CELL: THE BASIC UNIT OF LIFE

CELLS - are the basic structural and functional units of all living organisms. It is the smallest unit of an organism capable of independent life.
*4 main groups of tissue:
1. Muscular
2. Nervous
3. Connective
4. Epithelial
*Cell Structures:
 PLASMA MEMBRANE – the cell’s protective coat. This is the outer lining of a eukaryotic cell. This membrane serves to separate and
protect a cell from its surrounding environment and is made mostly from a double layer of proteins and lipids, fat-like molecules.
 CYTOSKELETON – the cell’s scaffold. It is an important, complex, and dynamic cell component. It acts to organize and maintain the
cell's shape; anchors organelles in place; helps during endocytosis, the uptake of external materials by a cell; and moves parts of the
cell in processes of growth and motility.
“bones and muscles” of the cell.
 CYTOPLASM – a cell’s inner space. It is a large fluid-filled space inside the cell, sometimes called the cytosol.
In eukaryotes, the cytosol is the "soup" within which all of the cell's organelles reside. It is also the home of the cytoskeleton.
 CYTOPLASMIC ORGANELLES - a set of "little organs", that are adapted and/or specialized for carrying out one or more vital functions.
Organelles are found only in eukaryotes and are always surrounded by a protective membrane.
 NUCLEUS – a cell’s center. It houses the cell's chromosomes and is the place where almost all DNA replication and RNA synthesis
occur. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
*Replication consists of three phases: initiation, elongation and termination. The basis of replication is the pairing of the four
bases found in DNA: adenine pairs with thymine, cytosine with guanine. The process, which results in two DNA helices instead of one,
is mediated by several dozen proteins. DNA is a double-stranded molecule that has a long chain of nucleotides. RNA is a single-
stranded molecule which has a shorter chain of nucleotides. DNA replicates on its own, it is self-replicating. RNA does not replicate on
its own.
 RIBOSOME – the protein production machine. Ribosomes are found in both prokaryotes and eukaryotes.
Looks like polka dots that transports materials between the cytoplasm and nucleus; make proteins in the cell. The ribosome is a large
complex composed of many molecules, including RNAs and proteins, and is responsible for processing the genetic instructions carried
by an mRNA.
 MITOCHONDRIA – the power generators. These are self-replicating organelles that occur in various numbers, shapes, and sizes in the
cytoplasm of all eukaryotic cells. Energy producer “powerhouse” of the cell and sausage like.
 ENDOPLASMIC RETICULUM - network of membranes. It has 2 types.
a) Rough ER- rough appearance because it has ribosomes; helps make protein.
b) Smooth ER- no ribosomes; makes fats or lipids.
 GOLGI APPARATUS - Made of saclike membrane; Sort and package proteins and carbohydrates; move materials within and out of the
cell.

 LYSOSOME - Sac of digestive enzymes found in Golgi bodies. Contains digestive enzymes to break down food, unwanted cells or cell
parts.

*Types of Lysosomes:
1. Primary Lysosomes - They have newly pinched-off vesicles from the Golgi apparatus.
The primary lysosomes are small in size and contain hydrolytic enzymes in the form of granules.
2. Secondary Lysosomes - Also called heterophagosome or digestive vacuole. A secondary lysosome is formed by the fusion of a food-
containing phagosome with a lysosome.
 3. Residual Bodies (Residual or Tertiary Lysosomes). They are those lysosomes in which only indigestible food materials have been left.

4. Autophagic Vacuoles( Autophagosome or Autolysosomes) - They are produced by the fusion of a number of primary lysosomes
around worn-out or degenerated and digested intercellular organelles.

*Significance of Lysosmes:
1. In WBC or leucocytes. Cells of leucocytes digest foreign proteins, bacteria, and viruses.

2. In autophagy. During starvation, the lysosomes digest stored food contents such as proteins, fats, and glycogen of the cytoplasm and
transport the necessary amount of energy to the cell.
3. In metamorphosis(Frog).
During the transformation of a tadpole into a frog, the embryonic tissues such as gills and tail are digested by the lysosomes and utilized by
other body cells.
4. In fertilization. The lysosomal enzymes present in the acrosome of sperm cells digest the limiting membrane of the ovum(egg). Thus, the
sperm is able to enter the ovum and start fertilization.
 CENTRIOLES - Log-like structures made of proteins; Pull chromosomes apart during cell division. Lines up beneath the plasma
membrane when a cell is about to make cilia or flagella.
Difference of Animal and Plant Cell:

*Some important BIOCHEMICAL REACTIONS:

1. Oxidation-Reduction Reaction (REDOX Reaction)
- reaction that involves the transfer of electrons between chemical species (the atoms, ions, or molecules involved in the reaction).
2. Hydrolysis - a reaction which involves the splitting of a covalent bond by water. Hydrolysis ("hydro" = water and "lysis" = break) involves
adding water to one large molecule to break it into multiple smaller molecules.
3. Condensation - involves forming large molecules from smaller building blocks . When a gas turns to a liquid.
4. Decarboxylation - The process by which a carbon atom - in the form of carbon dioxide - breaks off from a larger organic molecule.

