Chemical Level of Organization

CHEMICAL
LEVEL OF
ORGANIZATIO
N
 OBJECTIVES
Part 1
Ø Identify the main chemical elements of
the human body.
Ø Describe the structure of atoms, ions,
molecules, free radicals, and
compounds.
 OBJECTIVES
Part 2
Ø Define metabolism, and distinguish
between potential energy, kinetic energy,
and work.
Ø Distinguish major types of chemical
reactions that are important for studying
physiology.
Ø Describe the crucial role of
enzymes in metabolism.
 OBJECTIVES
Part 3
Ø Describe essential properties of water and
their significance in the body.
Ø Understand chemical properties of water
which affect the solubility of inorganic
and organic molecules.
Ø Distinguish the importance of pH and the
role of buffers in body fluids.
 OBJECTIVES
Part 4
Ø Describe the common elements of
organic compounds
Ø Discuss the structures and functions of
carbohydrates / lipids / proteins and all
their respective essential bodily functions
Ø Compare and contrast the structures
and functions of DNA and RNA.
1
Chemical level of organization
Ø First level on studying the human body

Ø Chemistry – a study of the structure of

matter

§ Matter
– Anything that occupies space and has mass
§ Mass
– The quantity or amount of material in matter
 ATOMS
Subatomic particles
Ø Protons (p+)
have a positive electrical charge
Ø Electrons (e–)
have a negative electrical charge
Ø Neutrons (n or n0)
are electrically neutral (uncharged)
Ø Nucleus
§ At the center of an atom
§ Contains one or more protons
§ May also contain neutrons

Ø Electron cloud
§ Created by whirl of electrons around the
nucleus
Atoms interact by means of their electrons to
produce larger, and more complex structures.
Atoms and its elements
§ normally contain equal numbers of
protons and electrons
Atomic number
§ total number of protons in an atom
Mass number
§ total number of protons and neutrons in
an atom
Element
§ substance composed only of atoms
with same atomic number
§ e.g. Oxygen
Hydrogen (H)
§ simplest atom
§ atomic number of 1
§ contains only 1
proton and 1
electron
§ proton in the center
of the atom (the
nucleus)
§ electron whirls around the nucleus in the
electron cloud
§ electrons are often shown in fixed orbit
Isotopes
§ atoms with same number of protons but
different numbers of neutrons
§ identical chemical properties
§ different mass number (tells number of
subatomic particles in nuclei)
Elements
Ø Principal elements
§ 13 most abundant elements by body
weight
Ø Trace elements
§ 14 other elements present in the body
in very small amounts
Ø All elements represented by a chemical
symbol based on:
§ English names
(e.g. H for hydrogen; O for oxygen)
§ Other language names
(e.g. Na for sodium; K for potassium)
 ELECTRONS
Atoms are electrically neutral

Ø every (+) proton is balanced by an (-)

electron

Ø electrons occupy an orderly series of

energy levels within the electron cloud
Energy levels
Ø Outermost energy level
(valence shell) is atom’s
“surface”
Ø Atoms with unfilled outer
shells are reactive
§ tend to react with
other atoms to fill
outer shell
§ e.g.: hydrogen,
lithium
Energy levels
Ø atoms with full outer
shells are inert
§ do not readily react
with other atoms;
more stable
§ e.g.: helium, neon
§ Noble gases
Ø Elements with unfilled valence shells are
reactive because they interact and combine
together with other atoms

Ø Atoms that have gained or lost electrons

are no longer electrically neutral and
become ions
Losing an electron means:
§ fewer electrons (-) than protons (+)
§ net positive charge
§ called a positive ion or cation
§ one missing electron = charge of +1
§ more electrons missing = more positive
charge (e.g. +2, +5, +7)
Gaining an electron means:
§ more electrons (-) than protons (+)
§ net negative charge
§ called a negative ion or anion
§ one extra electron = charge of –1
§ more electrons gained = more negative
charge (e.g., –2, –4, –6)
§ stabilizing interactions often form chemical
bonds
 CHEMICAL BONDS
Chemical bonding creates the ff:
Ø Compounds
§ chemical substance made up of atoms
of 2 or more different elements in a fixed
proportion, regardless of type of bond
joining them.

