BIOCHEMISTRY

The Study of Living Things

• Biochemistry is the study of the chemical substances found in living organisms and the chemical interactions of
these substances with each other.

• A biochemical substance is a chemical substance found within a living organism.

• science concerned with the chemical constituents of living cells and with the reactions and processes they undergo

• deals with cell biology, molecular biology and molecular genetics

VITAL FORCE THEORY

Scientists used to believe that compounds occurring in living matter were different from other substances and that they
contained some sort of intangible VITAL FORCE

• organic compounds are produced only by living things

• FRIEDRICH WOHLER

• German chemist who disproved this theory by synthesizing urea from a non-organic source (ammonium
cyanate)

Synthetic Organic Compounds

• This experiment gradually discredited the vital-force theory and opened the way for modern synthetic organic
chemistry

• Useful in the synthesis of pharmaceuticals and industrial chemicals

How does Biochemistry describe life processes?

The Composition of Living Organisms and Humans are complex and diverse

Biochemistry/ Biochemical Evolution

• Common to All living things:

– make use of the same types of biomolecules

– They all use energy

As a result, all living things can be studied using the methods of chemistry and physics

Field of Biochemistry draws on many disciplines

• allows it to use results from many sources to answer questions about the “molecular nature of life processes”

What are Biomolecules?

• Biomolecules are molecules found in living matter and are part of the subject matter of organic chemistry

• they are derived from monomers (smaller molecules) (Greek: mono + meros, single + part)

--amino acids --> proteins

--nucleotides --> nucleic acids

--monosaccharides polysaccharides
--lipids
Important applications

Made in:

• Medically related fields

• Understanding of health and disease at the molecular level leads to more effective treatment of illness of many
kinds

Biochemistry seeks to describe the structure, organization, and functions of living matter in molecular terms

Relevance of Biochemistry

• concerned with entire spectrum of life forms

• biochemical researches have impact on nutrition and preventive medicine

Types of biochemical substances:

Bioinorganic substances and Bioorganic substances.

– Bioinorganic substances : water (two-thirds the mass of human body) and inorganic salts (4%-5%).

– Bioorganic substances : make up only about one-fourth of body mass

Substances that contain carbon- carbohydrates, lipids, proteins, and nucleic acids

Biomolecules

Organic chemistry: the study of the compounds of carbon and hydrogen with their derivatives

=the cellular apparatus of living organisms is made up of carbon compounds

Functional group: an atom or group of atoms that shows characteristic physical and chemical properties
FUNCTIONAL GROUP (ALKANES)
ALKENE

FUNCTIONAL GROUP ALCOHOL

AMINE

• Molecules that contain carbon-nitrogen bonds

• It is a derivative of ammonia in which one or all three hydrogen atoms are replaced by hydrocarbon groups

AMIDE

• Molecules that contain nitrogen atoms connected to the carbon atom of a carbonyl group.

• Regarded as derivatives of carboxylic acids in which the hydroxyl group has been replaced by an amine or ammonia

What are Biomolecules?

• Biomolecules are molecules found in living matter.

• Two broad types: Small molecules and macromolecules

• Importance of Macromolecules:

a) Essential structures for the basis of life

b) Control and regulate these processes

c) Responsible for energy exchanges, irritability,

metabolism, mobility and reproduction

BIOMOLECULES

• living cells include very large molecules (proteins, nucleic acids, polysaccharides, lipids)

– these biomolecules are polymers (Greek: poly + meros, many + parts)

Informational Macromolecules

Level of Organization of Human Organism

Origin of Life

• The “big bang” theory

– all matter was originally confined in a very small space

– as the result of an explosion, it started to expand with great force

– the average temperature of the universe has been decreasing ever since

– in the earliest stages of the universe, the only elements present were H, He, and Li

– other elements formed by

• thermonuclear reactions in stars

• explosions of stars
 • the action of cosmic rays outside the stars

• Gases present in the atmosphere of the early earth included NH3, H2S, CO, CO2, CH4, N2, H2, and H2O but not O2

• Enzymes: a class of proteins that are biocatalysts

– the catalytic effectiveness of a given enzyme depends on its amino acid sequence

• Genetic code: the relationship between the nucleotide sequence in nucleic acids and the amino acid sequence in
proteins

– theories of the origin of life consider how such a coding system might have arisen

• Which came first…the chicken or the egg?

– catalytic activity associated with proteins

– coding associated with nucleic acids

Prokaryotes vs Eukaryotes

• Prokaryote: “before the nucleus”

– single-celled organisms

– includes bacteria and cyanobacteria

• Eukaryote: “true nucleus”

• contains a well-defined nucleus

• single-celled (yeasts and Paramecium), multicellular (animals and plants)

• eukaryotic cell

a. The nuclear body is bounded by a nuclear membrane

b. It contains one or more paired, lineaR chromosomes composed of (DNA)

c. A nucleolus is present.
d. The nuclear body is called a nucleus.

