Garcia - Organic Chemistry and Biochemistry

SPECIALIZATION: PHYSICAL SCIENCES
Focus: Organic Chemistry and Biochemistry

By: Prof. Nelson Garcia
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Competencies:
1. Classify simple organic compounds based on their formula and properties.
2. Compare the properties of organic compounds and inorganic compounds.
3. Give the importance of each of the biomolecules.
PART I – CONTENT UPDATE

ORGANIC CHEMISTRY
Organic chemistry is the study of carbon and its compounds. Aside from forming bonds
with the other elements like oxygen, nitrogen, sulfur and even with some metals like copper and
lithium, the carbon has the ability to form bonds with another carbon thereby forming numerous
compounds having diverse structures and functions.
Carbon compounds are so widely distributed – these can be found as natural component
of insects, plants and animals or as synthetic compounds like plastics and medicines. The
petroleum is a rich source of materials for the synthesis of organic compounds. It is a complex
mixture of crude oil and natural gas that were formed in the ground as a result of intense pressure
and temperature for millions of years. The sources for the carbon component of these mixtures
were the decaying plant and animal matter that were deposited in the ground.
The crude oil and natural gas are extracted from the ground, land or under oceans and
sent to refinery where it is processed and purified for commercial use. There are many products
that can be derived from the processing of the crude oil. Fuels, oils, waxes, asphalts are just
some of these products.
Classification of Hydrocarbon and Its Derivatives
Hydrocarbon is the simplest type of an organic compound. Based on structural terms,

hydrocarbon can be classified as alipathic or aromatic. Alipathic refers to straight chain carbon
atoms or cyclic carbon atoms. Alipathic hydrocarbons can be further classified as being saturated
or unsaturated. Saturated hydrocarbon contains only carbon-carbon single bond and carbon
hydrogen bonds. Unsaturated hydrocarbon contains carbon-carbon double bond and/or carbon-
carbon triple bond. It is also possible for the hydrogen of an unsaturated hydrocarbon to be
replaced by another atom like nitrogen, sulfur, oxygen, phosphorus and halogens. Aromatic
hydrocarbon contains an aromatic ring.
The functional group dictates the physical and chemical characteristics of an organic
molecule. The functional group is the reactive site in an organic molecule, enabling ease of
classification and synthesis of numerous organic compounds. The common functional group and
its representative structure is given in Table 1.
Table 1 Common Functional Group in Organic Compounds
Representative
Family of Organic Compounds
Structure
Alkene H2C CH2
Alkyne HC CH
Aromatic
Alkyl halides H3C Cl
Alcohol H3C OH
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O
Ether H3C CH3
O
Aldehyde
H3C H
O
Ketone
H3C CH3
O
Carboxylic acid
H3C
OH
O
Acid chlorides
H3C Cl
CH3 CH3
Anhydride
O O O
O
Ester O
H3C CH3
O
Amide
H3C NH2
Amine H3C NH2
Nitrile HC N
Nitro
Physical Properties of Organic Compounds
 Melting and Boiling Point
Organic compounds can be found as solid, liquid or gas. Examples of organic

compounds in the solid state are sugars, asphalts and waxes. Oils, kerosene, and jet
fuels oils are those in liquid state. Organic compounds such as methane, ethane,
propane and butane are in the form of a gas.
In general, the physical state of an organic compound can be attributed to the

number of carbon atoms it contains; especially for aliphatic hydrocarbons. Those
gaseous hydrocarbons have carbon atoms ranging from one (1) to four (4) carbon atoms,
while those in the liquid state have carbon atoms ranging from five (5) to twenty five (25)
carbon atoms. Fractional distillation is the method employed to obtain the desired
product from the crude oil. Table 2 shows the products obtained from this method and
the temperature at which it can be collected.
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Table 2 Products Obtained from Petroleum Refining
No. of carbon atom Products Temperature (0C)

C1 to C4 Refinery gases
C5 to C10 Gasoline (motor fuels) 40 to 180
C11 to C12 Kerosene (jet fuel) 160 to 250
C13 to C25 Gas oil (fuel oil, diesel oil) 220-350
Residue Lube oil, asphalt Above 350
 Solubility
A useful rule of solubility is that “like dissolves like”. Hydrocarbons are non-polar
and these are soluble in non-polar solvents. Similarly, polar organic compounds like
alcohol are soluble in water. There is a tendency however for some organic compounds
whose solubility in water decreases as the length of the carbon chain increases. This is
observed for alcohols. Propanol contains three (3) carbon atoms and is soluble in water
at any proportion. However, just an addition of one carbon atom decreases the solubility
of butanol, contains four carbon atoms, to 7.9 grams per 100mL water at room
temperature.
Bonds and IMFA in Organic Compounds
The types of bonding forces (intermolecular bonding) present between different

molecules are weaker than covalent bond. Still, the physical properties as well as biological
properties of the organic compounds are influenced by these types of bonding. The types of
intermolecular bonding are: ionic bonding, hydrogen bonding, dipole-dipole interactions and van
der waals interactions. The strongest among these is the ionic bonding and the weakest is van
der waals interactions.
 Ionic Bonding
Ionic bonding involves molecules having opposite charges, forming electrostatic

