3/19/2009

Why Study Chemistry?

The science that deals with the basic properties of
matter

MICROBIOLOGY
Chapter 2:
Chemical Principles

Chemical substances undergo changes and interact

with one another in chemical reactions
Metabolism is the use of nutrients for energy or for
making substances of cells
Understanding the basic principles of chemistry is
essential to understanding metabolic processes in
living things

Chemical Building Blocks and

Chemical Bonds

The Structure of Atoms

Atom: the smallest chemical unit of

matter

Protons: subatomic particle, located in the

nucleus of the atom and is positively charged

Matter composed of one kind of atom is

called an element

Neutrons: subatomic particle, located in the

nucleus of the atom and is neutral (no charge)

When two or more atoms combine

chemically, they form a molecule

Electrons: subatomic particle, orbits the

nucleus of the atom and is negatively charged

Molecules made up of atoms of two or

more elements are called compounds

Electrons

Electrons

Energy is the ability to do work

Electrons have energy due to their relative
orbital position (potential energy)

Each electron shell has a specific # of orbitals

Each orbital holds up to two electrons

Atoms with incomplete

electron orbitals are
more reactive

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Structure of Four Biologically Important

Atoms

Atomic number: The number of protons of a

particular element
Rule of octets
Ion: A charged atom produced when an
atom gains or loses one or more electrons
Cation: positively charged ion
Anion: negatively charged ion

Ions and Isotopes

Ions and Isotopes

Ions are atoms in which the number of

electrons does not equal that of protons

Isotopes are atoms with the same number of

protons but different numbers of neutrons

99% of all
carbon

Different
atomic mass
Same atomic
number

Atomic weight: the sum of the number of

protons and neutrons in an atom
Isotopes: Atoms of a particular element
that contain different numbers of neutrons
Gram molecular weight (mole)
Radioisotopes: the nuclei of unstable
isotopes tend to emit subatomic particles
and radiation

Molecules
A molecule is a group of atoms held together
by energy
The holding force is called a chemical bond
There are three kinds of chemical bonds
1. Ionic bonds
2. Covalent bonds
3. Hydrogen bonds

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Chemical bonds
Major chemical elements of life C, H, N, O, P,
S

Covalent Bonds Formed By

Sharing of Electrons

Bond in different ways to form various

molecules of life
Ionic bonds: result from the attraction
between ions that have opposite charges
Covalent bonds: strong bonds which share
pairs of electrons

Polar Compounds and Hydrogen

Bonding

Hydrogen bonds
Hydrogen Bonding

Hydrogen bonds
Form between hydrogen and
other electronegative elements
((O or N))
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)

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Hydrogen Bonds Give Water

Unique Properties

Water as a Biological Solvent

Polarity
Cytoplasm is aqueous and contains polar
molecules
Promotes hydrogen bonding (stability)
Promotes interaction within biomolecules
Forces nonpolar molecules (lipids) to aggregate

Water molecules are polar molecules

They can thus form hydrogen bonds with each
other and with other polar molecules

Each hydrogen bond is very weak

However, the cumulative effect of enormous
numbers can make them quite strong

Cohesiveness
H bonds are dynamic: forming, breaking, re
re--forming
Responsible for waters important properties:
1. High surface tension,
2. High specific heat
3. Surface ice insulates underlying water prevents
freezing (aquatic organisms can survive)

Hydrogen bonding is responsible for many of

the physical properties of water

Polarity and Water Molecules

Strong Surface Tension of

Water

Hydrogen Bonding Between

Water Molecules

Solutions and Colloids

Examples of mixtures

Mixture: consists of two or more

substances that are combined in any
proportion (not chemically bound)

Solution: mixture of two or more

substances
1. Solvent
2. Solute

Particles too large to form true solutions

can sometimes form colloids

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Acids, Bases, and pH

pH Values of Some Common

Substances

Acid: A hydrogen ion (H+) or proton

donor
Base: A p
proton acceptor,
p , or a
hydroxyl ion (OH-) donor
pH scale: relates proton
concentration to pH (logarithmic
scale)

Chemical Reactions
Typically involve the use of energy to form
chemical bonds and the release of energy as
chemical bonds are broken
Catabolism: breakdown of substances with
the release of energy (exergonic)
Anabolism: synthesis of substances with
energy used to create bonds (endergonic)

Forming Macromolecules

Complex Organic Molecules

Organic chemistry: the study of compounds
that contain carbon
Biochemistry: A branch of organic chemistry
that studies chemical reactions that occur in
living systems
Functional group: a part of a molecule that
generally participates in chemical reactions
as a unit and gives molecule some of its
chemical properties

Hydrocarbons

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

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Four Classes of Organic

Compounds Containing Oxygen

Major Classes of Large, Complex

Biochemical Molecules

Carbohydrates
Lipids
Proteins
Nucleic Acids

Carbohydrates
Serve as main source of energy for most living
things
Glycogen: storage form of energy
Monosaccharide
Disaccharide
Polysaccharide

Isomers

Glycosidic bond: sugar alcohol/sugar linkage

Glucose Molecule Represented Three Ways

Deoxy Sugars and Sugar

Alcohols

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Disaccharides and Polysaccharides

Lipids
Fats, phospholipids, and steroids
Relatively insoluble in water
Structural component of cells and
energy source
Saturated fatty acid vs. unsaturated
acid

The Structure of Fats

Saturated vs. Unsaturated Fatty Acids

Phospholipids

Micelle Aggregate

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Proteins

Steroids

Composed of building blocks called amino acids

Amino acids have at least one amino ((-NH2) group
and one acidic carboxyl ((--COOH) group
Each amino acid is distinguishable by a different
chemical group (R group)
Peptide bonds: covalent bond that links an amino
group of one amino acid to carboxyl group of
another

Amino Acids

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Peptide Linkage

The Structure of Proteins

Three Levels of Protein Structure

Primary structure: consists of the specific

amino acids in a polypeptide chain
Secondary structure: consists of the folding
or coiling or amino acids chains into a
particular pattern
Tertiary structure: folding of the protein into
globular shapes or fibrous threadlike strands
Quaternary structure: the association of
several tertiary
tertiary--structured polypeptide chains

Quaternary Protein Structure

Classification of Proteins
Structural proteins: contribute to the threethreedimensional structure of cells, cell parts,
and membranes
Enzymes: protein catalysts substances
that control the rate of chemical reactions in
cells

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Enzymes
Increase the rate at which chemical reactions
take place within living organisms
Active site: the site on the enzyme which
combines with substrate
Substrate: the substance on which an
enzyme acts

Nucleotides and Nucleic Acids

Nucleotides join to form nucleic acids

Functions:
1. Storage
g of energy
gy in highhigh
g -energy
gy
bonds
2. Store information that directs protein
synthesis
3. Information can be transferred from
parent to progeny

Nucleotides

ATP--Adenosine Triphosphate
ATP

Nucleotide
1. A nitrogenous base
2 A five2.
five-carbon sugar
3. One or more phosphate groups

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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

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