HANDOUTS IN BIOCHEMISTRY

I. Overview of Biochemistry

Biochemistry – is the study of the chemical substances found in living organisms and the chemical
interactions underlying life processes.
- is a field in which new discoveries are made almost daily about how cells
manufacture the molecules needed for life and how the chemical reactions by
which life is maintained occur.
- the scientific study of the chemical substances, processes, and reactions that occur
in living organisms
- this science is a branch of both Chemistry and Biology; the prefix bio- comes from
bios, the Greek word for “life.”

The chief goal of Biochemistry is to understand the structure and behavior of biomolecules. These are
the carbon-containing compounds that make up the various parts of the living cell and carry out
the chemical reactions that enable it to grow, maintain and reproduce itself, and use and store
energy.

Biochemical Analysis – an analysis relating to the chemical substances present in living organisms and
the reactions and methods used to identify or characterize them.

Importance of Biochemistry:

1. It is used in clinical diagnosis, manufacture of various biological products, treatment of diseases, in

nutrition, agriculture etc.
2. Helps one understand the actual chemical concepts of biology.
3. Biochemistry is a valuable subject in medicine without which there would have been no such
advancement in the field.
 Physiology: Biochemistry helps one understand the biochemical changes and related
physiological alteration in the body
 Pathology: Based on the symptoms described by the patient, the physician can get a clue on the
biochemical change and the associated disorder. For example, if a patient complains about
stiffness in small joints, then the physician may predict it to be gout and get confirmed by
evaluating uric acid levels in the blood. As uric acid accumulation in blood results in gout.
4. Almost all the diseases or disorders have some biochemical involvement. So the diagnosis of any
clinical condition is easily possible by biochemical estimations.
5. In agriculture, biochemistry plays a valuable role in farming, fishery and poultry.
 Prevent diseases: It helps for prevention, treatment of diseases and also increases the
production or yield.
 Enhance growth: Biochemistry gives an idea of how the use of fertilizers can increase plant
growth, their yield, quality of food etc.
 Enhance Yield: Some hormones promote growth, while other promote flowering, fruit formation
etc. In fisheries, use of substances to promote fish growth, their reproduction etc can be
understood.

II. The Organization of Cells and its Functions:

Cell - the basic structural and functional unit of all living organisms.
- discovered by Robert Hooke

Cell Theory – German botanist Matthias Schleiden and German zoologist Theodor Schwann, working
together, recognize the fundamental similarities between plant and animal cells and propose that all
living things are made up of cells.
 Cells form the basic building blocks of living organisms
 Cells arise by the division of pre-existing ones
 Cells contain inherited information w/c controls their activities
 Cell is the functioning unit of life; metabolism takes place in cells
 Given suitable conditions, cells are capable of independent existence

Cell Structures:

Organization of Cells:

Cell Tissue Organ System Organism

Classification of Cells:

a. Prokaryotic Cell – simple cell without nucleus: a cell whose DNA is not contained within a
nucleus, e.g. a bacterium
b. Eukaryotic Cell- cell with visible nuclei and organelles.

Cell Structures and Functions:

A. Prokaryotic Cell – found in bacteria
 Plasma Membrane – surrounds the entire cell &regulates the inflow and outflow of
materials
 Nucleoid – contains the genetic material, DNA
 Ribosome - coordinate the synthesis of proteins
B. Eukaryotic Cell –found in fungi, plants and animals
 Cell membrane or plasma membrane – encloses and protects the cell contents
 Nucleus – the control center of the cell, plays the central role in the cellular reproduction
and directs the metabolic activities of the cell
 Nuclear membrane - encloses and protects the nucleus; regulates what passes in and out
of the nucleus
 Chromosomes – bear the genes, the basic units of heredity & determine the
characteristics of the cells
  Nucleoli – responsible for protein synthesis
 Cytoplasm – semi-fluid substance of the cell
 Mitochondria – the “power houses” of the cell because they supply energy
 Ribosomes – manufacture proteins
 Endoplasmic reticulum – system of membrane-enclosed canals forming a network in the
cytoplasm to transport materials in and out of the cell
Types:
a. Rough ER – lined with ribosomes
b. Smooth ER –lack ribosomes
 Golgi Apparatus – involved in the secretion of several chemical products, membrane
repair and transport in and out of the cell
 Lysosome – cell’s recycling center and garbage disposal; contain powerful enzymes and
break down worn-out organelles
 Centriole – play an important role in organizing the spindle during cell division
 Chloroplast – structure where photosynthesis takes place, contain the green pigment
chlorophyll
 Cell wall - surrounds and protects the plasma membrane; protective outer support in
plant cell
 Vacuole – membrane-enclosed cavities w/c serves as fluid tank of the cell
 Cytoskeleton – set of fibers responsible for cell shape, movement and physical texture

III. Review of Functional Groups:

Organic Molecules based on Functionality:

Functional groups:
 are collections of atoms in organic chemistry molecules that contribute to the chemical
characteristics of the molecule and participate in predictable reactions.
 These groups of atoms contain oxygen or nitrogen or sometimes sulfur attached to a
hydrocarbon skeleton.
The most common functional groups can be divided into three types:
1. Hydrocarbons – compounds containing only the elements of Carbon and Hydrogen
Like:
 Alkanes- have only C - C single bonds and no functional group. Ex. Ethane (CH3 - CH3)
 Alkenes – have a C – C double bond as their functional group. Ex. Ethylene (CH2 = CH2)
 Alkynes – have C – C triple bond as their functional group. Ex. Acetylene (HC ≡ CH)
 Aromatic Hydrocarbons – contain a benzene ring , a six-membered ring with three double
bonds

Hydrocarbons
General Functional
Type of Compound Example Name
Structure Group
 Alkane R-H CH3 - CH3 Ethane -
Carbon – Carbon
Alkene Ethylene double bond

Carbon – Carbon
Alkyne Acetylene
triple bond

Aromatic
Benzene Benzene ring
Hydrocarbon

2. Compounds containing a single bond to a heteroatom

Heteroatom - a non-carbon atom in a heterocyclic compound.
Compounds Containing a Carbon-Heteroatom Single Bond
General
Type of Compound Example Name Functional Group
Structure

Methyl
Alkyl Halide
Bromide

Methyl
Alcohol
Hydroxide

Ether Dimethyl
Ether

Amine Methylamine

Thiol - an organosulfur
compound that contains a
carbon-bonded Methanethiol
sulfhydryl or sulphydryl
(–C–SH or R–SH) group

3. Compounds containing C=O group

Compounds Containing a Carbon-Heteroatom Single Bond
Type of Functional
General Structure Example Name
Compound Group
Acetaldehyde
Aldehyde
(Ethanal)

Dimethyl Ketone
Ketone
(acetone)
 Carboxylic Acid Acetic Acid

Dimethyl Ester
Ester ( Methyl
Methanoate)

Acetamide
Amide
(ethanamide)

1. Hydroxyl Functional Group

Also known as the alcohol group.

The hydroxyl group is an oxygen atom bonded to a hydrogen atom.

Hydroxyls are often written as OH on structures and chemical formulas.

2. Aldehyde Functional Group

Aldehydes are made up of carbon and oxygen double bonded together and hydrogen bonded to
the carbon.

Aldehydes have formula R-CHO

This is the general structure of the aldehyde functional group

3. Ketone Functional Group

A ketone is a carbon atom double bonded to an oxygen atom that appears as a bridge
between two other parts of a molecule.

Another name for this group is the carbonyl functional group.

Note how the aldehyde is a ketone where one R is the hydrogen atom.

