03 Chemistry of Life AJH

8/13/2019 03 Chemistry of Life AJH

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The Chemistry of Life

Chapter 2



Isn’t this a BIOLOGY class?

Why study chemistry?



Chemistry Review… Just a few concepts and their biological connections

Electrons

Chemical Bonds Properties of Water

pH and Buffer Systems

Chemical Reactions and Energy Functional Groups



Electrons

Electrons – negatively charged subatomic particles

that interact with other atoms

involved in chemical bonds Involved in chemical reactions

Electron arrangements determine the chemical

properties of an atom

An atom is most stable (least reactive) when its

outer electron shell is full



Electrons and Chemical Bonds

To achieve stability, atoms:

give up or accept electrons or

share electrons with another atom

Loss of electron

H2 molecule has

two shared electrons

... which canresult in the

formation of

chemical

bonds



Chemical Bonds

Chemical Bond – union between electronstructures of atoms

Types Found in Biological Molecules

Ionic Bonds – attraction between ions

Covalent Bonds – sharing of electrons between atoms

Polar Non-polar

Hydrogen Bonds – weak interactions between atomsinvolved in polar covalent bonds



Ionic Bonds

Table salt is a crystal composedof two ions held together by

i on ic bonds

Cl –

Na+

Loss ofelectron

Gain ofelectron

Sodium ionhas positive

charge

Chloride ionhas negative

charge



Covalent Bonds: Nonpolar

nonpolarcovalent bond

Hydrogen atoms each haveone unpaired electron

H2 molecule has twoequally shared electrons



Covalent Bonds: Polar

polar covalent bonds

Electrons are sharedunequally , so partial

charges exist onthe O and H atoms

Electronegativity – tendency of an atom to attract electrons to itself

O >> N > C ≈ H



Understanding Bonds

What determines whether two atoms will form a an

ionic bond, a nonpolar covalent bond or a polar

covalent bond?

Electronegativity – the ability of an atom to attract

electrons to itself

Dependent upon: Number of protons in the atom’s nucleus

Atomic radius - distance between the nucleus and the

outer shell in which electrons are orbiting



Electronegativity

A

t o m i c r a d i u s

Protons in atomic nucleus

less more

small

large



Electronegativity

A

t o m i c r a d i u s

Protons in atomic nucleus

less more

small

large

HIGH

electronegativity

LOW

electronegativity



Electronegativity & Chemical Bonds

The difference in electronegativity between two atoms

determines the type of bond that will form.

ElectronegativityDifference

Type of BondFormed

Zero – very small(equal electron sharing)

Intermediate(unequal electron sharing)

Large(electron transfer)

Ionic Bond

PolarCovalent Bond

NonpolarCovalent Bond



Continuum of Electron Sharing




Examples:

Na – ClCl = 3.16

Na = 0.93

Difference: 2.23 (large) Ionic Bond

C – HC = 2.25

H = 2.20

Difference: 0.35 (very small) Nonpolar Covalent Bond




Example:

O – HO = 3.44

H = 2.20

Difference: 1.24 (intermediate) Polar Covalent Bond

Electrons are sharedunequally , so partialcharges exist onthe O and H atoms thatparticipate in the bond

slight negative charge at this end

slight positive charge at this end



Hydrogen Bonds

Hydrogen Bonds - weak interactions

between a slightly positive hydrogen

atom and a slightly negative atom

(both involved in polar covalent bonds)



Hydrogen Bonds

Individually, hydrogen bonds are weak interactions

(much weaker than covalent bonds)

But… when acting in concert, a large number of hydrogen

bonds can create a very strong interaction

Example: DNA (deoxyribonucleic acid)



Hydrogen Bonds Between Water

Molecules

-

++

-

+

+

+

++

+-

-



Hydrophilic and Hydrophobic

Polar molecules Interact with polar (and charged) molecules

Hydrophilic (water-loving)

