02: water and carbon: the chemical basis of life

7/28/2019 02: Water and Carbon: The Chemical Basis of Life

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2011 Pearson Education, Inc.

Lectures by Stephanie Scher Pandolfi

BIOLOGICAL SCIENCE

FOURTH EDITION

SCOTT FREEMAN

2Water and Carbon: The

Chemical Basis of Life


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Key Concepts

Molecules form when atoms bond to each other. Chemical bonds

are based on electron sharing. The degree of electron sharing

varies depending on the type of bond formed.

Of all small molecules, water is the most important for life. Water

is highly polar and readily forms hydrogen bonds, making it an

extremely efficient solvent.


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Key Concepts

Energy is the capacity to do work or supply heat, and can be (1) a

stored potential or (2) an active motion. Chemical energy is a

form of potential energy, stored in chemical bonds.

Chemical reactions tend to be spontaneous if they lead to lower

potential energy and higher entropy, and nonspontaneous if they

require an input of energy.

Most of the important compounds in organisms contain carbon.


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Basic Atomic Structure

Atoms are composed of:

Protonspositively charged particles Neutronsneutral particles

Electronsnegatively charged particles

Protons and neutrons are located in the nucleus.

Electrons are found in orbitals surrounding the nucleus.


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ElementsThe Building Blocks of Chemical Evolution

Every different atom has a characteristic number of protons inthe nucleus, called the atomic number.

Atoms with the same atomic number have the same chemicalproperties and belong to the same element.

Forms of an element with different numbers of neutrons areisotopes.

The mass number is the number of protons + neutrons of the most

common isotope.



Electron Arrangement around the Nucleus

Electrons move around atomic nuclei in specific regions called

orbitals.

Each orbital can hold up to two electrons.

Orbitals are grouped into levels called electron shells.

Electron shells are numbered, with smaller numbers closer tothe nucleus.

The electrons in the outermost shell are called valence

electrons.

Elements commonly found in organisms have at least one unpaired

valence electron. The number of unpaired electrons in an atom is its

valence.


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Chemical Bonding

Unfilled electron orbitals allow formation ofchemical bonds, and

atoms are most stable when each electron orbital is filled.

Covalent bond: Each atoms unpaired valence electrons are

shared by both nuclei to fill their orbitals.

Substances held together by covalent bonds are calledmolecules.

Ionic bond: Electrons are transferred from one atom to

another.


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Covalent Bonds

Electrons are not always shared equally. An atom in a molecule

with a high electronegativity will hold the electrons more tightly

and have a partial negative charge (), whereas the other atom will

have a partial positive charge (+).

Differences in electronegativity dictate how electrons are

distributed in covalent bonds.

Nonpolar covalent bond: Electrons are evenly shared between

two atoms and the bond is symmetrical.

Polar covalent bond: Electrons are asymmetrically shared.


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Covalent Bonds

BLAST Animation: Covalent Bonds
http://localhost/var/www/apps/conversion/tmp/scratch_3/Covalent_Bonds.html


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Ions and Ionic Bonds

An atom or molecule that carries a charge is called an ion.

Cation

: An atom that loses an electron and becomes positively

charged.

Anion: An atom that gains an electron and becomes negatively

charged.

The resulting attraction between oppositely charged ions is an ionic

bond.


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The Electron-Sharing Continuum

The degree to which electrons are shared in chemical bonds forms

a continuum, from equal sharing in nonpolar covalent bonds, to

unequal sharing in polar covalent bonds, to the transfer of

electrons in ionic bonds.


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C A ?


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How Many Bonds Can an Atom Have?

The number of unpaired electrons determines the number of bonds

an atom can make.

Atoms with more than one unpaired electron can form multiple

single bonds or double or triple bonds.


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R ti M l l


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Representing Molecules

The shape of a simple molecule is governed by the geometry of its

bonds.

Molecular formulas indicate the numbers and types of atoms in a

molecule (e.g., H2O, CH4).

Structural formulas indicate which atoms are bonded together and

whether the bonds are single, double, or triple bonds.

Ball-and-stick models and space-filling models show 3Dgeometry.


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Chemical Reactions


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Chemical Reactions

Chemical reactions occur when:

1. One substance is combined with another.

Atoms are rearranged in molecules, or small molecules

combine to form larger molecules.

2. One substance is broken down into another substance.

Molecules are split into atoms or smaller molecules.

In most cases, chemical bonds are broken and new bonds form.

Quantifying Molecules


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Quantifying Molecules

The molecular weight of a molecule is the sum of the mass

numbers of all the atoms in the molecule.

One mole, or 6.022 1023 molecules, has a mass equal to the

molecular weight expressed in grams.

The concentration of a substance in a solution is typically

expressed as molarity (M), which is the number of moles per liter.

Why Is Water Such an Efficient Solvent?


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Why Is Water Such an Efficient Solvent?

Life is based on water because water is a great solvent.

The covalent bonds in water are polar because oxygen has a greater

electronegativity than hydrogen.

Oxygen has a partial negative charge.

Hydrogen has a partial positive charge.

Hydrogen bonds are the weak electrical attractions between the

partially negative oxygen of one water molecule and the partially

positive hydrogen of a different water molecule. Can also form between a water molecule and another polar

molecule.


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Water and Hydrogen Bonds


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Water and Hydrogen Bonds

Ions and polar molecules stay in solution because of their

interactions with waters partial charges. These atoms and

molecules are said to be hydrophilic.

Uncharged and nonpolar compounds do not dissolve in water and

are said to be hydrophobic.

Hydrogen bonding makes it possible for almost any charged or

polar molecule to dissolve in water.


