chapter 2 - fall 08

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Biol 213

Cell Structure and Function

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iClicker Registration

Go to: www.iclicker.com/registration

Your student ID is your GMU email

username (Example: gfondufe)
http://www.iclicker.com/registrationhttp://www.iclicker.com/registration

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Chapter 2

The Chemical Context of Life

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Atomic Carbon, hydrogen, oxygen

Molecular DNA, proteins

Organelle Nucleus, mitochondria, etc.

Cellular Metabolism, cell signaling Tissue Smooth muscle, bone, etc.

Organ Heart, brain, liver, etc.

Organ System Circulatory, digestive, etc.

Organism Mouse, human, maize

Higher Levels Ecosystems, populations

Hierarchy of biological organization

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Fig. 1.4 Exploring levels of Biological Organization

The biosphere

Communities

PopulationsOrganisms

EcosystemsOrgans andorgan systems

CellsCell

Organelles

Atoms

MoleculesTissues

10 m

1 m50 m

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Cell Biology

Cell

Smallest unit that can carry out all the activities

required for the life of an organism

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Cell Biology

Cell Properties / Organism Properties

Ability to reproduce

Ability to grow

Ability to process energy

Ability to respond to the environment

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Cell Biology

Organisms are composed of cells

Some are unicellularsingle cell

Some are multicellularmultiple cells

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Cell Biology

Multicellular Organism

Starts as a single cell (zygote)

Reproduces by division (mitosis)

Cells differentiate

Have different form and/or properties

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Cell Biology

Cells may appear different, but they have

many similarities

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Cell Biology

In Cell Biology, we will be examining the many

similarities (and some differences) of cells

the similarities that make up the commonSTRUCTURAL and FUNCTIONAL

properties of cells

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Biology - Study of life, living things

Biology is a multidisciplinary science

Cell Biology- Study of cells

To understand structure and function of cells,we need a basic understanding of Chemistry

Cell Biology

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Basic Chemistry for Cell Biologists

Matter

Composed Elements and Compounds

Elements required by living organisms

Atomic structure

Chemical bonding

Chemical reactions

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Basic Chemistry -Matter

Matter

Anything which takes up spaceand has mass

Composed of elements

Exists in many forms

Rock, wood, water, air, plastic, human, etc

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Basic Chemistry - Matter

Element

Substance which cannot be broken down into

other substances by chemical means

92 natural elements + ~20 man-made

Has a symbolusually 1 or 2 letters of its

name (may be derived from Latin or German)

H = Hydrogen He = Helium

Na = Sodium (Natrium) Fe = Iron (Ferrum)

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Compound

Substance consisting of two or more elements

combined in a fixed ratio

Examples:

Water: H2O = 2 Hydrogen : 1 Oxygen

Table salt: NaCl = 1 Sodium : 1 Chlorine

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A compound has characteristics beyond those of

its combined elementsemergent properties

Example:Table salt: NaCl = 1 Sodium : 1 Chlorine

Sodium - very reactive (explosive) metal

Chlorine - poisonous gas

Combined = edible compound

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Matter

Elements and Compounds


Atomic structure

Chemical bonding

Chemical reactions

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Basic chemistryElements Required for Life

Number required by living organisms

Only about 25 of 92 natural elements

96% of living matter composed of:

Carbon, Hydrogen, Oxygen, Nitrogen

Other 4% composed of:

Phosphorus, Sulfur, Calcium, Potassium,

others

T bl 2 1 N t ll O i El t i th

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Table 2.1 Naturally Occurring Elements in theHuman Body

Symbol Element % (by body weight)

Elements that make up 96% of the human bodyO Oxygen 65

C Carbon 18.5

H Hydrogen 9.5

N Nitrogen 3.3Elements that make up about 4% of the human body

Ca Calcium 1.5

P Phosphorus 1.0

K Potassium 0.4S Sulfur 0.3

Na Sodium 0.2

Cl Chlorine 0.2

Mg Magnesium 0.1Copyright 2008 Pearson Education, Inc., publishing as Benjamin Cummings

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Basic Chemistry - Trace Elements

