Ch. 2 BASIC CHEMISTRY -...

Copyright © 2010 Pearson Education, Inc.

BASIC CHEMISTRY

Ch. 2


Matter and Composition of Matter

• Definition: Anything that has mass and

occupies space

• Matter is made up of elements –An

element cannot be broken down by ordinary

chemical means

• Atoms - are unique building blocks for

each element


Atomic Structure

• Neutrons

• No charge, In atomic nucleus

• Mass = 1 atomic mass unit (amu)

• Protons

• Positive charge,In atomic nucleus

• Mass = 1 amu


Atomic Structure

• Electrons

• Negative charge ,orbit nucleus

• Mass = 0 amu

• Equal in number to protons in atom

Copyright © 2010 Pearson Education, Inc. Figure 2.1

Helium atom Helium atom

Nucleus Nucleus

Proton Neutron Electron

cloud

Electron


Energy

• Definition: Capacity to do work or put matter

into motion

• Types of energy:

• Kinetic: energy associated with motion

• Potential: stored (inactive) energy

• Electrical : results from the movement of

charged particles (Na+, K+)


Identifying Elements

• Atoms of different elements contain different

numbers of protons

• Compare hydrogen, helium and lithium


Proton

Neutron

Electron

Helium (He) Lithium (Li)

Hydrogen (H)


Identifying Elements

• Atomic number =

• Mass number =

• Mass numbers of atoms of an element are not

all identical

• Isotopes = atoms of the same element that

differ in the # of neutrons they contain


Proton

Neutron

Electron

Deuterium (2H) Tritium (3H) Hydrogen (1H)


Atoms of Elements can combine Chemically to

form Molecules and Compounds

• Molecule: two or more atoms bonded together

(H2 or C6H12O6)

• Compound:


Chemical Bonds

• Electrons occupy up to seven electron shells

(energy levels) around nucleus

• Octet rule: Except for the first shell which is

full with two electrons, atoms interact in order

to have eight electrons in their outermost

energy level (valence shell)


Chemically Inert Elements

• Stable and unreactive

• Outermost energy level fully occupied or

contains eight electrons

Copyright © 2010 Pearson Education, Inc. Figure 2.4a

Helium (He)

Neon (Ne)

2e 2e 8e

(a) Chemically inert elements

Valence shell complete


Chemically Reactive Elements

• Valence shell not fully occupied by electrons

• Tend to gain, lose, or share electrons (form

bonds) with other atoms to achieve stability

Copyright © 2010 Pearson Education, Inc. Figure 2.4b

2e 4e

2e 8e

1e

(b) Chemically reactive elements

Valence shell incomplete

Hydrogen (H) Carbon ©

1e

Oxygen (O) Sodium (Na)

2e 6e


Ionic Bonds

• Ions are formed by:

• Anions (– charge) have gained one or more

electrons

• Cations (+ charge) have lost one or more

electrons

• Attraction of opposite charges results in: An

ionic bond


Sodium atom (Na)

Chlorine atom (Cl)

Sodium ion (Na+) Chloride ion (Cl–)

Sodium chloride (NaCl)

+ –


Covalent Bonds

• Formed by sharing of two or more valence

shell electrons

• Allows each atom to fill its valence shell at

least part of the time


+

Hydrogen

atoms

Carbon

atom

Molecule of

methane gas (CH4)

(a) Formation of four single covalent bonds:

or

Resulting molecules Reacting atoms


or

Oxygen

atom

Oxygen

atom

Molecule of

oxygen gas (O2)

(b) Formation of a double covalent bond:


+

Copyright © 2010 Pearson Education, Inc. Figure 2.7c

+ or

Nitrogen

atom

Nitrogen

atom

Molecule of

nitrogen gas (N2)

(c) Formation of a triple covalent bond:.



Covalent Bonds

• Sharing of electrons may be equal

or unequal

• Equal sharing produces:

Electrically balanced nonpolar

molecules


Covalent Bonds

• Unequal sharing by atoms with different electron-attracting

abilities produces: polar covalent bonds

• H2O


Hydrogen Bonds

• Attractive force between electropositive

hydrogen of one molecule and an

electronegative atom of another molecule

• Important in intramolecular bonds, holding a

large molecule in a three-dimensional shape


(a) The slightly positive ends (+) of the water

molecules become aligned with the slightly

negative ends (–) of other water molecules.

