CHAPTER 2: Chemical Principles

Isotopes atoms with different

numbers of neutrons in their nuclei
Atom the smallest component of a

Have the same number of protons

pure substance that exhibits physical and

Atomic weight differ because of the

chemical properties of that substance
difference in the number of neutrons

Cannot be subdivided into smaller

Electron Shells regions
substances without losing its properties

Smallest units of matter that enter

into chemical reactions

Atoms interact with each other in

certain combinations to form molecules
corresponding to different
Chemistry the science of the
energy levels
interaction between atoms and molecules
The arrangement is called

Every atom has a centrally located

electronic configuration
nucleus (bears a net positive charge)
How Atoms Form Molecules : Chemical
and particles called electrons that move
Bonds
around the nucleus in regions called
electron shells
Valence or combining capacity,
of an atom is the number of extra
Protons positively (+) charged
or missing electrons in its
particles
outermost electron shell
Neutrons uncharged (neutral)
particles
Compound a molecule that
Electrons negatively (-) charged
contains at least two different
particles
kinds of atoms such as H2O
Charge a property of some
Chemical Bonds molecules
subatomic particles that produces an
hold together because the
attractive or repulsive force between them
valence electrons of the

Particles of opposite charge attract

combining atoms form attractive
each other
forces between the atomic nuclei

Particles of the same charge repel

2 ways for atoms to form
each other
bonds:
Gaining/losing electrons
Atomic Number the number of
from their outer electron
protons in the nucleus
Atomic Weight the total number of
shell
Sharing outer electrons
protons and neutrons in an atom
Na Latin name, natrium to
distinguish it from N and S

92 naturally occurring elements

26 elements commonly found in living

organisms

Ionic Bond when atoms gained

or lost outer electrons
Covalent Bond when outer
electrons are shared
Ionic Bonds

 Ion negatively or positively

charged atom
Electron Donor gaining
electrons
Electron Acceptor losing
electrons

Molecular Weight and Moles

Molecular weight the sum of the
atomic weights of all its atoms
Mole unit
- of a substance is its molecular
weight expressed in grams

Chemical Reactions
Ionic Bond - an attraction
Chemical reactions involve the
between ions of opposite charge
that holds them together to formmaking or breaking of bonds between atoms
a stable molecule
Chemical energy occurs when
An attraction between
bonds between atoms are formed or broken
atoms in which one atom
during chemical reactions
loses electrons and another
atom gains electrons
Endergonic reaction

Antigen-Antibody reactions
(endo=within) a chemical reaction that
reactions in which molecules produced by theabsorb more energy than it releases; energy is
immune system (antibodies) combine with
directed inward
foreign substances (antigens) to combat
Exergonic reaction (exo=out)
infection
a chemical reaction that

Cations - positively charged ions

Anions negatively charged ions
Covalent Bonds

Covalent Bond a chemical bond

formed by two atoms sharing one or more
pairs of electrons

Single covalent bond 1 pair of

electrons formed

Double covalent bond 2 pair of

electrons formed

Triple covalent bond 3 pair of

electrons formed
Hydrogen Bonds

Hydrogen Bond - in which hydrogen

atom that is covalently bonded to one oxygen
or nitrogen atom is attracted to another
oxygen or nitrogen atom

Such bonds are weak & do not bind

atoms into molecules

Serves as bridges

releases more energy than it

absorb; energy is directed
outward
3 Basic Types of Chemical Reaction
common to living cells
Synthesis reaction when two
or more atoms, ions, or molecules
combine to form new and larger
molecules
Forms new bonds

A+B

AB

A , B reactant
AB - product
Arrow - indicates the direction
in which the reaction proceeds
Anabolic reaction /
anabolism pathways of
synthesis reactions in living
organisms

 Decomposition reaction
reverse of a synthesis
To decompose means to
break down into smaller
parts
Bonds are broken