4. Amine Functional Group

Amine functional groups are derivatives of ammonia (NH3) where one or more of the
hydrogen atoms are replaced by an alkyl or aryl functional group.

5. Amide Functional Group

Amides are a combination of a carbonyl group and an amine functional group.

6. Ether Functional Group
An ether group consists of an oxygen atom forming a bridge between two different
parts of a molecule.
Ethers have formula ROR.

7. Ester Functional Group

The ester group is another bridge group consisting of a carbonyl group connected to
an ether group.
Esters have formula RCO2R.

8. Carboxylic Acid Functional Group

Also known as the carboxyl functional group.

The carboxyl group is an ester where one substituent R is a hydrogen atom.
The carboxyl group is usually denoted by -COOH

IV. The BIOMACROMOLECULES found in the cell.

A vast array of biomolecules is present in the cell. The structure of each biomolecule determines
in what chemical reactions it is able to participate, and hence what role it plays in the cell's life
processes.

BIOMACROMOLECULES – are biochemical substances found within a living organism.

Two Groups of Biochemical Substances:

1. Bioinorganic Substances w/c include: (do not contain Carbon)
a. water
b. salts
2. Bioorganic Substances w/c include:(contain Carbon)
a. Carbohydrates
b. Lipids
c. Proteins
d. Nucleic Acids
V. Water: The Solvent for Biochemical Reactions

Properties of water and their important roles as the major constituent of living system.

Water is a polar inorganic compound that is at room temperature a tasteless and odorless liquid,
nearly colorless with a hint of blue.

Density: 1,000 kg/m³

Formula: H2O
Boiling point: 100 °C
Molar mass: 18.01528 g/mol
IUPAC ID: Water, Oxidane
WATER is one of the major constituent of living matter. Around 50 to 90 percent of the weight
of living organisms is water. The basic material of living cells, known as protoplasm, consists of a
solution in water of fats, carbohydrates, proteins, salts and similar chemicals. Hence, water acts as a
solvent which transports, combines, and chemically breaks down these substances.

Water quality

Water quality is the physical, chemical and biological characteristics of water. It is a measure of
the condition of water relative to the requirements of one or more biotic species and or to any human
need or purpose. The desired quality of water must be related to the actual use of water supply. In
terms of water quality, there are a number of chemical contaminants of water which are of great
concern. These are lead, aluminum, nitrates and pesticides residues. It has been found that much of the
lead present in domestic water supplies has arisen from the use of lead pipes. Lead is dissolved in water
at a slow rate and thus it is the greatest concern in cases of slow-moving or stagnant water which has
got an acidic pH. Lead also gets into the environment through the use of lead-based chemicals as a
petrol additive. However, this source of lead is most significant as a contaminant of air. Aluminum,
instead, enters water supplies either as a natural component of water which has passed through acidic
soils or as the compound aluminum sulfate which is used in the clarification of peaty water. It has also
been suggested that aluminum and the disease known as Alzheimer are closely linked but this is still
being disputed. Nitrates in the water supply result mainly from the leaching of agricultural land. They
are also present in discharges from sewerage plants.

Moreover, some water supplies may contain chemicals which result in the hardness of the
water. This hardness is usually caused by the calcium salts and magnesium salts found in the water.
Normally, water found in kitchens, laundries, boilers and water-based heating systems do contain these
salts and these minerals can be removed from the water by a simple process known as water filtration.
This is imperative to be performed as drinkable water must be free from bacteria harmful to the health
of human beings. The coliform bacteria are used as indicators of bacteriological water quality. These are
associated with pathogenic organisms and are often indicators that a water supply has been
contaminated with sewerage. If these bacteria are present in the water, there is a big possibility of fecal
contamination and the presence of a number of micro-organisms which may cause gastro-intestinal
infections in humans. These organisms might include species of Salmonella and Shigella, Vibrio cholera,
viral hepatitis A amongst others. They are destroyed by heat and chlorine-based disinfectants but can
be a hazard in drinking water, water used in the kitchen and last but not least, ice.

Water and living organisms

Water has a number of roles in living organisms:

 solvent
 temperature buffer
 metabolite
 living environment

These roles can be explained once we have understood the structure and bonding in a water
molecule, and between water molecules.

A molecular compound

Water is a molecular compound, with molecular formula H2O. The atoms in a water molecule
are held together by strong covalent bonds. These are very difficult to break.

The dot-and-cross diagram for a water molecule shows there are

two bonding pairs of electrons and two non-bonding pairs of electrons. The
four pairs repel one another, forming a tetrahedral pattern. In this way they
are as far from one another as possible. The molecule itself (the spatial distribution of atoms) is
described as 'bent', 'angular' or 'non-linear'.

The two electrons in each oxygen-hydrogen bond are not shared equally. They are more strongly
attracted to the oxygen atom. The bond is polar, it has a 'negative end' (the oxygen atom) and a
'positive end' (the hydrogen atom).

A hydrogen bond forms between a non-bonding pair of electrons on the oxygen atom of one
water molecule and the hydrogen atom ('positive end') of another water molecule. The hydrogen bond
is about ten times weaker than a single covalent bond.

With this understanding we can begin to understand how water fulfils its various roles in biological
systems.

Solvent

Most compounds with ionic bonding, e.g. metal salts, dissolve in water. The oxygen atoms of
water molecules are attracted to cations (ions with a positive charge) and water molecules surround it.
These water molecules attract more water molecules and hydrogen-bonds form between them. The
result is a cluster of water molecules around the ion. We say the ion is hydrated.
 Similarly anions (ions with a negative charge) become surrounded by clusters of water
molecules. This time it is the positive ends of the water molecule, the hydrogen atoms, that are
attracted to the anion.

A wide range of molecular compounds also dissolve in water, including sugars, amino acids,
small nucleic acids and proteins. All these molecules are polar. This means they have a positive end and
a negative end as the result of polar covalent bonds within them. Of the important biological molecules
only the non-polar lipids (fats and oils) and large polymers (e.g. polysaccharides, large proteins and
DNA) do not dissolve.

The water acts as a solvent for chemical reactions and also helps transport dissolved compounds
into and out of cells.

Another important property is that many compounds dissolve and transfer a proton (a hydrogen
nucleus) to a water molecule. The result is an acidic solution with pH < 7. Compounds that release a
proton in this way are called acids. For example,

CH3COOH (aq) + H2O (aq) CH3COO- (aq) + H3O+ (aq)

H3O+(aq) is called a hydroxonium ion and is responsible for the acidic properties of the solution.

Some molecules receive a proton from a water molecule. The result is an alkaline solution with pH > 7.
Compounds that accept a proton in this way are called bases. For example, OH-(aq) is called a hydroxide
ion and is responsible for the alkaline properties of the solution.

Temperature buffer

Cells host a huge range of chemical reactions. Many of these are catalyzed by Enzymes. Enzyme
activity is sensitive to temperature and reactions only occur in a narrow range of temperatures. Water
helps to buffer temperature changes because of its relatively high specific heat capacity (the heat
required to raise 1 kg of water by 1 oC). It also has relatively large enthalpy of vaporization (heat energy
required to convert a liquid to a gas) and enthalpy of fusion (heat energy required to convert a solid to
a liquid). This is reflected in the unusually high boiling and melting points of water:

Liquid Molecular Bpt / oC Mpt / oC Specific heat capacity / kJ kg-1 oC -1

formula
Water H2O 100 0 4.18
Ethanol C2H5OH 79 -117 2.46
Benzene C6H6 80 6 1.05
Tetrachloromethane CCl4 77 -23 0.86

Metabolite

Chemical reactions take place in cells. Collectively these reactions together are
called metabolism, i.e. all the chemical and physical processes within a cell. The chemicals involved are
called metabolites. Water is a metabolite in many reactions, either as a reactant or as a product of
reaction. For example, it's involved in photosynthesis, digestion and aerobic respiration.
 When water reacts with a chemical to break it into smaller molecules the reaction is described
as hydrolysis.

