M1 Introduction

Hello Everyone! Before we start with today’s lesson and all other lessons ahead, I want you to
always remember this phrase:

 
 
 
 
 
 
 
 
 
 
 
 
Biochemistry is sometimes called biological chemistry. It can be seen as a study of the
components and composition of living things and how they come together to become life.  It is
the study of chemical processes that give rise to the complexity of life. It is also related to
molecular biology that concerns genetic information encoded in DNA as well as understanding
the structures, functions, and interactions of biological macromolecules. The following lessons
and activities will enhance your knowledge, understanding, and how to deal with the complexity
of life.
M1 Lesson 1 - Significance and Relation of Biochemistry to other Fields of Sciences
Biochemistry Overview:
Understanding biochemistry begins with defining it according to different approaches, giving its
significance and relation to other fields of sciences.
Biochemistry is defined as a branch of science exploring the chemical processes within and
related to living organisms. As a laboratory science, it brings together biology and chemistry that
uses chemical knowledge and techniques to understand and solve biological problems.
Biochemistry focuses on processes happening at a molecular level to understand how the
structure of a molecule relates to its function and to predict how molecules will interact. It
focuses on what is happening inside the cells, studying components like proteins, lipids,
carbohydrates, nucleic acids, and organelles. It also looks at how cells communicate with each
other especially during growth or fighting illness.
Biochemistry is a description of life at the molecular level that includes a description of all the
complex interrelated chemical changes within the cell called metabolism. The processes of
growth, reproduction, and heredity are intimately related to intermediary metabolism.
Multicellular organisms exhibiting these properties and capacities can be attributed to the
properties of the individual cells of that organism where the behavior of each individual cell can
be understood in terms of its chemical structure and the chemical changes occurring within that
cell.
Biochemistry includes the study of the chemical substances and processes that occurs in plants,
animals, and microorganisms as well as the changes they undergo during development and life. It
deals with a chemistry of life where it draws on the techniques of analytic, organic, physical
chemistry as well as physiology concerning the molecular basis of vital processes. Metabolism
describes all these chemical changes within the organisms, the degradation, building up of
complex molecules, and gaining energy necessary for life processes. Enzymes are organic
catalysts that act on these chemical changes wherein their existence depends on the genetic
apparatus of the cell. On this premise, biochemistry enters into the investigation of chemical
changes in disease, drug action, and other aspects of medicine, nutrition, genetics, and
agriculture.
Biochemistry involves a study of the molecules that make up all living things which are
inherently interesting and help us better understand how organisms operate and therefore covers
wide application. In medicine, biochemistry can help us figure out how microorganisms operate
and figure out ways to kill them. It also allows us to understand the different effects that
medication would have on our body so that the harmful effects of drugs can be known mitigated.
In agriculture, biochemistry can help you to develop pesticides that kill weeds and insects without
causing excessive damage to the crops. Biochemistry has many applications that can help the
human race and that is the reason why it is important to understand how biological organisms
function at the chemical level.
Biochemistry covers a range of scientific disciplines that includes genetics, microbiology,
forensics, plant science, and medicine where advances in this field of study are exciting and
fascinating.
Biomedical Importance
Biochemical studies have shed light on many aspects of health and disease that open up new areas
of biochemistry. Biochemistry makes significant contributions to the fields of cell biology,
physiology, immunology, microbiology, pharmacology, and toxicology, as well as the fields of
inflammation, cell injury, and cancer. These close relationships, therefore, emphasize that life
depends on biochemical reactions and processes.
Additional Learning Materials:  You may want to learn more about biochemistry by reading
and viewing the following learning materials.         
M1 Lesson 2 - Properties of Water and Chemical Reactions in the Cell
Properties of water
Water is the most abundant molecule in cells, accounting for 70% or more of total cell mass.  The
interactions between water and the other constituents of cells are of central importance in
biological chemistry. Water is a polar molecule with the hydrogen atoms having a slight positive
charge and the oxygen with a slight negative charge. This polarity enables water molecules to
form hydrogen bonds with each other or with other polar molecules, as well as interacting with
positively or negatively charged ions. As a result of these interactions, ions and polar molecules
are readily soluble in water (hydrophilic). In contrast, nonpolar molecules, which cannot interact
with water, are poorly soluble in an aqueous environment (hydrophobic). Consequently, nonpolar
molecules tend to minimize their contact with water by associating closely with each other
instead. Such interactions of polar and nonpolar molecules with water and with each other play
crucial roles in the formation of biological structures, such as cell membranes.
Water has a number of roles in living organisms such as solvent, temperature buffer, metabolite,
and living environment. It acts as a solvent for many chemical reactions and also helps transport
dissolved compounds into and out of cells. It is a metabolite in many chemical reactions like
photosynthesis, digestion, and aerobic respiration.
The manner in which water interacts with a solvated biomolecule influence the structure both of
the biomolecule and of water itself. Water becomes a reactant or product in many metabolic
reactions as an excellent nucleophile.
 Regulation of water balance depends upon hypothalamic mechanisms that control thirst, on
antidiuretic hormone (ADH), on retention or excretion of water by the kidneys, and on
evaporative loss. Nephrogenic diabetes insipidus, which involves the inability to concentrate
urine or adjust to subtle changes in extracellular fluid osmolarity, results from the
unresponsiveness of renal tubular osmoreceptors to ADH. 
For more discussion please read this PowerPoint presentation: Properties of
waterppt.pptx  download
Chemical reactions in the Cells
Most activities that take place within cells involve the interactions of atoms and
molecules where bonds between atoms are broken and new bonds form to make different
molecules. Energy is needed to form bonds between atoms, and energy is released when bonds
break. Cells use chemical energy for life activities.
M2 Introduction
Carbohydrates