interactions. Amines and carboxylic acids form these bonds.
 Hydrogen Bonding
Hydrogen bonding exists for hydrogen-fluorine, hydrogen nitrogen and hydrogen-

oxygen. The functional groups that can form hydrogen bonds are alcohols, phenols,
carboxylic acids, amines and amides.
 Dipole-Dipole Interactions
The presence of an atom that is more electronegative than the other tom creates
a slightly positive and slight negative charge in the molecule. The carbonyl group
exhibits this type of interaction.
 van der waals Interactions
Long chain hydrocarbons such as alkanes form this type of interactions. There is
a weak charge that momentarily exists in a part of the molecule due to movements of
electrons. This will result in a region in the molecule that will be slightly positive and
another region to be slightly negative and these two regions will attract. Another term
that denotes this type of interaction is hydrophobic interactions.
Table 3 gives a comparison on the effect of the number of carbon atoms in alcohol and its
solubility in water. The solubility of the alcohol in water decreases as the number of carbon
atoms increases due to the diminishing hydrogen bonds and in effect, hydrophobic interactions
predominate.
Table 3: Number of Carbon atoms in Alcohol and Its Solubility
Number of
Compound Solubility (g/100gwater)
Carbon Atoms
Propanol Three (3) miscible
Butanol Four (4) 8.3
Pentanol Five (5) 2.4
Hexanol Six (6) 0.6
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All the molecules in Table 4 contain three (3) carbon atoms, differing only in its functional
group. The differences in the boiling point are attributed to the type of bonding interactions as
influenced by the functional group of the molecule.
Table 4: Different Functional Groups Having Three (3) Carbon Atoms and Its Boiling Point
Molecular mass Boiling Point

Compound Bonding Interactions
(g/mol) (0C)
Propane 58 -42 Hydrophobic interactions
Propanone 58 56 Dipole-dipole interactions
Propanal 58 49 Dipole-dipole interactions
Propanol 60 97 H-bonding
Table 5 presents a comparison on some of the general properties of organic and inorganic
compounds.
Table 5. Comparison on the General Properties of Organic and Inorganic Compounds
Property Organic compounds Inorganic compounds

Bonding Covalent Ionic
Physical state at room
Liquids or gases solid
temperature
Soluble in water Insoluble high
Boiling Point (0C) Low (<200) High (> 1000)
Flammability Flammable nonflammable
Polymers
An important industrial application of organic reaction is polymerization. Polymers are

large molecules consisting of simple repeating units called monomers. The polymerization
reaction involves the joining together of monomers thereby forming large molecules. Polymers
can be natural or synthetic. Its description is given below.
1. Naturally polymers – polysaccharides, proteins, nucleic acids.
2. Synthetic – man made polymers and can be classified as

Fibers – threadlike
Plastics – molded objects
Elastomers – rubber-like
The polymers produced can thermosets or thermoplasts. Thermosets form an infusible or

insoluble product upon heating while thermoplasts melt when heated and hardens when cooled.
General polymerization reactions can be chain reaction or addition polymerization and the other
is step-reaction or condensation polymerization.
A. Chain-reaction/addition involves the joining of monomer units (homopolymer).
The stages involved in this reaction are:

1. Initiation step – formation of radicals and the addition of radicals to the double bond.
2. Propagation step – addition of monomers forming longer chain.
3. Termination step – combination of two radicals in chain that ends the reaction.
The monomers for this reaction and its product are given below.
Monomer Polymer
Ethene (ethylene) Polyethylene
Chain-reaction
Propene (propylene) Polypropylene
Reaction
Vinyl chloride Polyvinyl
Styrene Polystyrene
2. Step-reaction/Condensation involves the joining together of two different monomers with the
elimination of small molecule (water). The monomers and its product is given below.
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Monomers Polymer
Hexamethylene diamine
and Nylon
Adipic acid
Step – reaction Dimethyl terphthalate
Polymerization and Polyester
ethylene glycol
Butadiene
and Synthetic rubber
styrene
BIOCHEMISTRY
Certain groups of molecules essential to cellular functioning are commonly found among
plants, animals, humans, insects and even microorganisms. These are termed as biomolecules.
Biomolecules share common structural template among its group thereby allowing these to be
easily categorized. The functional groups in organic chemistry are the same functional groups
that can be seen among biomolecules, albeit as a derivatives of biomolecules. For instance, in
organic chemistry, alcohol has the functional group, -OH but in the context of biomolecules, OH
group can also be found in carbohydrates and lipids.
The four (4) biomolecules are the amino acids and proteins, carbohydrates and
polysaccharides, lipids and nucleic acids. Among the four (4) biomolecules, the lipid family has
no structural template that will categorize it as a lipid. The molecules belonging to the family of
lipid is based on its solubility and structural functions or properties.
Amino acids and Proteins
Amino acids are the building blocks of proteins. There are twenty (20) amino acids
having a general structure that contains a carboxyl group and an amino group attached to an
alpha – carbon (α-C). The physical and chemical properties of an amino acid molecule depend
on the type of the side chain or R-group that is attached to the alpha-carbon. The side chain or R
group in the amino acid can be polar (charged or neutral), nonpolar; acidic or basic. Except for
the amino acid glycine (G), the alpha-carbon in the twenty (20) amino acids is a stereogenic
center, making the amino acid chiral. Almost all the configuration of amino acid is in the L-
configuration.
At physiological pH, the amino acid has a neutral charge because it exists as zwitterion,
a molecule containing both positive and negative charges. The negative charge comes from the
ionization of the carboxyl group while the positive charge comes from the protonated amino
group.
Figure taken from: http://chemistry2.csudh.edu/rpendarvis/aminoacids.html
When two amino acids are linked together, it forms a bond belonging to the functional
group, amide. In biochemistry, it is termed as peptide bond. Two amino acids joined together are
said to be a dipeptide while for three amino acids, tripeptide. The amino acids in a polypeptide
are now called residues. Most often, polypeptides containing more than thirty (30) amino acid
residues are called proteins.
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Figure taken from: http://chemistry2.csudh.edu/rpendarvis/aminoacids.html
Among the twenty (20) amino acids, there are ten (10) amino acids that cannot be
synthesized by the body and have to be supplied from a balanced diet of meat and vegetables.
These are called essential amino acids. Table 6 lists the twenty amino acids, including the one
(1) and three (3) letter abbreviations.
Table 6: The Twenty Amino Acids
Three Letter
Amino acids
Abbreviation
Alanine (A) Ala
Arginine (R) * Arg
Asparagine (N) Asn
Aspartic acid (D) Asp
Cysteine (C) Cys
Glutamic acid (E) Glu
Glutamine (Q) Gln
Glycine (G) Gly
Histidine (H) * His
Isoleucine (I) * Ile
Leucine (L) * Leu
Lysine (K) * Lys
Methionine (M) * Met
Phenylalanine (F)* Phe
Proline (P) Pro
Serine (S) Ser
Threonine (T) * Thr
Tryptophan (W) * Trp
Tyrosine (Y) Tyr
Valine (V) * Val
Essential amino acids are marked with asterisk (*).
Table 7 groups the amino acid according to the nature of its side chains or R groups.
Table 7: The Nature of the Amino Acid Side Chains
Characteristics of the Amino Acid

