Lesson 1: Functional Groups

Functional Groups
● Atoms that exhibit a characteristic reactivity
● Have characteristic names that often carry over in the naming of individual compounds
● A specific structural arrangement of atoms or bonds that imparts o characteristic
chemical reactivity to the molecule
● Key structural elements that define how organic molecules react

Family name General Formula Suffix

alkane RH -ane

alkene 𝑅2𝐶 = 𝐶𝑅2 -ene

alkyne RC≡CR -yne

alcohol ROH -ol

thiol RSH -thiol

ether ROR ether

aldehyde -al

ketone -one

carboxylic acid -oic acid

esters -oate
 amines and amides -amine

Notes for remembering:

● Alkanes, alkenes, and alkynes - only have C and H, the difference is the presence of
bonds: alkane (single bond), alkene (double bond), alkyne (triple bond)
● Alcohols - single bond OH (magkasama ung OH, hindi magkahiwalay na nakakabit sa
isang carbon)
● Thiol- nag-iisang may Sulfur (S)
● Ether- may oxygen sa pagitan ng 2 alkyl groups (aka alkane, -ene, and -yne)
● Aldehyde- double bond [O] and [H] ay nakaattach sa carbon atom (di magkasama O and
H, separately attached sila kaya double bond ung O)
● Ketone- double bond [O] only, difference nya sa aldehyde is walang kasamang [H] na
nakaattach sa carbon
● Carboxylic acid- nagkababy ketone (=O) at alcohol (-OH); may double bond [O] at [OH]
na nakaattach sa isang carbon atom (sa iisang carbon atom sila nakaattach)
● Esters- may nakattach na double bond [O] at single bond [O] sa iisang carbon
● Amines and amides- presence of nitrogen
● Amide has a nitrogen attached to a carbonyl group (carbon atom double bonded to an
oxygen atom)
Alcohols
● Class of organic compounds characterized by one or more hydroxyl (-OH) groups
attached to a carbon atom of an alkyl group (hydrocarbon chain)
● May be considered as organic derivatives of water
● Covalent molecules (do not behave like bases such as NaOH and KOH which are ionic
compounds)
● Among the most common organic compounds
● Used as sweeteners, perfume making, and valuable intermediates in the synthesis of
other compounds
● Methanol- used as a solvent, raw material for formaldehyde, and special resins
● Ethanol (ethyl alcohol)- important alcohol for human use; produced by some species of
yeast and found in alcohol and beer
● Most alcohols are colorless liquids or solids at room temperature
Naming of Alcohols
 ● Comes from the hydrocarbon (alkyl group) from which it was derived. The final -e (eg.
pentane) is replaced by -ol (eg. pentanol).
● The carbon atom to which the -OH group is bonded is indicated by a number placed
before the name. (eg. 2-pentanol)
Ethers
● Contain the functional group -O-
● Do not have a designated suffix like the other types of molecules
● Diethyl ether
○ most widely used ether which is first used as an anesthetic in 1846
○ Used primarily as solvents for gums, fats, waxes, and resins
● Tertiary-butyl methyl ether
○ used as an additive for gasoline
○ Classified as an oxygenate due to its capacity to increase the oxygen content of
gasoline
Naming of ethers:

○ IUPAC- the oxygen atom and the smaller carbon branch are named as an alkoxy
substituent (yung branch na shaded na red sa example above is the “alkoxy”.
Madedetermine kung ano ung alkoxy by the smaller carbon branch or branch na
may lesser carbons. In this case, the smaller carbon branch is a methane, take
the prefix {meth-} then add the suffix {-oxy}, so magiging methoxy. Last step, add
sa name ung longer carbon chain, which in thise case is ethane. Ang IUPAC
name ng compound above is: methoxyethane
○ Common name- the two branches connected to the oxygen atom are named
separately followed by “ether”. Follow the naming rules for alkyl groups (chains
are named alphabetically). The common name of the compound above is
ethylmethyl ether
Aldehydes
● Contains a carbon-oxygen double bond (carbonyl group)
● The carbonyl group is bonded to atleast one hydrogen atom
● -CHO
● Its geometry is trigonal planar
● Commonly prepared by the oxidation of alcohols whose -OH functional group is located
at the end of the carbon chain
● Formaldehyde (HCHO)
○ a colorless gas with a pungent and irritating odor
○ Causes coagulation of proteins so it kills bacteria and stops many of the
biological processes that cause tissue to decay
○ Used for preserving tissue specimens and embalming bodies
○ Used to sterilize soil and other materials
 ○ Used in the manufacture of bakelite, a hard placing with high chemical and
electrical resistance
● Formalin- contains about 37% formaldehyde
Ketones
● Like aldehydes, it contains a carbon-oxygen double bond, however, instead of being
attached to a hydrogen atom, it is bonded to two other carbon atoms
● -CO-
● Its geometry is trigonal planar
● Synthesized from alcohols that have their -OH groups in the middle of the carbon chain
● Acetone (CH3COCH3)
○ Also known as dimethyl ketone
○ Made commercially by fermenting corn or molasses or by oxidation of 2-propanol
○ A colorless liquid
○ Solvent for lacquer, cellulose acetate, cellulose nitrate,. And many others
Carboxylic acids
● Contain a carbonyl group that contains an oxygen double bond and an oxygen single
bond that is attached to a hydrogen atom
● Weak acids, meaning they are not 100% ionized in water
● Generally about 1% of a carboxylic acid dissolved in water are ionized at any given time
● Prepared by the oxidation of aldehydes or alcohols whose -OH functional group is
located at the end of the carbon chain
● Formic acid (HCO2H)
○ Simplest carboxylic acid
○ Known since 1670
○ Comes from the Latin word formicus (ant)
○ First isolated by the distillation of red ants
○ Partially responsible for the pain and irritation of ant and wasp stings
○ Responsible for a characteristic odor of ants that can be sometimes detected in
their nests
● Acetic acid (CH3CO2H)
○ Constitutes 3-6% vinegar
○ Has a penetrating odor and produces painful burns
○ An excellent solvent for many organic and some inorganic compounds
○ Essential in the production of cellulose acetate, a component of many synthetic
fibers such as rayon
Esters
● Compounds that can be prepared by the reaction of a carboxylic acid with an alcohol
● They do not have hydrogen bonds between molecules and thus they have lower vapor
pressure than alcohols and carboxylic acids
● Contains a carbonyl group that contains an oxygen double bond and an oxygen single
bond that is attached to another carbon atom
● Produced by the reaction of acids with alcohols
● Cause of the distinctive and attractive odors and flavors of many flowers, perfumes, and
ripe fruit
 ● Most important natural esters:
○ Fats - lard, tallow, butter
○ Oils - linseed, cottonseed, olive oil
Amides
● Amide that has a single attached carbonyl group
● Also used to refer to the conjugate bases of amine (sodium amide) though it is
sometimes differentiated by being referred to as “amide bases”
● Lactam - cyclic amide
Isomers
● Molecules that have the same molecular formula, but have different arrangement of
atoms in space
Types of Structural Isomerism
1. Chain Isomerism
● Arise because of the possibility of branching in carbon chains
2. Position Isomerism
● The basic carbon skeleton remains unchanged but important groups are moved around
on that skeleton
● Can also appear in benzene rings
3. Functional Isomerism
● The isomers contain different functional groups from different families of compounds (or
homologous series)
Polymers
● Any class of natural or synthetic substances composed of very large molecules
(macromolecules)
● Materials made of long, repeating chains of molecules
● Monomers- smaller chemical units from macromolecules
● Copolymers- most natural and synthetic polymers are made up of two or more different
types of monomers
● Natural polymers - rubber and wood; synthetic polymers- plastics
Herman Staudinger
● A professor of organic chemistry at the University of Applied Sciences in Zurich
● The father of modern polymer development
● Awarded a Nobel Prize in Chemistry in 1953 “for his discoveries in the field of
macromolecular chemistry”
Polymerization
● The method of creating synthetic polymers by combining monomers into a chain held
together by covalent bonds.
Biomolecules
Dehydration Synthesis & Hydrolysis
● Two common reactions involving water that proteins, fats, and carbohydrates all use to
assemble and disassemble molecules
● Dehydration synthesis- occurs when two hydrogens and one oxygen are removed from
two separate molecules and the result is a single molecule and a water
 ● Hydrolysis- occurs when one large molecule is split (lysis means splitting) inro two
molecules with the addition of water and energy
1. Proteins
● The primary building materials of the body
● Amino acids- the basic building blocks of proteins
● Peptides- chain of amino acids
2. Lipids (Fats)
● Primary long-term energy storage molecules of the body
● Very compact and lightweight, thus an efficient way to store excess energy
● Made up of glycerol which is attached to 1-3 fatty acid chains
● Saturated fatty acids- have no double bonds and hold the maximum number of
hydrogens; the carbons are saturated with hydrogen; less healthier than unsaturated
fatty acids
● Unsaturated fatty acids- have some double bonds and hold fewer hydrogens
3. Carbohydrates
● Sugar is a source of quick energy for the body because it is easily metabolized (broken
down)
● Glucose- a 6-carbon sugar
● Starch
○ a polysaccharide which plants create for energy storage
○ The most common carbohydrate in the human diet
● Glycogen
○ A complex storage molecule made from glucose using insulin
○ Starch in animals
● Glycolysis
○ A process that breaks down glucose in order to release energy stored in the
carbon-carbon bonds
4. Nucleic Acids
● Contains the genetic code or all the information necessary to build the body
● Nucleotide- the basic unit of nucleic acids which is composed of a sugar-phosphate
backbone attached to one of four nitrogenous bases: cytosine, guanine, adenine, or
thymine
● Base Pairs: C-G & A-T (DNA) or C-G & A-U (RNA)