• prokaryotic cell

a. The nuclear body is not bounded by a nuclear membrane.

b. It usually contains one circular chromosome composed of deoxyribonucleic acid (DNA) associated with histone-like
proteins.
c. There is no nucleolus.
d. The nuclear body is called a nucleoid .

2.) cell division

eukaryotic cell
a. The nucleus divides by mitosis.
b. Haploid (1N) sex cells in diploid or 2N organisms are produced through meiosis

prokaryotic cell
a. The cell usually divides by binary fission. There is no mitosis.
b. Prokaryotic cells are haploid Meiosis is not needed.

3 BASIC PARTS OF CELL- NUCLEUS, CYTOPLASM, CELL MEMBRANE

cell membrane - the thin layer of protein and fat that surrounds the cell. The cell membrane is semipermeable, allowing
some substances to pass into the cell and blocking others.

centrosome - (also called the "microtubule organizing center") a small body located near the nucleus The centrosomes is
where microtubules are made.

cytoplasm - the jellylike material outside the cell nucleus in which the organelles are located.

Golgi body - (also called the Golgi apparatus or golgi complex) a flattened,layered, sac-like organelle that looks like a
stack of pancakes and is located near the nucleus. The Golgi body packages proteins and carbohydrates into membrane-
bound vesicles for "export" from the cell.

lysosome - (also called cell vesicles) round organelles surrounded by a membrane and containing digestive enzymes. This
is where the digestion of cell nutrients takes place.

nucleolus - an organelle within the nucleus - it is where ribosomal RNA is produced.

nucleus - The nucleus controls many of the functions Of the cell (by controlling protein synthesis) and contains DNA (in
chromosomes).

ribosome - small organelles composed of RNA-rich cytoplasmic granules that are sites of protein synthesis.
rough endoplasmic reticulum - (rough ER) a vast system of Interconnected, membranous, infolded and convoluted
sacks. Rough ER transports materials through the cell and produces proteins in sacks called cisternae
(which are sent to the Golgi body, or inserted into the cell membrane).

smooth endoplasmic reticulum - (smooth ER) a vast system of interconnected, membranous, infolded and convoluted
tubes. Smooth ER transports materials through the cell. It contains enzymes and produces and digests
lipids (fats) and membrane proteins.

PLANT CELL

Cell Wall
( Plant Cells Only )

 non living structure that surrounds the plant cell.

 protects + supports the cell.

 made up of a tough fiber called cellulose.

-mitochondria
-vacoules

Chloroplasts
Plant cells only )

 contains a green pigment known as chlorophyll which is important for photosynthesis.

-ribosomes
-E.R
-Golgi Body
-Lysosome
Nucleus

• Contains nucleolus and chromatin

• Location of main genome

Mitochondrion

• Site of oxidation reactions for the production of energy

Chloroplast

• Photosynthetic organelle

• Double-membrane

Endoplasmic reticulum

• Attached to cell membrane and nuclear membrane

• Rough and smooth ER

Golgi apparatus

• Involved in protein secretion from the cell

• Site in which sugars are linked to other cellular components

Lysosomes

• Secretes hydrolytic enzymes

Peroxisomes

• Contains the enzyme catalase

Vacuole

• Isolate waste substances that are toxic to the plant

Chemical Composition of Living Matter

• Water – 70-90% (free and bound water)

• Solids – 10-30%

• Inorganic substances – 1% (Na, K, Ca, Mg, NH4, Cl-, SO4, PO4-3, CO3-2, etc.

• Traces of Fe, I2, Cu, Mn, Co, Zn are also present in combination with organic radicals

• Rest- organic substances

Water

• This is the major component of the cell and is often referred to as an inert space filter in a living organism.

• It is a strong dipole and has a high dielectric constant.

• It is highly reactive with unusual properties different physically and chemically from other common liquids.

• Water and its ionization products H+ and OH- are important factors in determining the structure and biological
properties of proteins, nucleic acids, lipids, and other cell components.

IMPORTANCE OF WATER

• Supports existence of plant and animal life

• Every activity of every cell in the body takes place in a water environment.

PROPERTIES OF WATER

• It is a universal solvent

• It is an ideal biologic agent or medium for the ionization of substances and therefore hastens chemical reactions

• It has a high specific heat, that is, it takes up more heat to raise its temperature through 1oC, thus allowing the body
to store heat effectively without greatly raising its temperature.

• It possesses a high latent heat of evaporation

• It has the capacity to conduct heat readily

Water as an ideal biologic agent

• Water is a dipole, a molecule with chemical charge distributed asymmetrically about its structure.

• Hydrogen bonding enables water to dissolve many organic biomolecules that contain functional groups which can
participate in hydrogen bonding.

