The Stuff of Life Copyright © 2009 Pearson Education, Inc

The Stuff of Life

Copyright © 2009 Pearson Education, Inc.

Why are chemistry concepts essential to the study of life?

Facts, laws, and theories of the field apply to all living things.

Chemicals are at the base of the biological hierarchy.

Life results from the ordering of atoms into molecules and the interactions of these molecules within cells.


I. The Matter of Life (2.1-2.2)

A. Matter

1. Matter is…

2. Matter is composed of chemical elements

B. Elements

1. a substance that cannot be broken down to other substances.

2. 9292 naturally occurring elements

3. 2525 elements found in organisms; some found in minute amounts (trace elements)


II. Elements can combine to form compounds (2.3)

A. Chemical Compound

1. substance consisting of two or more different elements combined in a fixed ratio

2. Most in organisms contain C, H, O, and N (ex. Proteins & DNA)

3. Different arrangements of elements provide unique properties for each compound; different emergent properties appear

– Many compounds consist of only two elements, example water (H2O) and table salt (NaCl)


Sodium ChlorideChlorineSodium +

Check for Understanding:1.Which four chemical elements are most abundant in living things?2.How do the compounds water and salt differ from each other?3.*How is a compound different than a molecule?

B. Each element has its own kind of atom

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

– Atoms are made of over a hundred subatomic particles, but only three are important for biological compounds

2. Sub-Atomic Particles

– Proton—has a single positive electrical charge

– Electron—has a single negative electrical charge

– Neutron—is electrically neutral


III. Atomic Structure (2.4)

A. Nucleus protons (+) and neutrons

B. Energy Levels or Shells electrons (-)

1st orbital, max 2e-

2nd orbital, max 8e-

3rd orbital, max 8e-

C. Valence e-

D. An atom has no charge

http://www.shu.ac.uk/pri/scripts/resources/uploaded/images/atoms_pic.jpg

IV. Periodic Table- Appendix 2

A. Atomic number- # of protons

B. Atomic mass number - sum of protons + neutrons

C. Element symbol: P, Cl, Mg or He

D. Electron Distribution Diagram

Electroncloud

Protons

2e–Nucleus

Electrons

Massnumber = 4Neutrons

2

2

2

What element do these diagrams represent?

Why do the e- stay near the nucleus?

Check for Understanding

On an index card describe the structure of an oxygen atom on an index card. Reference your periodic table for its atomic number. In your answer include the terms electron, proton, neutron. Describe how you would identify the number of neutrons found in an atom of oxygen and state the answer.

Check for Understanding

In your notebook draw the atomic structure of oxygen. Include the element symbol, electron configuration, and indicate the number of neutrons and protons at the location where these subatomic particles would be found.

Electroncloud

Protons

6e–

Nucleus

Electrons

Massnumber = 12Neutrons

6

6

6

What element does this diagram represent?

V. COUNTING ATOMS

A. Molecular Formula, H2O

1. Subscript

2. Coefficient

B. Examples:

Water H2O

Aspirin C9H8O4

Acetic Acid (vinegar) 2C2H4O2

TNT (explosive) C7H5(NO2)3

http://www.princeton.edu/~chm112/project/water%20molecule.gif

What differs between Carbon-12, Carbon-13, and Carbon-14?

VI. Isotopes (2.4-2.5)

A. All atoms of an element have the same atomic number, some differ in mass number

1. The variations are isotopes, which have the same numbers of protons and electrons but different numbers of neutrons

2. For example, carbon isotopes

– One isotope of carbon has 8 neutrons instead of 6 (written 14C)

– Unlike 12C, 14C is an unstable (radioactive) isotope that gives off energy


B. Radioactive Isotopes(2.5)

1. Living cells cannot distinguish between isotopes of the same element

2. Use as tracers, detect with imaging instruments


PET image of healthy brain (left) and Alzheimer’s patient (right). Red and yellow indicate high level of PIB bound to beta-amyloid plaques. PIB contains the RI.

3. Benefits

- basic research (study processes such as photosynthesis)

- medical diagnosis

- radioactive dating using half lives

4. Dangers

– Uncontrolled exposure can cause damage to some molecules in a living cell, especially DNA

– Chemical bonds are broken by the emitted energy, which causes abnormal bonds to form


VII. Electron arrangement determines the chemical properties of an atom (2.6)

A. Only e- are involved in chemical activity

1. look at # of e- in the outermost shell

2. atoms want a filled outermost shell

- not filled, atom is unstable and reactive

- therefore atom will accept, donate, or share e- to become stable

- results in attraction between atoms called chemical bonds


Magnesium

Lithium

Hydrogen

Thirdshell

Firstshell

Secondshell

Sodium

Beryllium

Aluminum

Boron

Silicon

Carbon

Phosphorus

Nitrogen

Sulfur

Oxygen

Chlorine

Fluorine

Argon

Neon

Helium

What patterns or trends can you identify from this illustration of the periodic table of elements?