Biomolecules: Nucleic Acids

Biomolecules
● Any of numerous substances that are produced by cells and living organisms
● Have a wide range of sizes and structures and perform a vast array of functions
● Four main types:
○ Carbohydrates
○ Lipids
○ Nucleic acids
○ Proteins
Nucleic Acids
 ● Building blocks: nucleotides
● DNA and RNA
● Have the unique function of storing an organisms’s genetic code
● Naturally occurring chemical compounds that are capable of being broken down to yield
phosphoric acid, sugars, and a mixture of organic bases (purines and pyrimidines)
● The main information-carrying molecules of the cells
Nucleotide
● Each nucleotide consists of a nitrogen-containing aromatic base attached to a pentose
sugar, which is attached to a phosphate group
● Synthesized from readily available precursors in the cell
● Purines (two ring structure):
○ Adenine
○ Guanine
● Pyrimidines:
○ Cytosine
○ Thymine (found in DNA)
○ Uracil (found in RNA)
● Adenosine and thymine pairs through two hydrogen bonds
● Guanine and cytosine pairs through three hydrogen bonds
● Nucleoside
○ A sugar without an attached phosphate group
● Phosphodiester bonds
○ Linkages where the phosphate group connects successive sugar residues by
bridging the 5′-hydroxyl group on one sugar to the 3′-hydroxyl group of the lnext
sugar in the chain
● Kinase
○ Special enzyme that adds two phosphate groups using adenosine triphosphate to
form ribonucleoside triphosphate (immediate precursor of RNA)
Deoxyribonucleic acid (DNA)
● Master blueprint for life
● Constitutes the genetic material in all free-living organisms and most viruses
● Its pentose sugar does not have a hydroxyl group on the 2’ carbon of the sugar ring
● Gene
○ Section of a double-stranded DNA
Parts of a DNA:
 ● Purines (A and G) have two ring structures, pyrimidines (T and C) have one
● C and G have triple bonds, A and T have two
● A 3’end is attached to a sugar, a 5’ end is attached to a phosphate
Ribonucleic acid (RNA)
● Genetic material of certain viruses
● Plays an important role in making of proteins
● A single-stranded nucleic acid polymer of A, C, G, and U joined through a backbone of
alternating phosphate and ribose sugar residues
● The first intermediate in converting the information from DNA into proteins essential for
cell function
● Also serve direct roles in cellular metabolism
● Made by copying the base sequence of a gene into a piece of single-stranded nucleic
acid (transcription)
● Transcription is catalyzed by RNA polymerase
Types of RNA
A. Messenger RNA (mRNA)
● Delivers the information encoded in one or more genes from the DNA to the ribosome
● Cap
○ A structure in eukaryotes where the 5’-triphosphate residue is further esterified
● Splicing
○ An RNA makes an exact copy of itself
B. Ribosomal RNA (rRNA)
● Structural components of ribosomes
● Form extensive secondary structures and play an active role in recognizing conserved
portions of mRNA and tRNA
● Assist with the catalysis of protein synthesis
 ● Transcribed in the nucleolus
C. Transfer RNA (tRNA)
● Carries individual amino acids into the ribosome for assembly into the growing
polypeptide chain
● Codon
○ A sequence of three consecutive nucleotides in a DNA or RNA molecule that
codes for a specific amino acid
○ There are 61 codons used to code amino acids
● aminoacyl tRNA synthetases
○ Enzymes that load amino acids onto tRNAs
D. Ribozymes
● Discovered by Thomas Cech and Sidney Altman
● Certain RNAs that show enzymatic activity
E. Viral genomes
● Many viruses use RNA for their genetic material
● In some viruses, their entire genetic material is encoded in a single RNA molecule
● Reverse Transcriptase
○ Used by many RNA viruses (eg HIV) to replicate the virus through a DNA
intermediate
F. Small nuclear RNAs (snRNA)
○ RNA splicing