When water is formed as one of the products when two molecules join together the reaction is
described as condensation.

Living environment

Many organisms, such as fish, live in water and cannot survive out of it. They have adapted to living in it.

Ice floats on water. This is because ice is less dense than water. The reason is that ice has a giant
structure with every oxygen atom at the centre of a tetrahedral arrangement of hydrogen atoms (two
are covalently bonded and two are hydrogen-bonded).

In freezing weather, ice forms on the surface of ponds and lakes forming an insulating layer above the
water below. This provides a living environment for some organisms until the ice melts. Organisms can
also live under the ice.

The surfaces of ponds and lakes (and other forms of water) are covered in a 'skin' of water molecules.
While most objects break through this skin, it is strong enough to support small insects such as pond
skaters. The skin forms because of the increased attraction between water molecules (cohesive forces)
at the surface.

VI. Carbohydrates
Carbohydrates- are the most abundant class of bioorganic molecules on planet earth. Although their
abundance in the human body is relatively low, carbohydrates constitute about 75% by mass of
dry plant materials.

Green (chlorophyll containing) plants produce carbohydrates via photosynthesis. In this process, CO2
from the air and H2O from the soil are the reactants, and sunlight absorbed by chlorophyll is the energy
source.

Chemical Equation:
chlorophyll
CO2 + H2O + solar energy Carbohydrates (C6H12O6) + O2
Plant enzymes
Main Uses of Carbohydrates produced by Plants:
1. Serve as structural elements in the form of cellulose
2. Provide energy reserves for plants in the form of starch
Dietary intake of plant materials is the major dietary source for human and animals.

Functions of Carbohydrates in Humans:

1. Carbohydrate oxidation provides energy.
2. Carbohydrate storage in the form of glycogen, provides a short-term energy reserve.
3. Carbohydrates supply carbon atoms for the synthesis of other biochemical substances (proteins,
lipids, and nucleic acids).
4. Carbohydrates form part of the structural framework of DNA and RNA molecules.
5. Carbohydrates linked to lipids are structural components of cell membrane,
 6. Carbohydrates linked to proteins function in a variety of cell-cell and cell-molecule recognition
processes.

General Formula of Carbohydrates:

CnH2nOn
Carbohydrate is:
 a polyhydroxy aldehyde
 a polyhydroxy ketone
 a compound yields polyhydroxy aldehyde or polyhydroxy ketone upon hydrolysis

Ex.

Classification of Carbohydrates on the basis of molecular size:

1. Monosaccharide – ( simple sugar) is a carbohydrate that contains a single polyhydroxy aldehyde
or polyhydroxy ketone unit. It cannot be broken down into simplier units by hydrolysis. Pure
monosaccharides are water-soluble, white, crystalline solids.
Ex. Fructose(honey sugar) and glucose(grape sugar)

2. Oligosaccharide – is a carbohydrate that contains two to ten monosaccharide units covalently

bonded to each other.
Disaccharide – is the most common oligosaccharide containing two monosaccharide units.
Crystalline and water soluble. Ex. Sucrose(cane sugar) and Lactose (milk sugar). Within the
human body, oligosaccharides are often found associated with proteins and lipids complexes
and have both structural and regulatory functions.
Complete hydrolysis of an oligosaccharide produces monosaccharide. Upon hydrolysis, a
disaccharide produces two monosaccharides.
 3. Polysaccharide is a polymeric carbohydrate that contains many monosaccharide units covalently
bonded to each other. Polysaccharides often contain several thousand monosaccharide units.
Polymers: May contain a few 100s to > million monosaccharide units

Examples:
Cellulose: Paper, cotton, wood
Starch: Bread, pasta, potatoes, rice, corn, beans, peas, etc.

Chemical Formula for Sugars

Sugars are a white crystalline group of soluble carbohydrates that are sweet tasting in nature.
These sugar molecules include glucose, sucrose, lactose, fructose, maltose, lactose and galactose. Sugar
molecules are classified as monosaccharides or disaccharides. The following table lists the common
sugar molecules are their chemical formula.

Name Type of sugar (mono =1 or di =2 sugar units) Chemical formula of sugar

Glucose Monosaccharide C6H12O6
Fructose Monosaccharide C6H12O6
Galactose Monosaccharide C6H12O6
Lactose Disaccharide (glucose + galactose) C12H22O11
Sucrose Disaccharide (glucose + fructose) C12H22O11
Maltose Disaccharide (glucose + glucose) C12H22O11

 CHIRALITY: Handedness in Molecules

Monosaccharides are the simplest type of carbohydrate. Before considering specific
structures and specific reactions of monosaccharides, we will consider an important general
structural property called HANDEDNESS, which most saccharides exhibits.
Most monosaccharides exists in two forms w/c are related to each other:
1. Left-handed form
2. Right-handed form
The relationship is of the mirror images. This concept is the key to understanding molecular
handedness. A mirror image is the reflection of an object in a mirror. Objects can be divided into two
classes:
1. Objects with superimposable mirror images- are images that coincide at all points when the
images are laid upon each other.
2. Objects with nonsuperimposable mirror images – are images where not all points coincide when
the images are laid upon each other.
Chiral Molecule – is a molecule whose mirror images are not superimposable and have handedness.
Achiral Molecule - whose mirror images are superimposable
Chiral Center – is an atom in a molecule that has four different groups tetrahedrally bonded to it.
 Ex. An organic molecule that contains a carbon atom with four different groups attached to it in a
tetrahedral orientation.
Like: A trisubstituted methane molecule such as Bromochloroiodomethane.
H CHO
A chiral monosaccharide is a three carbon
Br – C – Cl H – C – OH monosaccharide called glyceraldehyde

I CH2OH

Bromochloroiodomethane glyceraldehyde

Chiral Centers within molecules are often designated by a small asterisk. Note the chiral centers of the
following molecules.
H CH3

CH3 – CH2 – *C – CH3 CH3 – CH2 – CH2 – *C – CH2 – CH3

OH H
2 - Butanol 3 – Methylhexane
Organic molecules may contain
more than one chiral center.

 STEREOISOMERISM: Enantiomers and Diastereomers

Isomers – are the left and right-handed forms of a chiral molecule.
Stereoisomers – are isomers that have the same molecular and structural formulas but differ in
the orientation of atoms in space.

The Two Major Structural Features that Generate Stereoisomerism:

1. The presence of a chiral center in a molecule
2. The presence of “structural rigidity” in a molecule

Structural Rigidity:
 is caused by restricted rotation about chemical bonds
 it is the basis for the cis - trans isomerism, a phenomenon found in some substituted
cycloalkanes and alkenes

Two Types of Stereoisomers:

1. Enantiomers – are stereoisomers whose molecules are nonsuperimposable mirror images of
each other. It comes from the Greek word “enantios” w/c means opposite.
- left and right handed forms of a molecule
2. Diastereomers – are stereoisomers whose molecules are not mirror images of each other
- Cis-trans isomers (of both the alkene and the cycloalkane types) are
diastereomers.
 Enantiomers Diastereomers

The diagram showing the “Thinking pattern” involved in using the terms stereoisomers,
enantiomers and diastereomers.
No Do molecules have the same Yes
molecular formula?

The molecules are The molecules are

not isomers isomers

Yes Are the atoms bonded in the same

No
order in the two molecules?