Trace Elements

required only in very small quantities

Examples:

Iron (Fe)hemoglobin, other proteins

Iodine (I)thyroid hormone

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Fig. 2.4b Goiter due toiodine deficiency

Iodine- thyroidhormone

a daily intake of0.15 mg of iodine isrequired for normalactivity of the humanthyroid gland

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Matter



Atomic structure

Chemical bonding

Chemical reactions

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Basic Chemistry - Atomic Structure

Atomic structure determines behavior of element

Atoms combine by chemical bonding to form

molecules

Weak chemical bonds are important

Shape of molecule is related to function

Chemical reactions make and break bonds

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Atom

Smallest unit of matter that still retains

properties of an element

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Atom

Composed of three types of particles

Neutrons - no electrical charge

Protons - positive electrical charge (+1)

Electrons - negative electrical charge (-1)

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Atom

Neutrons and Protons

Packed together in dense core

Atomic Nucleus

Electrons

Located in a cloud or shell around thenucleus

Attracted to nucleus by positively charged

protons

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Cloud of negativecharge (2 electrons)

Nucleus2 protons2 neutrons

Electrons

(b)(a)

Basic ChemistryAtomic structure

Fig. 2.5 Models of a Helium (He) atom

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Nucleus

Small in comparison to entire atom (5/1000)

Electrons orbit at a distance from nucleus

Accounts for nearly all of the weight Protons + neutrons (electron weight is

negligible)

Neutrons & protons - about the same mass ~1 dalton (~1.7 x 10-24g)

After John Dalton, a British scientist

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Atomic Number

Number of protons in an atom

Unique for each element

Written as a subscript to left of chemical

symbol 2He, 8O, 16S, 26Fe

Number of protons and electrons are

generally the same - no net charge

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Mass Number

Number of protons and neutrons

Written as a superscript to left of chemical

symbol - 4He, 16O, 32S, 55Fe Atomic Weight

approximately the mass number

proton and neutron each 1 dalton

4He has a mass number of 4

estimated atomic weight of 4 daltons (4.003)

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Number of Neutrons

No. of protons = Atomic Number

No. of protons and neutrons = mass number

Mass number - Atomic Number =Number of neutrons

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Number of Neutrons

Can the number of neutrons vary in atoms of

an element?

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Yes! Number of Neutrons may vary!

Isotopes- different numbers of neutrons

Carbon- 12C - 6 protons + 6 neutrons

13C - 6 protons + 7 neutrons

14C - 6 protons + 8 neutrons

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Isotopes

Stability of an isotope

Unstable (radioactive) -

breaks down (decays) and loses particles

12C and 13C are stable

14C is unstable (radioactive isotope)

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Radioactive IsotopesUseful in scientific research and medicine

Tracing atoms through metabolic processes

Diagnosing medical disorders

Also useful in dating fossils

Unfortunately, they pose a hazard to life

Decay particles damage cellular molecules

From nuclear reactor accidents or a dirty

bomb

Fi 2 6 U i R di ti I t

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Fig. 2.6 Using Radioactive Isotopes

Compounds includingradioactive tracer(bright blue)

Humancells

Incubators

1 2 3

4 5 6

7 8 9

50C45C40C

25C 30C 35C

15C 20C10C

Humancells are

incubatedwith compounds used tomake DNA. One compound islabeled with 3H.

1

2 The cells areplaced in testtubes; their DNA isisolated; andunused labeledcompounds are

removed.

DNA (old and new)

Fig 2 6 Using Radioacti e isotopes

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Fig. 2.6 Using Radioactive isotopes

The test tubes are placed in a scintillation counter.3

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U i R di ti I t

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Using Radioactive Isotopes

Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Cells containing

radioactive DNA

are exposed to

a photographicemulsion. Then

the emulsion is

developed and

viewed under amicroscope.