• Hydrogen bonds account for the surface tension, viscosity, liquid state at room temperature, and solvent power of
water.

• Compounds that contain O, N or S can serve as hydrogen bond donors or acceptors.

IMPORTANCE OF WATER

• Essential in the processes of digestion, circulation, elimination and the regulation of body temperature.

• Acts as a solvent, it dissolves sugar, salt and alcohol.

• Water intake = water output

Water intake > water output = edema

Water intake < water output = dehydration

PROPERTIES OF WATER

• Pure water is colorless, odorless, tasteless

Tap water taste comes from dissolved gases and minerals.

Blue color of oceans, and lakes is due to reflection of the sky and presence of finely divided solid materials .
• Water volume at room temperature contracts as it cools but further cooling (4oC ) causes volume expansion (ice),
decreasing its density. (lighter).

• Density of water is 1g/mL; (mass at 4oC = 1g)

• Boiling point of pure water is 100oC at 1atm pressure.

• Freezing point of water is 0oC.

• Heat is necessary for water to evaporate. The amount of heat necessary so that evaporation to take place is
called heat of vaporization = 540 cal/g. (perspiration)

• For ice to melt, amount of heat required is 80cal/g.

• Calorie is the amount of heat required to change the temperature of 1g of water by 1oC

What is a polar bond:

• Electrons are unequally shared,more negative charge found closer to one atom.

• Due to difference in electronegativity of atoms involved in bond.

• Polar nature of water molecule is responsible for its property of dissolving many materials

• The unsymmetrical distribution of electrons i.e., the bond or molecule contains (+) and (-) poles resulting into a
dipole.
-Ionic compounds (KCl) and low molecular-weight polar covalent compounds (e.g.C2H5OH and CH3COCH3) dissolve
in water

• Each water molecule can be involved in 4 hydrogen bonds: 2 as donor, and 2 as acceptor

• • Due to the tetrahedral arrangement of the water molecule

Hydrogen Bond

• Hydrogen bonding: important in stabilization of 3-D structures of biological molecules (DNA, RNA, proteins)

• Even though hydrogen bonds are weaker than covalent bonds, they have a significant effect on the physical
properties of hydrogen-bonded compounds
CARBOHYDRATES

Carbohydrate: A polyhydroxyaldehyde or polyhydroxyketone, or a substance that gives these compounds on

hydrolysis.

Monosaccharide: A carbohydrate that cannot be hydrolyzed to a simpler carbohydrate.

• Monosaccharides have the general formula CnH2nOn, where n varies from 3 to 8.

• Aldose: A monosaccharide containing an aldehyde group.

• Ketose: A monosaccharide containing a ketone group.

Monosaccharides

• The suffix -ose indicates that a molecule is a carbohydrate.

• The prefixes tri-, tetra-, penta-, and so forth indicate the number of carbon atoms in the chain.

• Those containing an aldehyde group are classified as aldoses.

• Those containing a ketone group are classified as ketoses.

• There are only two trioses:

• Often aldo- and keto- are omitted and these compounds are referred to simply as trioses.

• Although “triose” does not tell the nature of the carbonyl group, it at least tells the number of carbons.

Fischer projection: A two-dimensional representation for showing the configuration of tetrahedral stereocenters.

• Horizontal lines represent bonds projecting forward from the stereocenter.

• Vertical lines represent bonds projecting to the rear.

• Only the stereocenter is in the plane.

In 1891, Emil Fischer made the arbitrary assignments of D- and L- to the enantiomers of glyceraldehyde.

• D-monosaccharide: the -OH on its penultimate carbon is on the right in a Fischer projection.

• L-monosaccharide: the -OH on its penultimate carbon is on the left in a Fischer projection.
 • The most common D-tetroses and D-pentoses are:

• The three most common D-hexoses are:

Amino Sugars

Amino sugars contain an -NH2 group in place of an -OH group.

• Only three amino sugars are common in nature: D-glucosamine, D-mannosamine, and D-galactosamine.
N-acetyl-D-glucosamine is an acetylated derivative of D-glucosamine.

Physical Properties of Monosaccharides

• Colorless, crystalline solids

• -OH Group: polar, hydrogen bonding

• All monosaccharides are soluble in water

• Slightly soluble with ethanol and other nonpolar solvents (diethyl ether, dichloromethane, benzene)

Cyclic Structure

• Aldehydes and ketones react with alcohols to form hemiacetals (Chapter 17).

• Cyclic hemiacetals form readily when hydroxyl and carbonyl groups are part of the same molecule and
their interaction can form a five- or six-membered ring.