Carbohydrates represent a broad group of substances which include sugars, starches, gums, and
celluloses. The common attributes of carbohydrates are that they contain only the elements
carbon, hydrogen, and oxygen and that their combustion will yield carbon dioxide plus one or
more molecules of water. The formulas of many carbohydrates can be written as carbon hydrates,
Cn(H2O)n, .

Carbohydrates are widely distributed in plants and animals; they have important structural and
metabolic roles. Chemically carbohydrates are aldehydes or ketone derivatives of polyhydric
alcohols. Glucose is the most important carbohydrate; the major metabolic fuel of mammals
(except ruminants) and are the universal fuel of the fetus. It is the precursor for the synthesis of
all the other carbohydrates in the body.
M2 Lesson 1 - Definition, Sources, Properties and Functions of Carbohydrates
M2 Lesson 1 Definition of Carbohydrates (1).pptx  download
 
DEFINITION:
Carbohydrates, called sugars and starches, are polyhydroxy aldehydes or ketones, or compounds
that can be hydrolyzed to them. They are synthesized in green plants through photosynthesis,
whereby energy from the sun is stored as chemical energy in carbohydrates. In the body, they are
used for bursts of energy needed during exercise in the form of glucose.
Sources of Carbohydrates
Carbohydrates in foods include all sugars
A] sucrose [table sugar],
B] glucose,
C] fructose,
C] lactose,
D] maltose and
E] starches (found in pasta, bread, and grains). These carbohydrates can be digested by the body
and provide energy for cells.
There are other carbohydrates that the human body doesn't digest, including insoluble fiber,
A] cellulose from plants, and
B] chitin from insects and other arthropods.
Unlike sugars and starches, these types of carbohydrates don't contribute calories to the human
diet.
                                    https://www.thoughtco.com/examples-of-carbohydrates-603884 (Links to
an external site.)