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Fig. 2.7 PET(Positron Emission Tomography) SCAN

Cancerous

throattissue

Radioactively-taggednutrient is given

and monitored

Decay of isotope is

detected and colorindicates amount of

isotope present

Intensely coloredareas indicate high

metabolic rate - i.e.,

CANCER

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Electrons

Involved in chemical reactions between atoms

Energy levels of electrons vary (potential

energy)

Discrete steps called electron shells

Low energy near nucleus

High energy further away

Fig 2 8 Energy levels of an atoms electrons

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Fig. 2.8 Energy levels of an atoms electrons

(a) A ball bouncing down a flightof stairs provides an analogy

for energy levels of electrons

Third shell (highest energy

level)

Second shell (higherenergy level)

Energyabsorbed

First shell (lowest energylevel)

Atomicnucleus

(b)

Energylost

Different amounts of

potential energy are

stepwise changes

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Electron configuration

Determines chemical properties of elements

Depends upon the number of electrons in its

outermostshell

Termed valence shelland valence

electrons

The periodic table of elements shows the

electron distribution of elements

Fig 2-9 Electron distribution diagrams for the first 18

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Fig. 2-9 Electron distribution diagrams for the first 18elements in the periodic table

Hydrogen

1H

Lithium

3LiBeryllium

4BeBoron

5BCarbon

6CNitrogen

7NOxygen

8OFluorine

9FNeon

10Ne

Helium

2HeAtomic number

Element symbol

Electron-distributiondiagram

Atomic mass

2He

4.00Firstshell

Secondshell

Third

shell

Sodium

11NaMagnesium

12MgAluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16SChlorine

17ClArgon

18Ar

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Electron configuration

Valence shell and valence electrons

Completed shell is unreactivechemicallyinert

Helium, Neon, Argon

Other atoms transfer or share electrons to

complete valence shell

Chemical bonds

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Electron shells or Orbitals

Once thought to be like planets orbiting the

sun, but dont know exact path

An orbitalis where electron is 90% of time

Only 2 electrons per orbital at any time

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Electron orbitals

First energy shell - 2 electrons

1s orbital - 2 e-

Second energy shell - 8 electrons

2s orbital - 2 e-

Three 2p orbital - 6 e-

Neon, with two filled shells (10 electrons)Fig. 2.10 Electron Orbitals

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Electron-distributiondiagram

(a)

(b)

Separate electronorbitals

First shell Second shell

1sorbital 2sorbital Three 2porbitals

(c)

Superimposed electronorbitals

1s, 2s, and 2porbitals

x y

z

Fig. 2.10 Electron Orbitals

B i Ch i t At i St t

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The presence of unpaired electrons in one ormore orbitals of their valence shells accounts for

the reactivity of an atom

Atoms interact with certain other atoms in order

to complete their valance shells

Such interactions result in atoms stayingclose together, and held by attractions

called chemical bonds

Basic ChemistryAtomic Structure

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Matter



Atomic structure

Chemical bonding

Chemical reactions

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Covalent Chemical Bonds

Sharing of valence electrons

Strongest of the chemical bonds

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Covalent Bond

Sharing of a pair of valence electrons by two

atoms

If unshared orbitals overlap, each atom cancount both electrons toward its goal of filling the

valence shell

Fig. 2.11 Formationof aHydrogen

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covalent bondHydrogen

atoms (2 H)

Hydrogen

molecule (H2)

When two hydrogen atoms approach,the electron of each atom is also attracted

to the proton in the other nucleus.

The two electrons become shared in a

covalent bond, forming an H2 molecule

In eachhydrogen atom, the single

electron is held in its orbital by itsattraction to the proton in the nucleus

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Basic Chemistry - Molecules

Two or more atoms held together by covalentbonds constitute a molecule

The molecular formulaindicates the number

and types of atoms present in a single molecule

For molecular hydrogen: H2

Structural formulaFor molecular hydrogen: HH

Covalent Bonds

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A single covalent bond, or single bond

sharing of one pair of valence electrons

A double covalent bond, or double bond

sharing of two pairs of valence electrons

Covalent Bonds

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Animation: Covalent Bonds


Covalent Bonds - Animation
http://localhost/var/www/apps/conversion/tmp/scratch_5/02_12CovalentBonds_A.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_5/02_12CovalentBonds_A.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_5/02_12CovalentBonds_A.html