Objects and Mirror Images

• Most monosaccharides exist in two forms: a “left handed” and “right handed” form - same as two hands

• Two types of objects:

- Superimposible on their mirror images: -- images that coincide at all points when the images are laid upon each other --
a dinner plate with no design features -- Achiral

- Non-superimposible on their mirror images: Chiral (handedness)

Chirality

• Chiral Center: C atom attached to 4 different groups

• A molecule with chiral center is a chiral molecule

• Best way to visualize - look at all C atoms and see if there are at least two H atoms then that can’t be a
chiral center

• C atoms with less than one H atoms are worth looking at for their chirality.
 • Be careful as a C atom may apparently look similar but may not have four DIFFERENT groups.

• E. g. 3-bromopentane - C has two CH2-CH3 groups – so it is achiral A chiral C is usually denoted by *

Chiral Objects

• Chiral compounds have the same number of atoms arranged differently in space.

• A chiral carbon atom has four different groups attached

Mirror Images

• The three-dimensional structure of a chiral compound has a mirror image.

• Your hands are chiral. Try to superimpose your thumbs, palms, back of hands, and little fingers. Is it possible?
Why or why not?

Haworth Projections

• A five- or six-membered cyclic hemiacetal is represented as a planar ring, lying roughly perpendicular to
the plane of the paper.

• Groups bonded to the carbons of the ring then lie either above or below the plane of the ring.

• The new carbon stereocenter created in forming the cyclic structure is called the anomeric carbon.

• Stereoisomers that differ in configuration only at the anomeric carbon are called anomers.

• The anomeric carbon of an aldose is C-1; that of the most common ketose is C-2.

In the terminology of carbohydrate chemistry,

• b means that the -OH on the anomeric carbon is on the same side of the ring as the terminal -CH2OH.

• a means that the -OH on the anomeric carbon is on the side of the ring opposite from the terminal -
CH2OH.

• A six-membered hemiacetal ring is called a pyranose, and a five-membered hemiacetal ring is called a
furanose because these ring sizes correspond to the heterocyclic compounds furan and pyran.
 • Aldopentoses also form cyclic hemiacetals.

• The most prevalent forms of D-ribose and other pentoses in the biological world are furanoses.

• The prefix “deoxy” means “without oxygen.”

• D-Fructose (a 2-ketohexose) also forms a five-membered cyclic hemiacetal.

Chair Conformations

• For pyranoses, the six-membered ring is more accurately represented as a strain-free chair conformation.

• In both Haworth projections and chair conformations, the orientations of groups on carbons 1- 5 of b-D-
glucopyranose are up, down, up, down, and up and all are equatorial.

Mutarotation

• Mutarotation: The change in specific rotation that accompanies the equilibration of a- and b-anomers in aqueous
solution.

• Example: When either a-D-glucose or b-D-glucose is dissolved in water, the specific rotation of the
solution gradually changes to an equilibrium value of +52.7°, which corresponds to 64% beta and 36%
alpha forms.

Formation of Glycosides

• Treatment of a monosaccharide, all of which exist almost exclusively in cyclic hemiacetal forms, with an alcohol
gives an acetal.

Formation of Glycosides

• A cyclic acetal derived from a monosaccharide is called a glycoside.

• The bond from the anomeric carbon to the -OR group is called a glycosidic bond.

• Mutarotation is not possible for a glycoside because an acetal, unlike a hemiacetal, is not in equilibrium
with the open-chain carbonyl-containing compound.

• Glycosides are stable in water and aqueous base, but like other acetals, are hydrolyzed in aqueous acid to
an alcohol and a monosaccharide.

• Glycosides are named by listing the alkyl or aryl group bonded to oxygen followed by the name of the
carbohydrate in which the ending -e is replaced by -ide.

Reduction to Alditols

• The carbonyl group of a monosaccharide can be reduced to an hydroxyl group by a variety of reducing agents,
including NaBH4 and H2 in the presence of a transition metal catalyst (H2/Pt).
 • The reduction product is called an alditol.

• Alditols are named by changing the suffix -ose to -itol.

ALDITOS

• Sorbitol is found in the plant world in many berries and in cherries, plums, pears, apples, seaweed, and
algae.

• It is about 60 percent as sweet as sucrose (table sugar) and is used in the manufacture of candies and as a
sugar substitute for diabetics.

• These three alditols are also common in the biological world. Note that only one of these is chiral.

Oxidation to Aldonic Acids

• The aldehyde group of an aldose is oxidized under basic conditions to a carboxylate anion.

• The oxidation product is called an aldonic acid.

• A carbohydrate that reacts with an oxidizing agent to form an aldonic acid is classified as a reducing sugar
(it reduces the oxidizing agent).

• 2-Ketoses (e.g. D-fructose) are also reducing sugars.

Aldonic Acids

• The body uses glucuronic acid to detoxify foreign alcohols and phenols.

• These compounds are converted in the liver to glycosides of glucuronic acid and then excreted in the
urine.

• The intravenous anesthetic Propofol is converted to the following water-soluble glucuronide and
excreted.