The molecules are The molecules are

STEREOISOMERS CONSTITUTIONAL ISOMERS

Are the molecules NONSUPERIMPOSABLE

MIRROR IMAGES? No
Yes

The molecules are

The molecules are
DIASTEREOMERS
ENANTEOMERS

DESIGNATING HANDEDNESS USING FISCHER PROJECTION FORMULAS

A Fischer Projection Formula – is a two-dimensional structural notation for showing the spatial
arrangement of groups about chiral centers in molecules. Originated
by a German Chemist Hermann Emil Fischer.
- In this formula, a chiral center is represented as the intersection of vertical and
horizontal lines.
- The atom at the chiral center, w/c is almost always carbon, is not explicitly shown.
chiral

- The tetrahedral arrangement of the four groups attached to the atom at the chiral
center is governed by the following conventions(agreements):
1. Vertical lines from the chiral center represent bonds directed to the printed
page.
2. Horizontal lines from the chiral center represent bonds directed out of the
printed page.
The Fischer projection formulas for monosaccharides:
 The monossacharide carbon chain is positioned vertically with carbonyl group (aldehyde or
ketone) at or near the top. The smallest monosaccharide that has a chiral center is the
compound glyceraldehyde (2,3 dihydroxypropanal).

 The two enantiomers of glyceraldehyde:

 The enantiomer with the chiral center OH group on the right, is a right-handed isomer (D-
glyceraldehyde)where D –means Dextro (right)
 The enantiomer with the chiral center OH group on the left, is a left-handed isomer (L-
glyceraldehyde) where L- means Levo (left)
  The Fischer formula projection for the compound 2,3, 4-trihydroxybutanal, a monosaccharide
with four carbons and two chiral centers.

 There are four stereoisomers for this compound – two pairs of enantiomers

First enantiomeric pair Second enantiomeric pair

The D, L system used to designate the handedness of glyceraldehyde enantiomers is extended to

more than one chiral center in the following manner.
1. The carbon chain is numbered starting at the carbonyl group end of the molecule
2. The highest-numbered chiral center is used to determine D or L configuration and nomenclature.

D-erythrose L-erythrose D-threose L-threose

Based on the structures,compounds:

A and B – first enatiomeric pair
C and D – second enatiomeric pair
A and C – first diastereomeric pair
A and D –second diastereomeric pair
B and C –third diastereomeric pair
B and D -fourth diastereomeric pair

Epimers – members of each four pairs of diastereomers. They are diastereomers whose molecules differ
only in the configuration at one chiral center.
EXERCISES:
1. Draw a Fisher projection formula for the enantiomer of each of the following monosaccharides and
classify each as a D or an L enantiomer.

a. b. c. d.

2. Characterize the following pairs of structures as enantiomers and diastereomers.

a. b.

and and

c.

and

CONSTITUTIONAL ISOMERS AND STEREOISOMERS

 H
H

PROPERTIES of ENATIOMERS:
Constitutional isomers and Diastereomers – differ in most physical and chemical properties. They have
different boiling points and melting points.
Enantiomers – nearly all the properties of a pair of enantiomers are the same. They have the same
boiling and melting points.
Enantiomers exhibit different properties in only two areas:
1. Their interaction w/ plane polarized light –optically active and called optical isomers
2. Their interaction w/ other chiral substances
Chiral molecules - optically active and Achiral molecules – optically inactive

Plane-polarized light – is an ordinary light passed through a polarizer, an instrument with lenses or
filters containing special types of crystals.
Polarimeter – an instrument used to measure the degree of rotation of plane-polarized light by
enantiomeric compounds.
Optically active compound- rotates the plane-polarized light

“When plane-polarized light is passed through a solution containing a single enantiomer, the plane-
polarized light is rotated counter-clockwise ( to the left or levorotatory) or clockwise (to the
right or dextrorotatory) depending on the enantiomer.”

“The two enantiomers of a pair rotate the plane-polarized light the same number of degrees, but in
opposite directions.”
 The notation (+) means rotation to the right(clockwise) while notation (-) means rotation to the left
(counter-clockwise)

CLASSIFICATION OF MONOSACCHARIDES:
Although there is no limit to the number of carbon atoms that can be present in a monosaccharide, only
monosaccharide with three to seven carbon atoms are commonly found in nature.

Monosaccharides are classified as: ( on the basis of type of carbonyl group)

1. Aldoses – contain an aldehyde functional group
2. Ketoses – contain a ketone functional group

Monosaccharides are often classified by both their number of carbon atoms and their functional
group. (Structural Characteristics)
Three-carbon monosaccharide is called TREOSE
Four - carbon monosaccharide is called TETROSE
Five- carbon monosaccharide is called PENTOSE
Six- carbon monosaccharide is called HEXOSE
Example:
1. Aldohexose – has 6 carbon atoms and aldehyde functional group
2. Ketopentose – has 5 carbon atoms and ketone functional group

Monosaccharides are also often called SUGARS w/c has sweet taste.

EXERCISES:
Classify each of the following monosaccharides according to both the number of carbon atoms
and the type of carbonyl group present.

THE FISCHER PROJECTION FORMULAS OF D-ALDOSES

THE FISCHER PROJECTION FORMULAS OF D-KETOSES
 BIOCHEMICALLY IMPORTANT MONOSACCHARIDE
1. D-Glyceraldehyde and Important intermediates in the process of glycolysis, a series of reactions
Dihydroxyacetone whereby glucose is converted into two molecules pyruvate.
2. D-Glucose Tastes sweet, nutritious and important in human diet. A grape sugar (20 -
30% by mass). Other names are dextrose and blood sugar. Blood sugar
normal concentration in the human body is in the range of 70-100mg/dL.
Cells use glucose as primary source of energy. Two hormones insulin and
glucagon controls glucose blood concentration within the normal range.
Abnormal functioning leads to diabetes.
3. D-Galactose Synthesized from glucose in the mammary glands for use in lactose(milk
sugar). Consists of glucose and galactose units. A brain sugar because it is
a component of glycoproteins(protein-carbohydrates compound) Present
in the chemical markers to distinguish blood types.
4. D-Fructose Known as levulose and fruit sugar and honey sugar. The sweetest-
tasting among sugars.Use as sweetener in the form of high fructose
corn syrup( HFCS)
5. D-Ribose Component of a variety of complex molecules, including ribonucleic
acids (RNA) and energy-rich compounds such as Adenosine
Triphosphate (ATP)Component of DNA molecules(2-deoxy-D-ribose)

HAWORTH PROJECTION FORMULAS

- by British Chemist Walter Norman Haworth

The structural presentations of the CYCLIC FORMS OF MONOSACCHARIDES

The cyclic forms of monosaccharides result from the ability of their carbonyl group to react
intramolecularly with the hydroxyl group.

The result is a cyclic hemiacetal ring system viewed “edge on” with oxygen ring atom at the
upper right (six-membered ring) or at the top (five-membered ring).

The hemiacetals have both an –OH group and an –OR group attached to the same carbon
atom. In the cyclic hemiacetals that monosaccharides form, it is the carbonyl carbon atom that
bears the –OH and –OR groups.

The D and L form of monosaccharide is determined by the position of the terminal CH2OH group
on the highest-numbered ring carbon atom.
D form - if the terminal CH2OH is positioned above the ring and L if the terminal CH2OH is
positioned below the ring.