+

–

–

– –

–

+

+

+

+

+

Hydrogen bond

Figure 2.8


Synthesis Reactions

• A + B AB

• Always involve bond formation

• Anabolic

• Endergonic


Example

Amino acids are joined to

Form protein.

(a) Synthesis reactions

Smaller particles are bonded

together to form larger,

molecules.

Amino acid

molecules

Protein

molecule


Decomposition Reactions

• AB A + B

• Reverse synthesis reactions

• Involve breaking of bonds

• Catabolic

• Exergonic


Example

Glycogen is broken down to release

glucose units.

Bonds are broken in larger

molecules, resulting in smaller,

less complex molecules.

(b) Decomposition reactions

Glucose

molecules

Glycogen


Classes of Compounds

• Inorganic compounds

• Do not contain carbon (ex. Water, salts, and

many acids and bases)

• Organic compounds

• Contain carbon, usually large, covalently

bonded (ex’s. carbohydrates, fats, proteins,

nucleic acids)


Water

• 60%–80% of the volume of living cells

• Most important inorganic compound in living

organisms because of its properties


Salts

• Ionic compounds that dissociate into ions in

water

• Ions (electrolytes) conduct electrical currents

in solution


Acids

• Acids : Proton (H+) donors (release H+ in

solution)

• HCl H+ + Cl–


Bases

• Bases: Proton acceptors (take up H+ from

solution)

• NaOH Na+ + OH–


Acid-Base Concentration

• Acid solutions contain higher amounts of H+

• As [H+] increases: acidity increases

• Basic solutions contain higher concentrations

of OH–

• As [H+] decreases (or as [OH–] increases):

alkalinity increases

• pH = measure of the acidity/bascisity of a

solution


Acid-Base Concentration

• Neutral solutions:

• pH = 7

• Contains equal numbers of H+ and OH–

• Acidic solutions

• [H+], pH

• pH = 0–6.99

• Basic solutions

• [H+], pH

• pH= 7.01–14


Carbohydrates

• Sugars and starches whose building blocks =

• Three classes

• Monosaccharides -Simple sugars containing

three to seven C atoms (glucose)

• Disaccharides -Double sugars that are too

large to pass through cell membranes

• Polysaccharides - Three/more simple sugars,

e.g., starch and glycogen; not very soluble


Carbohydrates

• Functions

• Primary role: Major source of cellular fuel

(glucose)


Example

Hexose sugars (the hexoses shown

here are isomers)

Example

Pentose sugars

Glucose Fructose Galactose Deoxyribose Ribose

(a) Monosaccharides

Monomers of carbohydrates


PLAY Animation: Disaccharides

Example

Sucrose, maltose, and lactose

(these disaccharides are isomers)

Glucose Fructose Glucose Glucose Glucose

Sucrose Maltose Lactose

Galactose

(b) Disaccharides

Consist of two linked monosaccharides

disaccharides.mov


PLAY Animation: Polysaccharides

Example

This polysaccharide is a simplified representation of

glycogen, a polysaccharide formed from glucose units.

(c) Polysaccharides

Long branching chains (polymers) of linked monosaccharides

Glycogen

polysaccharides.mov


Lipids

• Insoluble in water

• Main types:

• Triglycerides

• Phospholipids

• Steroids


Triglycerides

• Defined as:solid fats and liquid oils

• Building blocks = three fatty acids bonded to a

glycerol molecule

• Main functions

• Energy storage

• Insulation

• Protection


Glycerol

+

3 fatty acid chains Triglyceride,

or neutral fat

3 water

molecules

(a) Triglyceride formation


Phospholipids

• Similar to triglycerides:

• Building blocks = Glycerol + two fatty acids

and a phosphorus (P)-containing group

• “Head” and “tail” regions have different

properties

• Important in cell membrane structure


Phosphorus-

containing

group (polar

“head”)

Example

Phosphatidylcholine

Glycerol

backbone

2 fatty acid chains

(nonpolar “tail”)

Polar

“head”

Nonpolar

“tail”

(schematic

phospholipid)

(b) “Typical” structure of a phospholipid molecule

Two fatty acid chains and a phosphorus-containing group are

attached to the glycerol backbone.