Ø Molecules
§ chemical structure consisting of atoms of
1 or more elements held together by
covalent bonds
Ionic bonds
§ one of the most common types of chemical
bonds

§ created by electrical attraction between

cations and anions

§ Involves the transfer of 1 or more electrons

from 1 atom to another to achieve stability

§ e.g. sodium chloride

Covalent bonds
§ involves sharing of electrons between atoms
§ forms molecules = chemical structure
consisting of one or more elements held
together by covalent bonds.
Ø Single covalent bond
§ shares 1 pair of electrons
§ 1 electron given by each atom
Ø Double covalent bond
§ shares 2 pairs of electrons
§ 2 electrons given by each atom
Nonpolar molecule
§ formed by a
typical covalent
bond

§ electrons shared
equally between atoms

§ no electrical charge
on the molecule
Polar molecule
§ formed by polar
covalent bonds

§ unequal sharing of
electrons between
atoms

§ e.g. water molecule

(H2O)
 STATES OF MATTER
Matter exists in one of three states at a time

Ø Solid
§ particles held tightly together
§ maintains volume and shape at normal
temperatures and pressures
Ø Liquid
§ particles held less tightly together
§ has a constant volume
§ shape is determined by its container
Ø Gas
§ particles independent of each other
§ has neither a constant volume nor a
fixed shape
§ can be compressed or expanded
§ will fill a container of any size
Ø Solid
Ø Liquid
§ interactions of polar water molecules
allow this state to exist in a wide
range of temperatures
Ø Gas (water vapor)
Hydrogen bond
§ attraction of small (+) charges on hydrogen
atoms (of a polar molecule) to (-) charges
on atoms in other polar molecules

§ can pull molecules together or change

their shape
Effects of hydrogen bonds on water properties
§ constantly forming and breaking in liquid
state

§ locks in place when freezing

§ becomes vapor when all hydrogen

bonds are broken

§ slows rate of evaporation

§ responsible for surface tension

Water as a solvent
§ polar charges on
water molecules
allow water to disrupt
ionic bonds (dissolve)
a variety of inorganic
compounds

§ human body fluids

contain at least 29
dissolved elements
2
 CHEMICAL REACTIONS
Cells remain alive by controlling chemical
reactions
Ø New chemical bonds are forming
Ø Existing bonds being broken
Ø Reactants
§ atoms in the reacting substances
Ø Products
§ results of the reactions
Ø Metabolism
§ all of the reactions in the body at any
moment
Each cell is a “chemical factory”
Ø Complex chemical reactions are required
for essential functions such as:
§ Providing energy
§ Maintenance
and repair
§ Growth
§ Cell division
§ Secretion
§ Contraction
Work
Ø Movement of an object or change in
physical structure of matter

Ø Can be macroscopic (e.g., moving

muscles) or microscopic (e.g., synthesis of
molecules)
Energy = capacity to perform work
Ø Potential energy
§ stored energy
§ has the potential to do work
§ e.g.: a stretched spring
Ø Kinetic energy
§ energy of motion
§ can be transferred to another object and
do work
§ e.g.: skeletal muscles contracting
Ø Conversion of energy is never 100 percent
efficient
§ some energy is released as heat
§ e.g.: body temperature rises as muscles
contract
Chemical notation
Ø simple “chemical shorthand”
Ø allows precise and brief description of
complex events
Ø may be used to calculate weights of
reactants in a reaction
Chemical notation for atoms
Ø Symbol of element indicates one atom
of that element
§ H = one atom of hydrogen
§ O = one atom of oxygen
Ø Number preceding symbol indicates
more than one atom of that element
§ 2 H = two atoms of hydrogen
§ 2 O = two atoms of oxygen
Chemical notation for molecules
Ø Subscript following symbol indicates a
molecule with that number of atoms of that
element
§ H2 = hydrogen molecule, composed of
two hydrogen atoms
§ O2 = oxygen molecule, composed of
two oxygen atoms
§ H2O = water molecule, composed of two
hydrogen atoms and one oxygen atom
Chemical reactions
Ø Reactants
§ participants at reaction start
§ usually on the left
Ø Products
§ generated at end of reaction
§ usually on the right
Ø Arrow indicates direction of reaction from
reactants to products
Ø Represented by chemical equations
§ e.g.: 2 H + O → H2O
Ø Chemical reactions rearrange atoms
into new combinations