Beta (β) if the CH2OH of the 5th Carbon and OH of the 1st Carbon are at the same side.
Alpha (α) if the CH2OH of the 5th Carbon and OH of the 1st Carbon are at opposite sides.
EXERCISES:
Draw the HAWORTH PROJECTION FORMULAS OF THE FOLLOWING.
1) 2) 3)

D - Talose D - Fructose
D - Mannose
 REACTIONS OF MONOSACCHARIDES:

Five Important Reactions of Monosaccharides: ( Aldoses and Ketoses, undergo similar reactions)
1. OXIDATION to Acidic Sugars
The redox of Chemistry monosaccharides is closely linked to that of the alcohol and aldehyde
functional groups.
Summary Diagram of the Reaction:

 Monosaccharide
oxidation can yield different types of ACIDIC SUGARS.
 The oxidizing agent used determines the product such as:
1) Tollen’s solution
2) Benedict’s solution

A. WEAK OXIDIZING AGENTS like TOLLEN’S and BENEDICT’S solutions, can oxidize the aldehyde end of
an aldose to give an ALDONIC ACID.
o Oxidation of the Aldehyde end of Glucose ----- produces GLUCONIC ACID
o Oxidation of the Aldehyde end of Galactose -----produces GALACTONIC ACID

Weak
oxidizing agent

 Aldoses and Ketoses are reducing sugars. With Tollen’s solution, glucose reduces Ag + to Ag and
with Benedict’s solution, glucose reduces Cu++ ion to Cu+ ion.
 Reducing sugar is a carbohydrate that gives a positive test with Tollen’s and Benedict’s
solutions.
 Aldoses acts as reducing agent while ketoses undergo a structural rearrangement that produces
an aldose and aldose then reacts. Thus both are reducing agents.
 Tollen’s and Benedict’s Tests – can be used to test for glucose in urine, a symptom for diabetes.
 For Benedict’s Test – if glucose is not present in urine (normal condition) the Benedict’s solution
remains blue.
 The presence of glucose is indicated by the formation of red precipitate.
 Test for the presence of glucose in the clinical laboratory uses Diastrix – reagent trips for
urinalysis.

B. STRONG OXIDIZING AGENTS - can oxidize both ends of a monosaccharide at the same time (the
carbonyl group and the primary alcohol group). To produce a dicarboxylic acid.
  Such polyhydroxy dicarboxylic acids are known as ALDARIC ACID.
 For GLUCOSE, the oxidation produces GLUCARIC ACID.

C. BIOCHEMICAL SYSTEMS ENZYMES – can oxidize the primary alcohol end of an aldose like GLUCOSE,
without oxidation of the aldehyde group, to produce an ALDURONIC ACID.
 For GLUCOSE, such an oxidation produces D – GLUCURONIC ACID.

2. REDUCTION to Sugar Alcohols

The Carbonyl group present in a monosaccharide (either an aldose or a ketose) can be reduced to a
hydroxyl group using Hydrogen as the reducing agent.
 For aldoses and ketoses, the product of the reduction is the corresponding HYDROXY
ALCOHOL, w/c is sometimes called a SUGAR ALCOHOL.
Example:
The reduction of D – Glucose gives D – GLUCITOL.

D – Glucitol is also known by the common name D-Sorbitol. Hexahydroxy alcohols such as D-Sorbitol
have properties similar to those of the trihydroxy alcohol GLYCEROL.
 These alcohols are used as:
o Moisturizing agents in foods and cosmetics because of their affinity for water.
o D- Glucitol is used as sweetening agent in chewing gum
 - Bacteria in tooth decay cannot use polyhydroxy alcohols as source of food
- Accumulation of D-Sorbitol in the eye is a major factor in the formation of cataracts
due to diabetes.

3. GLYCOSIDE Formation
Hemiacetals can react with alcohols in acid solution to produce acetals.
Hemiacetals – are the cyclic forms of monosaccharide.
- they have two –OR groups attached to the same carbon atom.

β –D - Glucose Methyl -β –D - Glucoside

The general name for monosaccharide acetals is GLYCOSIDE.

 A GLYCOSIDE is an acetal formed from a cyclic monosaccharide by replacement of the
hemiacetal carbon –OH group with an –OR group.
 A glycoside produced from glucose is called Glucoside and from galactose is
galactoside, and so on.
 Glycosides can exist in both α and β forms.
 Glycosides are named by listing the alkyl or aryl group attached to the oxygen, followed
by the name of the monosaccharide involved, with the suffix –ide appended to it.

α β
BLOOD TYPES and Monosaccharide type present:
Human blood is classified into four types: A, B, AB and O. Type “O” a universal donor while “AB”
a universal recipient.
The biochemical basis for the various blood types involved monosaccharides. The plasma
membrane of the red cells
carries biological markers
made up of
monosaccharides.
4. PHOSPHATE ESTER Formation
The hydroxyl group of a monosaccharide can react with inorganic oxyacids to form into inorganic
esters. Phosphate esters, formed from phosphoric acid and various monosaccharides, are commonly
encountered in biochemical systems.

Example:
Specific enzymes in the human body catalyze the esterification of the hemiacetal group (carbon
1) and the primary alcohol group (carbon 6) in glucose to produce the glucose 1-phosphate and
glucose 6-phosphate.

5. AMINO Sugar Formation

If one of the hydroxyl groups of a monosaccharide is replaced with an amino group, an amino sugar
is produced. In naturally occurring amino sugars, of w/c there are three common ones, the amino
group replaces the carbon 2 hydroxyl group.

The Three Common Amino Sugars are:

Amino sugars and their N-acetyl derivatives are important building blocks of polysaccharides
found in Chitin and hyaluronic acid. The N-acetyl derivatives of D-glucosamine and D-galactosamine
are present in the biochemical markers on red blood cells, w/c distinguish the various blood types.
An acetyl group has the structure:

It can be considered to be derived from acetic acid by removal of the –OH portion of that structure.

Acetic Acid

DISACCHARIDES
A monosaccharide that has a cyclic form (hemiacetal forms) can react with an alcohol to form a
glycoside (acetal). The same type of reaction can be used to produce a disaccharide, a carbohydrate in
w/c two monosaccharide are bonded together. In disaccharide formation, one of the monosaccharide
reactants functions as a hemiacetal, and the other functions as an alcohol.

Chemical reaction:
Monosaccharide + Monosaccharide Disaccharide + H2O
(Functioning as a (Functioning (Glycoside)
hemiacetal) as an alcohol)

The bond that links the two monosacchaides of a disaccharide (glycoside) together is called a
GLYCOSIDIC Linkage.
A GLYCOSIDIC LINKAGE is the bond in a disaccharide resulting from the reaction between the
hemiacetal carbon atom –OH group of one monosaccharide and an –OH group on the other
monosaccharide. It is always a carbon-oxygen-carbon bond in a disaccharide.

Maltose
Maltose – often called malt sugar, is produced whenever the polysaccharide starch breaks down, as
happens in plants when seeds germinate and in human beings during starch digestion.
Malt (germinated barley that has been baked and ground) contains maltose; hence the name malt
sugar.
- common ingredient in baby foods and is found in malted milk.
- it is made up of two D-glucose units, one of w/c must be α-D-Glucose.

The Formation of Maltose from two Glucose molecules:

 The glycosidic linkage between the two glucose units is called an α(1 4) linkage. The two –OH groups
that form the linkage are attached respectively, to carbon 1 of the first glucose unit (in an α configuration) and to
the carbon 4 of the second.
Maltose is a reducing sugar because the glucose unit on the right has a hemiacetal carbon atom (C-1).
Thus this glucose unit can open and close; it is in equilibrium with its open-chain aldehyde form.

Three forms of the maltose molecule: α-maltose, β-maltose and the open-chain form.

