BIO 1010 Chapter 2 - Chemistry

Why study chemistry?

Corpse flower

Devil’s Gardens

Why are there 800 year old stands of only lemon trees in the middle of the

Amazon rain forest?

Some Basic Chemistry

Take any biological system apart, and you eventually end up at the chemical level.

Chemical reactions are always occurring in the human body and our environment.

Figure 1.2-3

Organisms5

12

3

4

7

6

8

109

BiosphereEcosystems

Populations

Communities

Organ Systemsand Organs

Tissues

Cells

OrganellesMolecules and Atoms

NucleusAtom

Are Chemicals Bad or Good for you?

Misconceptions and Concerns about chemicals

Appreciation for chemical nature of our bodies and our world

Potential harms and benefits

Several chemicals are added to food for a variety of reasons

–Help preserve it–Make it more

nutritious

–Make it look better

Matter: Elements and Compounds

Matter is anything that occupies space and has mass.

Matter is found on Earth in three physical states:

solid,

liquid, and

gas.

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Matter is composed of chemical elements.

An element is a substance that cannot be broken down into other substances by chemical reactions.

There are 92 naturally occurring elements on Earth.

All of the elements are listed in the periodic table.

Matter: Elements and Compounds

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Elements & AtomsElement: a substance that can neither be broken down nor converted to another substance by chemical reactions. Pure substance that contains only one type of atom

Figure 2.1a

Atomic number(number of protons)

Mass number(number of

protons plus neutrons)

Element symbol

12

6

C

He

Ne

Se Br

Cl

F

Ar

Kr

Xe

ONCB

SPSiAl

I

Ge AsGa

TeSbSnIn

MnCr

Po At RnPb BiTI

CoFeV CuNi Zn

Tm Yb LuHo ErDy

BeLi

MgNa

K ScCa Ti

MoNb RuTc PdRh AgYSrRb Zr

H

Cd

LaBa TaHf OsRe IrW AuPt HgCs

BhSg MtHs RgDs CnFr AcRa Rf Db

Md No LrEs FmCfAm Cm BkNp PuU

Eu Gd TbPm SmNd

Pa

Pr

Th

Ce

Figure 2.1b

Thermometers, dental fillings and batteriesMercury in the air settles into water. It can pass through the food chain and build up in fish, shellfish and animals that eat fish. Exposure to high levels can damage the brain and kidneys. Can damage the kidneys and the nervous system, and interfere with development of the brain in the very young children

Mercury

Figure 2.1c

Deficiencies of copper can cause premature hair graying, sterility and premature wrinkling of the skin.

Figure 2.1d

Affects nearly all system: Hearing loss, kidney problems, lower IQ, children are more vulnerable because they tend to place things in their mouths.Houses built before ‘78, present toys, pipes, faucets

Lead

Twenty-five elements are essential to people.

Four elements make up about 96% of the weight of most cells:

oxygen,

carbon,

hydrogen, and

nitrogen.

Matter: Elements and Compounds

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ELEMENTS, ATOMS, AND MOLECULES

What is matter?There are 92 chemical elements in nature

Life requires 25 essential elements; some are called trace elements.

Figure 2.2

Oxygen (O):65.0%

Carbon (C): 18.5%

Calcium (Ca): 1.5%

Magnesium (Mg): 0.1%

Chlorine (Cl): 0.2%

Sodium (Na): 0.2%

Sulfur (S): 0.3%

Potassium (K): 0.4%

Phosphorus (P): 1.0%

Hydrogen (H):9.5%

Nitrogen (N):3.3%

Trace elements: less than 0.01%

Iron (Fe)Iodine (I)Fluorine (F)Copper (Cu)Cobalt (Co)Chromium (Cr)Boron (B)

Zinc (Zn)Vanadium (V)Tin (Sn)Silicon (Si)Selenium (Se)Molybdenum (Mo)Manganese (Mn)

Trace elements are

required in only very small amounts and

essential for life.

An iodine deficiency causes goiter.

Fluorine

is added to dental products and drinking water and

helps to maintain healthy bones and teeth.

Matter: Elements and Compounds

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Trace elements are common additives to food and water

–Without iron, your body cannot transport oxygen

–An iodine deficiency prevents production of thyroid hormones, resulting in goiter

-Deficiencies of copper can cause premature hair graying, sterility and premature wrinkling of the skin.

Figure 2.3

Elements can combine to form compounds.

Compounds are substances that contain two or more elements in a fixed ratio.

Common compounds include

NaCl (table salt) and

H2O (water).

Matter: Elements and Compounds

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Sodium Chloride(Kitchen salt)

Chlorine(poisonous gas)

Sodium(metal)

+

Compound—a substance consisting of two or more different elements combined in a fixed ratio

Atoms

Each element consists of one kind of atom.

An atom is the smallest unit of matter that still retains the properties of an element.

