CHEM 113: BIOCHEMISTRY

LECTURE 2: Functional Groups

___________________________________________________________________________________________________________

SIR. JESSIE MAGNO – DEPARTMENT OF CHEMISTRY

1ST SEMESTER | A.Y 2022 - 2023

UNIT EXPECTED OUTCOMES COMPOUND STRUCTURE

At the end of this unit, the students are expected to: Molecular
1 Classify accordingly the structure of different organic Formula –
compounds CH4 Methane
2 Categorize appropriately the IUPAC names of different
organic compounds
Complete
ORGANIC VS INORGANIC COMPOUNDS Structural
Formula –
• Organic Chemistry – Study of hydrocarbons (only Show all the Complete Structural Formula
carbon and hydrogen atoms) and their various atoms and
derivatives. bonds in a
• Inorganic Chemistry – Study of all substances other molecule
than hydrocarbons and their derivatives.
• Condensed Structural Formulas – Leave out some
BONDING CHARACTERISTICS OF CARBON ATOM bonds and/or atoms from the structural

• C-atom always makes total of 4 Bonds

• The sharing of four valance electrons requires the
formation of four covalent bonds which are
represented by four lines.

FUNCTIONAL GROUPS
NOMECLATURE/NAMING SYSTEM
• are groups of atoms in organic molecules that are
responsible for the characteristics, chemical reactions • IUPAC – International Union of Pure and Applied
of those molecules. Chemistry
• Simple molecules that contain the same functional o All names end with -ane
group in their structure can be expected to react in o Root part of an alkane’s name indicates how
similar ways. many carbon atoms it contains
• More complicated chemical molecules may contain • Scientist also rely on a combination of systematic,
more than one functional group within their structure. semisystematic, and common names to identify
organic compounds
HYDROCARBONS • Some organic compounds are best known for their
common names
• Carbon has 4 valence electrons, therefore will always • Branched-Chain Alkanes – One or more alkyl
form four covalent carbon-hydrogen bounds groups
o Remembering this will help you complete and o Hydrocarbon substituent
correct structures for organic molecules - Substituent: atom or group of atoms that
can take the place of a hydrogen atom on a
TYPES OF FORMULAS parent hydrocarbon molecule
o Consist of an alkane with one hydrogen removed
• Structural Formulas o Radicals
o Convenient to write o Change the suffix -ane from the parent structure
o Two-dimensional representations of three- to -yl
dimensional molecules
• Straight-Chain Alkanes
o Any no. of carbon atoms, one after the other, in a
chain
o Always end in -ane
o write the symbol for carbon as many times as
necessary to get the proper chain length
o Fill in with hydrogens and lines representing
covalent bonds
- Each covalent bond is equivalent to two
electrons ALKENES

