The Chemical Level of Organization professor edit

© 2012 Pearson Education, Inc.

PowerPoint® Lecture Presentations prepared by

Jason LaPres

Lone Star College—North Harris

2 The Chemical Level of Organization__professor edit


An Introduction to the Chemical Level of

Organization • Chemistry

• Is the science of that deals with the structure of

matter

• Matter is defined as anything that takes up space

and has mass (weight)

• Topics of this chapter include:

• The structure of atoms

• The basic chemical building blocks

• How atoms combine to form increasingly complex

structures


2-1 Atoms and Atomic Structure

• Matter

• Atoms are the basic particles of matter

• Atoms join together to form chemicals with different

characteristics

What do atoms have to do with the human body?

Think, pair, share…..



• Elements

• Pure substance composed of atoms of only one

kind.

• Cannot be broken down into simpler substances

• Carbon is always carbon, oxygen is always oxygen


Table 2-1 Principal Elements in the Human Body


Table 2-1 Principal Elements in the Human Body


Can you give examples of what happens to the human

body when there is too much or too little of these

elements?

-calcium

-sodium

-iron

Think, pair, share…..



• Atoms are composed of subatomic particles

• Proton p+

• Positive charge

• Neutron n

• Neutral, similar to size and mass of a proton

• Electron e-

• Negative charge, much lighter than protons



• Atomic Structure

• Atomic number

• Number of protons

• Nucleus

• Contains protons and neutrons

• Electron cloud

• Contains electrons (which are attracted to protons)


Figure 2-2 The Arrangement of Electrons into Energy Levels

The first energy level

can hold a maximum of

two electrons.

The second and third

energy levels can

each contain up to 8

electrons.

Hydrogen, H

Atomic number: 1

1 electron

Lithium, Li

Atomic number: 3

(3 protons 3 neutrons)

3 electrons

Hydrogen (H). A typical hydrogen atom has one proton and one electron. The electron orbiting the nucleus occupies the first energy level, diagrammed as an electron shell.

Helium (He). An atom of helium has two protons, two neutrons, and two electrons. The two electrons orbit in the same energy level.

Neon, Ne

Atomic number: 10


10 electrons

Lithium (Li). A lithium atom has three protons, three neutrons, and three electrons. The first energy level can hold only two electrons, so the third electron occupies a second energy level.

Neon (Ne). A neon atom has 10 protons, 10 neutrons, and 10 electrons. The second level can hold up to eight electrons; thus, both the first and second energy levels are filled.

Helium, He

Atomic number: 2


2 electrons



• Electrons and Energy Levels

• Electrons in the electron cloud determine the reactivity of an

atom

• The electron cloud contains shells, or energy levels that hold a

maximum number of electrons

• Lower shells fill first

• Outermost shell is the valence shell, and it determines

bonding


2-2 Molecules and Compounds

• Chemical Bonds

• Involve the sharing, gaining, and losing of electrons in the

valence shell

• Three major types of chemical bonds

1. Ionic bonds

• Attraction between cations (+ charged) and anions (- charged)

2. Covalent bonds

• Strong electron bonds involving shared electrons

3. Hydrogen bonds

• Weak polar bonds based on partial electrical attractions



• Chemical Bonds

• Form molecules and/or compounds

• Molecules

• Two or more atoms joined by strong bonds

• Compounds

• Two or more atoms OF DIFFERENT ELEMENTS

joined by strong or weak bonds

• Compounds are all molecules, but not all molecules are

compounds

• H2 = molecule only H2O = molecule and compound



• Ionic Bonds

• One atom—the electron donor—loses one or more

electrons and becomes a cation, with a positive

charge (if you lose negativity, you become positive)

• Another atom—the electron acceptor—gains those

same electrons and becomes an anion, with a

negative charge (if you gain negativity, you become

more negative)

• Attraction between the opposite charges then draws

the two ions together Opposites attract!