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Oxygen has 6 electrons in valence shell

Needs to add 2 e-to complete its valence

shell

Two oxygen atoms can form a molecule by

sharing two pairs of valence electrons

Forms a double covalent bond

Covalent Bond - O2

Fi 2 12 C l t B d O

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Fig. 2.12 Covalent Bond - Oxygen

(b) Oxygen (O2)

Name andMolecularFormula

Electron-distribution

Diagram

Lewis DotStructure and

StructuralFormula

Space-fillingModel

B i Ch i t V l

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Basic Chemistry - Valence

Every atom has a characteristic total number

of covalent bonds that it can form - an atoms

valence

The valence of hydrogen is 1Oxygen is 2

Nitrogen is 3

Carbon is 4

Phosphorus has a valence of 5, forming 3

single covalent bonds and 1 double bond

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Covalent Bonds

Can form between atoms of the same element or

atoms of different elements.

While both types are molecules, the latter are

also compounds

Water, H2O, is a compound in which two

hydrogen atoms form single covalent bonds

with an oxygen atom

Fig. 2.12 Covalent Bond - Hydrogen

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Fig. 2.12 Covalent Bond Hydrogen

(a) Hydrogen (H2)

Name andMolecularFormula

Electron-distribution

Diagram

Lewis DotStructure and

StructuralFormula

Space-fillingModel

Fig 2 12 Covalent Bond - Water

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Fig. 2.12 Covalent Bond - Water

(c) Water (H2O)

Name and

MolecularFormula

Electron-

distributionDiagram

Lewis Dot

Structure andStructuralFormula

Space-

fillingModel

Fig. 2-12 Covalent Bond - Methane

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g Co a e t o d et a e

(d) Methane

(CH4)

Name and

MolecularFormula

Electron-

distributionDiagram

Lewis Dot

Structure andStructuralFormula

Space-

fillingModel

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Covalent Bonds

Sharing of electrons between atoms

Equal- nonpolar covalent bond

Unequal- polar covalent bond

Some atoms have a greater attraction for an

electron

Electronegativityis a measure of the degree

of attraction

P l C l B d

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Polar Covalent Bonds

Form between atoms with different

electronegativity

Water: Oxygen - high electronegativity

Hydrogen - low electronegativity

partial negative charge near the strongly

electronegative atom

partial positive charge near the weakly

electronegative atom

Fig. 2.13 Polar covalent bonds in a water

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gmolecule

+ +H H

O

H2OPartial positive Partial positive

Partial negative

Oxygen is more electronegative than hydrogen


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Chemical Bonds

Covalent bonds

Nonpolar

Polar

Ionic bonds

Hydrogen bonds

Van der Waals interactions

Basic Chemistry Ionic Bonds

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Basic Chemistry - Ionic Bonds

Transfer of electrons between atoms

After such a transfer, both atoms have charges

A charged atom (or molecule) is called an ion

A cationa positively charged ion

An aniona negatively charged ion

An ionic bondis the attraction between ananion and a cation

Basic Chemistry Ionic Bonds

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Basic Chemistry - Ionic Bonds

Sodium and Chlorine

Sodium has one electron in valence shell

Chlorine has seven

Transfer one electron from sodium to chlorine

Sodium becomes positively charged - cation

Chlorine becomes negatively charged - anion

Both have complete valence shell

Fig. 2.14 Electron Transfer and Ionic Bonding

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Fig. 2.14 Electron Transfer and Ionic Bonding

Na Cl Na Cl

NaSodium atom Chlorine atom

Cl Na+Sodium ion(a cation)

ClChloride ion

(an anion)

Sodium chloride (NaCl)

Electron Transfer

Ionic Bonds - Animation

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Animation: Ionic Bonds


Ionic Bonds Animation

Ionic Compounds
http://localhost/var/www/apps/conversion/tmp/scratch_5/02_14IonicBonds_A.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_5/02_14IonicBonds_A.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_5/02_14IonicBonds_A.html