• Said to be saturated compounds because they

contain a maximum no. of hydrogens
 CHEM 113: BIOCHEMISTRY
LECTURE 2: Functional Groups
___________________________________________________________________________________________________________
SIR. JESSIE MAGNO – DEPARTMENT OF CHEMISTRY
1ST SEMESTER | A.Y 2022 - 2023
• Alkenes and Alkynes – Contain double and triple
bonds
• They are said to be unsaturated compounds because
they contain fewer no. of hydrogens in their structure
ALKYNES
• Containing carbon-carbon triple covalent compounds
• Unsaturated compounds
• Not plentiful in nature
• Simplest alkynes are: ethyne, propyne, butyne
• Ethyne is commonly called acetylene
ALCOHOLS, PHENOLS AND THIOLS
• An alcohol is an organic compound in which an -OH
group is bonded to a saturated carbon atom
• A saturated carbon atom is a carbon atom that is
bonded to four other atoms
• The -OH group, the functional group is characteristic
of an alcohol, is called a hydroxyl group
NOMECLATURE FOR ALCOHOLS
• Common name exists for alcohols with simple
(generally C1 through C4) alkyl groups. To assign a
common name:
o Rule 1: Name all of the carbon atoms of the
molecule group as a single alkyl group
o Rule 2: Add the word alcohol, separating the
words with a space
ALCOHOL WITH MORE THAN ONE HYDROXLY GROUP
• Polyhydroxy alcohols – alcohols that possess more
than one hydroxyl group
• An alcohol in which two hydroxyl groups are present
in named as a diol, one containing three hydroxyl
groups is name as a triol, and so on. In these names
for diols, triols, and so forth, the final -e of the parent
alkane name is retained for pronunciation reasons
METHYL ALCOHOL (METHANOL)
• Methyl alcohol, which one carbon and one -OH group,
is the simplest alcohol
• This colorless liquid is a good fuel for internal
combustion engine. (Methyl alcohol fires are easier to
put out than gasoline fires because water mixes and
dilutes methyl alcohol)
• Methyl alcohol also excellent solvent properties, and it
is the solvent of choice for paints, shellacs, and
varnishes
• Methyl alcohol is sometimes call woof alcohol,
terminology that draws attention to an early method
for its preparation – the heating of wood to a high
temperature in the absence of air
• Drinking methyl alcohol is very dangerous. Within the
human body, it is oxidized by the liver enzyme alcohol
dehydrogenase to the toxic metabolites formaldehyde
and formic acid
• Formaldehyde can cause blindness (temporary or
permanent). Formic acid causes acidosis
ETHYL ALCHOHOL (ETHANOL)
• Long-term excessive use of ethyl alcohol may cause
undesirable effects such as cirrhosis of the liver, loss
of memory, and strong physiological addiction
• Links have also been established between certain
birth defects and the ingestion of ethyl alcohol by
women during pregnancy (fetal alcohol syndrome)
ISOPROPYL ALCOHOL (2-PROPANOL)
• A 70% isopropyl alcohol-30% water solution is
marketed as rubbing alcohol
• Isopropyl alcohol’s rapid evaporation rate creates a
dramatic cooling effect when it is applied to the ski,
hence its use for alcohol rubs to combat high body
temperature
• Has a bitter taste. Its toxicity is twice that of ethyl
alcohol, but it causes few fatalities because it often
induces vomiting and thus doesn’t stay down long
enough to be fatal
 CHEM 113: BIOCHEMISTRY
LECTURE 2: Functional Groups
___________________________________________________________________________________________________________
SIR. JESSIE MAGNO – DEPARTMENT OF CHEMISTRY
1ST SEMESTER | A.Y 2022 - 2023
• Large amounts (about 150 mL) of ingested isopropyl
alcohol can be fatal. Death occurs from paralysis of
the central nervous system
GLYCEROL (1, 2, 3 – PROPANETRIOL)
• Normally present in the human body because it is a
product of fat metabolism
• Present, in combined form, in all animal fats and
vegetable oils
• In some artic species, glycerol functions as a
“biological antifreeze”
• Has a great affinity for water vapor (moisture), it is
often added to pharmaceutical preparations such as
skin lotions and soap
• Florists sometimes use glycerol on cut flowers to help
retain water and maintain freshness
• Its lubricate properties also make it useful in shaving
creams and applications such as glycerol
suppositories for rectal administration of medicines
AMINES
• Carbon-hydrogen-nitrogen compounds
• Numerous drugs used for the treatment of mental
illness, hay fever, heart problems, and other physical
disorders are amines or amides
STRUCTURE AND CLASSFICICATION OF AMINES
• An amine is organic derivative of ammonia (NHB) in
which one or more alkyl, cycloakly, or aryl groups
are attached to the nitrogen atom
o Primary Amine – Nitrogen atom is bonded to
one hydrocarbon group and two hydrogen atoms
o Secondary Amine – Nitrogen atom is bonded to
two hydrocarbon group and one hydrogen atoms
o Tertiary Amine – Nitrogen atom is bonded to
three hydrocarbon groups and no hydrogen
atoms
PHYSICAL PROPERTIES OF AMINES
• The methylamines (mono-, di-, and tri-) and
ethylamine are gases at room temperature and have
ammonia-like odors
• Most other amines are liquids, and many have odors
resembling that of raw fish
• A few amines, particularly diamines, have strong,
disagreeable odors
• The foul odor arising form dead fish and decaying
flesh is due to amines released by the bacterial
decomposition of protein
• Two of these “odiferous” compounds are the diamines
putrescine and cadaverine
• The simpler amines are irritating to the skin, eyes,
and mucous membranes and are toxic by ingestion
• Aromatic amines are generally toxic. Many are readily
absorbed through the skin and affect both the blood
and the nervous system
• The boiling point of amines are intermediate
between those of alkanes and alcohols of similar
molecular mass
• They are higher than alkane boiling points, because
hydrogen bonding is possible between amine
molecules but not between alkane molecules
• Intermolecular hydrogen bonding of amines involves
the hydrogen atoms and nitrogen atoms of the amino
groups
SELECTED BIOCHEMICALLY IMPORTANT AMINES
• Neurotransmitter – A chemical substance that is
released at the end of a nerve, travels across the
synaptic gap between the nerve and another nerve,
and them bonds to a receptor site on the other nerve,
triggering a nerve impulse
• Norepinephrine – A compound secreted by adrenal
glands into the blood, helps maintain muscle tone in
the blood vessel
• Dopamine – Found in the brain. A deficiency of this
neurotransmitter results in parkinson’s disease, a
degenerative neurological disease
• Serotonin – Also a brain chemical, is involved in
sleep, sensory perception, and the regulation of body
temperature
• Epinephrine – Known as adrenaline, has some
neurotransmitter functions but is more important as a
central nervous system stimulant
• Histamine – Responsible for the unpleasant effects
felt by individuals susceptible to hay fever and
various pollen allergies
o Alkaloids – A nitrogen-containing organic
compound extracted from the plant material
o Morphine – One of the most effective
painkillers known, its painkilling properties
are about a hundred times greater than
those of aspirin
o Codeine – Is less potent than morphine,
having a painkilling effect about one-sixth
month that of morphine
 CHEM 113: BIOCHEMISTRY
LECTURE 2: Functional Groups
___________________________________________________________________________________________________________