 
Healthy sources of carbohydrates include both food sources-animal and plant products, such as
fresh fruits, vegetables, corn, potatoes, milk and milk products.
Unhealthy sources include soda, white bread, artificial sugar, pastries, and other highly
processed foods. Carbohydrate foods are an important source of fiber and other
nutrients. Sugars and starches provide glucose, the main energy source for the body.
Major sources of Healthy Carbohydrates
Vegetables, fruits, whole grains, milk, and milk products are the major food sources of
carbohydrates 
Good Carbs:
 Vegetables: All of them. ...
 Whole fruits: Apples, bananas, strawberries, etc.
 Legumes: Lentils, kidney beans, peas, etc.
 Nuts: Almonds, walnuts, hazelnuts, macadamia nuts, peanuts, etc.
 Seeds: Chia seeds, pumpkin seeds.
  Whole grains: Choose grains that are truly whole, as in pure oats, quinoa, brown rice, etc.
Carbohydrates have six major functions in the body:
providing energy,
regulating blood glucose,
sparing the use of proteins for energy,
breaking down fatty acids,
providing dietary fiber and
natural sweetener for foods.
Note: Glucose energy is stored as glycogen, with the majority of it in the muscle and liver.
Primary Function of Carbohydrates.
The primary role of carbohydrates is to supply energy to all cells in the body. Many cells prefer
glucose as a source of energy versus other compounds like fatty acids. Some cells, such as red
blood cells, are only able to produce cellular energy from glucose.
What is a GOOD Carbohydrate?
Carbohydrates are all about energy and are found in foods like fruits, vegetables, bread, pasta,
and dairy products. Your body uses these foods to make glucose, which is your body's main
energy source. ... "Carbohydrates provide the body with the energy it needs and is a good
source of many vitamins and minerals. Those kinds of carbohydrates are described
as good carbs or low glycemic foods. Good carbs include vegetables, low glycemic fruits such as
berries and apples, as well as legumes and unprocessed high fiber whole grains.
M2 Lesson 2 - Classifications of Carbohydrates
Chemical classification of carbohydrates
Carbohydrates, also called Carbs, are defined as aldehydic or ketonic compounds with some
number of oxydrilic groups (so polyhydroxy aldehydes or ketones as well).
Many of them, but not all, have general formula (CH2O)n ,  in addition to carbon (C), oxygen (O),
and hydrogen (H), include nitrogen or sulfur.
On the basis of the number of forming units, three major classes of carbohydrates can be defined:
monosaccharides, oligosaccharides, and polysaccharides.
  Monosaccharidesor simply sugars are formed by only one polyhydroxy aldehydic or ketonic
unit.
The most abundant monosaccharide is D-glucose, also called dextrose.
 Oligosaccharides are formed by short chains of monosaccharide units (from 2 to 20) linked
one to the next by chemical bonds, called glycosidic bonds.
The most abundant oligosaccharides are disaccharides, formed by two monosaccharides, and
especially in the human diet the most important are sucrose (common table
sugar), lactose, and maltose. Within cells many oligosaccharides formed by three or more
units do not find themselves as free molecules but linked to other ones, lipids or proteins, to
form glycoconjugates.
 Polysaccharides are polymers consisting of 20 to 107 monosaccharide units; they differ each
other for the monosaccharides recurring in the structure, for the length and the degree of
branching of chains or for the type of links between units.
Whereas in the plant kingdom several types of polysaccharides are present, in vertebrates
there is only a small number.
Polysaccharides are defined as:
homopolysaccharides if they contain only one type of monosaccharide as starch, glycogen, and
chitin;
heteropolysaccharides, instead, contain two or more different kinds (e.g. hyaluronic acid).
Note: the term “saccharide” derives from the Greek word “sakcharon”, which means sugar.
Physiological classification of carbs
On the basis of their degree of polymerization, they can be classified as:
 simple: mono- and disaccharides (also known as “sugars”) and tri- and tetrasaccharides
(oligosaccharides);
 complex: the polysaccharides.
A further classification lays the foundations on the possibility of being used directly for energy
purpose, so:
 available, as glucose, fructose, galactose between monosaccharides,
sucrose, lactose, maltose and maltodextrin between oligosaccharides,
and starch and glycogen between polysaccharides;
  not available, as xylose (monosaccharide), lactulose (see lactose), and raffinose (respectively
di- and trisaccharide), fiber (cellulose, hemicellulose, lignin, pectins, etc.) and resistant or not
digestible starch(polysaccharides). The members of this class, also if ingested, are not
digestible nor absorbable and will be fermented by intestinal flora with the release of short-
chain fatty acids and so yielding some energy.
M2 Lesson 3 - Isomerism: Fischer Structure and Haworth Structure
Key Takeaways: Structural or Constitutional Isomerism
1.Structural or constitutional isomers share the same chemical formulas, but their atoms are
arranged differently.
2.The three types of structural isomers are skeletal isomers, positional isomers, and functional
group isomers.
3.Structural isomers differ from stereoisomers, which share the same chemical formulas and the
same order of atoms, but have different three-dimensional configurations.
Types of Structural Isomers
There are three categories of structural isomers:
  Skeletal isomerism (also called chain isomerism) - structural isomers in which components
of the skeleton are arranged in a different order. This is most commonly seen when the
skeleton or backbone consists of a carbon chain.
 Position isomerism (also called regioisomerism) - constitutional isomers in which a
functional group or substituent changes position on a parent structure.
 Functional group isomerism - structural isomers with the same molecular formula, but with
atoms connected differently so dissimilar functional groups are formed.
Structural Isomer Examples
1.Butane and isobutane (C4H10) are structural isomers of each other.
2.Pentan-1-ol, pentan-2-ol, and pentan-3-ol are structural isomers that exhibit position
isomerism.
3.Cyclohexane and hex-1-ene are examples of functional group structural isomers.
Molecules that have multiple stereocenters become difficult to draw quickly.  The Fischer
projection is a convention for drawing molecules and quickly designating stereochemistry
without laboriously trying to use wedges and hashes to specify the 3-D relationships.