Amino Acids
Side chains
Non polar A, L, G, P, V
(Hydrophobic) F, M, W, I
Q, S, N
Neutral (Polar)
C, T, Y
Acidic D, E
Basic R, H, K
The proteins serve many functions and these are given below:
 Structural component – these provide support as either part of a structure or the structure
itself as covering. Examples are feathers, collagen and keratin.
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 Transport and storage – hemoglobin delivers oxygen to the cell and removes carbon
dioxide from cells. Examples of protein as storage are albumin found in egg white.
 Catalyst – enzymes are made up of protein and acts as catalyst. Enzymes carry many
important reactions in the cell like oxidation-reduction reactions, protein hydrolysis and
many others.
 Messenger – one way for to cells communicate with other cells and organ inside the body
is through hormones. Hormones are considered as chemical messengers. Some of
these hormones are proteins like insulin which sends message inside the cell to regulate
carbohydrate metabolism.
 Mobility – proteins like actin and myosin found in the muscle cells allows muscle
contraction and mobility for the organism.
 Immunity – higher animals produce antibodies in the form of globular proteins to protect it
from biological entities that cause disease.
Carbohydrates and Polysaccharides
Carbohydrates are the most abundant group among biomolecules. The common term for
carbohydrates is sugar. Energy source and structural components are its two (2) major functions.
In plants, carbohydrate is formed from the conversion of carbon dioxide and water to sugars and
oxygen in the presence of sunlight. The plant is capable of using the carbohydrate as its energy
source and cell wall structural component. The industrial importance of carbohydrate is evident in
the manufacture of fibers such as cotton by the textile industries; alcohol production from the
fermentation of sugars, and the manufacture of paper and its products from the pulp and paper
industries.
The empirical formula for carbohydrates is Cn(H2O)n. The simplest carbohydrates are the
monosaccharides. Two monosaccharide units comprise the disaccharide. Oligosaccharides
refer to carbohydrates containing fewer than ten (10) monosaccharide units and polysaccharides
denote enormous long chain of carbohydrate units. The bond that links between two sugar units
is called the O-glycosidic bond.
In terms of structure, a sugar may be an aldose or a ketose. Aldose sugars bear a

carbonyl group on the first carbon, resembling the functional group, aldehyde. Ketose sugars
bear a carbonyl group on the second carbon, resembling the functional group, ketone. The
carbon bearing the carbonyl group in monosaccharides is termed as anomeric carbon.
The stereochemical configuration of monosaccharides in Fischer projection is in the D-