Biomolecules: Proteins
Protein
● Building blocks: amino acids
● Highly complex substance that is present in all living organisms
● Of great nutritional value and are directly involved in the chemical process essential for
life
● Derived from the Greek word prōteios meaning “holding first place” (Jöns Jacob
Berzelius)
● Proteins of one species differ from those of another species (species-specific)
● Peptide - small protein
● Animals can synthesize serine but not cysteine or cystine
● Have neither acidic nor basic properties
● -ine general prefix for amino acids (not all)
● Arginine is found in all proteins
Enzymes
● -ase is the general suffix for enzymes
● Catalysts of all metabolic reactions
● Enable an organism to build up the chemical substances necessary for life
Hemoglobin
● Respiratory protein
● Acts as oxygen carrier in the blood, transporting oxygen from the lungs to body organs
and tissues
Collagen
● Protein of the connective tissue of animals
Biomolecules: Carbohydrates
Carbohydrates
● Building blocks: monosaccharides
● Class of naturally occurring compounds and derivatives formed from them
● “Watered carbon”
● General formula: CxH2O
● The most abundant and widespread organic substances in nature
● Essential constituents of all living things
● Formed by green plants from carbon dioxide and water during the process of
photosynthesis
● Serve as energy sources and as essential structural components in organisms
● The generic nomenclature ending for monosaccharides is -ose
● Frequently referred to as aldopentoses or ketopentoses/ aldohexoses or ketohexoses
Major Carbohydrate Groups
1. Monosaccharides
● Simple sugars
● Three of the most important:
○ Glucose - also known as dextrose, grape sugar, and corn sugar
○ Fructose - fruit sugar
○ Galactose - usually combined with other simple sugars in order to form larger
molecules
● The degree of sweetness of various sugars differs according to the arrangement of the
hydroxyl groups that compose part of the molecular structure
● It is not yet possible to predict the taste of sugar by knowing its specific structural
arrangement
● The energy in the chemical bonds of glucose indirectly supplies most living things with a
major part of the energy that is necessary for them to carry on their activities
2. Disaccharides
● Two simple sugars
● Examples;
○ Sucrose (table sugar)- glucose and fructose
○ Lactose (milk sugar)
○ maltose
3. Oligosaccharides
● Consist of three to six monosaccharide units
● Infrequently found in natural sources although a few plant derivatives have been
identified
4. Polysaccharides
● “Many sugars”
● Large sugar molecules that may consist as many as 10,000 monosaccharide units
● Vary considerably in size, structural complexity, and sugar content
● Examples:
 ○ Cellulose - the principal structural component of plants; Most common
polysaccharide
○ Starch (stercan meaning “to stiffen”) - found mostly in seeds, roots, and stems
where it is stored as an available energy source for plants
○ Glycogen
■ found in animals
■ formed in the liver and muscles and is stored as an energy source
■ a highly branched molecule that has a superficial resemblance to that of
the amylopectin component of starch
■ Glycogen is rapidly broken down to glucose under conditions of stress in
animals
■ Acts as an immediate carbohydrate reserve
■ When adequate food supplies are available, both glycogen and fat
reserves of the body increase (it decreases rapidly when the food intake
falls below the minimum energy requirement)
Biological Significance of Carbohydrates:
● Carbohydrates are generally available as an immediate energy source for both animals
and plants
● Glucose, the prevalent uncombined sugar circulating in the blood of higher animals is
essential to cell function
● The proper regulation of glucose metabolism is of paramount importance to survival
Role of Carbohydrates in the Biosphere
● Photosynthesis - results in both the release of oxygen gas into the atmosphere and the
transformation of light energy into the chemical energy of carbohydrates
● The energy stored in plants during the formation of carbohydrates is used by animals to
carry out mechanical work and to perform biosynthetic activities
● During photosynthesis, an immediate phosphorus containing product (3-phosphoglyceric
acid) is formed, which is then transformed into cellulose, sucrose, starch, or
polysaccharides
Role of Carbohydrates in Human Nutrition
● Calorie - the amount of heat necessary to raise the temperature of 1,000 grams of water
from 15 to 16 C (kilocalorie)
● The total caloric requirement for an individual generally ranges between 2,000 and 4,000
calories per 24-hour period
● A high proportion of an individual’s daily energy requirement may be supplied by
carbohydrates, with most of the remainder coming from a variety of fat resources
Role of Carbohydrates in Energy Storage
● Starches - major plant-energy-reserve polysaccharides used by humans consist of a
mixture of two components:
○ Amylose - has a straight-chain or linear structure
○ Amylopectin - has a branched-chain structure and is a somewhat more compact
molecule
● Parenchymatous cells
○ Specialized cells which functions as storage of starch in plants
 ○ Can be found in root vegetables and tubers
● The highest concentration of starch is found in seeds and cereal grains (contains up to
80% of their total carbohydrates)
● Most plant species store starch as approximately 25% amylose and 75% amylopectin
● Some varieties of corn have been developed to produce starch that contains 70%
amylose, which is more easily digested by humans than amylopectin
● Some plants (Jerusalem artichoke and rye grass) form polysaccharides composed of
fructose than glucose
● Fructose polysaccharides cannot be digested by higher animals
Role of Carbohydrates in Plant and Animal Structure
● Most carbohydrates occur as structural components in the cell walls of plants
● Chitin - found in insects and other arthropods
Classes of Carbohydrates:
Monosaccharides
Naturally-occurring Monosaccharides:

● D-glucose
○ From the Greek word “glykys” meaning sweet
○ sucrose, cellulose, starch, glycogen
○ Constituent of the two most common disaccharides: sucrose and lactose
○ Generally prepared from either potato starch or cornstarch
● D-mannose
○ seeds, ivory nut
● D-fructose
○ sucrose, artichokes, honey
● D-galactose
○ lactose, agar, gum arabic, brain, glycolipids
○ Common constituent of both oligosaccharides and polysaccharides
○ Occurs in glycolipids (found in the brain and other nervous tissues of most
animals)
○ Galactose is generally prepared by acid hydrolysis (breakdown involving water)
of lactose (composed of galactose and glucose)
○ Animals do not require galactose in the diet
○ Galactosemia - hereditary defect where a human does not have the ability to
metabolize galactose
● D-xylose (pentose)
○ corncobs, seed hulls, straw
○ Found in most plants in the form of a polysaccharide called xylan
● L-arabinose (pentose)
○ mesquite gum, wheat bran
● D- ribulose
○ intermediate in photosynthesis
● 2-deoxy-D-ribose
○ constituent of deoxyribonucleic acid
 ● L-fucose
○ marine algae, seaweed
● L-rhamnose
○ poison-ivy blossom, oak bark
● D-mannoheptulose
○ avocado
● D-altroheptulose
○ numerous plants
Chemical reactions of monosaccharides
● As sugars contain free aldehyde or keto groups they can be oxidized to form products
which was the basis for detecting reducing sugars]
● Glucose oxidase - used for the analysis of blood and urinary glucose which catalyzes the
oxidation of glucose to products that include hydrogen peroxide
● Aldonic acids
○ formed when the aldehyde group of glucose reacts with alkaline iodine
○ Ascorbic acid - essential dietary component for humans and guinea pigs
○ Does not occur with keto sugars
● Alditols
○ Sugar alcohols
○ Compounds formed by reducing an aldehyde or keto group
○ Sorbitol (d-glucitol) - reduction of the aldehyde carbon of D-glucose; also formed
when L-sorbose is reduced
○ Mannitol - results in the reduction of mannose
○ Dulcitol - results in the reduction of galactose
Disaccharides and oligosaccharides
Disaccharides
● A specialized type of glycoside in which the anomeric hydroxyl group of one sugar has
combined with the hydroxyl group of a second sugar with the elimination of water
● Only a limited number of disaccharides are of biological significance
● The unusual type of linkage between the two anomeric hydroxyl groups of glucose and
fructose means that neither a free aldehyde group nor a free keto group is available to
react unless the linkage between the monosaccharides is destroyed (this makes sucrose
a nonreducing sugar)
● Sucrose solutions do not exhibit mutarotation which involves the formation of an
asymmetrical center at the aldehyde or keto group
● The change in the sign of optical rotation from positive to negative makes sucrose an
invert sugar
● Cane final molasses / blackstrap molasses
○ The residual syrupy material from the harvest of sucrose crystals
○ Used in the preparation of antibiotics, sweetening agents, and in the production
of alcohol by yeast fermentation
● Trehalose
○ Composed of two molecules of α-D-glucose
○ Nonreducing sugar
 ○ Present in young mushrooms and in the resurrection plant Selaginella
○ Found in the circulating fluid (hemolymph) of many insects which may be used to
provide an immediate source of energy for the insects
● Lactose
○ Found mostly common in human diets
○ A reducing sugar
○ Constitutes about 7% of human milk
○ Consists of two aldohexoses:
■ β-D-galactose
■ glucose
● Maltose
○ Not found by itself in nature
○ A reducing sugar
○ Product of the enzymatic breakdown of starches during digestion
○ Readily hydrolyzed to glucose and can be metabolized by animals
Polysaccharides (glycans)
● There are not many polysaccharides composed of more than three or four different
monosaccharides; most contain one or two
Homopolysaccharides
● Polysaccharides formed from only one type of monosaccharide
● Have well-defined chemical structure
● Glycogen synthesis and breakdown are controlled by hormones
● Examples: (polysaccharide - sugar component - function - sources)
○ Cellulose - glucose - structural - found in plants
○ Amylose - glucose - food storage -starches
○ Chitin - N-acetylglucosamine - structural - insect and crustacean skeleton
○ Inulin - fructose - food storage - artichokes, chicory
○ Xylan - xylose - structural - all land plants
○ Glycogen - glucose - food storage - liver and muscles of animals
○ Amylopectin - glucose - food storage - starches
○ Dextran - glucose - unknown - bacterial
○ Agar - galactose - structural - seaweeds
Heteropolysaccharides
● Polysaccharides containing two or more different types of monosaccharides
● Closely associated with lipids or proteins
● The most important ones are found in the connective tissues of all animals
● Major types:
○ Connective-tissue polysaccharides
○ Blood group substances
○ Glycoproteins (carbohydrates and proteins)
○ Glycolipids (carbohydrates and lipids)
● Hyaluronic acid
○ The major component of join fluid in animals that functions as a lubricating agent
and shock absorber
Biomolecules: Lipids
Lipids
● Building blocks: glycerol
● Diverse group of fats, oils, and hormones
● Hydrophobic
● Triglycerides
○ Sequestered as fat in adipose cells,which serve as the energy-storage depot for
organisms and also provide thermal insulation
● Steroid hormones
○ Chemical messengers between cells, tissues, and organs
● Amphipathic lipids
○ some parts are hydrophilic and other parts are hydrophobic
○ Spontaneously form ordered molecular aggregates; hydrophilic ends are on the
outside and the hydrophobic parts are on the inside
● Major Groups of Lipids:
○ Fatty acids
○ Fatty acid derivatives
○ Cholesterol
○ Cholesterol derivatives
○ Lipoproteins
Fatty acids
● amphipathic
● Rarely occur as free molecules in nature
● usually found as components of many complex lipid molecules such as fats (energy
storage compounds) and phospholipids (primary lipid components of cellular
membranes)
● Low water solubility
● The most chemically reactive portion is the acidic carboxyl group (COOH)
● Reacts with alcohol to form esters
● Members of carboxylic acids
● the more highly unsaturated the fatty acid, the more easily it is oxidized
● Acyl group
○ The fragment of a carboxylic acid not including the hydroxyl group
Saturated fatty acids
● All of the hydrogen atoms are each bonded to a carbon
Unsaturated fatty acids
● there is at least one double bond within the fatty acid chain
Essential fatty acids
● Fatty acids that animals need in their diet but cannot synthesize on their own
Trans polyunsaturated fatty acids
● Produced by microorganisms in the gut of ruminant animals (cows and goats)
● Produced synthetically by partial hydrogenation of fats and oils in the manufacture of
margarine
Polymorphs
● The details of the molecular packing may vary which gives rise to these different crystal
forms
Triglycerides
● The main source of fatty acids
● Hydrophobic
● Soluble in only some organic solvents
● Neutral lipids (possess no electric charge)
● Generally called fats
● Consist of three fatty acid molecules, each linked by an esterbon to one of the three OH
groups
● Principal means of storing fatty acids in biological systems
● Example: tristearin (simple triglyceride)
● Mixed triglyceride
○ When two or more triglycerides in a given molecule are different
Waxes
● consist of a long-chain fatty acid linked through an ester oxygen to a long-chain alcohol
● completely water-insoluble and generally solid at biological temperatures
● Hydrophobic
● serve as energy-storage substances in plankton
Lipases
● Pancreatic enzymes
Lipoproteins
● Large molecular complexes that are transported in the lymph and blood to recipient
organs
Three Principal Classes of Lipids that form the bilayer matrix of biological membranes
A. Glycerophospholipids
● Most abundant in biological membranes
● ampiphatic
B. Sphingolipids
C. Sterols
● a prominent member of isoprenoids that are widely distributed in nature
● major components of biological membranes in eukaryotes but are rare in prokaryotes
● Cholesterol - principal sterol in animals
● Ergosterol - principal sterol in fungi
● Sitosterol - principalsterol in plants
● Bile acids
○ Detergents that emulsify fats in the gut during digestion