A historical note:  this was developed at a time before it was possible to experimentally prove
absolute configuration for any molecule.  Emil Fischer, an early carbohydrate chemist, developed
it so that it could continue to be used correctly and consistently even after experimental proof of
configuration was developed.

The definition is that every carbon is specified completely by a cross designating the carbon (at
the center) and the four bonds to that carbon.  The stereochemistry of the bonds is defined (now)
as the horizontal bonds are in front of the plane (coming toward you, the viewer); the vertical
bonds are behind the plane (going away from you).  Sometimes (often, even), bonds to hydrogen
are omitted.
M3 Introduction
Have you ever wondered why oil and water do not mix?  Or what do butter, oil, fatty acids,
cholesterol, and vitamin A have in common?  Well, they all belong to a group of compounds
called lipids. 
Lipid is a family of substances that are insoluble in water but soluble in nonpolar solvents and
solvents of low polarities, such as diethyl ether.  They are not defined by functional groups, thus
they have a variety of structures and functions.
They contain many nonpolar C—C and C—H bonds and few polar bonds resulting in their water
insolubility.  The lipids found in biological systems are either hydrophobic or amphipathic.
Examples of Lipids
M3 Objectives

At the end of the module,  you will be able to:

Properties of Lipids
Lipids are a heterogeneous group of compounds that are related more by their physical than by
their chemical properties.  They are relatively insoluble in water and soluble in a non-polar
solvent.  It is greasy to touch and leaves a permanent oily stain on the paper.   Lipids are lighter
than water.   
Pure lipids are colorless with bland odor and taste.  When heated strongly, undergoes
decomposition forming acrid flammable vapors and when ignited, they burn with a sooty flame.
Lipids are poor conductors of heat and electricity and therefore serve as excellent insulators for
the body, slowing the loss of heat through the skin.
Functions of Lipids:
Lipids are a major source of energy for the body, and they also provide the hydrophobic barrier
that permits partitioning of the aqueous contents of cells and subcellular structures.  
They serve additional functions in the body, for example, some fat-soluble vitamins have
regulatory or coenzyme functions, and the prostaglandins and steroid hormones play major roles
in the control of the body’s homeostasis.  
Lipids also act as precursors for other lipids and play a role in the transport of other lipids in the
body.  They also function as emulsifying agents in the gastrointestinal tract.
Deficiencies or imbalances of lipid metabolism can lead to some of the major clinical problems
encountered by physicians, such as atherosclerosis and obesity.
Reactions of Lipids:
 1.Hydrolysis
Fats and oils can be hydrolyzed in the presence of an acid, a base, or specific enzymes known
as lipases.  The hydrolysis of fats and oils in the presence of a base is used to make soap and is
called saponification. 
2.Hydrogenation
The double bonds in fats and oils can undergo hydrogenation.  The hydrogenation of vegetable
oils to produce semisolid fats is an important process in the food industry. Chemically, it is
essentially identical to the catalytic hydrogenation reaction described for alkenes.
In commercial processes, the number of double bonds that are hydrogenated is carefully
controlled to produce fats with the desired consistency (soft and pliable).  In the preparation of
margarine, for example, partially hydrogenated oils are mixed with water, salt, and nonfat dry
milk, along with flavoring agents, coloring agents, and vitamins A and D, which are added to
approximate the look, taste, and nutrition of butter. 
3.Oxidation
Fats and oils that are in contact with moist air at room temperature eventually undergo oxidation
and hydrolysis reactions that cause them to turn rancid, acquiring a characteristic disagreeable
odor.  One cause of the odor is the release of volatile fatty acids by hydrolysis of the ester bonds.