Steroids

• Steroids—interlocking four-ring structure

• Examples are cholesterol, vitamin D, steroid

hormones, and bile salts


Example

Cholesterol (cholesterol is the

basis for all steroids formed in the body)

(c) Simplified structure of a steroid

Four interlocking hydrocarbon rings form a steroid.


Proteins

• Building blocks = amino acids

• After amino acids are linked together they often undergo

a natural folding process

• This folding process results in four different levels of

protein structure: primary, secondary, tertiary, quaternary


(a) Generalized

structure of all

amino acids.

(b) Glycine

is the simplest

amino acid.

(c) Aspartic acid

(an acidic amino acid)

has an acid group

(—COOH) in the

R group.

(d) Lysine

(a basic amino acid)

has an amine group

(–NH2) in the R group.

(e) Cysteine

(a basic amino acid)

has a sulfhydryl (–SH)

group in the R group,

which suggests that

this amino acid is likely

to participate in

intramolecular bonding.

Amine

group

Acid

group


(a) Primary structure:

The sequence of amino acids forms the polypeptide chain.

Amino acid Amino acid Amino acid Amino acid Amino acid

PLAY Animation: Primary Structure

primary_structure.mov


a-Helix: b-Sheet:

(b) Secondary structure:

The primary chain forms spirals (a-helices) and sheets (b-sheets).

PLAY Animation: Secondary Structure

secondary_structure.mov


(c) Tertiary structure:

PLAY Animation: Tertiary Structure

tertiary_structure.mov

Copyright © 2010 Pearson Education, Inc. Figure 2.19d

(d) Quaternary structure:

Two or more polypeptide chains, each with its own tertiary structure,

combine to form a functional protein.

PLAY Animation: Quaternary Structure

quaternary_structure.mov


Protein Denaturation

• Shape change and disruption of active sites

due to environmental changes

• A denatured protein is nonfunctional


Enzymes

• Are proteins

• Biological catalysts

• Increase the speed of a reaction

• Allows for millions of reactions/minute


Substrates

Enzyme

Active site

+

Enzyme Function


Nucleic Acids

• DNA and RNA

• Building blocks = nucleotide, composed of N-

containing base, a pentose sugar, and a

phosphate group


Deoxyribonucleic Acid (DNA)

• Four Nitrogen containing bases:

• adenine (A), guanine (G), cytosine (C), and

thymine (T)

• Double-stranded, helical

• Replicates before cell division, ensuring

genetic continuity

• Provides instructions for protein synthesis


Deoxyribose

sugar

Phosphate

Sugar-phosphate

backbone

Adenine nucleotide Hydrogen

bond

Thymine nucleotide

Phosphate Sugar:

Deoxyribose Phosphate Sugar Thymine (T) Base:

Adenine (A)

Adenine (A)

Thymine (T)

Cytosine (C)

Guanine (G)

(b)

(a)

(c) Computer-generated image of a DNA molecule


Ribonucleic Acid (RNA)

• Four bases:

• adenine (A), guanine (G), cytosine (C), and uracil (U)

• Single-stranded

PLAY Animation: DNA and RNA

DNA_and_RNA.mov


Adenosine Triphosphate (ATP)

• Adenine-containing RNA nucleotide with two

additional phosphate groups


Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP)

Adenosine monophosphate (AMP)

Adenosine

Adenine

Ribose

Phosphate groups

High-energy phosphate

bonds can be hydrolyzed

to release energy.


Function of ATP

• Phosphorylation:

• The chemical energy contained in the high

energy phosphate bonds can be used to

perform cellular work


Solute

Membrane

protein

Relaxed smooth

muscle cell

Contracted smooth

muscle cell

+

+

+

Transport work

Mechanical work

Chemical work

(a)

(b)

(c)

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