3/19/2009

Why Study Chemistry?

ƒ The science that deals with the basic properties of
matter

MICROBIOLOGY ƒ Chemical substances undergo changes and interact

with one another in chemical reactions

ƒ Metabolism is the use of nutrients for energy or for

Chapter 2: making substances of cells
Chemical Principles
ƒ Understanding the basic principles of chemistry is
essential to understanding metabolic processes in
living things

Chemical Building Blocks and The Structure of Atoms

Chemical Bonds
ƒ Atom: the smallest chemical unit of ƒ Protons: subatomic particle, located in the
matter nucleus of the atom and is positively charged

ƒ Matter composed of one kind of atom is ƒ Neutrons: subatomic particle, located in the
called an element nucleus of the atom and is neutral (no charge)

ƒ When two or more atoms combine

chemically, they form a molecule ƒ Electrons: subatomic particle, orbits the
nucleus of the atom and is negatively charged
ƒ Molecules made up of atoms of two or
more elements are called compounds

Electrons Electrons

ƒ Energy is the ability to do work ƒ Each electron shell has a specific # of orbitals
ƒ Electrons have energy due to their relative ƒ Each orbital holds up to two electrons
orbital position (potential energy)

Atoms with incomplete

electron orbitals are
more reactive

1
 3/19/2009

Structure of Four Biologically Important

Atoms ƒ Atomic number: The number of protons of a
particular element

ƒ Rule of octets

ƒ Ion: A charged atom produced when an

atom gains or loses one or more electrons

ƒ Cation: positively charged ion

ƒ Anion: negatively charged ion

Ions and Isotopes Ions and Isotopes

ƒ Ions are atoms in which the number of ƒ Isotopes are atoms with the same number of
electrons does not equal that of protons protons but different numbers of neutrons

99% of all
carbon

Different
atomic mass

Same atomic
number

Molecules
ƒ Atomic weight: the sum of the number of
protons and neutrons in an atom ƒ A molecule is a group of atoms held together
by energy
ƒ Isotopes: Atoms of a particular element
that contain different numbers of neutrons ƒ The holding force is called a chemical bond

ƒ Gram molecular weight (mole) ƒ There are three kinds of chemical bonds
ƒ 1. Ionic bonds
ƒ Radioisotopes: the nuclei of unstable ƒ 2. Covalent bonds
isotopes tend to emit subatomic particles
and radiation ƒ 3. Hydrogen bonds

2
 3/19/2009

Chemical bonds Covalent Bonds Formed By

Sharing of Electrons
ƒ Major chemical elements of life – C, H, N, O, P,
S

ƒ Bond in different ways to form various

molecules of life

ƒ Ionic bonds: result from the attraction

between ions that have opposite charges

ƒ Covalent bonds: strong bonds which share

pairs of electrons

Polar Compounds and Hydrogen

Hydrogen bonds Bonding
Hydrogen Bonding
ƒ Hydrogen bonds
ƒ Form between hydrogen and
other electronegative elements
((O or N))
ƒ Increased number provides
stability to molecules
Water: the shared electrons ((--) are
closer to the O than H nucleus,
so there is also a charge
separation (polarity)

3

Hydrogen Bonds Give Water
Unique Properties
ƒ Water molecules are polar molecules
ƒ They can thus form hydrogen bonds with each
other and with other polar molecules
ƒ Each hydrogen bond is very weak
ƒ However, the cumulative effect of enormous
numbers can make them quite strong
ƒ Hydrogen bonding is responsible for many of
the physical properties of water
Polarity and Water Molecules
Strong Surface Tension of
Water
3/19/2009
Water as a Biological Solvent
ƒ Polarity
ƒ Cytoplasm is aqueous and contains polar
molecules
ƒ Promotes hydrogen bonding (stability)
ƒ Promotes interaction within biomolecules
ƒ Forces nonpolar molecules (lipids) to aggregate
ƒ Cohesiveness
ƒ H bonds are dynamic: forming, breaking, re re--forming
ƒ Responsible for water’s important properties:
1. High surface tension,
2. High specific heat
3. Surface ice insulates underlying water – prevents
freezing (aquatic organisms can survive)
Hydrogen Bonding Between
Water Molecules
Solutions and Colloids
Examples of mixtures
ƒ Mixture: consists of two or more
substances that are combined in any
proportion (not chemically bound)
ƒ Solution: mixture of two or more
substances
1. Solvent
2. Solute
ƒ Particles too large to form true solutions
can sometimes form colloids
4
 3/19/2009

pH Values of Some Common

Acids, Bases, and pH
Substances
ƒ Acid: A hydrogen ion (H+) or proton
donor

ƒ Base: A p
proton acceptor,
p , or a
hydroxyl ion (OH-) donor

ƒ pH scale: relates proton

concentration to pH (logarithmic
scale)