Intermolecular Forces
● The properties of liquids are intermediate between gases and solids
● The properties of liquids are more similar to solids
Intramolecular forces
● The covalent bonds that hold atoms together in molecules and polyatomic ions
Intermolecular forces
● Hold molecules together in a liquid or solid
● Generally much weaker than covalent bonds
● Determine bulk properties:
○ Melting point of solids
○ Boiling point of liquids
● Electrostatic in nature (stationary electric charges)
● Arise from the interaction between positively and negatively charged species
● The sum of both attractive and repulsive components
● Very important in keeping the molecules of solids and liquids together
● Important for gases only at very high pressures
● Non polar molecules
○ symmetric with no unshared electrons (CO2)
● Polar molecules
○ symmetric, either containing lone pairs of electrons on a central atom or having
atoms with different electronegativities bonded.
● Van der Waals forces
○ London dispersion forces
○ Dipole-dipole forces
Kinds of Intermolecular Forces
1. Dipole-dipole Interactions
● The bonded atoms have localized fractional charges that are equal but opposite
● Net dipole moment
○ The structure of a molecule such that the individual bond dipoles do not cancel
one another
● Molecules with net dipole moments tend to align themselves so that the positive end of
one dipole is near the negative of another
● Arrangements where the positive and negative ends are adjacent are more stable than
two positive or negative ends are adjacent
● Molecules in a liquid always experience both attractive and repulsive dipole-dipole
interactions simultaneously because they move freely and continuously
● The attractive dipole-dipole interactions dominate
● The strength of the intermolecular interactions increases as the dipole moment of the
molecules increases
● Dipole-dipole interactions are significantly stronger in small polar molecules than London
forces
2. London Dispersion Forces
● Fritz London (1900-1954)
○ German physicist who proposed that temporary fluctuations in the electron
distributions within atoms and nonpolar molecules could result in the formation of
short-lived instantaneous dipole moments which produced attractive forces called
London dispersion forces between nonpolar substances
● Force exclusive for nonpolar substances
● Induced dipole
 ○ The temporary formation of a dipole due to the effect that the first atom causes
on its adjacent atom
● Polarizability
○ The ease of deformation of the electron distribution in an atom or molecule
○ Heavier substances are easier to deform or more polarizable than lighter ones
○ London dispersion forces get stronger with increasing molecular size
○ Determines how a substance interacts with ions and species that possess
permanent dipoles
○ Responsible for the general trend toward higher boiling points with increased
molecular mass and greater surface area in a homologous series of compounds
● The strength of these forces depend significantly on molecular shape because it
determines how much of one molecule can interact with its neighboring molecules at any
given time
● Larger molecules have stronger London forces than smaller molecules
● Polar and nonpolar forces are attracted to one another by London dispersion forces
3. Hydrogen Bonds
● Electronegative atoms
○ O, N, F
○ Cl and S (to a much lesser extent)
○ Tend to exhibit unusually strong intermolecular interactions
● Lightest elements of groups 14-17 are anomalously high for compounds with such low
molecular masses
● The very strong dipole-dipole interactions that result from the combination of large bond
dipoles and short dipole-dipole distances
● Hydrogen bond donor
○ Elements O, N, and F
● Hydrogen bond acceptor
○ The atom that has the lone pair of electrons