configuration. A cyclic sugar structure is formed for monosaccharides containing five (5) to six
(6) carbon. The ring formed from the intramolecular arrangement of monosaccharides gives rise
to the formation of stereoisomers having two configurations, the alpha (α) and beta (β) anomers.
The figure below is a Haworth projection of glucose, showing the alpha and beta anomer
configuration.
(figure taken from http://chemistry2.csudh.edu/rpendarvis/monosacch.html)
The three (3) important monosaccharides in the human diet are glucose (also called
dextrose), galactose and fructose. Glucose and galactose are aldose sugars while fructose is a
ketose sugar. Glucose and galactose differ only in the position of the OH group in the fourth
carbon. Glucose is the sugar being used by the cell as its principal energy source.
The three (3) important disaccharides are sucrose, lactose and maltose. The
disaccharides are formed from the reaction of the alcohol group with the anomeric carbon of the
sugar.
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Maltose is made up of two (2) α-glucose units. The anomeric carbon of the first glucose
unit is linked to the hydroxyl group of the fourth carbon of the second glucose unit. The linkage is
denoted as α(1 → 4). The disaccharide cellobiose is also made up of two (2) glucose units but
the linkage is of the β(1 → 4) type. Maltose can be incorporated in the human diet and digested
but cellobiose cannot be digested.
Lactose or milk sugar consists of a galactose and a glucose unit. The anomeric carbon
of β-galactose is linked with the hydroxyl group of the fourth carbon of the glucose. The official
name for lactose is galactose- β(1 → 4)-glucose. In the consumption of lactose, the enzyme β-
galactosidase hydrolyzes the disaccharide, freeing the galactose and glucose units.
Sucrose, common table sugar, is a made up of one glucose and one fructose unit. The
α,β (1 → 2) glycosidic bond formed from these two monosaccharides denote the specific
anomers of the sugars, glucose is in the alpha anomeric configuration while fructose is in the beta
anomeric configuration.
The three (3) important polysaccharides are the cellulose, starch and glycogen.
Cellulose is the most widely distributed structural polysaccharides while starch and glycogen are
both stored form of energy in plants and mammals respectively.
Cellulose consists of very long chain glucose units linked through β(1 → 4). The
cellulose forms a linear chain, forming sugar units packed closely together in fibers. This
arrangement makes cellulose a very good structural component because it does not allow
solvents to be trapped inside.
Starch consists of many glucose units and is a mixture of two types of polymeric glucose,
amylose and amylopectin. The linear unbranched chain is the amylase, linked by α(1 → 4).
The branched type is the amylopectin. The main backbone of the amylopectin is linked by a α(1
→ 4) O-glycosidic bond similar to amylase while the branch connected to the backbone is via α(1
→ 6) O-glycosidic bond. When consumed as part of the human diet, the saliva in the mouth
degrades the starch, yields maltose and other oligosaccharide products.
Glycogen is very similar to amylopectin, the backbone and the branch have the same
linkages. The difference lies in the numerous α(1 → 6) branch and shorter branch and has much
higher molecular mass than amylopectin.
The figure below shows some of the structures of the disaccharides and polysaccharides.
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Taken from http://chemistry2.csudh.edu/rpendarvis/monosacch.html
Lipids
The members of the family of lipids are categorized based on solubility and physical
properties, biological functions rather than a common structure that can be found in other
biomolecules like amino acids and carbohydrates.
Lipids play many important roles in cellular processes and are listed below:
 Energy source and storage – the oxidation of lipids in the form of fats releases more
energy than carbohydrates. The storage of lipids in the cell in the form of fats is very
compact, allowing more energy to be stored without occupying much space.
 Structural component – cell membranes are made up of diverse family of lipids whose
main function is to regulate the entry of solvents, ions and molecules in and out of the
cell. The other function of the lipids is to facilitate cell to cell communication.
 Messenger and transporters – example of lipids that carry out these functions are the
prostaglandins as signal molecules and ubiquinones as electron carriers.
In terms of classification, a lipid can be saturated or unsaturated. This classification

applies to fatty acids as family member of lipids. The difference lies in the presence of double
bonds in the molecule. The unsaturated fatty acid has a lower melting point compared to the
saturated fatty acids; saturated fatty acids are solids at room temperature while unsaturated fatty
acids are liquid. The orientation of the double bonds in the unsaturated fatty acids is in the cis-
configurations. Table 8A and Table 8B list the common saturated and unsaturated fatty acid with
its respective melting points.
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Table 8A: Common Saturated Fatty acids & Its Melting Points
Common Name of Melting

RCOOH
Common Saturated Fatty Acid IUPAC Point
Formula
(no. of carbon) (oC)
Capric (10) Decanoic C9H19COOH 32
Lauric (12) Dodecanoic C11H23COOH 44
Myristic (14) Tetradecanoic C13H27COOH 54
Palmitic (16) Hexadecanoic C15H31COOH 63
Stearic (18) Octadecanoic C17H35COOH 70
Table 8B: Common Unsaturated Fatty acids & Its Melting Point
Common Name of
Melting
Common Unsaturated Fatty Acid RCOOH
IUPAC Point
(no. of carbon, no of double bonds Formula
(oC)
and its position)
Palmitoleic (16; 1; Δ9) cis-9-Hexadecanoic C15H29COOH 0
Oleic (18; 1; Δ9) cis-9-Octadecanoic C17H33COOH 16

cis,cis-9,12-
Linoleic (18; 2; Δ9, Δ12) C17H31COOH 5
Octadecadienoic
All cis-9, 12, 15-
Linolenic (18; 3; Δ9, Δ12, Δ15) C17H29COOH -11
Octadecatrienoic
All cis-5, 8, 11, 14-
Arachidonic (20; 4; Δ5, Δ8, Δ11, Δ14) C19H31COOH -50
Eicosatetraenoic
Legend:
The Δ indicates the position of the double bond in the molecule. For instance, Δ9 indicates that
the position of the double bond is between carbon 9 and 10.
Another way to classify lipids is its backbone structure. Phospholipid has triacylglycerol
as its backbone whereas shingolipid has sphingosine as its backbone. The components of
biological membrane are phospholipids while the nerve and brain cells are made of sphingolipids.
General structure of a triacylglycerol