E.g. sugars, ions

Nonpolar molecules Interact with nonpolar molecules

Hydrophobic (water-fearing)

E.g. fatty acids, methane

Amphipathic molecules Some polar and some nonpolar groups on the

same molecule

E.g. proteins, phospholipids



Properties of Water

Excellent Solvent

High Cohesion and Adhesion (and surface tension)

Low-density Freezing High Energy-absorbing Capacity

These properties are a result of the polarity of

water molecules…

… and their ability to form hydrogen bonds



Excellent Solvent

Salt in absenceof water

Salt dissolved in water

Solution – liquid homogeneous mixture of 2 or more substances

Solute – substance dissolved in a solution

Solvent – fluid in which substances are dissolved - dissolving agent



Cohesion, Adhesion and Surface Tension

Cohesion

Surface Tension

Meniscus Formation

Capillary

Action



Low-Density Freezing

Liquid Water – no lattice/more dense

Ice – crystal lattice/less dense



Ionization of Water

pH – measure of H+

concentration in a solution

pH = -log[H+]

H2O H+ + OH-

Very low concentration of ions: 1x10 -7 M



Acids and Bases

Acids

donate protons when dissolved in water

increase H+ concentration

pH < 7

Bases

accept protons when dissolved in water

lower H+ concentration

pH > 7



pH Scale

Oven cleaner

Milk of magnesia

Household ammoniaHousehold bleach

Milk

Baking sodaSeawater

Urine

Human bloodPure water

Wine

Lemon juice

Black coffee

Tomatoes

Stomach acid

Vinegar, soft drinks, beer

Acidic

Neutral

Basic

Logarithmic scale

pH change of 1 = 10x difference in [H+]



pH: Why is this important?

A pH change can alter the chemical behavior of a

molecule

Aspartate(an amino acid)

ABLE to

participate in

ionic bonds

UNABLE to

participate in

ionic bonds

H

Lower pH(more acidic)



Buffer System

Buffer – compound (weak acid) that minimizes variations in pH

Buffer System – partnership between a weak acid and the base

that forms when the acid dissolves in water

EXAMPLE: carbonic acid / bicarbonate (partner base)



Buffer System: Example

If [H+ ] in blood is too low (high pH, basic)…

H2CO3 HCO3- + H+

If [H+ ] in blood is too high (low pH, acidic)…

HCO3- + H+ H2CO3

Chemical reactions: reactants and products



Chemical reactions & energy

Energy (the capacity to do work) exists in many

different interconvertible forms, such as:

Solar/Light (radiant)

Chemical

Heat (thermal)

Mechanical

Electrical Nuclear

Sound



L f Th d i



Laws of Thermodynamics:Rules of Energy Transformation

First Law of Thermodynamics (Law of Conservation of Energy)

Energy cannot be created or destroyed, but it can

be transferred and transformed (changed from

one form to another)

Where does the chemical (potential) energy

stored in the carbohydrates in fruits andvegetables originate?

Where does the chemical energy stored in meat

originate?

L f Th d i



Laws of Thermodynamics:Rules of Energy Transformation

Second Law of Thermodynamics (Law of Increasing Entropy)

Energy cannot be changed fromone form to another without a lossof usable energy

Things spontaneously move towarda state of disorder; entropy

increases in a closed system

Entropy (S) – measure of the amount ofdisorder in a system



Moving Toward Disorder (Entropy)

Glucose• More organized

•

Less entropy (less stable)

Carbon Dioxide + Water• Less organized

• More entropy (more

stable)

ΔS = S(products) – S(reactants)

Which has more energy: reactant or products?



Understanding Functional Groups

In chapter 3 you will be

learning the properties of the

four classes of biomolecules.

It will help greatly if you first

learn the names, structures,

and significance of these

functional groups.

Doing so will be easier if you

apply your understanding ofpolar/nonpolar features ,

acid/base functions , and

hydrogen bonding conditions.

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03 Chemistry of Life AJH