Rust Formation Photosynthesis Respiration

 HYDROCARBONS

Hydrocarbons - The simplest organic compounds are those composed of only two elements: carbon and hydrogen.

*Fundamental Series of Hydrocarbons:

1. ALKANES Series - Also called the saturated hydrocarbon because all the carbon atoms are joined by single bonds only.
The general formula for alkanes is CnH2n + 2.

Naming for Alkanes:

a. n + chemical name - This is used for straight chain only.
b. ISO - For chains that have a branch in carbon number 2 this prefix is added to the name of the carbon chain.
c. Tert - This prefix is used when there are 2 branches attached in carbon number two.
2. Alkenes Series - In this family there is at least one carbon–carbon double bond. It has a general formula of CnH2n.
Ethylene System - (CH2=CH2) this is the basic formula for ethylene, the word ethylene is added to the last name of the compounds.
3. Alkynes Series - Alkynes are series of unsaturated aliphatic hydrocarbons characterized by triple covalent bonds between carbon atoms.
NOMENCLATURE - Naming alkynes follows the same rules we discussed earlier for the IUPAC nomenclature rules for alkanes.
This is the brief summary of steps:
Step 1. Identify the parent chain.
Step 2. Identify the substituents.
Step 3. Number the parent chain giving the triple bond the lowest locant
Step 4. Put everything together having the substituents in alphabetical order.
 Module 2: MACROMOLECULES

A. CARBOHYDRATES – called hydrates de carbon and has a formula (C.H2O)n. It is defined as polyhydroxy aldehydes or polyhydroxy
ketones or substances that when hydrolyzed yield polyhydroxyaldehydes or polyhydroxyketones. It contains oxygen, carbon and
hydrogen. Carbohydrates are formed in the plants by photosynthesis from carbon dioxide and water in the presence of sunlight.
Cellulose - a carbohydrate from which our papers and cotton clothing fibers are derived from.

*Classification of Carbohydrates:
1. Monosaccharides - Monosaccharides are the simplest carbohydrates. Thus, they cannot be hydrolyzed to simpler carbohydrate units.
Monosaccharides are the basic carbohydrate unit of cellular metabolism. These are the building blocks of all carbohydrates.
*Classification of monosaccharides:
a. According to chain length or the number of carbon atoms in the molecule.
Trioses is the simplest of all monosaccharides has three carbon atoms
Example: Trioses: C3H6O3 Hexoses: C6H12O6
b. According to kind of carbonyl group present.
An aldose is a sugar that contains the functional group aldehyde (-CHO) while a ketose is a ketone-containing sugar.
c. As an isomer.
 Glucose - the most important monosaccharide. It is an aldohexose and is found in free state in plant and animal tissue. It is also
known as dextrose or grape sugar. Glucose is the body's key sugar and is carried by the bloodstream to all parts of the body.
Blood Sugar – the most abundant carbohydrate in the blood.
Hyperglycemia sets in when glucose level exceeds the normal range. Diabetes mellitus is a disease due to the inability of cells to
acquire glucose from the blood.
 Galactose - an aldohexose that differs structurally from D-glucose only in the configuration of the -H and –OH group on carbon 4. It is
synthesized in the mammary glands to make the lactose of milk. It is also a constituent of glycolipids and glycoproteins in many cell
membranes, such as those in nervous tissues. Galactose is less than half as sweet as glucose.
Galactosemia is an inherited condition characterized by the inability of infants to metabolize galactose.
 Fructose - also known as levulose and fruit sugar. It is a ketohexose that occurs in fruit juices, honey, and vegetables. It is the sweetest
of all the common sugars as it is about twice as sweet as glucose. This is why high-fructose corn syrup and honey are very sweet. It is
used as commercial sweetener in processed food products and is the energy source for sperm.