The most important chemical reaction of maltose is HYDROLYSIS. Hydrolysis of D-maltose ,

whether in a laboratory or in living organism, produces two molecules of D-glucose.
Acidic condition or the enzyme maltase is needed for the hydrolysis to occur.

D-Maltose + H2O H+ or maltase 2 D-glucose

Cellobiose
Cellobiose is produced as an intermediate in the hydrolysis of the polysaccharide cellulose. Like
maltose, cellobiose contains two D-glucose monosaccharide units. It differs from maltose in that one of
the D-glucose units- the one functioning as a hemiacetal-must have a β configuration instead of the α
configuration for maltose. This change in configuration results in a β(1-4) glycosidic linkage.
The difference between the structural notation for an α(1-4) glycosidic linkage and β(1- 4) glycosidic
linkage.
α(1- 4)

Monosaccharide C-1 C- 4 Monosaccharide

β(1-4)

Like maltose, cellobiose is a reducing sugar, has three isomeric forms in aqueous solution, and
upon hydrolysis produces two D-glucose molecules.

D- Cellobiose + H2O H+ or cellobiase 2 D-glucose

Despite similarities, Maltose can be digested by humans and readily fermented by yeast but cellobiose
cannot be digested by humans and fermented by yeast.

Lactose
Lactose is made up of a β-D-glucose unit joined by β(1- 4) glycosidic linkage.
- The principal carbohydrate in milk. About 7- 8% in human mother’s milk and only 4 – 5% in cow’s milk.
- For people who has a problem on lactose digestion and absorption, the problem is lactose intolerance.
They lack the enzyme lactase needed hydrolyze lactose to galactose and glucose. Galactose has to be
converted into glucose before it can be used by cells.
- Souring of milk is caused by bacteria which converts lactose to lactic acid. Milk has to be pasteurized to
kill bacteria.

Lactose + H2O Lactase Glucose + Galactose

Sucrose
Sucrose - a common table sugar and is the most abundant of all disaccharides and occurs throughout
plant kingdom.
- A non-reducing sugar
- Exist only in one form-there is no α and β isomers, and an open-chain form is not possible.
- It is produced commercially from sugar cane juice (20% by mass sucrose) and sugar
beets(17% by mass sucrose).
- D-sucrose composed of two monosaccharide units α-D-glucose and β-D-fructose.
- The glycosidic linkage is an α, β(1 – 2). The –OH group on carbon 2 of D-fructose(the
hemiacetal carbon) reacts with the –OH group on carbon 1 of D-glucose (the hemiacetal
carbon).

α, β(1 – 2)

α-glucose

β - fructose sucrose
 - Sucrase, the enzyme needed to break the α, β(1 – 2) linkage in sucrose
- It is easily digested substance in human body
- Sucrose hydrolysis(digestion) produces an equimolar mixture of glucose and fructose called
invert sugar. (Invert due to its rotation to plane polarized light from + to - ).

D-Sucrose + H2O H+ or sucrase D-glucose + D-fructose

POLYSACCHARIDES invert sugar

Polysaccharide - is a polymer that contains many monosaccharide units bonded to each other by
glycosidic linkages.
- often called Glycan

Important parameters that distinguish various polysaccharide from each other:

1. The identity of the monosaccharide repeating units in the polymer chain.
Homopolysaccharide – is a polysaccharide with only one type of monosaccharide monomer is
present. Ex. Starch, glycogen, cellulose and chitin(cell wall of fungi)
Heteropolysaccharide - is a polysaccharide with two or more monosaccharide monomers.
Ex. Hyaluronic acid and heparin (anticlotting agent present in the body).
2. The length of the polymer chain. Polysaccharide chain length can vary from less than a hundred
monomer units up to million units.
3. The type of glycosidic linkage between monomer units.
4. The degree of branching of the polymer chain. The ability to form branched-chain structures.

Polymer Chain:
• Polymers of many
monosaccharide
units bonded with
glycosidic linkages

• Two types:
– Linear - homo
– branched, -
hetero-
polysaccharides
STORAGE POLYSACCHARIDE
Storage Polysaccharide – a storage form for monosaccharides and used as an energy source in cells.

Starch
– Glucose is the monomeric unit
– Storage polysaccharide in plants
– Two types of polysaccharides isolated from starch:
– Amylose: Straight chain polymer - 15 - 20% of the starch and has alpha (1  4) glycosidic
bonds
– Molecular Mass: 50,000 (up to 1000 glucose units)
• Amylopectin:
- Branched chain polymer - 80 - 85 % of the starch alpha (1-4) glycosidic bond for straight chain
and alpha (1-6) for branch
- Molecular Mass: 300,000 (up to 100,000 glucose units) - higher than amylose
- Amylopectin is digested more readily by humans (can hydrolyze alpha linkages but not beta
linkages)
Glycogen
– Human and animal storage polysaccharide
– Contains only glucose units
– Branched chain polymer – alpha (14) glycosidic bonds in straight chains and alpha
(16) in branches
– Molecular Mass: 3,000,000 (up to 1,000,000 glucose units)
– Three times more highly branched than amylopectin in starch
– Excess glucose in blood stored in the form of glycogen
Glycogenesis
Glucose Glycogen
Glycogenolysis

STRUCTURAL POLYSACCHARIDE
Structural Polysaccharide – serves as a structural element in plant cell walls and animal exoskeleton.

Cellulose
• Linear homopolysaccharide with beta (14) glycosidic bond
• Up to 5000 glucose units with molecular mass of ~900,000 amu
– Cotton ~95% cellulose and wood ~50% cellulose
– Humans don’t have enzymes that hydrolyze beta (14) linkages - so they can not digest
cellulose -- animals also lack these enzymes but they can digest cellulose because they
have bacteria in their guts to hydrolyze cellulose
– It serves as dietary fiber in food-- readily absorbs water and results in softer stools
– 20 - 35 g of dietary fiber is desired everyday
HO

HO O O
OH
HO O O
OH (1-4) OH
HO O O
OH (1-4)
O O OH
OH (1-4)
O OH
OH

Chitin
– Similar to cellulose in both function and structure
 – Linear polymer with all beta (14) glycosidic linkages - it has a N-acetyl amino derivative
of glucose
– Function is to give rigidity to the exoskeletons of crabs, lobsters, shrimp, insects, and
other arthropods

N-acetyl
Β-D-glucoseamine

ACIDIC POLYSACCHARIDE
• Acidic polysaccharides - polysaccharides with a repeating disaccharide unit containing an amino
sugar and a sugar with a negative charge due to a sulfate or a carboxyl group.
• Structural polysaccharide present in connective tissue associated with joints, cartilage, synovial
fluids in animals and humans
– Primary function is lubrication necessary for joint movement
– These are heteropolysaccharides - have more than one type of monosaccharide
monomers is present.
• Examples:

Hyaluronic Acid:
– Alternating residues of N-acetyl-beta-D-glucosamine and D-glucuronic acid.
– Highly viscous - serve as lubricants in the fluid of joints and part of vitreous humor of the
eye.