Sucrose

• Table sugar, obtained from the juice of sugar cane and sugar beet.

Lactose

• The principle sugar present in milk.

• About 5 - 8% in human milk, 4 - 5% in cow’s milk.

Maltose

• From malt, the juice of sprouted barley and other cereal grains.

Polysaccharides

Polysaccharide: A carbohydrate consisting of large numbers of monosaccharide units joined by glycosidic bonds.

Starch: A polymer of D-glucose.

• Starch can be separated into amylose and amylopectin.

• Amylose is composed of unbranched chains of up to 4000 D-glucose units joined by a-1,4-glycosidic

bonds.

• Amylopectin contains chains up to 10,000 D-glucose units also joined by a-1,4-glycosidic bonds. At branch
points, new chains of 24 to 30 units are started by a-1,6-glycosidic bonds.
 • Glycogen is the energy-reserve carbohydrate for animals.

• Glycogen is a branched polysaccharide of approximately 106 glucose units joined by a-1,4- and a-1,6-
glycosidic bonds.

• The total amount of glycogen in the body of a well-nourished adult human is about 350 g, divided almost
equally between liver and muscle.

Cellulose is a linear polysaccharide of D-glucose units joined by b-1,4-glycosidic bonds.

• It has an average molecular weight of 400,000 g/mol, corresponding to approximately 2200 glucose units
per molecule.

• Cellulose molecules act like stiff rods and align themselves side by side into well-organized water-
insoluble fibers in which their -OH groups form numerous intermolecular hydrogen bonds.

• This arrangement of parallel chains in bundles gives cellulose fibers their high mechanical strength.

• It is also the reason why cellulose is insoluble in water.

• Humans and other animals can not digest cellulose because their digestive systems do not contain
b-glycosidases, enzymes that catalyze the hydrolysis of b-glycosidic bonds.

• Termites have such bacteria in their intestines and can use wood as their principal food.

• Ruminants (cud-chewing animals) and horses can also digest grasses and hay.

• Humans have only a-glucosidases; hence, the polysaccharides we use as sources of glucose are starch and
glycogen.

• Many bacteria and microorganisms have b-glucosidases.

Acidic polysaccharides: a group of polysaccharides that contain carboxyl groups and/or sulfuric ester groups, and
play important roles in the structure and function of connective tissues.

• There is no single general type of connective tissue.

• Rather, there are a large number of highly specialized forms, such as cartilage, bone, synovial fluid, skin,
tendons, blood vessels, intervertebral disks, and cornea.

• Most connective tissues are made up of collagen, a structural protein, in combination with a variety of
acidic polysaccharides.

• Heparin is synthesized and stored in mast cells of various tissues, particularly the liver, lungs, and gut.

• The best known and understood of its biological functions is its anticoagulant activity.

• It binds strongly to antithrombin III, a plasma protein involved in terminating the clotting process.
(chapter 3)

Atomic Structure and the Periodic Table

INTERNAL STRUCTURE OF ATOM

Subatomic Particle

• A very small particle that is a building block for atoms.

Three Types of Subatomic Particles

• The atom contains:

 Electrons – found outside the nucleus; possesses a negative electrical charge; smallest mass.

 Protons – found in the nucleus; positive charge equal in magnitude to the electron’s negative charge.

 Neutrons – found in the nucleus; no charge; virtually same mass as a proton.

• The nucleus is:

 Small compared with the overall size of the atom.

 Extremely dense; accounts for almost all of the atom’s mass.

 Positively charged center of an atom.

CHARGE NEUTRALITY OF AN ATOM

An atom as a whole is electrically neutral (no net electrical charge).

# of Protons = # of Electrons

• Atomic Number (Z) – # of protons in the nucleus of an atom.

• Mass Number (A) – sum of the # of protons and the # of neutrons in the nucleus of an atom.

ELEMENT

• A pure substance in which all atoms present have the same atomic number.

• All atoms with the same atomic number have the same chemical properties and are atoms of the same element.

Isotopes

• Atoms of an element that have the same number of protons and the same number of electrons but different
numbers of neutrons.

• Show almost identical chemical properties; chemistry of atom is due to its electrons.

• Physical properties are often slightly different because they have different masses.

• In nature most elements contain mixtures of isotopes

ATOMIC MASS

• Elements occur in nature as mixtures of isotopes.

• Carbon = 98.89% 12C

13
1.11% C

<0.01% 14C

• Calculated average mass for the isotopes of an element expressed on a scale where
serves as the reference point.

Average Atomic Mass for Carbon

98.89% of 12 amu + 1.11% of 13.0034 amu =

(0.9889)(12 amu) + (0.0111)(13.0034 amu) =

12.01 amu

THE PERIODIC LAW AND PERIODIC TABLE

• Periodic Law – When elements are arranged in order of increasing atomic number, elements with similar chemical
properties occur at periodic (regularly recurring) intervals.