Taken from: http://chemistry2.csudh.edu/rpendarvis/ester-fats.html
General structure of a phospholipid

Taken from: http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/lipid.htm
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Structure of sphingosine
Taken from: http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/lipid.htm
The structure of fatty acids, phospholipids and sphingolipids belong to the linear, open
chain type of lipids. Another group from the family of lipids that contains ring in its structure are
the steroids. The familiar molecule that belongs to this family of lipid is the cholesterol.
Cholesterol is the precursor of sex hormones and contains four (4) fused rings. The function of
cholesterol is in regulating the fluidity of the biological membrane. Cholesterol and its derivatives
present in plasma proteins are called lipoproteins.
The function of lipoproteins is to transport cholesterol in peripheral tissues to be used as

material in the construction of cell membrane and as precursor of many other important biological
materials.
Cholesterol structure
Taken from:http://www.abc.net.au/health/library/stories/2006/08/03/1829380.htm
Nucleic acids
The biomolecules that are involved in the storage, transfer and expression of the physical
traits organisms are the nucleic acids. The hair, eye and skin color, height and body built are
governed by the sequence of the nucleotides in the parent’s genes. The two families of nucleic
acid are the DNA, deoxyribonucleic acid, and the other is the RNA, ribonucleic acid. The DNA is
the molecule that is responsible for such genetic traits since it carries the genetic code or
information that will produce the many biomolecules that make up the human being.
Nucleic acids are linear polymers whose monomers are called nucleotides. A nucleotide
consists of a five member ring aldose sugar; ribose; a phosphate group and a nitrogenous base.
In RNA, the sugar is a ribose, while for DNA, a deoxyribose. When phosphate is not present, the
molecule is termed as nucleoside.
There are four (4) types of nitrogenous base in the nucleic acids and the nitrogenous
bases can be a derivative of either of the two heterocyclic molecule, purine or pyrimidine.
Adenine (A) and guanine (G) belong to the purine based ring while the cytosine (C), thymine (T)
and uracil (U) belong to the pyrimidine based ring. Thymine can only be found in the DNA and
uracil can only be found in the RNA. Adenine, guanine and cytosine can be found in the DNA and
RNA.
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Structure of the nitrogenous bases in nucleic acids

Taken from: http://chemistry2.csudh.edu/rpendarvis/NuclAcids.html
The name of the nitrogenous base is changed to indicate that the molecule being referred
to is either a nucleoside or a nucleotide. The nomenclature is summarized in Table 9.
Table 9: Nomenclature of Nucleosides and Nucleotides
Nucleic Nitrogenous
Ring Nucleoside Nucleotide
acid Base
Adenine Deoxyadenosine Deoxyadenosine-5’monophosphate
Purine
Guanine Deoxyguanosine Deoxyguanosine-5’monophosphate
DNA
Cytosine Deoxycytidine Deoxycytidine-5’monophosphate
Pyrimidine
Thymine Deoxythymidine Deoxythymidine-5’monophosphate
Adenine Adenosine Adenosine-5’monophosphate
Purine
Guanine Guanosine Guanosine 5’monophosphate
RNA
Cytosine Cytidine Cytidine 5’monophosphate
Pyrimidine
Uracil Uridine Uridine 5’monophosphate
Nucleic acids are formed from nucleotides linked through the phosphate group, forming
3’-5’-phosphodiester bond. The 3’ refers to the third carbon of the sugar of the first nucleotide
while the 5’ refers to the fifth carbon of the sugar of the second nucleotide. Between the 3’ and 5’
is a phosphate group that serves as linked for the two nucleotides.
Structure showing how nucleotides are linked

Taken from: http://chemistry2.csudh.edu/rpendarvis/NuclAcids.html
The DNA consists of two polynucleotide strands, folded into a double helix shape while
that of the RNA consists only of a single strand, folded into conformations containing different
structural elements. In a DNA double helix, the two strands of DNA are wound round each other.
The two (2) DNA strands are organized in an anti parallel direction; one strand is oriented in a 5’
→ 3’ direction while the other is oriented in a 3’ → 5’ direction.. The nitrogenous bases are
positioned inside the strands while the sugar phosphate backbone is located outside. Adenine
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pairs with thymine, forming two (2) hydrogen bonds while guanine pairs with cytidine, forming
three (3) hydrogen bonds. These specific base pairings make the two (2) strands of the DNA to
be complimentary with one another.
The transfer of biological information as proposed by Crick (1958) is known as the
Central Dogma of Molecular Biology. Its stages are summarized as follows:
 REPLICATION: The DNA makes it own copy, producing new DNA molecules.
 TRANSCRIPTION: The DNA molecule is transcribed to produce an RNA, complimentary

to the DNA.
 TRANSLATION: The RNA sequence is translated to produce the corresponding amino

acids forming the desired protein.
The figure shows the process in the transfer of biological information.