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Hydrogen Bonds and Water


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Hydrogen Bonds and Water

BLAST Animation: Hydrogen Bonds in Water

Correlation of Waters Structure and Properties
http://localhost/var/www/apps/conversion/tmp/scratch_3/Hydrogen_bonds_water.html


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Correlation of Water s Structure and Properties

Water is unique due to its small size, bent shape, highly polar

covalent bonds, and overall polarity.

Water also has several remarkable properties, largely due to its

ability to form hydrogen bonds. Water is:

1. Cohesive

2. Adhesive

3. Denser as a solid than a liquid

4. Able to absorb large amounts of energy

A Closer Look at the Properties of Water


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A Closer Look at the Properties of Water

Cohesionbinding between like molecules

Results in high surface tension

Adhesionbinding between unlike molecules

Water expands as it changes from a liquid to a solid. This is why ice floats!

Water has an extraordinarily large capacity for absorbing heat.

High specific heat

High heat of vaporization


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The Properties of Water


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p

Web Activity: Properties of Water

AcidBase Reactions and pH
http://localhost/var/www/apps/conversion/tmp/scratch_3/PropertiesOfWater.html


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p

Proton [hydrogen ion (H+)] concentration is the basis of the pH

scale.

pH expresses proton concentration in a solution.

The pH of pure water is 7.

Acids have a pH of less than 7.

Bases have a pH of greater than 7.

In acidbase reactions, a proton donor (acid) transfers a proton to

a proton acceptor (base).

The pH Scale and Buffers


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p

The pH scale is logarithmic:

pH = log [H+]

Greater H+ concentrationlower pHmore acidic

Lower H+ concentrationhigher pHmore basic/alkaline

Buffers are compounds that minimize changes in pH.


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How Do Chemical Reactions Happen?


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pp

Chemical reactions have reactants and products. For example:

CO2(g) + H2O(l) H2CO3(aq)

Chemical equilibrium occurs when the forward and reverse

reactions proceed at the same rate and the quantities of reactants

and products remain constant.

Endothermic reactions must absorb heat to proceed, but

exothermic reactions release heat.

What Is Energy?


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Energy is the capacity to do work or supply heat. This capacity

exists in one of two waysas a stored potential or as an active

motion.

Potential Energy and Kinetic Energy


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Stored energy is called potentialenergy. An objects position

determines its ability to store energy. For example:

Electrons in an outer shell (farther from the positively

charged nucleus) have more potential energy than do

electrons in an inner shell.

The energy of movement is called kineticenergy orthermal

energy, which is measured as temperature.

Low-temperature objects have slower molecules than high-

temperature objects.


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Heat and the First Law of Thermodynamics


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Heat is the thermal energy transferred between objects of different

temperatures.

The first law of thermodynamics states that energy is conserved

it cannot be created or destroyed, but it can be transferred or

transformed.


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What Makes a Chemical Reaction Spontaneous?


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Chemical reactions are spontaneous if they proceed on their own,

without any continuous external influence such as added energy.

The spontaneity of a reaction is determined by two factors:

1. The amount of potential energy

Products of spontaneous reactions have less potential energy

than the reactants.

2. The degree of order

Products of spontaneous reactions are less ordered than the

reactants.

The Second Law of Thermodynamics


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Entropy (S) is the amount of disorder in a group of molecules.

The second law of thermodynamics states that entropy always

increases.

In other words, chemical reactions result in products with less

ordered (usable) energy.

In general, physical and chemical processes proceed in the direction

that results in lower potential energy and increased disorder.


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Gibbs Free-Energy Change


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The Gibbs free-energy change (G) determines whether a

reaction is spontaneous or requires energy.

G < 0 is an exergonic spontaneous reaction.

G > 0 is an endergonic reaction that requires energy input.

G = 0 is a reaction that is at equilibrium.

Temperature and Concentration Affect Reactions


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Breaking and forming bonds depends on collisions between

substances.

This allows electrons to interact.

The rate of a reaction depends upon the number of collisions.

The number of collisions is dependent on the temperature and

concentration of the reactants:

Higher temperature more collisions faster reaction

Higher concentration

more collisions

faster reaction


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Energy Inputs and the Start of Chemical Evolution


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Formation of formaldehyde (H2CO) and hydrogen cyanide (HCN)

is the first step in chemical evolution and requires energy input.

Photons are packets of light energy emitted by the Sun.

High-energy photons can break molecules apart by knocking

electrons away from valence shells. The resulting free radicals

have unpaired electrons and are extremely unstable and highly

reactive.


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Chemical Energy Is a Form of Potential Energy


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Significant amounts of H2CO and HCN could form under the

temperature and concentration conditions that were likely on

ancient Earth. These products have more potential energy than the reactants.

Potential energy stored in chemical bonds is called chemical

energy.

Thus: solar energy (energy of the Sun) was converted into chemical

energy (in H2CO and HCN).

The Importance of Carbon


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Carbon is the most versatile atom on Earth. Because of its four

valence electrons, carbon can form many covalent bonds.

Carbon-containing molecules can form an almost limitless arrayof molecular shapes with different combinations of single and

double bonds.

The formation of carboncarbon bonds was an important event inchemical evolution.


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Functional Groups: Determinants of Chemical Behavior


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The carbon atoms in an organic molecule furnish the skeleton that

gives the molecule its overall shape.

Amino and carboxyl groups: Attract or drop a proton,

respectively

Carbonyl groups: Sites of reactions that link molecules intolarger, more-complex compounds

Hydroxyl groups: Act as weak acids

Phosphate groups: Have two negative charges

Sulfhydryl groups: Link together via disulfide bonds


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02: water and carbon: the chemical basis of life

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