Butter, for example, releases foul-smelling butyric, caprylic, and capric acids.  Microorganisms
present in the air furnish lipases that catalyze this process. Hydrolytic rancidity can easily be
prevented by covering the fat or oil and keeping it in a refrigerator.
M3 Lesson 2 - Classification of Lipids
Based on their reaction with water:
1.Hydolyzable lipids
 – These are compounds that can be converted into smaller molecules by hydrolysis.
 – These are compounds that are derived from fatty acids.
Examples:  Fats, oils, waxes, phospholipids, lipoproteins
2.Non-hydolyzable lipids
– These are compounds that cannot be cleaved into smaller molecules by hydrolysis.
Examples:  steroids, prostaglandins, vitamins, hormones
Based on their structure:
1.Simple lipids
– Esters of fatty acids with various alcohols.
Examples:  triglycerides and waxes
2.Complex lipids
– Lipids containing parts other than fatty acids and alcohol.
– Found in cell membranes, brain, nervous tissues, myelin sheaths of nerves, and blood platelets
Examples:  phospholipids, sphingolipids, glycolipids, and lipoproteins
3.Derived lipids
– These compounds are products of hydrolysis of simple and complex lipids
Examples:  steroids, prostaglandins, vitamins, hormones
M3 Lesson 3 - Fatty Acids
Fatty acids are carboxylic acids with long, unbranched carbon chains.  Naturally occurring fatty
acids have an even number of carbon atoms.  They contain a polar end and a non-polar end. 
Apart from the carboxylic acid (-COOH) group, fatty acids have no functional groups, except that
some do have double bonds.
Fatty acids can be classified as saturated or unsaturated.  Saturated fatty acids only contain
single bonds while unsaturated fatty acids contain at least one double bond. 
Unsaturated fatty acids with one double bond are called monounsaturated fatty acids while
those with two or more double bonds are called polyunsaturated fatty acids. 

 
Unsaturated fatty acids can be classified as cis fatty acids or trans-fatty acid.  cis Fatty acids have
two hydrogen atoms on the same side of the double bond, which creates a kink in the
structure.  trans Fatty acids have two hydrogen atoms on the opposite side of the double bond,
which results in a similar structure to that of saturated fatty acid.
You can check out this video to learn more about fatty acids:
Naming Fatty Acids
Fatty acids can be named using a shorthand nomenclature.  First, count the number of carbons. 
Next, count the number of double bonds and note their position: Delta – starting from the
carboxylic end, and omega – starting from the methyl end.

 
            Write the number of carbons followed by a colon and the number of double bonds present,
if any.  For unsaturated fatty acids, indicate if you started counting from the delta or omega end.
For example:

10:1 Δ7
Essential fatty acids are fatty acids that cannot be produced by the body.  It includes alpha-
linolenic acid (ALA) and linoleic acid (LA).
 
o α-linolenic acid is the parent fatty acid of the omega-3 family
o Linoleic acid is the parent fatty acid of the omega-6 family
M3 Lesson 4 - Simple and Complex Lipids
Simple Lipids 
1.Triglycerides
 Also known as triacylglycerols
 Humans store energy as triglycerides in adipose cells below the surface of the skin, in the
breast area, and surrounding internal organs.
 Hydrolyzed by enzymes called lipases to produce energy. 
 Complete metabolism of a triglycerides yields: CO2, H2O, and energy.
a. Fats 

 o
 A mixture of triglycerides containing a high proportion of long-chain, saturated fatty
acids
  Mostly obtained from animals 
  Fats have higher melting points
  Solids at room temperature.
1.Oils

o
 A mixture of triglycerides containing a high proportion of long-chain, unsaturated
fatty acids, or short-chain, saturated fatty acids
  Oils are fats in the liquid state 
  Oils have lower melting points
   Liquids at room temperature.
  Mostly obtained from plants and fish
2.Waxes 
 They are esters of fatty acids with high molecular weight alcohols.
 Because of their long nonpolar C chains, waxes are very hydrophobic.
 Form protective coating on plants and fruits, and in animal
 