(Taken from: http://www.accessexcellence.org/RC/VL/GG/central.php)
PART II – ANALYZING TEST ITEMS

1. All of the following contain C, H and N atoms EXCEPT?
a. Purine c. Pyrimidine
b. Amino acid d. Sucrose
Explanation: The answer is D. Sucrose contains H, C, and O atoms only. The rest
contains N atoms .
2. An organic compound was isolated and was found to be soluble in hexane and insoluble in
ethanol and acetone. What best describe the isolated compound?
a. The compound contains alcohol group
b. The compound contains long chain alkyl group
c. The compound contains double bond in its structure
d. The compound contains carboxylic group in its structure
Explanation: The answer is B. The long alkyl group exhibits non-polar character and
non-polar compounds are soluble in non-polar solvents like hexane.
3. Which of the following differentiates a plant from an animal?

a. Growth c. Photosynthesis
b. Reproduction d. REDOX reactions
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Explanation: The answer is C. Plants have chlorophyll that is needed for

photosynthesis while animals don’t have.
4. What is the product when amino acids are joined together forming peptides?
a. ammonia c. water
b. carbon dioxide d. ATP
Explanation: The answer is C. Once the amino acid joined together their C-terminal
releases OH group that abstracts the H atom from the N-terminal which
then form water.
5. Which among the following physical properties given below distinctly differentiates organic
compound from inorganic compound?
i. Melting and boiling point.

ii. Solubility in water.
iii. Physical state of the substance.
iv. Optical activity.
a. i and iv. c. iii and iv.

b. ii and iv. d. i and iii.
Explanation: The answer is A. Inorganic compounds have unusual high melting points
and optical activity is a special property exhibited by organic compounds.
6. What is the orientation of the double bond in an unsaturated fatty acid?

a. Cis configuration. c. Depends on the temperature.
b. Trans configuration. d. Depends on the type of species.
7. A certain refrigerant contains chlorine and fluorine atoms as substituent in an organic

molecule. Where does this organic molecule belong?
a. Belongs to alcohol group c. Belongs to organic halide group
b. Belongs to carbonyl group d. Belongs to carboxylic acid group
8. Two (2) compounds were isolated from the depth of the ocean. Both compounds have a
molar mass of 1 ATP 00 g/mol. What test WILL NOT differentiate the two compounds?
a. Solubility in water c. Phase test
b. Melting point d. Combustibility
9. What will join the monomeric units in nucleic acid?

a. H-bonding link c. O-glycosidic link
b. N-glycosidic link d. Phosphodiester link
10. Which shows hydrophobic interactions among the pairs of functional groups given
below?
i. Carbonyl compounds and saturated hydrocarbons.

ii. Alcohols and saturated hydrocarbons.
iii. Saturated and unsaturated hydrocarbons.
iv. Aromatics.
a. i and iv. c. iii and iv.

b. ii and iv. d. iv only.
11. An alcohol was synthesized and found to be soluble in almost all non-polar solvents.
Which among the following best describes the synthesized alcohol?
a. It is hydrophobic in nature.
b. It contains short alkyl group.
c. It is capable of hydrogen bonding.
d. It contains halogen as one of its substituent.
12. Which biomolecule is concern with the transfer of genetic information from parents to
offspring?
a. Lipids c. Nucleic acids
b. Amino acids d. Polysaccharides
13. Which of the following statement is CORRECT if a plastic material cannot be blended
with other plastic during heat processing?
a. It is a thermoset. c. It contains many impurities.
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b. It is a thermoplastic. d. It has been recycled many times.
14. In DNA, what is the correct complementary pairing of the nitrogenous bases?
a. AG & CT c. AC & GC
b. AA & GG d. AT & GC
15. A phospholipid with a very low melting point is likely to be .
a. Highly hydrophobic c. Highly unsaturated
b. Highly hydrophilic d. Highly saturated
16. A certain organic compound was found to be unsaturated. Which of the following test will
confirm that the compound is unsaturated?
a. Bromine test c. Solubility test
b. Melting point d. Oxidation test
17. The solubility of alcohol decreases as the number of carbon atoms increases. Which of
the following best explains the statement above?
a. The polarity of the molecule increases.
b. The non-polar character predominates.
c. The polarity of the molecule decreases.
d. There is crowding of carbon atoms in the chain.
18. Which functional group classifies an organic molecule as alkyl halide?

a. Ether groups c. Halogen groups
b. Hydrohalogens d. Methyl & ethyl groups
19. Unsaturated fatty acids are fatty acids whose physical state is liquid at room
temperature. This is attributed to the lowering of hydrophobic interactions among the
molecules. Which among the given fatty acids will have the lowest melting point if it were
to contain certain number of double bonds?
a. It depends on the carbonyl.
b. Unsaturated fatty acid that has one double bond.
c. Unsaturated fatty acid that has two double bonds.
d. Unsaturated fatty acid that has three double bonds.
20. What is the role best played by lipids in living system?

a. Biomarkers c. Structural membrane
b. Energy source d. Immunity enhancement
21. Which among the given set of amino acid belongs have the same solubility?
a. K, A, L c. P, Y, H
b. K, E, D d. W, D, E
22. In the central dogma of protein synthesis, which part involves the production of
information prior to protein synthesis?
a. Replication c. Transcription
b. Translation d. Reverse transcriptio
23. What anomer configuration/projection is exhibited by cellulose?

a. Chiral projection c. Beta configuration
b. Fischer projection d. Alpha configuration
24. What functional group is found in ketones and aldehydes?

a. Oxygen c. Nitro group
b. Alkyl group d. Carbonyl group
25. What biomolecular structure mediates the passage of molecules and nutrients in and out
of the cell?
a. Lipid c. Nucleic acids.
b. Protein d. Polysaccharides
PART III – ENHANCING TEST TAKING SKILLS

1. Which pairs of functional group given below are most capable of forming hydrogen bonds
with water?
Pair 1:Alcohols and amines.