Figure 2-3a The Formation of Ionic Bonds

Formation of ions

Sodium atom Sodium ion (Na)

Attraction between opposite charges

Formation of an ionic compound

Sodium chloride (NaCl)

Chloride ion (Cl) Chlorine atom

Formation of an ionic bond. A sodium (Na) atom loses an electron, which is accepted by a chlorine (Cl) atom. Because the sodium (Na) and chloride (Cl) ions have opposite charges, they are

attracted to one another. The association of sodium and chloride ions forms the ionic compound sodium chloride.

1

3

2


Figure 2-3b The Formation of Ionic Bonds

Chloride ions

(Cl)

Sodium ions

(Na)

Sodium chloride

crystal. Large

numbers of sodium and

chloride ions form a

crystal of sodium

chloride (table salt).



• Covalent Bonds

• Involve the sharing of pairs of electrons between

atoms

• One electron is donated by each atom to make the pair

of electrons


Figure 2-4 Covalent Bonds in Four Common Molecules

Molecule Electron Shell Model and

Structural Formula

Hydrogen

(H2)

Oxygen

(O2)

Carbon

dioxide

(CO2)

Nitric

oxide

(NO)

HH

OO

OCO

NO



• Covalent Bonds

• Nonpolar covalent bonds

• Involve equal sharing of electrons because atoms

involved in the bond have equal pull for the electrons

• Polar covalent bonds

• Involve the unequal sharing of electrons because one

of the atoms involved in the bond has a

disproportionately strong pull on the electrons

• Form polar molecules — like water


Figure 2-5 Polar Covalent Bonds and the Structure of Water

Hydrogen atom

Hydrogen atom

Hydrogen atom

Oxygen atom

Oxygen atom

2



• Hydrogen Bonds

• Bonds between adjacent molecules, not atoms

• Involve slightly positive and slightly negative

portions of polar molecules being attracted to one

another

• Hydrogen bonds between H2O molecules cause

surface tension

• Because of the extensive hydrogen bonding in water, the molecules tend to

stick to each other in a regular pattern. The tension on the surface of water

occurs when water molecules on the outside of the system align and are

held together by hydrogen bonding to create an effect similar to a net made

of atoms. For example, the surface tension of water allows water spiders to

literally walk on water.


Figure 2-6 Hydrogen Bonds between Water Molecules

KEY

2

Hydrogen

Oxygen

Hydrogen bond

2

2

2

2 2

2

Do you see the

net/regular pattern

being formed?



• States of Matter

• Solid

• Constant volume and shape

• Liquid

• Constant volume but changes shape

• Gas

• Changes volume and shape


2-3 Chemical Reactions

• In a Chemical Reaction

• Either new bonds are formed or existing bonds are broken

• Reactants

• Materials going into a reaction

• Products

• Materials coming out of a reaction

• Metabolism

• All of the reactions that are occurring at one time


Figure 2-7 Chemical Notation

Atoms

The symbol of an element indicates one atom of that element. A number preceding the symbol of an element indicates more than one atom of that element.

VISUAL REPRESENTATION CHEMICAL NOTATION

one atom

of hydrogen one atom

of hydrogen

one atom

of oxygen

one atom

of oxygen

two atoms

of hydrogen

two atoms

of hydrogen

two atoms

of oxygen two atoms

of oxygen



Molecules

A subscript following the symbol of an element indicates a molecule with that number of atoms of that element.

hydrogen molecule composed of two

hydrogen atoms

hydrogen

molecule composed of two

oxygen atoms

oxygen

molecule

oxygen molecule

water molecule composed

of two hydrogen atoms

and one oxygen atom

water

molecule




In a description of a chemical reaction, the participants at the start of the reaction are called

reactants, and the reaction generates one or more products. An arrow indicates the direction of

the reaction, from reactants (usually on the left) to products (usually on the right). In the following

reaction, two atoms of hydrogen combine with one atom of oxygen to produce a single molecule

of water.

Reactions

Chemical reactions neither create nor destroy

atoms; they merely rearrange atoms into new

combinations. Therefore, the numbers of atoms

of each element must always be the same on

both sides of the equation for a chemical

reaction. When this is the case, the

equation is balanced.