Ø Number of atoms must be the same on

both sides of the equation to be balanced
§ Example of balanced equation
§ 2 H2 + O2 → 2 H2O
§ Example of unbalanced equation
§ H2 + O2 → H2O
Chemical notation for ions
Ø A superscript plus or minus following
symbol indicates an ion
§ Single plus sign indicates cation with +1
§ Atom has lost one electron
§ e.g.: Na+
§ Single minus sign indicates anion with –1
§ Atom has gained one electron
§ e.g.: Cl–
§ Number before sign indicates more than
one electron lost or gained
§ e.g.: Ca2+
 TYPES OF CHEMICAL
REACTIONS
Decomposition reactions

Ø Break a molecule into smaller fragments

Ø Occur inside and outside cells

Ø e.g.: digestion of food for absorption

Ø Hydrolysis
§ specific type of decomposition reaction
that involves water.
§ one of the bonds in a molecule is broken
§ components of water molecule (H
and OH) are added to the
fragments
Ø Catabolism
§ collective term for decomposition
reactions in the body
§ refers to breaking covalent bonds (form
of potential energy)
§ release kinetic energy that can perform
work
§ body can use energy for growth,
movement, and reproduction
Synthesis reactions

Ø Opposite of decomposition

Ø Assemble smaller molecules into larger

molecules

Ø Always involve formation of new chemical

bonds
Ø Dehydration synthesis
§ formation of a complex molecule by
removing a water molecule
§ opposite of hydrolysis
Ø Anabolism
§ collective term for synthesis reactions
§ refers to forming new chemical bonds
§ requires energy
§ energy usually comes from other
catabolic reactions
Ø Decomposition and synthesis reactions are
often coupled together
§ Many biological reactions are freely
reversible (they can operate in either
direction)
Ø At equilibrium, rates of both reactions are
in balance
Exchange reactions

Ø Parts of the reacting molecules are shuffled

around to produce new products

Ø May involve both decomposition and

synthesis reactions
Most chemical reactions require energy to
activate reactants
Ø Activation energy
§ Minimum energy required to activate
reactants in a reaction and allow
reaction to proceed
§ Outside the body, may be acquired by
extremes in temperature, pressure, or
lethal chemical factors
§ Inside the body, cells use special proteins
called enzymes
Enzymes
Ø Promote chemical reactions

Ø Lower the required activation energy

Ø Allow reactions to proceed under

conditions compatible with life

Ø Function as catalysts
§ accelerate chemical reaction
without being permanently changed
or consumed
§ reactions continue until equilibrium is
reached
Metabolic pathway
Ø Series of complex reactions occurring in
the body

Ø Each reaction interlocking with next step

Ø Each reaction controlled by specific

enzyme
Ø Reactions may absorb or release energy
on completion
§ Exergonic (exo-, outside)
§ Overall net release of energy
§ Common in the body and help to
maintain body temperature
§ Endergonic (endo-, inside)
§ More energy is required to begin than is
released
§ Include reactions to build molecules
Metabolites