Pair 2:Amines and alkyl halides.
Pair 3: Alcohols and alkyl halides.
Pair 4: Carboxylic acids.
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_
a. pairs 1 and 4. c. pairs 3 and 4.

b. pairs 2 and 4. d. pair 4 only.
2. The data below shows the boiling point and molecular mass of selected compounds.
Which compounds exhibit strong hydrogen bonding?
Molecular Mass and Boiling Point of Selected compounds
Molecular
Compound mass Boiling Point (0C)
(g/mol)
A 32 62
B 38 35
C 45 78
D 77 50
a. Compounds A and B. c. Compounds A and C.

b. Compounds C and D. d. Compounds B and D.
3. What is the compliment of the DNA sequence GCCAAA?

a. CGGTTT c. TTTCGG
b. AAAGCC d. CGGUUU
4. A certain compound was analyzed and found to contain three (3) carbon atoms. Further
tests showed that there is the presence of a double bond between carbon atoms. There
was only one (1) hydrogen atom present and the rest were chlorine atoms. Which of the
following statement best describes the compound?
Statement 1
The compound is organic due to the presence of halogens.
Statement 2
The compound is organic and is considered saturated.
Statement 3
The compound is organic and is considered unsaturated.
Statement 4
The compound can be an organic or inorganic. Further tests are necessary.
a. Statement 1 and 2. c. Statement 3 only.

b. Statement 1 and 3. d. Statement 4 only.
5 Which among the following physical and chemical properties below are generally exhibited
by organic compounds?
i. High boiling point, highly soluble in water.
ii. Low melting point, less soluble in water.
iii. Flammable, form ionic bonds.
iv. Flammable, form covalent bonds.
a. i and iii. c. ii and iv.

b. ii and iii. d. iii and iv.
6. Which among the given components differentiate between DNA and RNA in terms of
structure?
i. The nucleoside sequence.
ii. The type of sugar present.
iii. The type of nitrogenous bases.
iv. The sugar-phosphate backbone sequence.
a. i and ii c. iii and iv

b. ii and iii d. i and iv
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7. Which pairs of functional groups display the carbon-nitrogen bond?
Pair 1: Nitriles and carbonyl compounds.
Pair 2: Alcohol and ammonia.
Pair 3: Amines and nitriles.
a. pairs 1 and 2. c. pair 3 only.

b. pairs 2 and 3. ` d. pairs 1, 2 and 3.
8. Which of the following are NOT considered as an organic compound(s)?

a. Vanilla b. Ethyl alcohol c. Chalk d. menthol
9. The three (3) important monosaccharides are glucose, galactose and fructose. What
sugar unit makes up the table sugar or sucrose?
a. Glucose and glucose c. Glucose and galactose
b. Glucose and fructose d. Galactose and fructose
10. Which of the following organic compounds DO NOT contain oxygen atoms?
a. amides and esters. c. aldehydes and ketones.
b. amines and nitriles. d. acid anhydrides and acid chlorides.
11. The amino acid glycine has no stereogenic center whereas alanine possesses one
stereogenic center. Which of the following statement is correct?
Statement 1
Alanine will have a mirror image.
Statement 2
Glycine will have a mirror image.
Statement 3
The presence of stereogenic center makes the amino acid acidic.
Statement 4
The presence of stereogenic center increases the isoelectric point of amino acid.
a. Statement 1. c. Statement 1 & 3.

b. Statement 2. d. Statement 2 & 4.
12. A certain fatty acid was isolated from a marine species. The fatty acid has a melting
point of – 20 0C and three (3) moles of hydrogen is consumed upon hydrogenation. From
the given data, which of the following statement is correct about the isolated fatty acid?
Statement 1
The fatty acid is solid and highly saturated.
Statement 2
The fatty acid is liquid and highly unsaturated.
Statement 3
There are three (3) double bonds in the fatty acid.
Statement 4
There are six (6) double bonds in the fatty acid.
a. Statement 1 & 3. c. Statement 2 & 3.

b. Statement 1 &4. d. Statement 2 & 4.
13. Which of the following explains the solubility of OH group in water?

a. The capability to form hydrogen bond.
b. The chance for van der waals interactions.
c. The chance for hydrophobic interactions.
d. The presence of strong dipole-dipole interactions.
14. Why is there a need to separate the study of carbon from other elements?
Statement 1
Carbon is capable of forming polymers.
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Statement 2
Compounds formed from carbon are stable.
Statement 3
Compounds formed from carbon exhibit isomerism.
Statement 4
Carbon is capable of forming multiple bonds with any metals.
a. Statement 1 and 2. c. Statement 2 and 3.