Balanced equation

Unbalanced equation




Ions

A superscript plus or minus sign following the symbol of an element indicates an ion. A single plus

sign indicates a cation with a charge of 1. (The original atom has lost one electron.) A single minus

sign indicates an anion with a charge of 1. (The original atom has gained one electron.) If more than

one electron has been lost or gained, the charge on the ion is indicated by a number preceding the

plus or minus sign.

sodium ion chloride ion calcium ion sodium

ion

chloride

ion calcium

ion the chlorine

atom has gained

one electron

the calcium

atom has lost

two electrons

A sodium atom becomes a sodium ion

Electron lost

Sodium atom (Na)

Sodium ion (Na)

the sodium

atom has lost

one electron




• Basic Energy Concepts

• Energy

• The power to do work

• Work

• A change in mass or distance

• Kinetic energy

• Energy of motion

• Potential energy

• Stored energy

• Chemical energy

• Potential energy stored in chemical bonds



• Types of Chemical Reactions


2-3 Chemical Reactions • Breaking chemical bonds

• AB A + B

• Hydrolysis (You are breaking up A-B [hydro = water; lysis =

break]; A-H and HO-B are the products)

• A-B + H2O A-H + HO-B

• Forming chemical bonds

• A + B AB

• Dehydration synthesis (You are removing water from A and B

[dehydrating them]; water and A-B are the products)

• A-H + HO-B A-B + H2O

Forming A-B

Breaking A-B


2-4 Enzymes

• Chemical Reactions

• In cells cannot start without help

• Activation energy is the amount of energy needed to

get a reaction started

• Enzymes are protein catalysts that lower the

activation energy of reactions

• Promote the chemical reaction


Figure 2-8 The Effect of Enzymes on Activation Energy

Without

enzyme

Activation energy

required

Reactants

Stable

product

With enzyme

En

erg

y

Progress of reaction


2-5 Organic and Inorganic Compounds

• Nutrients

• Essential molecules obtained from food

• Metabolites

• Molecules made or broken down in the body

• Inorganic Compounds

• Molecules not based on carbon and hydrogen

• Carbon dioxide, oxygen, water, and inorganic acids, bases, and salts

• Organic Compounds

• Molecules based on carbon and hydrogen

• Carbohydrates, proteins, lipids, and nucleic acids


2-6 Properties of Water

• Water

• Accounts for up to two-thirds of your total body weight

• A solution is a uniform mixture of two or more

substances

• It consists of a solvent (water) in which atoms,

ions, or molecules of another substance, called a

solute (NaCl—table salt), are individually

dispersed

• Concentration

• The amount of solute in a solvent (a salty solution

like brine has a high concentration of NaCl)



• Solubility

• Water’s ability to dissolve a solute in a solvent to

make a solution

• Reactivity

• Most body chemistry occurs in water

• High Heat Capacity

• Water’s ability to absorb and retain heat

• Lubrication

• To moisten and reduce friction (think about joints)



• High Heat Capacity

• When molecules are heated, they get excited. They

move around faster as they gain more energy. Water

is a polar molecule (has a plus end and a minus end).

Positive attracts to negative and water molecules

stick together through strong bonds. Because the

molecules are being held tightly in place by these

bonds, the H2O molecules do not move much when

heated. It takes more and more heat to move the

molecules, causing water to have a high specific heat

capacity.



• The Properties of Aqueous Solutions

• Ions and polar compounds undergo ionization, or

dissociation in water

• NaCl becomes Na+ ion and Cl- ion in water


Table 2-2 Important Electrolytes that Dissociate in Body Fluids




• Electrolytes and body fluids

• Electrolytes are inorganic ions that conduct electricity

in solution

• Electrolyte imbalance seriously disturbs vital body

functions

Why is electricity important in our body?

Think, pair, share…




• Hydrophilic and hydrophobic compounds

• Hydrophilic

• hydro- = water, philos = loving

• Interacts with water

• Includes ions and polar molecules

• Hydrophobic

• phobos = fear

• Does NOT interact with water

• Includes nonpolar molecules, fats, and oils


2-7 pH and Homeostasis

• pH

• The concentration of hydrogen ions (H+) in a solution

• Neutral pH

• A balance of H+ (hydrogen) and OH (hydroxide)

• Pure water = 7.0



• Acidic pH Lower Than 7.0

• High H+ concentration

• Low OH concentration

• Basic (or alkaline) pH Higher Than 7.0

• Low H+ concentration

• High OH concentration

• pH of Human Blood

• Ranges from 7.35 to 7.45

Where in the body is

the pH not near 7?