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Electroncloud

Protons

2e–Nucleus

Electrons

Massnumber = 4Neutrons

2

2

2

Atoms consist of protons, neutrons, and electrons

Electrons are kept in orbit by the attraction between the negatively charged electrons and positively charged protons

Atomic number: 2 (number of protons)

Mass number: 4 (sum of the number of protons and neutrons in its nucleus

The Structure of Atoms

Atoms are composed of subatomic particles.

A proton is positively charged.

An electron is negatively charged.

A neutron is electrically neutral.

Most atoms have protons and neutrons packed tightly into the nucleus.

The nucleus is the atom’s central core.

Electrons orbit the nucleus.

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Atomic Number

C12Mass number(atomic weight)

( # Protons + # Neutrons)

6Atomic Number(# of Protons in an atom)

Atomic Symbol(Carbon)

The atomic number determines which

element it is.

# protons = atomic number# electrons = atomic number

(in an uncharged atom)# neutrons = mass number – atomic number

Elements differ in the number of subatomic particles in their atoms.

The number of protons, the atomic number, determines which element it is.

Mass is a measure of the amount of material in an object.

An atom’s mass number is the sum of the number of protons and neutrons in its nucleus.

The Structure of Atoms

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Isotopes

Isotopes are alternate mass forms of an element.

Isotopes

have the same number of protons and electrons but

differ in their number of neutrons.

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Atomic Weight (Mass Number) May Vary

Isotope: a variant form of an atom with same number of protons but different numbers of neutrons

Naturally occurring carbon 99% ~1% Minute quantities

Stable isotopes Radioactive: the nucleus decays

Atomic number:

Mass number:

Table 2.1

The nucleus of a radioactive isotope decays spontaneously, giving off particles and energy.

Radioactive isotopes have many uses in research and medicine.

They can be used to determine the fate of atoms in living organisms.

They are used in PET scans to diagnose heart disorders and some cancers.

Isotopes

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Radioisotopes in Medicine & Research

when radioactive compounds are used in metabolic processes, they act as radioactive tracers

An imaging instrument that uses positron-emission tomography (PET) detects the location of injected radioactive materials

Normal Alzheimer’s

C isotope studies can be used to identify areas with histories of vegetation change

How the Maya were able to sustain such large populations is still a question today.

Use of Carbon Isotopes in Determining Ancient Maya Land Use

Jungle: C3 Plants

Discriminate more against CO2 containing 13C isotope

Maize: C4 Plants

Why is the energy emitted in radioactive decay hazardous?

.

Radioactive Isotopes Can Harm

Uncontrolled exposure to radioactive isotopes can harm living organisms by damaging DNA.

The 1986 Chernobyl nuclear accident released large amounts of radioactive isotopes.

Naturally occurring radon gas may cause lung cancer.

Electron arrangement determines the chemical properties of an atom

Only electrons are involved in chemical activity

Electrons occur in energy levels called electron shells The number of electrons in

the outermost shell determines the chemical

properties of an atom

Electron Arrangement and the Chemical Properties of Atoms

Electrons orbit the nucleus of an atom in specific electron shells.

The farther an electron is from the nucleus, the greater its energy.

The number of electrons in the outermost shell determines the chemical properties of an atom.

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The number of electrons in the valence shell (outermost shell) determines the chemical properties of the atom

Elements whose outer shells contain unfilled

orbitals are chemically reactive

When all the orbitals are filled, the element

is inactive (inert)

An uncharged atom of gold has an atomic number of 79 and a mass number of 197. This atom has _________ protons, _______ neutrons, and __________ electrons.

a. 79 …118 …79

b. 118 …79 …118

c. 276 …118 …79

d. 79 …276 …79

The most abundant element found in the human body by weight is _________.

a. oxygen

b. carbon

c. fluorine

d. hydrogen

Isotopes of atoms differ in their number of __________.

a. neutrons

b. electrons

c. protons

d. atomic nuclei

Intro to Atoms, Ions etc

http://www.youtube.com/watch?v=UhXS-iR2L3U

Chemical Bonding and Molecules

Chemical reactions enable atoms to give up or acquire electrons, completing their outer shells.

Chemical reactions usually result in atoms

staying close together and

being held together by attractions called chemical bonds.

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NaSodium atom

Transfer ofelectron

ClChlorine atom

Ionic bonds are attractions between ions of opposite charge

The octet rule:atoms are moststable when theirouter most energyshells are either fullor empty

Ions: atoms electrically charged as a result of gaining or losing electrons

Complete transfer of electrons. Attraction between ions of opposite charge

NaSodium atom

Transfer ofelectron

ClChlorine atom

Na+

Sodium ionCl–

Chloride ion

Sodium chloride (NaCl)

+ –

Na+

Cl–

Covalent bonds join atoms into molecules through electron sharing

A covalent bond results when atoms share outer-shell electrons

– A molecule is formed when atoms are held together by covalent bonds

Covalent BondsThe number of covalent bonds an atom can form is equal to the number of additional electrons it needs to fill its valence shell

– A single bond forms when two electrons are shared between two atoms

– A double bond forms when four electrons are shared between two atoms

– A triple bond forms when ______ electrons are shared between two atoms

Electrons are Unequally Shared in Polar Covalent Bonds

Fig 2.8

Oxygen draws sharedelectrons towards itselfOxygen becomes “a little” negativeHydrogens become “a little” positiveResults in Hydrogen Bonds betweenneighboring molecules