• Periodic Table – Tabular arrangement of the elements in order of increasing atomic number such that elements
having similar chemical properties are positioned in vertical columns.

The Periodic Table

• Periods – horizontal rows of elements

• Groups – elements in the same vertical columns; have similar chemical properties

Groups

• Table of common charges formed when creating ionic compounds.

Group Charge

Alkali Metals (1A) 1+

Alkaline Earth Metals (2A) 2+

Halogens (7A) 1-

Noble Gases (8A) 0

Metal

• An element that has the characteristic properties of luster, thermal conductivity, electrical conductivity, and
malleability.

Nonmetal
 • An element characterized by the absence of the properties of luster, thermal conductivity, electrical conductivity,
and malleability.

Electron Shells

• A region of space about a nucleus that contains electrons that have approximately the same energy and that spend
most of their time approximately the same distance from the nucleus.

• Electrons that occupy the first electron shell are closer to the nucleus and have a lower energy than electrons in the
second electron shell.

Electron Subshells

• A region of space within an electron shell that contains electrons that have the same energy.

Subshell Number of Electrons

s 2

p 6

d 10

f 14

Electron Orbitals

• A region of space within an electron subshell where an electron with a specific energy is most likely to be found.

• An electron orbital can accommodate a maximum of 2 electrons.

Subshell Number of Orbitals

s 1

p 3

d 5

f 7

Electron Spin

• As an electron “moves about” within an orbital, it spins on its own axis in either a clockwise or a counterclockwise
direction.

• When two electrons are present in an orbital, they always have opposite spins.
Rules for Assigning Electrons to Various Shells, Subshells, and Orbitals

1. Electron subshells are filled in order of increasing energy.

2. Electrons occupy the orbitals of a subshell such that each orbital acquires one electron before any orbital acquires a
second electron. All electrons in such singly occupied orbitals must have the same spin.

3. No more than two electrons may exist in a given orbital – and then only if they have opposite spins.

Electron Configurations

• A statement of how many electrons an atom has in each of its electron subshells.

• An oxygen atom as an electron arrangement of two electrons in the 1s subshell, two electrons in the 2s subshell,
and four electrons in the 2p subshell.

Oxygen: 1s22s22p4

Orbital Diagrams

• A notation that shows how many electrons an atom has in each of its occupied electron orbitals.

Oxygen: 1s22s22p4

Distinguishing Electron

• Last electron added to the electron configuration for an element when electron subshells are filled in order of
increasing energy.

• This last electron is the one that causes an element’s electron configuration to differ from that of an element
immediately preceding it in the periodic table.

• A system based on selected physical properties of the elements, in which they are described as metals or
nonmetals.

• A system based on the electron configurations of the elements, in which elements are described as noble-gas,
representative, transition, or inner transition elements.
CHAPTER 4

Chemical Bonding: The Ionic Bond Model

A Chemical Bond

• Attractive force that holds two atoms together in a more complex unit.

• Form as a result of interactions between electrons found in the combining atoms.

Two Types of Chemical Bonds

• Ionic Bonds

• Covalent Bonds

Ionic Bond

• Chemical bond formed through the transfer of one or more electrons from one atom or group of atoms to another
atom or group of atoms.

• Ionic Compound

– A compound in which ionic bonds are present.

Covalent Bond

• Chemical bond formed through the sharing of one or more pairs of electrons between two atoms.

• Molecular Compound (Covalent Compound)

– A compound in which atoms are joined through covalent bonds.

Bonding

• Most bonds are not 100% ionic or 100% covalent.

• Most bonds have some degree of both ionic and covalent character.

Two Fundamental Concepts Of Chemical Bond

1. Not all electrons in an atom participate in bonding. Those that participate are called valence electrons.

2. Certain arrangements of electrons are more stable than others, as is explained by the octet rule.

Valence Electron

• An electron in the outermost electron shell of a representative element or noble-gas element.

• Valence electrons are found in either s or p subshells.

Lewis Symbol

• Chemical symbol of an element surrounded by dots equal in number to the number of valence electrons present in
atoms of the element.
Lewis Symbols for Selected Representative and Noble-Gas Elements

THE OCTET RULE

• Certain arrangements of valence electrons are more stable than others.

• The valence electron configurations of the noble gases are considered the most stable of all valence electron
configurations.

• In forming compounds, atoms of elements lose, gain, or share electrons in such a way as to produce a noble-gas
electron configuration for each of the atoms involved.

THE IONIC BOND MODEL

Ion

• An atom (or group of atoms) that is electrically charged as a result of the loss or gain of electrons.

• If an atom gains one or more electrons, it becomes a negatively charged ion.

• If an atom loses one or more electrons, it becomes a positively charged ion.