Macromolecules giant molecules

Inorganic Compounds

Water
One of the most abundant
Every water molecule is capable of
forming hydrogen bonds with nearby water
molecules
Strong attraction between water
Catabolic reaction /
catabolism - decomposition molecules
100 deg. Celsius (boiling point)
reactions that occur in living
Excellent dissolving medium or
organisms
solvent
Reactant or product in many chemical
Exchange reactions actually
reactions
part of synthesis and part of
Key reactant in the digestive
decomposition
processes of organisms
Also involved in synthetic reactions
Strong hydrogen bonding between
water molecules makes water an excellent
temperature buffer

AB
B

A+

AB + CD
+ BC

AD

Polar molecule having unequal

distribution of charges
The reversibility of Chemical
Reactions

Acids, Bases, and Salts

Ionization / Dissociation break

Reversible reaction a chemical apart into ions

reaction that is readily reversible; indicated by
Acid a substance that dissociates
two arrows
into one or more hydrogen ions ( H+) and
one or more negative ions
Proton donor (H+)
Important Biological Molecules

A+B

AB

Inorganic compounds molecules,

usually small and structurally simple, which
typically lack carbon and in which inorganic
bonds may play an important role (O2, CO2,
salts, acids, bases)

Organic compounds always

contain carbon and hydrogen and typically
are structurally complex

Base dissociates into one or more

positive ions plus one or more
negatively charged hydroxide ions
(OH-) that can accept or combine with
protons
Salt a substance that dissociates in
water into cations and anions, neither
of H+ or OH-

Acid-Base Balance : The Concept of pH

Bonding of other elements with carbon
Biochemical reactions chemical
and hydrogen forms characteristic functional
reactions in living systems , extremely
groups, specific group of atoms that are most
sensitive to even small changescommonly
in the
involved in chemical reactions and
acidity or alkalinity of the environments
are responsible for most of the characteristic
in which they occur
chemical properties of a particular organic

compound
pH - potential of hydrogen, ranges
Alcohol (-OH) hydrophilic and thus
from 0 14
attracts water molecules to it. This
calculation for a solutions pH : -log10 [H+]
attraction helps dissolve organic molecules
Acidic
containing hydroxyl groups
More H+
Carboxyl group (-COOH) source of
pH lower than 7
hydrogen ions, molecules containing it have
Basic
acidic properties
More OHAmino group (-NH2) functions as
bases
because they readily accept hydrogen
pH buffers compounds that help
ions
keep the pH from changing drastically
Sulfhydryl group (-SH) helps
Fungi best able to tolerate acidic
stabilize the intricate structure of many
proteins
conditions
Cyanobacteria prokaryotes, do well R remainder of the molecule ( R-OH)
in alkaline habitats
Macromolecules - very large
Propionibacterium acnes amolecules

Polymers formed by covalent

bacterium that causes acne, has its
natural environment human skin, tends
bonding of many repeating small
to be slightly acidic, pH of about 4
molecules called monomers
Thiobacillus ferrooxidans a
bacterium that metabolizes elemental Dehydration synthesis /
Condensation
reaction a molecule of
sulfur and produces sulfuric acid,
pH
water is released
from 1-3.5
Sulfuric acid produced from this
Carbohydrates
bacterium in mine water is important in
dissolving uranium and copper from
Are a large and diverse group of
low-grade ore
organic compounds that includes sugars
Organic Compounds

and starches

Common elements that attach to C are Deoxyribose sugar, building block

of deoxyribonucleic acid (DNA), the
H, O, N
molecule that carries hereditary information
Less often are S, P

Carbon skeleton - chain of carbon

atoms in an organic molecule

Simple carbohydrates used in the

synthesis of amino acids and fats or fatlike

substances, which are used to build cell

membranes and other structures

different structures and

properties
Hydration disaccharides can
Macromolecular
be broken down into smaller,
carbohydrates - functions as
simpler molecules when water is
food reserves
added; reverse of dehydration
synthesis
Function of carbohydrates is
Polysaccharides consist of tens or
mainly to fuel cell activities with hundreds
a
of monosaccharides joined through
ready source of energy
dehydration synthesis