Water molecule

Polar molecule: opposite charges on opposite ends

Weak electrical attractions

Hydrogen bond

Water molecules are electrically attracted to oppositely charged regions on neighboring molecules

Because the positively charged region is always a hydrogen atom, the bond is called a hydrogen bond

Hydrogen bonds are weak bonds important in the chemistry of life

Type Chemical basis Strength Example

Covalent bonds Atoms share electron pairs

Strong Hydrocarbons, methane

Ionic bonds Atoms donate one or more electrons to other atom of opposite charge

Moderate Sodium chlorideSodium iodide

Hydrogen bonds Atoms with partial negative charge attract hydrogen atoms

Weak Water, DNA

Chemical bonds and attractive forces

WATER’S LIFE-SUPPORTING PROPERTIES

WATER AND LIFE

Life on Earth began in water and evolved there for 3 billion years.

Modern life remains tied to water.

Your cells are composed of 70–95% water.

The abundance of water is a major reason Earth is habitable.

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Water’s Life-Supporting Properties

The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties.

Water molecules stick together.

Water has a strong resistance to change in temperature.

Frozen water floats.

Water is a common solvent for life.

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Biology and Society: More Precious than Gold

A drought is

a period of abnormally dry weather that changes the environment and

one of the most devastating disasters.

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Figs 2.12, 2.13

Surface Tension Capillary Action

Cohesion: attraction between molecules (water= hydrogen bonds)

Hydrogen bonds give water a high surface

tension

Droughts can cause

severe crop damage,

shortages of drinking water,

dust storms,

famine,

habitat loss, and

mass migration.

Biology and Society: More Precious than Gold

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Throughout human history, droughts have helped wipe out societies and even whole civilizations.

Droughts are catastrophic because life cannot exist without water.

Biology and Society: More Precious than Gold

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Water resistance to temperature change stabilizes ocean temperatures.

Evaporative cooling: when a substance evaporates, the surface of the liquid remaining behind cools down

Water’s hydrogen bonds moderate temperature

Because of hydrogen bonding, water has a greater ability to resist temperature change than other liquids.

The efficiency of evaporative cooling is affected by humidity.

Water Expands When Frozen

Fig 2.15

Fewer molecules than an equal volume of liquid

What is a solution? Example

What is a solvent? Example

What is an aqueous solution?

What is a solute? Example

Ionic bond between Na+ and Cl- holds

ions together in a solid crystal

Dissolve in water:The chloride anion (-) attracts the (+) pole of water

The sodium cation (+) attracts the (-) pole of water

Dissolved ions cannot

re-associate into a solid

Water is a polar solvent:A polar molecule has opposite charges on opposite ends

Ion insolution

Saltcrystal

Water is the solvent of life

Fig 2.17

Ionization of Water:Water dissociates

hydrogen ions H+

hydroxide ions OH-

Bases: release OH- (or accept H+): decrease [H+]

Sodium Hydroxide Na+ & OH -

Acids: release H+ (or accept OH-): increase [H+]

Hydrochloric acid: HCl H+ & Cl- (in your stomach)

The chemistry of life is sensitive to acidic and basic conditions

Figure 2.17a

OH−

OH−

OH−

OH−

OH−

OH−H

H

Basic solution

OH−

OH−

OH−OH−

H

H

H

H

OH−

OH−

H

H

HH

H

H

Neutral solution

Acidic solution

The pH Scale

A pH scale (pH = potential of hydrogen) is used to describe whether a solution is acidic or basic.

–pH ranges from 0 (most acidic) to 14 (most basic)

–A solution that is neither acidic or basic is neutral (pH = 7)

Acid rain Water reacting with pollutants (SO2, NO)pH 2-3

Normal rain:pH 5.6

Buffers minimize changes in pH

Buffers Act as H+ reservoirs

• Take up H+ ions when they are abundant, release them when they are scarce.

• Keep proton concentration steady.

• A buffer that maintains pH 7:

• accepts protons if pH is < 7,

• releases protons if pH is > 7

The Carbonic-Acid-Bicarbonate Buffer in Blood

When we exercise, we increase the H+ concentration in our blood stream:

[H+] increases

Blood pH decreases

Our blood contains a buffering system

Chemical reactions make and break bonds, changing the composition of matter

You learned that the structure of atoms and molecules determines the way they behave

– Remember that atoms combine to form molecules

– Hydrogen and oxygen can react to form water

2 H2 O2 2 H2O

Reactants

Product

You should now be able to

1. Describe the importance of chemical elements to living organisms

2. Explain the formation of compounds

3. Describe the structure of an atom

4. Distinguish between ionic, hydrogen, and covalent bonds

5. Define a chemical reaction and explain how it changes the composition of matter

6. List and define the life-supporting properties of water

7. Explain the pH scale and the formation of acid and base solutionsCopyright © 2009 Pearson Education, Inc.