Atoms tend to gain or lose electrons until they have obtained an electron configuration that is the same as that of a noble
gas.

• Example: K+ (1s22s22p63s23p6)

• Lost one electron to obtain electron configuration for Ar (1s22s22p63s23p6).

• Metal atoms containing one, two, or three valence electrons tend to lose electrons to acquire a noble-gas electron
configuration.

Group Charge

IA 1+

IIA 2+

IIIA 3+
2. Nonmetal atoms containing five, six, or seven valence electrons tend to gain electrons to acquire a noble-gas
electron configuration.

Group Charge

VIIA 1–

VIA 2–

VA 3–

3. Elements in Group IVA occupy unique positions relative to the noble gases (could gain or lose four electrons).

Isoelectronic Species

• A series of ions/atoms containing the same number and configuration of electrons.

O2-, F-, Ne, Na+, Mg2+, and Al3+

1s22s22p6

Formation of an Ionic Compound

• Ion formation requires the presence of two elements:

– A metal that can donate electrons.

– A nonmetal that can accept electrons.

• The electrons lost by the metal are the same ones gained by the nonmetal.

• The positive and negative ions simultaneously formed from such electron transfer attract one another.

Lewis Structure

• Combination of Lewis symbols that represents either the transfer or the sharing of electrons in chemical bonds.

The Reaction Between Sodium and Chlorine

The Reaction Between Sodium and Oxygen

The Reaction Between Calcium and Chlorine

• Ionic compounds are always neutral; no net charge is present.

• The ratio in which positive and negative ions combine is the ratio that achieves charge neutrality for the resulting
compound.

Writing Chemical Formulas for Ionic Compounds

1. The symbol for the positive ions is always written first.

2. The charges on the ions that are present are not shown in the formula.

3. The subscripts in the formula give the combining ratio for the ions.

Example

• Compound formed between Li+ and O2–

– Need two Li+ to balance out the 2- charge on oxygen.

• Formula is Li2O.

Solid Ionic Compounds

• Consists of positive and negative ions arranged in such a way that each ion is surrounded by nearest neighbors of
the opposite charge.

• Any given ion is bonded by electrostatic attractions to all the other ions of opposite charge immediately
surrounding it.

Formula Unit

• Smallest whole-number repeating ratio of ions present in an ionic compound that results in charge neutrality.

• Chemical formulas for ionic compounds represent the simplest ratio of ions present.

Naming Compounds

• Binary Compounds:

 Composed of two elements

 Ionic and covalent compounds included

• Binary Ionic Compounds:

 Metal-nonmetal

 Metal is always present as the positive ion, and the nonmetal is always present as the negative ion.
 • The full name of the metallic element is given first, followed by a separate word containing the stem of the
nonmetallic element name and the suffix –ide.

Naming Ionic Compounds (for Metals with Variable Charges)

• Metals in these compounds form more than one type of positive charge.

• Charge on the metal ion must be specified.

• Roman numeral indicates the charge of the metal cation (positively charged ion).

• Transition metal cations usually require a Roman numeral.

Examples

CuBr Copper(I) bromide

FeS Iron(II) sulfide

PbO2 Lead(IV) oxide

Polyatomic Ion

• Ion formed from a group of atoms (held togethePolyatomic Ion

• r by covalent bonds) through loss or gain of electrons.

• Must be memorized (see Table 4.3 on pg. 99 in text).

• Examples of compounds containing polyatomic ions:

NaOH Sodium hydroxide

Mg(NO3)2 Magnesium nitrate

(NH4)2SO4 Ammonium sulfate

Generalizations

1. Most of the polyatomic ions have a negative charge.

2. Two of the negatively charged polyatomic ions, OH– and CN–, have names ending in –ide and the rest of them have
names ending in either –ate or –ite.

3. A number of –ate, –ite pairs of ions exist. The –ate ion always has one more oxygen atom than the –ite ion. Both the
–ate and –ite ions of a pair carry the same charge.

4. A number of pairs of ions exist wherein one member of the pair differs from the other by having a hydrogen atom
present. In such pairs, the charge on the ion that contains hydrogen is always 1 less than that on the other ion.

5. Determined in the same way as those for ionic compounds that contain monatomic ions.

6. The positive and negative charges present must add to zero.

1. Na+ and OH– form NaOH.

2. Mg2+ and NO3– form Mg(NO3)2.

3. NH4+ and SO42– form (NH4)2SO4.

 PERIODIC TABLE

 Dmitri Mendeleev often considered as the “Father” of the Periodic Table

 Discovery of the individual elements

 In 1649, the first scientific discovery of element by Hennig Brand - Phosphorus

 In 1869, a total of 63 elements had been discovered

 Scientists began to device the periodic table using their knowledge of atomic masses.