Essential QuestionEssential Question::Why do atoms combine to form molecules or Why do atoms combine to form molecules or compounds?compounds?

1. Valence shell not filled unstable and reactive.

2. Lose/Gain e- ion (charged atom) will be attracted to oppositely charged ion

Remember atoms are electrically neutral unless they gain or lose an electron.

VIII. Ionic Bonding (2.7)

A. Ion

1. an atom or molecule with an electrical charge resulting from gain or loss of electrons

2. Cation- atom loses e-, a (+) charge results

3. Anion- atom gains e-, a (-) charge results

B. Ionic Bond- attraction holding together a cation and an anion

C. Bond easily broken


NaSodium atom

Transfer ofelectron

ClChlorine atom

1.What will be the charge on the sodium ion?2.What will be the charge on the chlorine ion?3.What is a cation?4.What is an anion?5.How are ions different from atoms?

Understanding Ionic Bonds

NaSodium atom

Transfer ofelectron

ClChlorine atom

Na+

Sodium ionCl–

Chloride ion

Sodium chloride (NaCl)

+ –

Understanding Ionic Bonds

Na+

Cl–

Figure 2.7B A crystal of sodium chloride.

IX. Covalent Bonding (2.8)

A. results when atoms share outer-shell electrons

B. a molecule is formed when atoms are held together by covalent bonds

C. Strong, not easily broken

D. Can have:

1. 1 pair share, single bond, H-H, H2

2. 2 pair share, double bond, O=O, O2

3. 3 pair share, triple bond, N=N, N2


Structural formula

--

Molecular formula

What does a structural formula show you that a molecular formula does not?

E. Atoms in a covalently bonded molecule continually compete for shared electrons

– The attraction (pull) for shared electrons is called electronegativity

– More electronegative atoms pull harder

F. In molecules of only one element, the pull toward each atom is equal, b/c each atom has the same electronegativity

– bonds formed called nonpolar covalent bonds


G. In molecules with different elements, like water, atoms have different electronegativities

– Oxygen attracts the shared e- more strongly than hydrogen

– shared e- spend more time near oxygen

– result is a polar covalent bond

H. Polar molecules (2.9)

- molecule with unequal distribution of charge

- ex, H2O the oxygen atom has a slight (-) charge and the hydrogens have a slight (+) charge


(–) (–)

O

HH

(+) (+)

Check for Understanding:1.Which element in water is the electronegative atom?2.What is the overall net charge of a water molecule?3.How might being polar help water molecules stick together?

Hydrogen bond

X. Hydrogen Bonding (2.0)

A. Weaker than covalent bond

B. Hydrogen, as part of a polar covalent bond, will share attractions with other electronegative atoms (like O and N)

C. B/C the (+) charged region is always a H atom, the bond is called a hydrogen bond


Animation: Water Structure

XI. Chemical Reactions (2.18)A. Atoms react due to their electron configurations

B. Chemical rxns rearrange matter by making and breaking chemical bonds

C. All chem rxn accompanied by change in energy

1. exothermic- E (heat) released to surroundings

2. endothermic- E (heat)absorbed from surroundings

D. Some rxns can be spontaneous while others require activation energy


A + B AB

Reactants Products

E. Balancing Chemical Reactions

1. Conservation of Mass

2. # and type of atoms on reactants side must be found on products side

3. H2 + O2 H2O, balance the equation


yields

http://www.sfrisch.com/images/chem_cov.jpg

WATER’S LIFE-SUPPORTING PROPERTIES


I. H bonds make liquid water cohesive (2.11)

A. H bonding causes molecules to stick together, a property called cohesion

– Cohesion is much stronger for water than other liquids

B. Cohesion is related to surface tension—a measure of how difficult it is to break the surface of a liquid

– Hydrogen bonds are responsible for surface tension


C. Cohesion is the tendency for _______________________

D. Adhesion is the tendency for _______________________

In what ways does this property of water support life?

Water-conductingcells

Adhesion

Cohesion

150 µm

Directionof watermovement

What effect does soap have on surface tension? _________________________

Soap has a water loving end and a

water hating end.

When it is added to water, it separates the

water molecules and reduces surface

tension.

II. Water’s H bonds moderate temperature (2.12)

A. Due to H bonds, water has a greater ability to resist temperature change than other liquids

1. Heat is the energy associated with movement of atoms and molecules in matter

2. Temperature measures the intensity of heat

B. Heat must be absorbed to break H bonds; heat is released when H bonds form


Q: In what ways does this property of water support life?