Ø Substances synthesized or decomposed in

our bodies

Ø Processed by enzymatic reactions

Nutrients
Ø Essential metabolites normally obtained
from our diet
Ø Can be classified as:
§ Organic compounds
§ always contain carbon and hydrogen
§ e.g.: sugars, fats, proteins
§ Inorganic compounds
§ generally do not contain carbon and
hydrogen
§ e.g.: carbon dioxide, water, salts
Ø Macromolecule = large molecule made
up of monomer subunits
Ø Monomer = molecule that can be bonded
to other identical molecules to form a
polymer
Ø Repeating monomers join through
dehydration synthesis to form polymers
Ø Hydrolysis reactions separate polymers to
form monomers
3
 WATER
Water

Ø Most important component of your body

Ø About 2/3 of total body weight

Ø Comprises all physiological systems

Important properties of water

Ø Lubrication

Ø Chemical reactant

Ø High heat capacity

Ø Solvent
Water (H2O) can dissociate into hydrogen ions
(H+) and hydroxide ions (OH–)

Ø Hydrogen ion (H+)

§ hydrogen atom that has lost electron
§ extremely reactive in a solution
§ body concentrations are regulated
precisely

Ø Hydroxide ion (OH–)

§ Produced when water dissociates
 PH
pH

Ø Measure of H+ concentration in body fluids

Ø Ranges from 0 to 14
§ Acidic: below 7
§ Neutral: equal to 7
§ Alkaline (basic): above 7

Ø Change in one unit is tenfold change in

H+ ion concentration
Normal pH of blood is 7.35–7.45

Ø Beyond range damages cells and tissues

by:
§ break in chemical bonds
§ changes in the shapes of proteins
§ altered cellular functions
Ø Acidosis = below 7.35
§ pH below 7.0 causes coma
Ø Alkalosis = above 7.45
§ pH above 7.8 causes uncontrollable,
sustained skeletal muscle
contractions
Acid

Ø Solute that dissociates and releases

hydrogen ions

Ø Often referred to as proton donors

§ e.g.: hydrochloric acid
(HCl)
Base

Ø Solute that removes hydrogen ions from

solution

Ø Proton acceptor
§ e.g.: sodium hydroxide (NaOH)
Salt

Ø Inorganic compound composed of any

cation (except hydrogen) and any anion
(except hydroxide)

Ø Held together by ionic bonds

Ø Many dissociate completely in water,

releasing cations and anions
Buffers
Ø Compounds that stabilize the pH of a
solution by removing or replacing
hydrogen ions
Ø Help to maintain normal pH of body fluids

Buffer systems
Ø Help maintain pH within normal limits
Ø Usually involve a weak acid and its related
salt
Ø e.g.: Sodium bicarbonate (NaHCO3)
4
Organic compounds

Ø Always contain carbon and hydrogen and

generally oxygen

Ø Functional groups
§ attached groupings of atoms that occur
commonly in many organic molecules
§ influence the properties of the overall
molecule

Ø Many allow cells to transfer and capture

energy as high-energy compounds
 Carbohydrates

Ø Organic molecules containing carbon,

hydrogen, and oxygen in ratio near 1:2:1

Ø e.g.: sugars and starches

Ø Roughly 1.5 percent of total body weight

Ø Most important energy source

Types of Carbohydrates

1. Monosaccharide = simple sugar

Ø Contains three to seven carbon atoms

§ Triose / Tetrose / Pentose / Heptose
§ Hexose (six-carbon) (glucose, most
important fuel in the body)
Isomers

Ø Molecules with the same molecular

formula but different structures

Ø Can be important in molecular function

Ø e.g.: glucose and fructose

2. Disaccharide

Ø Two monosaccharides joined

§ e.g.: sucrose
Ø Dehydration synthesis creates
disaccharides
Ø Hydrolysis breaks them down to
monosaccharides
3. Polysaccharides

Ø Complex carbohydrates formed

from multiple disaccharides and/or
monosaccharides
Ø e.g.: Starches / Glycogen
 Lipids

