH-), the Solution is GREATER than the number of Hydoxide Ions (OH-), the Solution is an ACID.  an ACID.  Acids tend to have a SOUR Taste and in concentrated Acids tend to have a SOUR Taste and in concentrated forms are Highly Corrosive.forms are Highly Corrosive. BASEBASE - If a Solution contains MORE Hydroxide Ions (OH-) than - If a Solution contains MORE Hydroxide Ions (OH-) than Hydronium Ions (HHydronium Ions (H33O+) it is defined as a BASE.  O+) it is defined as a BASE.  Bases tend to Bases tend to FEEL Slippery (soap) and have a BITTER Taste.FEEL Slippery (soap) and have a BITTER Taste.

BUFFERSBUFFERS

Buffer System = counter slight shifts in pH.Buffer System = counter slight shifts in pH.

Ex: Body fluids – pH of blood rises, Ex: Body fluids – pH of blood rises, carbonic acid neutralized the excess OH- carbonic acid neutralized the excess OH- by releasing H+ ions, which combine w/ by releasing H+ ions, which combine w/ OH- to form water, HOH- to form water, H22O.O.

Massive swings in blood pH can be Massive swings in blood pH can be deadly.deadly.