Heparin
– An anticoagulant-prevents blood clots.
Polysaccharide with 15–90 disaccharide residues per chain

Dietary Considerations and Carbohydrates:

Nutrition
• Foods high in carbohydrate content constitute over 50% of the diet of most people of the world
-- a balanced dietary food should contain about 60% of carbohydrate:
– Corn in South America
– Rice in Asia
– Starchy root vegetables in parts of Africa
 – Potato and wheat in North America
• Nutritionists divide dietary carbohydrates into two classes:
– Simple carbohydrates: dietary monosaccharides or disaccharides - sweet to taste
commonly referred to as sugars - 20 % of the energy in the US diet
– Complex carbohydrates: Dietary polysaccharides -- starch and cellulose - normally not
sweet to taste

Glycemic Foods
• A developing concern about intake of carbohydrates involves how fast the given dietary
carbohydrates are broken down to glucose within the human body
• Glycemic effect refers to:
– how quickly carbohydrates are digested
– how high blood glucose rises
– how quickly blood glucose levels return to normal
• Glycemic index (GI) has been developed for rating foods

GLYCOLIPIDS AND GLYCOPROTEINS: Cell Recognition

• A glycolipid is a lipid molecule that has one or more carbohydrate (or carbohydrate derivative)
units covalently bonded to it.
• A glycoprotein is a protein molecule that has one or more carbohydrate (or carbohydrate
derivative) units covalently bonded to it.
• Such carbohydrate complexes are very important in cellular functions such as cell-cell
recognition, cell adhesion and cellular communication.

VII. Lipids

Structure and Classification of Lipids

• Lipid: An organic compound found in living organisms that is insoluble (or only sparingly soluble)
in water but soluble in non-polar organic solvents.
• Unlike other biomolecules, lipids do not have a common structural features that serves as the
basis for defining such compounds.
• Classification: Based on two methods
– Biochemical function
– Saponification (hydrolysis under basic conditions)

Classification based on Biochemical Function:

• For purposes of simplicity of study lipids are divided into five categories based on their
biochemical function:
– Energy-storage lipids - triacylglycerols
– Membrane lipids - phospholipids, sphingoglycolipids, and cholesterol
– Emulsification lipids - bile acids
– Chemical messenger lipids - steroid hormones and eicosanoids)
– Protective-coating lipids - biological waxes
Classification Based on Saponification:
• Saponification reaction: Hydrolysis reaction that occurs in a basic solution.
• Based on saponification reactions lipids are divided into two categories :
– Saponifiable lipids – triacylglycerols phospholipids, sphingoglycolipids, cholesterol and
biological waxes
 – Nonsaponifiable lipids - bile acids, steroid hormones and eicosanoids)
Structure:
• Lipids exhibit structural diversity
• Some are esters, some are amides, and some are alcohols (acyclic and cyclic) and some are
polycyclic.

Five Categories of Lipids on the basis of Lipid Functions:

1. Energy-storage lipids (triacylglycerols)
2. Membrane lipids (phospholipids,sphingoglycolipds,and cholesterol)
3. Emulsification lipids ( bile acids)
4. Messenger lipids ( steroid hormones and eicosanoids)
5. Protective coating lipids ( biological waxes)

Fatty Acids

Fatty Acids – is a naturally occurring monocarboxylic acid.

• Carboxylic acids with linear (unbranched) carbon chain
• Even # of Carbon atoms:
– Long chain fatty acids: C12 - C26
– Medium chain fatty acids: C6 - C11
– Short-chain fatty acids: C4 - C5
• Two Types of Fatty Acids::
– Saturated - all C-C bonds are single bonds
– Unsaturated
• Monounsaturated: one C=C bond
• Polyunsaturated: 2 or more C=C bonds present - up to six double bonds are present in fatty
acids

Saturated Fatty Acids

• Fatty acid with a carbon chain in which all C-C bonds are single bonds
 • Numbering starts from the end of -COOH group
• Structural notation: it indicates number of C atoms
• Example - Lauric acid has 12 C atoms and no double bonds so it is (12:0)
O

H 3C (CH) 10 C OH
O
or
C
11 9 7 5 3 1 OH
12 10 8 6 4 2
Unsaturated Fatty Acids
• A monounsaturated fatty acid is a fatty acid with a carbon chain in which one carbon–carbon
double bond is present.
• Different ways of depicting the structure

Polyunsaturated Fatty Acids (PUFAs)

• A polyunsaturated fatty acid is a fatty acid with a carbon chain in which two or more carbon–
carbon double bonds are present.
• Up to six double bonds are found in biochemically important PUFAs.
• Two types of unsaturated fatty acids.
– Omega (ω)-3 fatty acids - An unsaturated fatty acid with its endmost double bond three
carbon atoms away from its methyl end.
– Omega (ω)-6 fatty acid is an unsaturated fatty acid with its endmost double bond six
carbon atoms away from its methyl end.

Selected Fatty Acids of Biological Importance

Structural Notation Common Name Structure
Saturated Fatty Acids
12:0 Lauric Acid
14:0 Myristic Acid
16:0 Palmitic Acid
18:0 Stearic Acid
20:0 Arachidic Acid
Monounsaturated Fatty Acids
16:1 9 ω -7 Palmitoleic Acid
18:1 9 ω -9 Oleic Acid
Polyunsaturated Fatty Acids
18:2 9,12
ω-6 Linoleic Acid
18:3 9,12,15
ω-3 Linolenic Acid
20:4 5,8,11,14
ω-6 Arachidonic Acid
20:5 5,8,11,14,17
ω-3 EPA (Eicosapentaenoic Acid)
22:6 4,7,10,13,16,19
ω-3 DHA(Docosahexaenoic Acid)
Omega Acids
• Essential Fatty Acids: Must be part of diet
• Nutritionally important Omega-3 and Omega-6 fatty acids
– Linolenic acid – Omega-3
– Linoleic acid – Omega-6
• Linoleic Acid Deficiency:
– Skin redness - becomes irritated
– Infections and dehydration
– Liver abnormalities
– Children need it the most
– Human milk has more than cow’s milk
  Distinguish between a triglyceride, phosphatidic acid, and a phosphoacyglyceride.
 Find out the physical properties of fatty acids.
 Determine the structure and classification of lipids.
 List down the major physiological functions of fatty acids.
 Know the names and structures of the saturated and unsaturated fatty acids from C12 to C20.
VIII. Proteins
 Lists all the characteristics of proteins and determine its properties.
 Describe the structural characteristics of protein, its classifications and functions.
 Distinguish the different biochemically important peptides.
 Explain protein hydrolysis and protein denaturation.
IX. Enzymes
 Describes the general characteristics of enzymes, enzyme structures.
 Name and classify the different types of enzymes.
 Describes enzymes specificity.
 Determine the factors that affect enzyme activity.