Ø Contain carbon, hydrogen, and oxygen

Ø Much less oxygen compared to

carbohydrates with similar number of
carbon atoms

Ø e.g.: fats, oils, waxes

Ø Most are insoluble in water

§ Special transport mechanisms for them in
the blood
Fatty acids

Ø Long carbon chains with attached

hydrogen atoms

Ø Two ends
§ Hydrophilic Head
§ Hydrophobic Tail

Ø Two types
§ Saturated fatty acid
§ Unsaturated fatty acid
Glycerides

Ø Fatty acid chains attached to a glycerol

molecule

Ø Three types formed through dehydration

synthesis
§ Monoglyceride (glycerol + one fatty
acid)
§ Diglyceride (glycerol + two fatty acids)
§ Triglyceride (glycerol + three fatty acids)

Ø Hydrolysis breaks glycerides into fatty

acids and glycerol
Lipids in the body

Ø Essential components of all cells

Ø Important as energy reserves and provide

twice as much energy as carbohydrates

Ø Normally account for 12–18 percent of

total body weight for men and 18–24
percent for women

Ø Some fatty acids are only obtained by

humans from the diet
 Proteins
Ø Most abundant organic molecule in the
body and in many ways, are most
important

Ø Normally account for 20 percent of total

body weight

Ø Consist of long chains of

amino acids
§ 20 different amino acids in the body
§ Typical protein contains 1000 amino
acids
Amino acids

Ø All have same structural components

§ Central carbon attached to four
different groups
§ Hydrogen atom
§ Amino group
§ Carboxyl group
§ R group
Peptides

Ø Amino acids linked through dehydration

synthesis

Ø Covalent bond connects the carboxylic

acid group of one amino acid to the
amino group of another
§ This covalent bond is called a peptide
bond
Ø Dipeptide = 2 amino acids linked together

Ø Polypeptides = 3 or more amino acids

linked together

Ø Peptides of over 100 amino acids are

called proteins
Denaturation

Ø Change in protein tertiary or quaternary

structure

Ø Protein shape changes and function

deteriorates
Ø Occurs under extreme conditions
§ Body temperature above 43ºC or 110ºF

Ø Fatal due to denaturation of structural

proteins and enzymes

Ø Irreparable damage can occur to tissues

and organs
 ENZYMATIC REACTIONS
Ø Active site
§ specific region of an enzyme where
substrates must bind
§ site shape determined by tertiary or
quaternary structure of enzyme
Ø Substrates
§ reactants in enzymatic reactions
§ interactions among substrates yield
specific products
Ø Substrate and enzyme fit in a “lock and
key” fashion

Ø Each enzyme binds only to substrate with

particular shape and charge

Ø Each enzyme catalyzes only one type of

reaction
§ Characteristic called specificity
Control of reaction rates

Ø Multiple enzymes in each cell

Ø Each enzyme is active under its

own set of conditions

Ø Enzyme activation or inactivation is

important method of short-term control
over reaction rates and pathways
Saturation limit

Ø Substrate concentration required to have

maximum rate of reaction

Ø Every enzyme molecule is cycling through

reaction sequence
 DNA & RNA
Nucleic acids

Ø Large organic molecules

Ø Composed of carbon, hydrogen, oxygen,
nitrogen, and phosphorus

Ø Two classes
1. Deoxyribonucleic acid (DNA)
2. Ribonucleic acid (RNA)
Ø Primary function is storage and
transfer of information
DNA molecule

Ø Consists of a pair of nucleotide chains

called complementary strands
§ Strands twist around each other to
form a double helix (like a spiral
staircase)
§ Have complementary base pairs due
to the shapes of the bases
§ Adenine–Thymine (A–T)
§ Cytosine–Guanine (C–G)
RNA molecule

Ø Single chain of nucleotides

Ø Shape and function depend on order of
nucleotides and interactions between
them

Ø Three types
§ Messenger RNA (mRNA)
§ Transfer RNA (tRNA)
§ Ribosomal RNA (rRNA)
END