Properties of Liquids
1. Surface Tension
● Measure of the elastic force on the surface of a liquid
● Amount of energy required to stretch or increase the surface of a liquid by a unit area
● Manifested as some sort of skin or elastic film in the surface of a liquid or in a drop of
liquid
● Allows needles and paper clips to float in water
● Explains why drops of water are spherical in shape
● Molecules within a liquid are pulled in all directions by intermolecular forces
● Molecules at the surface are pulled downward towards other molecules, not away from
the surface
● Strong intermolecular force = high surface tension
2. Capillary Action
● Tendency of a liquid to rise in narrow tubes or be drawn into small openings
● Also known as capillarity
 ● Result of intermolecular attraction between the liquid and solid materials
● Types of forces in capillary action:
○ Cohesion- intermolecular attraction between similar molecules
○ Adhesion- attraction between dissimilar molecules
● Meniscus
○ Shape of the surface of a liquid in a cylindrical container
○ Convex- cohesive forces are greater than the adhesive forces
○ Concave- cohesive forces are lesser than the adhesive forces
3. Viscosity
● The resistance of a liquid to flow
● The thickness or thinness of a liquid
● Stronger intermolecular force = higher viscosity
4. Vapor Pressure
● Pressure exerted by vapor when in equilibrium with liquid or solid
● Strong intermolecular forces = low vapor pressure
5. Boiling Point
● The temperature at which its vapor pressure is equal to the external or atmospheric
pressure
● Normal boiling point
○ The temperature at which a liquid boils under 1 atm
● Greater intermolecular force = higher energy needed to increase the kinetic energy of
the molecules to break the forces
6. Heat of Vaporization
● Amount of heat required to vaporize one mole of a substance at its boiling point
● Boiling point increases as heat of vaporization increases
Properties of Water
● Colorless, odorless, and tasteless liquid
● Turns to ice at 0 degrees celsius and 1 atm
● Turns to steam or gas at 100 degrees celsius
● Water is a good solvent
● Water has a high specific heat
● The boiling point of water is unusually high
● Solid water is less dense and floats on liquid water
● The molecules in solid water are farther apart than liquid water
Specific heat
● Amount of heat or energy needed to raise the temperature of one gram of a substance
by 1 degree C
Types of Solids
1. Crystalline solids
● Highly regular arrangement of particles
● Have well-defined crystal lattice
Types of Crystalline Solids
● Ionic
○ Ions
 ○ Ionic
○ Hard, high melting point
○ Insulating as solid but conducting when dissolved (in water)
● Molecular
○ Discrete molecules
○ Dipole-dipole or London dispersion
○ Soft; low melting point
● Metallic
○ Metal atoms
○ Delocalized covalent
○ Wide range of hardness and melting points
● Network
○ Nonmetal atoms
○ Directional covalent
○ Hard, high melting point
● Group 8A
○ Noble gases
○ London dispersion forces
○ Very low melting point:
2. Amorphous solids
● Considerable disorder in the structure of particles
● Formed rapidly that its constituents do not have time to align or organize into a more
crystalline lattice
Lattice
● A three dimensional system of points designating the positions of the components (ions,
atoms, or molecules) that make up a crystal
● Kinds (lattice or unit cell?):
○ Cubic
○ Tetragonal
○ Monoclinic
○ Hexagonal
○ Rhombohedral
○ Triclinic
○ Orthorhombic
Unit cell
● Smallest repeating unit of lattice