X. Vitamins
 Explain the general characteristics of vitamins.
 Classify the vitamins based on water or fat solubility.
 To determine the iodine value of some oils.
 To compare the iodine values of several oils.
XI. Nucleic Acids
 Identify the type of nucleic acids and different nucleotides as its building blocks.
 Describe the nitrogenous bases and sugars found in nucleic acids
 Describe the formation of nucleosides and nucleotides.
 Draw the some primary nucleic acid structure.
 Differentiates DNA from RNA.
 Summarize the central dogma.
 Describe mutations and DNA sequencing.
XII. Biochemical Energy Production
 Distinguish between anabolic and catabolic processes.
 Discuss the relationship between catabolic and anabolic processes in cellular metabolism.
 Determine the important intermediate compounds in metabolic pathways.
 Summarize the citric acid cycle and electron transport chain.
XI. Carbohydrate Metabolism
 State the primary function of the glycolytic pathway.
 Outline the steps involved in the conversion of glucose to pyruvate.
 Name the types of reactions involved in glycolysis. Indicate which reaction involves the
production of use of ATP.
 Name the enzyme that catalyzes each reaction in glycolysis and specify the enzymes that take
part in the regulation of glycolysis
XIII. Lipid Metabolism
 Differentiate between the different types and classifications of fatty acid obtained from our
diet.
  Explain how fats, cholesterol and fat-soluble vitamins are digested and absorbed.
 Distinguish the relationship between lipogenesis and citric acid cycle intermediates.
 Distinguish the relationships between lipid and carbohydrate metabolism.
XIV. Protein Metabolism
 Describes the protein digestion and absorption.
 Explain the importance of protein in the diet.
 Define nitrogen balance and state under what conditions a positive nitrogen balance and
negative nitrogen balance occur.
 Define each of the following pathways in protein metabolism and state their importance:
transamination, oxidative deamination, urea biosynthesis, gluconeogenesis.
 TOPICS OBJECTIVES
Orientation  Discuss the MVGO of the institution and the School of Arts and
1. Vision, Mission, Goals Sciences
and Objectives of the  Discuss the Greening CHMSC and Gender and Development
Institution and School  Relate the role of the course in the attainment of the
of Arts and Sciences institutional MVGO and the departmental goals & objectives.
2. Greening CHMSC  Identify the different class expectations
awareness  .Familiarize with the course content and course requirement.
3. Gender and
Development
Awareness
I. Overview of Biochemistry  Define the terms used in Biochemistry and biochemical analysis.
 Appreciate the role of biochemists in the society.
II. The Organization of Cells  Define the cell theory.
and Its Functions  Differentiate the prokaryotic cell from a eukaryotic cell.
 Identify the parts of the cell and give its functions.
III. Water: The Solvent for • Explain the properties of water which are important to its role as
Biochemical Reactions the major constituent of living system.
IV. Review of the Functional • Review classes of organic molecules based on functionality i.e.,
Groups alcohol, aldehyde, ketone, carboxylic acid, forms of the
carboxylate ion, primary and secondary amines, ammonium
forms.
• Know the names of the biomacromolecules found in the cell.
V. Carbohydrates  Classify the different types of carbohydrates, its occurrence and
functions.
 Identify stereoisomers and distinguish between enantiomers and
diastereomers, including epimers and anomers.
 Draw the Fisher projection formulas for aldoses and ketoses and
classify the molecules according to the type of stereoisomer.
 Write the equations for monosaccharides undergoing reduction,
oxidation, esterification, and glycoside formation.
VI. Lipids  Distinguish between a triglyceride, phosphatidic acid, and a
phosphoacyglyceride.
 Find out the physical properties of fatty acids.
 Determine the structure and classification of lipids.
 List down the major physiological functions of fatty acids.
 Know the names and structures of the saturated and
unsaturated fatty acids from C12 to C20.
VII. Proteins  Lists all the characteristics of proteins and determine its
properties.
 Describe the structural characteristics of protein, its
classifications and functions.
 Distinguish the different biochemically important peptides.
 Explain protein hydrolysis and protein denaturation.
VIII. Enzymes  Describes the general characteristics of enzymes, enzyme
structures.
 Name and classify the different types of enzymes.
 Describes enzymes specificity.
 Determine the factors that affect enzyme activity.
IX. Vitamins  Explain the general characteristics of vitamins.
 Classify the vitamins based on water or fat solubility.
 To determine the iodine value of some oils.
 To compare the iodine values of several oils.
X. Nucleic Acids  Identify the type of nucleic acids and different nucleotides as its
building blocks.
 Describe the nitrogenous bases and sugars found in nucleic acids
 Describe the formation of nucleosides and nucleotides.
 Draw the some primary nucleic acid structure.
 Differentiates DNA from RNA.
 Summarize the central dogma.
 Describe mutations and DNA sequencing.
XI. Biochemical Energy  Distinguish between anabolic and catabolic processes.
Production  Discuss the relationship between catabolic and anabolic
processes in cellular metabolism.
 Determine the important intermediate compounds in metabolic
pathways.
 Summarize the citric acid cycle and electron transport chain.
XI. Carbohydrate  State the primary function of the glycolytic pathway.
Metabolism  Outline the steps involved in the conversion of glucose to
pyruvate.
 Name the types of reactions involved in glycolysis. Indicate
which reaction involves the production of use of ATP.
 Name the enzyme that catalyzes each reaction in glycolysis and
specify the enzymes that take part in the regulation of glycolysis
XII. Lipid Metabolism  Differentiate between the different types and classifications of
fatty acid obtained from our diet.
 Explain how fats, cholesterol and fat-soluble vitamins are
digested and absorbed.
 Distinguish the relationship between lipogenesis and citric acid
cycle intermediates.
 Distinguish the relationships between lipid and carbohydrate
metabolism.
XIII. Protein Metabolism  Describes the protein digestion and absorption.
 Explain the importance of protein in the diet.
 Define nitrogen balance and state under what conditions a
positive nitrogen balance and negative nitrogen balance occur.
 Define each of the following pathways in protein metabolism
and state their importance: transamination, oxidative
deamination, urea biosynthesis, gluconeogenesis.
 LABORATORY EXPERIMENTS IN BIOCHEMISTRY:
Experiment.
Experiment Titles Objectives
Nos.
1 Water  To determine the properties of water that
make it a suitable medium for sustaining
life in biological systems
2 Buffers and Buffers Capacity  To prove that buffers solutions maintain
pH.
 To show that buffers maintain pH within
certain limits.
 To enable students to undertake
calculations on pH changes in buffer
systems.
3 Colloids and their Properties  To determine the properties of colloids
and how they function in physiological
systems.
4 Separation and Identification  To separate a dye mixture into its
of a Dye Mixture components.
 To evaluate the efficiency of a
chromatographic process in separating
mixtures.
5 Lipids  To examine some physical and chemical
properties of lipids
 To prepare soap.
 To compare the properties of soap with
detergents.
6 Analysis and Denaturation of  To be able to identify the different amino
Proteins acids in a protein sample.
7 Effects of Antibiotics on Lactic • To determine the effect of different
Acid Fermentation antibiotics on lactate fermentation.
8 Enzymes and Factors that  To isolate and determine the properties
Affect enzyme Activity of catalase.
 To determine the effect of sulfides on
catalase activity.
 To prove the presence of a protein factor
in enzymes.
 To determine the effect of temperature
on enzyme activity.
9 Determination of the Iodine  To determine the iodine value of some
Value of a Fat Sample oils.
 To compare the iodine values of several
oils.
10 Nucleic Acids  To isolate from RNA from yeast.
 To test the properties of the isolated
RNA.
11 Analysis of Urine  To test the presence of some normal
 products of metabolism in the urine.
 To test for the presence of some
pathological constituents of urine.
12 Analysis of Saliva • Determine the usual and unusal
components of saliva may help in the
diagnosis of a pathologic condition in an
individual.
13 Analysis of Blood • To determine the different constituents of
the blood.
• To differentiate oxyhemoglobin from
reduced hemoglobin.

Laboratory Manual:
 Department of Chemistry. (2013). Laboratory manual in biochemistry. Iloilo City:
University of San Agustin

Electronic Sources:
 https://trixiesolis.files.wordpress.com/2015/02/essential-biochemistry-third-edition-
charlotte-w-pratt.pdf
 http://www.cengagebrain.co.uk/content/9781285019772.pdf
 http://downloads.obsidian-
inc.com/Books/Introduction%20to%20Organic%20and%20Biochemistry%20(7th%20Editi
on).pdf
 https://umkcarnivores3.files.wordpress.com/2012/02/campbell-biochemistry-6th-ed-
1.pdf
 http://m-learning.zju.edu.cn/G2S/eWebEditor/uploadfile/20120925133308427.pdf
 http://www.student.oulu.fi/~taneliha/Harpers_Illustrated_Biochemistry_(29th_Edition).
pdf
 https://thephilomaths.files.wordpress.com/2013/03/lippincott__039_s_illustrated_revie
ws__biochemistry__5th_edition.pdf