Lack the characteristic sweetness of

Made up of C, H, and O atoms
sugars
Ratio of H to O is 2:1

Not usually soluble in water

Ribose (C5H10O5)

Glycogen composed of glucose

Glucose (C6H12O6)
subunits and is synthesized as a storage
Sucrose (C12H22O11)
material by animals and some bacteria

Cellulose glucose polymer, main

Formula is (CH2O)n
component of the cell walls of plants
and most algae
3 Major Groups Based on Size

Dextran produced as a sugary slime

Monosaccharides simple
by certain bacteria, used in a blood
sugars
plasma substitute
Each molecules has 3-7 carbon

Chitin makes up part of the cell wall

atoms
of most fungi and exoskeletons of
# of carbon atoms in the
lobsters, crabs, and insects
molecules of simple sugars is

Starch polymer of glucose produced

indicated by the prefix in its
by plants and used as food by humans
name (trioses, tetroses,

Amylase break bonds between the

pentoses, etc.)
glucose molecules in glycogen; but
Pentoses and Hexoses
cannot break the bond in cellulose
important to living organisms

Cellulase can digest cellulose

DNA has pentose
Lipids
Glucose common hexose,
main energy-supplying molecule

Essential to the structure and function

of living cells
of membranes that separate living cells
from their environment
Disaccharides 2

Has C, H, and O atoms; but lack the

monosaccharides bond in a
2:1 ratio of H and O atoms
dehydration synthesis reaction

Nonpolar molecules, no positive or

Disaccharide sucrose(table
negative end (pole)
sugar) glucose + fructose

insoluble in water, but dissolves easily

Disaccharide lactose (milk
in nonpolar solvents
sugar) glucose + galactose

provide structure of membranes

Isomers - two molecules with

energy storage
the same chemical formula but

Simple Lipids fats or

triglycerides contain an alcohol called
glycerol and group of compounds known as
fatty acids

A molecule of fat is formed when a

molecule of glycerol combines with 1-3
fatty acid molecules
Based on # of fatty acids :
monoglyceride, diglyceride,
triglyceride
Ester linkage the chemical
bond formed where the water
molecule is removed

polar (phosphate group &

glycerol) & nonpolar
regions (fatty acids)
Mycobacterium tuberculosis
a bacterium that causes
tuberculosis, is distinguish by its
lipid-rich content
Cell wall contains complex
lipids such as waxes and
glycolipids(lipids w/
carbohydrates attached) that
gives the bacterium distinctive
staining characteristics

Steroids structure of steroid

cholesterol with four interconnected carbon
Primary function of lipids is to rings that are characteristic of steroid
from plasma membranes that

Sterol when an OH group is

enclose cells
attached to one of the rings of the
Saturated - no double bonds,
steroid
the carbon skeleton contains the
Important constituent of the plasma
maximum number of hydrogen
membranes of animal cells and of one
atoms, becomes solid more easily
group of bacteria (mycoplasmas),
because they relatively straight
also found in fungi and plants
Separate the fatty acid chains and
and able to pack together more
closely than unsaturated chains
thus prevent the packing that would
Unsaturated the double bonds
harden the plasma membrane at low
create kinks in the chain, which
temperatures
keep the chains apart from one
Proteins
another
Cis fatty acid H atoms on the

Organic molecules that contain C, H,

same side
O, N ; some also contain S
Trans fatty acid H atoms on

Essential ingredients in all aspects of

opposite sides of the double bond
cell structure and function

Complex lipids contains

Enzymes are proteins that speed up
elements such as P, N, S in
biochemical reactions
addition to C, H, O
Transport proteins help transport
Phospholipids made up of
certain chemicals into and out of cells
glycerol, 2 fatty acids, and in
Bacteriocins produced by many
place of a third fatty acid is a
bacteria, kill other bacteria
phosphate group bonded to one
Exotoxins produced by some
or several organic groups
disease-causing microorganisms
builds membranes
Hormones regulatory functions
essential to a cells survival