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Ionic Compounds

Compounds formed by ionic bonds

Formula indicates ratio of elements

NaCl - 1 atom of sodium: 1 atom of chlorine

MgCl2: 1 atom of Mg : 2 atoms of Cl

Strength of ionic bonds depends on

environmental conditions

dry conditions - salts are hard

aqueous conditions - salts dissolve

C f C

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Chemical Bonds

Covalent bonds

Nonpolar

Polar

Ionic bonds

Hydrogen bonds


B i Ch i H d B d

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Basic Chemistry - Hydrogen Bonds

Weak type of bonding

Hydrogen atom covalently bonded to one

atom (strongly electronegative) is attracted toanother atom (also strongly electronegative)

The partially positive charged hydrogen atomin a covalent bond is attracted to negatively

charged (partial or full) molecules, atoms, oreven regions of the same large molecule.

Fig. 2.16 A hydrogen bond between water and ammonia

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+

+

+

+

+

Water (H2O)

Ammonia (NH3)

Hydrogen bond


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Chemical Bonds

Covalent bonds

Nonpolar

Polar

Ionic bonds

Hydrogen bonds


Van der Waals Interactions

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Because electrons are constantly in motion,there can be periods when partially positiveand negative regions accumulate by chancein one area of a molecule

This creates ever-changing regions ofnegative and positive charge within amolecule.

Molecules or atoms in close proximity can beattracted by these fleeting charge differences,creating van der Waals interactions.


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Such bonds, collectively, can be strong

as between molecules a geckos toe hairsand the surface of a wall

Function Relates to Shape

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Shape of a molecule

determined by the arrangement of electron

orbitals that are shared by the atoms involved

in a bond

A molecule with two atoms is always linear

However, a molecule with more than twoatoms has a more complex shape

Function relates to Shape

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sorbitalz

x

y

Three porbitals

Hybridization of orbitals

Four hybrid orbitals

Tetrahedron

(a)

For atoms with electrons in both s and p orbitals, the

formation of a covalent bond leads to hybridization ofthe orbitals to form four new orbitals in a tetrahedron

shape

Fig. 2.17a Hybridization of orbitals


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In a water molecule the hybrid orbitals thatoxygen shares with hydrogen atoms are

spread in a V shape.

In a methane molecule (CH4),

all four hybrid orbitals are shared

hydrogen nuclei are at the corners of thetetrahedron

Space-fillingModel

Ball-and-stickModel

Hybrid-orbital Model(with ball-and-stick

Fig. 2.17b

Molecular-shape

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Model Model (with ball-and-stickmodel superimposed)

Unbonded

electronpair

104.5

Water (H2O)

Methane (CH4)

Molecular shape

models


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Molecules with similar shapes can interact in similar

ways

Opiate drugs (such as morphine) are similar to

endorphins (the bodys natural pain killers)

Both morphine and endorphins can bind to

endorphin receptors on the surface of brain cells

thereby relieving pain and producing euphoria

Key

Carbon NitrogenFig 2.18 A molecular

mimic

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(a) Structures of endorphin and morphine

(b) Binding to endorphin receptors

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

Morphine

Natural endorphinHydrogen

gSulfurOxygen

mimic


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Matter



Atomic structure

Chemical bonding

Chemical reactions

Basic Chemistry - Chemical Reactions

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y

The making and breaking of chemical bonds

Chemical bonds are broken and reformed,

leading to new arrangements of atoms

The molecules at the beginning of a chemical

reaction are called reactants

The molecules at the end of a chemical

reaction are called products

B

Basic Chemistry Chemical reactions

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Reactants Reaction Products

2 H2 O2 2 H2O

Basic ChemistryChemical reactions

All of the atoms in the reactants must be accounted

for in the products

The reaction must be balanced


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Reactants Products

In Photosynthesis (summarized reaction):

6 CO2 + 6 H2O C6H12O6 + 6 O2

This is not what happens chemically, but is a

balanced equation of the summarized reaction


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Basic Chemistry Chemical Reactions

Reactants Products

Some reactions can go forward or reverse

3 H2 + N2 2 NH3

Reversible reactions indicated by the opposite headed arrows

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chapter 2 - fall 08

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