SIR. JESSIE MAGNO – DEPARTMENT OF CHEMISTRY

1ST SEMESTER | A.Y 2022 - 2023
o Heroin – Semi-synthetic compound, the
diacetyl ester of morphine, it is produced
from morphine
o Amines – A carboxylic acid derivative in
which the carboxyl -OH group has been
replaced with an amino or a substitute amino
group. The amide functional group is thus
depending on the degree of substitution

STRUCTURE AND CLASSIFICATION OF AMIDES

• Primary Amide – An amide which two hydrogen

atoms are bonded to the amide nitrogen atom
• Secondary Amide – An amide in which an alkyl (or
aryl) group and a hydrogen atom are bonded to the
amide nitrogen atom
• Tertiary Amide – An amide in which two alkyl (or aryl)
groups and no hydrogen atoms are bonded to the
amide nitrogen atom

SELECTED AMIDES AND THEIR USES

• Urea – a water soluble white solid produced in the

human body from carbon dioxide and ammonia
through a complex series of metabolic reactions

• With malfunctioning kidneys, urea concentrations in

the body can build to toxic levels, a condition called
uremia
• Melatonin – A hormone that is synthesized by the
pineal gland that regulates the sleep wake cycle in
humans
• Acetaminophen – A derivative of acetamide, which
in 1992 replace aspirin as the top selling over-the-
counter pain reliver
• Barbiturates – Which are cyclic acid amide
compounds, are a heavily used group of prescription
drugs that cause relaxation (tranquilizers), sleep
(sedatives), and death (overdose)