Chemical Reactions Complex Organic Molecules

ƒ Organic chemistry: the study of compounds
ƒ Typically involve the use of energy to form that contain carbon
chemical bonds and the release of energy as
chemical bonds are broken
ƒ Biochemistry: A branch of organic chemistry
that studies chemical reactions that occur in
ƒ Catabolism: breakdown of substances with living systems
the release of energy (exergonic)
ƒ Functional group: a part of a molecule that
generally participates in chemical reactions
ƒ Anabolism: synthesis of substances with
as a unit and gives molecule some of its
energy used to create bonds (endergonic) chemical properties

Forming Macromolecules Hydrocarbons

ƒ An organic molecule
consists of a carbon-
carbon-
based core with
special groups
attached
ƒ These groups have
special properties
and are referred to
as functional groups

5
 3/19/2009

Four Classes of Organic Major Classes of Large, Complex

Compounds Containing Oxygen Biochemical Molecules

ƒ Carbohydrates

ƒ Lipids

ƒ Proteins

ƒ Nucleic Acids

Carbohydrates
ƒ Serve as main source of energy for most living
things

ƒ Glycogen: storage form of energy

ƒ Monosaccharide Isomers
ƒ Disaccharide
ƒ Polysaccharide

ƒ Glycosidic bond: sugar alcohol/sugar linkage

Glucose Molecule Represented Three Ways

Deoxy Sugars and Sugar
Alcohols

6
 3/19/2009

Disaccharides and Polysaccharides Lipids

ƒ Fats, phospholipids, and steroids

ƒ Relatively insoluble in water

ƒ Structural component of cells and

energy source

ƒ Saturated fatty acid vs. unsaturated

acid

The Structure of Fats Saturated vs. Unsaturated Fatty Acids

Phospholipids Micelle Aggregate

7
 3/19/2009

Steroids Proteins
ƒ Composed of building blocks called amino acids

ƒ Amino acids have at least one amino (-

(-NH2) group
and one acidic carboxyl ((--COOH) group

ƒ Each amino acid is distinguishable by a different

chemical group (R group)

ƒ Peptide bonds: covalent bond that links an amino

group of one amino acid to carboxyl group of
another

Amino Acids

8
 3/19/2009

Peptide Linkage

The Structure of Proteins Three Levels of Protein Structure

ƒ Primary structure: consists of the specific
amino acids in a polypeptide chain

ƒ Secondary structure: consists of the folding

or coiling or amino acids chains into a
particular pattern

ƒ Tertiary structure: folding of the protein into

globular shapes or fibrous threadlike strands

ƒ Quaternary structure: the association of

several tertiary
tertiary--structured polypeptide chains

Quaternary Protein Structure Classification of Proteins

ƒ Structural proteins: contribute to the three-
three-
dimensional structure of cells, cell parts,
and membranes

ƒ Enzymes: protein catalysts – substances

that control the rate of chemical reactions in
cells

9
 3/19/2009

Enzymes Nucleotides and Nucleic Acids

ƒ Increase the rate at which chemical reactions ƒ Nucleotides join to form nucleic acids
take place within living organisms

ƒ Functions:
ƒ Active site: the site on the enzyme which
combines with substrate 1. Storage
g of energygy in high-
high
g -energy
gy
bonds
ƒ Substrate: the substance on which an 2. Store information that directs protein
enzyme acts synthesis
3. Information can be transferred from
parent to progeny

Nucleotides

ATP--Adenosine Triphosphate
ATP
Nucleotide

1. A nitrogenous base

2 A five-
2. five-carbon sugar

3. One or more phosphate groups

10
 3/19/2009

Nucleic Acid Structure

Two Nucleic Acids Found in Living
Organisms
1. Ribonucleic acid (RNA)

2 Deoxyribonucleic acid (DNA)

2.

Five Bases Found in Nucleic Acids

11