Complex Lipids
1.Phospholipids
 Also called phosphoglycerides or glycerophospholipids
 Long-chain fatty acids on a glycerol backbone attached to a phosphoric acid molecule
containing an alcohol substituent. (usually amino alcohol)
   The essential components of cell membranes and are found in small concentrations in other
parts of the cell.
2.Sphingolipids
 A class of lipids built from long-chained fatty acids attached to a sphingosine backbone rather
than glycerol.
a. Sphingomyelin  - Found in the myelin sheath surrounding nerve cells
Glycolipids - Often called cerebrosides because of their abundance in brain tissue
3.Lipoproteins
 Lipoproteins are the primary means of transport of cholesterol among tissues
 Secreted by the small intestine and liver into the circulating blood
 Composed of lipids and special proteins (apolipoproteins)a. Chylomicron
They are formed in the mucosal cell of the intestine. They deliver triglycerides to the adipose
tissue and muscle. They also deliver dietary cholesterol to the liver
b. Very Low-Density Lipoproteins
They are formed in the liver for the export of triglycerides. They transport triglycerides from the
liver to the muscle and adipose tissue for storage or energy.
c.  Low-Density Lipoproteins
They are primary carriers of cholesterol in the blood for delivery to the tissues.
d. High-Density Lipoproteins
They are scavengers for cholesterol from peripheral tissues. They also return cholesterol to the
liver for metabolism.
M3 Lesson 5 - Derived Lipids
Derived Lipids
1.Steroids
 Steroids are a group of lipids whose carbon skeletons contain several fused rings:
2.Sterols
 Also known as steroid alcohol
  Occur naturally in plants, animals, and fungi
  Plant sterols have cholesterol-lowering properties
a. Cholesterol

o
 Precursor for vitamins and hormones
 Elevated levels of cholesterol in the bloodstream lead to coronary artery disease,
heart attack, etc.
  Transported through the bloodstream by lipoproteins.
3.Bile Salts
 Bile salts are oxidation products of cholesterol.
 Bile salts are powerful detergents. 
 Responsible for fat emulsification
 The secretion of bile salts and cholesterol into the bile by the liver is the only mechanism by
which cholesterol is excreted.
4.Fat-Soluble Vitamins
 Vitamins are organic compounds and vital nutrients that an organism requires in limited
amounts.
 They cannot be produced by the body.
 Fat-soluble vitamins are stored in the body for long periods of time.
 They pose a greater risk of toxicity than water-soluble vitamins.
 Vitamins A, D, E, K
5.Hormones
 Hormones are chemical messengers that are secreted directly into the blood, which carries
them to organs and tissues of the body to exert their functions.
  Cholesterol is the starting material for the synthesis of steroid hormones.
a. Adrenocorticoid hormones
b.Sex hormones
 
6.Ketone Bodies
 Ketone bodies serve as an energy source for the heart, kidney, and skeletal muscles, thereby
preserving the limited glucose for use by the brain.
 Produced by the liver from the breakdown of fatty acids during periods of low food intake,
carbohydrate restrictive diets, starvation, prolonged intense exercise, or in untreated type 1
diabetes mellitus.
7.Eicosanoids
 Eicosanoids are metabolites of arachidonic acid. 
 Responsible for inflammatory responses, on the intensity and duration of pain and fever, and
on reproductive function.
 Inhibits gastric acid secretion
 Regulates blood pressure through vasodilation or constriction
 Inhibits or activates platelet aggregation and thrombosis.
a. Prostaglandins (PGs)
b.Thromboxanes (TXs)
c. Leukotrienes (LTs)
d.Lipoxins (LXs).