B. LAW OF TRIADS

 In 1817, Dobereiner noticed that the atomic weight of Sr fell midway between Ca and Ba

 In 1829, he observed that several elements could be classified into groups of three called, TRIADS

C. FIRST ATTEMPTS AT DESIGNING A PERIODIC TABLE

• A.E. Beguyer de Chancourtois described a list of elements positioned on a cylinder in terms of increasing atomic
weight

• first to recognize that elemental properties reoccur every seven elements

• * His chart included some ions and compounds in addition to the elements.

D. LAW OF OCTAVES

 John Newlands noticed that the known elements were arranged in order of atomic mass, every eighth element
has similar properties (LAW OF OCTAVES)

 Inadequate for elements beyond Calcium

DMITRI MENDELEEV

• In 1869, he proposed that elements showed recurring properties according to increasing atomic mass.

• This made possible of the prediction of the properties of several elements that had not been discovered.

LOTHAR MEYER

• He produced remarkably similar results as that of Mendeleev’s.

• Unfortunately for Meyer, Mendeleev’s table became available to the scientific community via publication before
his table appeared.

• He produced remarkably similar results as that of Mendeleev’s.

• Unfortunately for Meyer, Mendeleev’s table became available to the scientific community via publication before
his table appeared.

F. DISCOVERY OF THE NOBLE GASES

• Lord Rayleigh, in 1895 proved argon to be chemically inert.

• William Ramsey, in 1898 suggested that argon be placed in the family between chlorine and potassium (Zero
group)
G. ATOMIC STRUCTURE AND THE PERIODIC TABLE ERNEST RUTHERFORD

• In 1911, determined the nuclear charge

• Found that the nuclear charge on a nucleus was proportional to the atomic weight of the element.

HENRY MOSELEY

• In 1913, determined the atomic numbers of all the known elements from an experimental technique.

• Arranged the elements according to increasing atomic numbers.

• The PERIODIC LAW

THE PERIODIC LAW

“It states that the properties of the elements recur in a repeating pattern when arranged according to increasing atomic
number.”

GLENN SEABORG

• He worked on the last major changes to the Periodic Table

• He discovered all the transuranic elements from 92 to 102

• He reconfigured the Periodic table by placing the actinide series below

• Element 106 has been named in his honor

The Alexander Arrangement of the Elements

 originated by a science exhibit designer, Roy Alexander

 to eliminate the confusion and apparent inconsistencies in the flat table

 Elements were contiguously and continuously arranged according to the atomic number without disturbing the
accepted group and property interrelationships previously found in the periodic chart.

 The resulting 3-D form has three parts looping outwards from a relatively central point.

 The elements in Groups 0, Ia, IIa, IIIb, IVb, Vb, and VIIIb are in the narrowest and tallest part, which forms a tube
in the upper part, topped by a `crown' of Hydrogen.

 From the lower part of this component the sides branch to a more lengthy loop showing groups IIIa, IVa, Va, VIa,
VIIa, VIII, Ib, and IIb. From the lower half of this, a third, and longest loop protrudes, the f-block.

The Periodic Table

 The Elements are arranged in order of their increasing atomic number

 Periodic Law states that “the properties of the elements are periodic Functions of their atomic numbers.

 The Periodic Law tells us that if the elements are arranged in order of increasing atomic number, periodically we
encounter elements that have similar chemical and physical properties.

Parts of the Periodic Table

 The vertical columns are referred to as Group or Families

 Elements within a group have similar chemical and physical properties

  Periods – horizontal rows of elements

 Groups – elements in the same vertical columns; have similar chemical properties

Groups

 Table of common charges formed when creating ionic compounds.

Group Charge

Alkali Metals (1A) 1+

Alkaline Earth Metals (2A) 2+

Halogens (7A) 1-

Noble Gases (8A) 0

Metal

 An element that has the characteristic properties of luster, thermal conductivity, electrical conductivity, and
malleability.

Nonmetal

 An element characterized by the absence of the properties of luster, thermal conductivity, electrical conductivity,
and malleability.

Distinguishing Electron

 Last electron added to the electron configuration for an element when electron subshells are filled in order of
increasing energy.

 This last electron is the one that causes an element’s electron configuration to differ from that of an element
immediately preceding it in the periodic table.

 A system based on selected physical properties of the elements, in which they are described as metals or
nonmetals.

 A system based on the electron configurations of the elements, in which elements are described as noble-gas,
representative, transition, or inner transition elements.

Classification By Physical Properties

 Non-metal

 Metal
Classification By Electronic Properties

1. Representative Elements

- s area and first 5 columns of p area

- metals and non-metals

2. Noble Gas

- Last column of p area + He (s area)

- Non-metals

3. Transition Elements

- d area

- metals

4. Inner traansition elements

- f area

- metals

Groups with Special Names

1. Alkali Metal

2. Alkaline Earth Metal

3. Halogens

4. Noble gas