Antibodies- play a role in vertebrate

immune systems
Amino Acids

Building blocks of proteins

Attached to its alpha-carbon id at least
1 carboxyl group (-COOH) and 1 amino
group (-NH2) = alpha-amino acids;
also attached is a side group (R group),
which is the amino acids distinguishing
feature

Tyrosine an amino acid that has a

cyclic side group

Stereoisomers has two

configurations : D and L , 3D shapes
D right handed
L left handed

Peptide Bonds
Peptide bonds bonds
between amino acids
Dipeptide - 2 amino acids
joined by a peptide bond
Tripeptide 3 amino acids
Peptide 4-9 amino acids
Polypeptide 10-2000 or
more amino acids
Levels of Protein Structure

Hydrogen bonding
between O or N atoms
that are part of the
polypeptides backbone
Tertiary structure overall 3D
structure of a polypeptide chain
Folding is not repetitive or
predictable
Involves several
interactions between
various amino acid side
groups in the polypeptide
chain
Hydrophobic interaction
helps contribute to
tertiary structure
H bonds between side
groups & ionic bonds
between oppositely
charged side groups, also
contribute to tertiary
structure
Disulfide bridges proteins that
contain the amino acid cysteine form
strong covalent bonds
Contains (-SH) sulfhydryl groups
and S of one cysteine molecule
bonds with another S of the other
(S-S) by removal of H atoms

Quaternary Structures consist of

Primary structure amino an aggregation of 2 or more individual
polypeptide chains that operate as a single
acids are linked together to
functional unit
from a polypeptide chain

Globular shape compact and

Secondary structure
roughly
spherical
repetitious twisting or folding of

Fibrous shape threadlike

the polypeptide chain

Denaturation when a protein

Helices clockwise
encounters a hostile environment in
spirals
terms of temperature, pH, or salt
Pleated sheets - which
concentrations, it may unravel and lose
form from roughly
its characteristic shape ; protein is no
parallel portions of the
longer functional
chain

Simple proteins contains only

amino acids

Conjugated proteins combination

of amino acids with other organic or inorganic
components

Named by their non-amino acid

component

Glycoproteins - has sugars

Nucleoproteins has nucleic acids

Metalloproteins has metal atoms

Lipoproteins has lipids

Phosphoproteins has phosphate

groups; important regulators of activity
in eukaryotic cells

Nucleic Acids
Oswald Avery, Colin MacLeod,
Maclyn McCarty (1944) discovered DNA
the substance which genes are made

James Watson & Francis Crick

work with molecular models and X-ray
information

Maurice Wilkins & Rosalind

Franklin identified the physical structure of
DNA

Nucleic acids DNA & RNA

discovered in the nuclei of cells; nucleotides
structural unit and named according to their
nitrogen-containing base

Pentose sugar (deoxyribose or

ribose)
Phosphate group (phosphoric
acid)

Nucleoside combination of
purine or pyrimidine + pentose
sugar; no phosphate group
DNA

Consists of two long strands

wrapped around each other to
from a double helix
A & T held by 2 H bonds
G & C by 3 H bonds
No Uracil

Complementary when the

sequence of bases of one strand
is determined by the sequence of
bases of the other
RNA

Single-stranded
Pentose sugar is a ribose
which has 1 more Oxygen atom
than deoxyribose
RNAs bases is URACIL (U)
instead of Thymine
Messenger RNA
(mRNA)
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)

Nucleotides - 3 parts:
Nitrogen-containing base (cyclic
compounds that has C, H, N, O)
Adenine (A)
ATP
Thymine (T)
Cystosine (C )
Adenosine triphosphate principal
Gunaine (G)
energy-carrying molecule of all cells and is
Uracil (U)
indispensable to the life of the cell
A & G- double-ring

Stores chemical energy released by

structures called purines
chemical reactions
T, C, U single-ring

Provides energy for reactions that

structures called
require energy
pyrimidines

Adenosine unit adenine & ribose w/ 3

phosphate group attached; in other
words (adenine nucleotide or
adenine monophosphate or AMP) w/
2 extra phosphate groups

Releases large amount of energy when

the 3rd phosphate group is hydrolyzed
into ADP