b. Statement 1 and 3. d. Statement 3 and 4.
15. In humans, which among the following biomolecules store energy the most in terms of
quantity?
a. Lipids c. Starch and fats.
b. Proteins d. Polysaccharides
16 An unsaturated fatty acid consumes 3 moles of hydrogen gas. How many double bonds
are present in the said fatty acid?
a. 3 c. 9
b. 6 d. 12
17. A polymer was formed from a single monomer. What is the involved polymerization
reaction?
a. Thermosetty polymerization c. Step-reaction polymerization
b. Thermophilic polymerization d. Chain reaction polymerization
18. Which of the following will differentiate an amine from an amide in terms of structure?
a. Amine has carbonyl group
b. The amide has carbonyl group
c. Amide is directly linked to an alkyl group
d. Amine group is directly bonded to carbonyl group
19. An organic molecule is said to be soluble in polar solvent and possesses high boiling
point despite having a low molar mass. What functional group contributes to the said
characteristic of the organic molecule?
a. Ethers c. Hydroxyl
b. Alkenes d. Halogens
20. What classification does the sugar fructose belongs?

a. Aldoses c. Cellulose
b. Ketoses d. Anhydrides
21. What is the backbone of the lipid triglyceride?

a. Glycerol c. Phospholipid
b. Sphingolipid d. Sugar-phosphate
22. Which of the following involves DNA replication?

a. Formation of mRNA c. Formation of daughter strands
b. The presence of ribosome d. The copying of the genetic code
23. What is the stored form of carbohydrates in plants?

a. Starch c. Glycogen
b. Cellulose d. Cellobiose
24. How many stereogenic carbons are present in glucose?

a. 1 c. 3
b. 2 d. 4
25. What is the anomeric configuration/projection of the polysaccharide, starch?

a. Beta configuration c. Fischer projection
b. Alpha configuration d. Stereogenic projection
251

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SPECIALIZATION: PHYSICAL SCIENCES

Focus: Organic Chemistry and Biochemistry

SPECIALIZATION: PHYSICAL SCIENCES

PART I – CONTENT UPDATE

Classification of Hydrocarbon and Its Derivatives

Hydrocarbon is the simplest type of an organic compound. Based on structural terms,

Table 1 Common Functional Group in Organic Compounds

Alkene H2C CH2

Alkyl halides H3C Cl

Amine H3C NH2

Physical Properties of Organic Compounds

 Melting and Boiling Point

Organic compounds can be found as solid, liquid or gas. Examples of organic

In general, the physical state of an organic compound can be attributed to the

Table 2 Products Obtained from Petroleum Refining

No. of carbon atom Products Temperature (0C)

Bonds and IMFA in Organic Compounds

The types of bonding forces (intermolecular bonding) present between different

Ionic bonding involves molecules having opposite charges, forming electrostatic

Hydrogen bonding exists for hydrogen-fluorine, hydrogen nitrogen and hydrogen-

 van der waals Interactions

Table 3: Number of Carbon atoms in Alcohol and Its Solubility

Molecular mass Boiling Point

Table 5. Comparison on the General Properties of Organic and Inorganic Compounds

Property Organic compounds Inorganic compounds

An important industrial application of organic reaction is polymerization. Polymers are

1. Naturally polymers – polysaccharides, proteins, nucleic acids.

2. Synthetic – man made polymers and can be classified as

The polymers produced can thermosets or thermoplasts. Thermosets form an infusible or

A. Chain-reaction/addition involves the joining of monomer units (homopolymer).

The stages involved in this reaction are:

Amino acids and Proteins

Figure taken from: http://chemistry2.csudh.edu/rpendarvis/aminoacids.html

Figure taken from: http://chemistry2.csudh.edu/rpendarvis/aminoacids.html

Table 6: The Twenty Amino Acids

Essential amino acids are marked with asterisk (*).

Table 7: The Nature of the Amino Acid Side Chains

Characteristics of the Amino Acid

Carbohydrates and Polysaccharides

In terms of structure, a sugar may be an aldose or a ketose. Aldose sugars bear a

The stereochemical configuration of monosaccharides in Fischer projection is in the D-

(figure taken from http://chemistry2.csudh.edu/rpendarvis/monosacch.html)

Taken from http://chemistry2.csudh.edu/rpendarvis/monosacch.html

In terms of classification, a lipid can be saturated or unsaturated. This classification

Common Name of Melting

Oleic (18; 1; Δ9) cis-9-Octadecanoic C17H33COOH 16

General structure of a triacylglycerol

General structure of a phospholipid

The function of lipoproteins is to transport cholesterol in peripheral tissues to be used as

Structure of the nitrogenous bases in nucleic acids

Table 9: Nomenclature of Nucleosides and Nucleotides

Structure showing how nucleotides are linked

 TRANSCRIPTION: The DNA molecule is transcribed to produce an RNA, complimentary

 TRANSLATION: The RNA sequence is translated to produce the corresponding amino

The figure shows the process in the transfer of biological information.

PART II – ANALYZING TEST ITEMS

3. Which of the following differentiates a plant from an animal?

Explanation: The answer is C. Plants have chlorophyll that is needed for

i. Melting and boiling point.

a. i and iv. c. iii and iv.

6. What is the orientation of the double bond in an unsaturated fatty acid?

7. A certain refrigerant contains chlorine and fluorine atoms as substituent in an organic

9. What will join the monomeric units in nucleic acid?

i. Carbonyl compounds and saturated hydrocarbons.