III. Ice is less dense than liquid water (2.13)

*think about the arrangement of water molecules in a gas, liquid, and solid

A. At freezing, a water molecule can make 4 H bonds with neighbors

1. A 3-D crystal results

2. Space between molecules

B. Due to H bonds, ice is less dense than water, so it floats



Liquid waterHydrogen bonds

constantly break and re-form

IceHydrogen bonds

are stable

Hydrogen bond

IV. Water is the solvent of life (2.14)

A. Solution

1. liquid consisting of a uniform mixture of two or more substances2. The dissolving agent is the solvent3. The substance that is dissolved is the solute

B. Water is a versatile solvent

1. due to its polarity2. easily dissolves polar substances and ions



Ion insolution

Saltcrystal

Notice the orientation of the water molecules.

Why doesn’t oil dissolve in water?

Oil is non polar, so does not interact with water. It forms a single layer above it, sticking its water fearing

ends out.

2.15 The chemistry of life is sensitive to acidic and basic conditions

A few water molecules can break apart into ions

– Some are hydrogen ions (H+)

– Some are hydroxide ions (OH–)

– Both are extremely reactive

– A balance between the two is critical for chemical processes to occur in a living organism



Chemicals other than water can contribute H+ to a solution

– They are called acids

– An example is hydrochloric acid (HCl)

– This is the acid in your stomach that aids in digestion

An acidic solution has a higher concentration of H+ than OH–



Some chemicals accept hydrogen ions and remove them from solution

– These chemicals are called bases

– For example, sodium hydroxide (NaOH) provides OH– that combines with H+ to produce H2O (water)

– This reduces the H+ concentration



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)


Acidic solution

pH scale

Battery acid

0

1

2

3

4

5

Lemon juice, gastric juice

Grapefruit juice, soft drink,vinegar, beer

Tomato juice

Rain water

Human urine

Saliva

Pure water

6

7

Human blood,tears

Seawater

8

9

10

11

12

13

Milk of magnesia

Household ammonia

Household bleach

Oven cleaner

Neutral solution

Basic solution

NEUTRAL[H+]=OH–]

Incr

ea

sin

gly

AC

IDIC

(Hig

he

r c

on

cen

tra

tio

n o

f H

+)

14

Incr

ea

sin

gly

BA

SIC

(Lo

we

r c

on

cen

trat

ion

of

H+)

Acidic solution Neutral solution Basic solution

2.16 CONNECTION: Acid precipitation and ocean acidification threaten the environment

When we burn fossil fuels (gasoline and heating oil), air-polluting compounds and CO2 are released into the atmosphere

– Sulfur and nitrous oxides react with water in the air to form acids

– These fall to Earth as acid precipitation, which is rain, snow, or fog with a pH lower than 5.6

– Additional CO2 in the atmosphere contributes to the “greenhouse” effect and alters ocean chemistry


2.17 EVOLUTION CONNECTION: The search for extraterrestrial life centers on the search for water

An important question is, has life evolved elsewhere?

– Water is necessary for life as we know it

The National Aeronautics and Space Administration (NASA) has evidence that water was once abundant on Mars

– Scientists have proposed that reservoirs of water beneath the surface of Mars could harbor microbial life


August 1999 September 2005

New deposit

CHEMICAL REACTIONS


2 H2 O2 2 H2O

electron transferbetween atoms

creates

electron sharingbetween atoms

creates

ChemicalBonds

atomic number ofeach element

water

nonpolarcovalent bonds

(e)ions

(f) (g)

(h)

attraction betweenions creates

unequalsharing creates

can lead toexample is

equalsharing creates

has importantqualities due

to polarity and

have positivelycharged have neutral

have negativelycharged

number in outershell determines

formation of

number maydiffer in

number presentequals

(a)

Atoms

(b) (c)

(d)

atomic number ofeach element

have positivelycharged have neutral

have negativelycharged

number in outershell determines

formation of

number maydiffer in

number presentequals

(a)

Atoms

(b) (c)

(d)

electron transferbetween atoms

creates

electron sharingbetween atoms

creates

ChemicalBonds

water

nonpolarcovalent bonds

(e)ions

(f) (g)

(h)

attraction betweenions creates

unequalsharing creates

can lead toexample is

equalsharing creates

has importantqualities due

to polarity and

Potassium atomFluorine atom

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. List and define the life-supporting properties of water

6. Explain the pH scale and the formation of acid and base solutions

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


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The Stuff of Life Copyright © 2009 Pearson Education, Inc