Think, pair, share….



• pH Scale

• Has an inverse relationship with H+ concentration

• More H+ ions mean lower pH, less H+ ions mean higher

pH


Figure 2-10 pH and Hydrogen Ion Concentration

1 mol/L

hydrochloric

acid

Stomach

acid

Beer,

vinegar,

wine,

pickles

Tomatoes,

grapes

Extremely

acidic Increasing concentration of H Neutral Increasing concentration of OH Extremely

basic

Urine

Saliva,

milk

Blood Ocean water Pure

water Eggs

Household bleach Household

ammonia

Oven cleaner

1 mol/L sodium

hydroxide

14 13 12 11 9 10

1014 1013 1012 1011 1010 109 8

108 7

107 6

106 5

105 4

104 3

103 2

102 1

101 pH [H]

0 100

(mol/L)


2-8 Inorganic Compounds

• Acid

• A solute that adds hydrogen ions to a solution

• Proton donor

• Strong acids dissociate completely in solution

• Base

• A solute that removes hydrogen ions from a solution

• Proton acceptor

• Strong bases dissociate completely in solution

• Weak Acids and Weak Bases

• Fail to dissociate completely

• Help to balance the pH


2-8 Inorganic Compounds

• Buffers and pH Control

• Buffers

• Weak acid/salt compounds

• Neutralize either strong acid or strong base

• Sodium bicarbonate is very important in humans

• Antacids

• Basic compounds that neutralize acid and form a salt

• Alka-Seltzer, Tums, Rolaids, etc.


2-9 Carbohydrates

• Organic Molecules

• Contain H, C, and usually O

• Are covalently bonded

• Contain functional groups that determine chemistry

• Carbohydrates

• Lipids

• Proteins (or amino acids)

• Nucleic acids


2-9 Carbohydrates

• Carbohydrates

• Ex:

• Monosaccharide — simple sugar

• Disaccharide — two sugars

• Polysaccharide — many sugars


2-9 Carbohydrates

• Monosaccharides

• Simple sugars

• Glucose, fructose, galactose

• Disaccharides

• Two simple sugars combined by a chemical reaction

• Sucrose, maltose

• Polysaccharides

• Many monosaccharides combined by a chemical reaction

• Glycogen, starch, cellulose


Table 2-4 Carbohydrates in the Body

Why are carbohydrates important? What

are the consequences of a “low carb” diet?


2-10 Lipids

• Lipids

• Mainly hydrophobic molecules such as fats, oils, and waxes

• Made mostly of carbon and hydrogen atoms with a –COOH at

the end (carbon, oxygen, and hydrogen)

• Include:

• Fatty acids

• Eicosanoids

• Glycerides

• Steroids

• Phospholipids and glycolipids


2-10 Lipids

• Fatty Acids

• Long chains of carbon and hydrogen

• Are relatively nonpolar

• Fatty acids may be:

• Saturated with hydrogen (no covalent bonds)

• Unsaturated (one or more double bonds)


Figure 2-14b Fatty Acids

Unsaturated

A fatty acid is either saturated (has single

covalent bonds only) or unsaturated (has

one or more double covalent bonds). The

presence of a double bond causes a

sharp bend in the molecule also known as a “kink”

Saturated

Single bonds

create a

straight

molecule,

which can be

easily packed

together to

form a solid at

room

temperature,

like butter.

The double

bond

introduces a

kink in the

structure

(cannot pack

as tightly), so

it forms a

liquid, like

olive oil.