Phase Changes and Phase Diagrams

Phase Change
● Transformations of matter from one physical state to another
● Occur when energy is added or removed from a substance
● Characterized by changes in molecular order
● Greatest order- solid
● Greatesr disorder- gases
Types of Phase Changes
● Melting- solid to liquid
● Freezing- liquid to solid
● Vaporization/Evaporation - liquid to gas
● Condensation- gas to liquid
● Sublimation- solid to gas
● Deposition- gas to solid
Phase Diagrams
● Graphical representation of the physical states of a substance under different conditions
of temperature and pressure
● Gives possible combinations of pressure and temperature at which certain physical
state/s a substance would be observed
● Plots of pressure (atm) versus temperature (Celsius or Kelvin)
Features of a Phase Diagram
1. The three area
● Marked solid, liquid, and vapor
2. The Three Lines
● Lines that serve as boundaries between physical states
● Represent the combination of pressure and temperature at which two phases can exist
in equilibrium
● Define phase change points
3. Melting/Freezing Curve
● Represents the transition between liquid and solid states and vice versa
● Show the effect of pressure on the melting point of the solid
● There is equilibrium between the solid and liquid anywhere on this line
4. Vaporization/Condensation Curve
● Represents the transition between gaseous and liquid states
● Shows the effect of pressure on the boiling point of the liquid
● There is equlibrium between liquids and vapor anywhere on this line
5. Sublimation/Deposition Curve
● Represents the transition between gaseous and solid states
● Represents the effect of increased temperature on a solid at a very low constant
pressure
6. Triple Point
● The combination of pressure and temperature at which all three phases of matter are at
equilibrium
● The point on a phase diagram at which three states of matter coexist
7. Critical Point
● Terminates the liquid/gas line
● Set of temperature and pressure on a phase diagram where the liquid and gaseous
phases of a substance merge together into a single phase
8. Supercritical fluid
● The merged single phase beyond the temperature of the critical point
Physical Properties and Types of Solutions, and Energy of Solution
Formation

Mixture
● A combination of two or more substances that do not combine chemically but
remain the same individual substances
● Can be separated by physical means
Two Types of Mixtures
● Heterogeneous
○ “Hetero” means different
○ Consists of visibly different substances or phases
○ Can be separated by filtering
● Homogeneous
○ “Homo” means the same
○ Has the same uniform appearance and composition throughout
○ Maintain one phase of matter
○ Commonly referred to as solutions
Solution
● A mixture of two or more substances that is identical throughout
● Can be physically separated
● Composed of solutes and solvents
Solutes
● The substance being dissolved
● Usually present in a smaller amount
Solvents
● The substance that dissolves the solute
● Dissolving medium
● The largest part of the solution
Types of Solutions
● Gaseous solutions
● Liquid solutions
● Solid solutions

SOLUTE SOLVENT SOLUTION EXAMPLE

GAS GAS GAS Oxygen in Nitrogen

GAS LIQUID LIQUID Carbon dioxide in

water

GAS SOLID SOLID Hydrogen in

Palladium

LIQUID LIQUID LIQUID Ethanol in water

 LIQUID SOLID SOLID Mercury in Silver

SOLID LIQUID LIQUID Salt in water

SOLID SOLID SOLID Copper in tin (bronze)

*the phase of the solvent determines the phase of the solution
The Energies of Solution Formation
Mixing
● Spontaneous process that increases the entropy of the solution
● Heat transfers are inevitable in order to form solutions by distributing the solute
molecules evenly within the solvent molecules
● ΔH
○ change in heat energy found by subtracting the enthalpy of the reactant from that
of the product: Hproducts - Hreactants= ΔHsoln
Endothermic reaction (positive)
● any chemical reaction that absorbs heat from its environment
Exothermic reaction (negative)
● chemical reactions that produce heat
Three Step Approach to Finding the Enthalpy of Solution
1. Each molecule of solute is Separated from each other (expand the solute), endothermic
reaction. (ΔH1)
2. Each molecule of solvent is separated from each other (expand solvent), endothermic
reaction. (ΔH2)
3. The molecules of solute and solvent react with each other and a solution will result.
exothermic reaction (ΔH3)
Instant Hot and Cold Packs
● practical aids which utilize the heat of chemical reactions during solution formation
● Hot Packs
○ consist of a pouch of water and a dry chemical, either magnesium sulfate
(MgSO4) or calcium chloride
● Cold packs
○ made of water and ammonium nitrate (NH4NO3)

Concentration of Solutions

Concentration of Solution
● Refers to the amount of solute in a given amount of solvent
% by mass/ weight
% by volume

Proof number
● Twice the alcohol (ethanol) content by volume
● Proof number = 2(% by volume)

Parts per million (ppm)

Mole Fraction
● Ratio of the number of moles of one component to the total number of moles in a
solution
● Represented by capital X

●
● The mole fraction of solute and solvent must be equal to 1

Molarity
● Ratio of the number of moles of solute per solution, which is mathematically expressed
as;

Molality
● Defined as the number of moles of solute per kilogram of solvent