2-10 Lipids

• Eicosenoids:

• Leukotrienes

• Active in immune system

• Prostaglandins

• Local hormones, short-chain fatty acids


2-10 Lipids

• Glycerides

• Fatty acids attached to a glycerol molecule

• Have three important functions

1. Energy source

2. Insulation

3. Protection


2-10 Lipids

• Steroids

• Types of steroids:

• Cholesterol

• Component of plasma (cell) membranes

• Estrogens and testosterone

• Sex hormones

• Corticosteroids and calcitriol

• Metabolic regulation

• Bile salts

• Derived from steroids


2-10 Lipids

• Phospholipids and Glycolipids

• Contain either a phosphate group (phospholipid) or a

sugar (glycolipid)

• Generally, both have hydrophilic heads and

hydrophobic tails and are structural lipids,

components of plasma (cell) membranes


Figure 2-18c Phospholipids and Glycolipids

WATER

Hydrophilic

heads

Hydrophobic

tails

Phospholipid Glycolipid

In large numbers,

phospholipids and

glycolipids form micelles,

with the hydrophilic

heads facing the water

molecules, and the

hydrophobic tails on the

inside of each droplet.


Table 2-5 Representative Lipids and Their Functions in the Body

What happens when you eat too much saturated fats?

Think, pair, share…


2-11 Proteins

• Proteins

• Are the most abundant and important organic

molecules

• Contain basic elements

• Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)

• Basic building blocks

• 20 amino acids

DNARNAPROTEIN Genetic

information


2-11 Proteins

1. Support

• Structural proteins

2. Movement

• Contractile

proteins

3. Transport

• Transport (carrier)

proteins

4. Buffering

• Regulation of pH

5. Metabolic Regulation

• Enzymes

6. Coordination and Control

• Hormones

7. Defense

• Antibodies

• Seven Major Protein Functions


2-11 Proteins

• Protein Structure

• Long chains of amino acids


Figure 2-19 Amino Acids

Structure of an Amino Acid

Nitrogen containing group

Central carbon

-COOH group

•R group

•Different amino acids have different

•R groups.


2-11 Proteins

• Hooking Amino Acids Together

• Requires a dehydration synthesis

• Forms a peptide bond

• Resulting molecule is a peptide


Figure 2-20 The Fomation of Peptide Bonds

Peptide Bond Formation

Glycine (gly) Alanine (ala)

HYDROLYSIS DEHYDRATION

SYNTHESIS

Peptide bond


2-11 Proteins

• Protein Shape

• Primary structure

• The sequence of amino acids along a polypeptide

• Secondary structure

• Hydrogen bonds form spirals or pleats

• Tertiary structure

• Secondary structure folds into a unique shape

• Quaternary structure

• Final protein shape — several tertiary structures together


Figure 2-21 Protein Structure

A1 A2 A3 A4 A5 A8 A6 A7 A9

A1 A2 A3 A4

A5

A6 A7 A9 A8

A10

A11 A12 A13 A14

Pleated sheet

Hydrogen bond

OR

Alpha-helix

Hydrogen

bond

A1

A2

A3 A5

A6

A7 A9

Linear chain of amino acids

OR

Heme units

Hemoglobin

(globular protein)

Keratin or collagen

(fibrous protein)


2-11 Proteins

• Fibrous Proteins

• Structural sheets or strands

• Globular Proteins

• Soluble spheres with active functions

• Protein function is based on shape

• Shape is based on sequence of amino acids


2-11 Proteins

• Enzyme Function

• Enzymes are catalysts

• Proteins that lower the activation energy of a chemical

reaction

• Are not changed or used up in the reaction

• Enzymes also exhibit:

1. Specificity — will only work on limited types of

substrates (lock and key)


Figure 2-22 A Simplified View of Enzyme Structure and Function

Substrates bind to active site of enzyme



Once bound to the active site, the substrates are held together and their interaction facilitated

Enzyme-substrate

complex



Substrate binding alters the shape of the enzyme, and this change promotes product formation



Product detaches from enzyme; entire process can now be repeated


2-11 Proteins

• Cofactors and Enzyme Function

• Cofactor

• An ion or molecule that binds to an enzyme before

substrates can bind

• Coenzyme

• Nonprotein organic cofactors (vitamins)


2-11 Proteins

• Effects of Temperature and pH on Enzyme

Function

• Denaturation (not natural shape)

• Loss of shape and function due to heat or pH

We will talk about RNA

and DNA in the next

chapter. We will also

discuss why cells use

ATP as an energy

source.

Documents

The Chemical Level of Organization professor edit