2. Disaccharides - are carbohydrates made up of two monosaccharide units joined together by glycosidic bonds.
*Sucrose and Lactose are found in free state of nature.
 Sucrose - is commonly known as table sugar and exists throughout the plant kingdom. Sugar cane contains 15-20% sucrose, and sugar
beets 10-17%. Maple syrup and sorghum are also good sources of sucrose. Sucrose is made of two simple sugars, glucose and
fructose are joined in a dehydration reaction to form a glycosidic bond. In the process, a water molecule is lost.
 Lactose - is the sugar contained in milk. It is composed of glucose and galactose molecules and is found in nature mainly in the milk of
mammals. Human milk contains about 6.7% lactose and cow milk about 4.5% lactose.
Lactose Intolerance - The discomfort felt after drinking milk.
 Maltose - is found in fruit juices and sprouting grains. It is composed of two glucose molecules.

3. Oligosaccharides - oligosaccharides are comprised of a few (typically 3 to 9) sugar residues. Oligosaccharides are found bound, for
example, to sphingolipids (making cerebrosides or gangliosides) or proteins (making glycoproteins). Oligosaccharides in membrane
glycoproteins play important roles in cellular identity and recognition.

4. Polysaccharides - These are carbohydrates consisting of hundreds of thousands of monosaccharide units joined by glycosidic bonds.
These are macromolecular substances that can be hydrolyzed to yield many monosaccharide units.
 Glycogen - the energy storage carbohydrate of the animal kingdom. It is the animal equivalent of starch. It is a highly branched
molecule usually stored in liver and muscle tissues. It maintains the blood glucose levels because it serves as a repository of excess
glucose ingested from the blood. Whenever blood glucose levels decrease, glycogen is broken down to release glucose in a process
known as glycogenolysis.
 Starch - the most important energy storage carbohydrate of the plant kingdom. It is the stored form of sugars in plants. It is made up
of a mixture of amylose and amylopectin (both polymers of glucose).
 Cellulose - a tough fibrous material which holds together the plant structure. It is the most abundant organic substance found in
nature. It is the chief structure component of plants and wood.

*Reactions of Carbohydrates:
a. Reducing Properties - the basis of testing sugar in urine and in the blood.
Reducing sugars are sugars that react even with mild oxidizing agents. They reduce silver ions to free silver and Cu2+ ions to Cu1+ ions.
Benedict’s and Fehling’s Test are laboratory tests for the presence of glucose in urine.
In Tollen’s test, Tollen’s reagent is used which contains Ag+ ion in the form of Ag(NH3)2.
b. Oxidation
When the aldehyde end of a monosaccharide is oxidized, an onic acid is formed. Glucose for instance would be oxidized to gluconic acid.
When the alcohol end of a monosaccharide is oxidized, a uronic acid is formed, thus glucose is oxidized to glucuronic acid.
c. Reduction
Glucose Sorbitol
Galactose Dulcitol
Fructose Mannitol + Sorbitol
d. Fermentation
e. Reaction with Iodine
Iodine test is therefore used to detect starch's presence.

CARBOHYDRATE METABOLISM:
 1. Glycolysis. Glucose is the body’s most readily available source of energy. Cells in the body take up the circulating glucose in response
to insulin and, through a series of reactions called glycolysis, transfer some of the energy in glucose to ADP to form ATP.
2. Anaerobic Respiration. When oxygen is limited or absent, pyruvate enters an anaerobic pathway.
3. Aerobic Respiration. In the presence of oxygen, pyruvate can enter the Krebs cycle.
4. Krebs Cycle/Citric Acid Cycle/Tricarboxylic Acid Cycle.
The pyruvate molecules generated during glycolysis are transported across the mitochondrial membrane into the inner mitochondrial
matrix, where they are metabolized by enzymes in a pathway called the Krebs cycle. The Krebs cycle is also commonly called the citric
acid cycle or the tricarboxylic acid (TCA) cycle. During the Krebs cycle, high-energy molecules, including ATP, NADH, and FADH2, are
created.

2. LIPIDS AND MICRONUTRIENTS

Lipids - a heterogeneous group of organic compounds, including fats, oils, steroids, waxes, and related compounds, which are related more by
their physical than by their chemical properties. They show no common chemical structure.
*General properties of Lipids:
1. Lipid structures or molecules are relatively big, made up of many carbon molecules.
2. Lipids contain carbon, hydrogen, and oxygen; sometimes nitrogen and phosphorus.
3. Lipids cannot hydrogen-bond to the extent that carbohydrates can, they are said to be NONPOLAR. Thus, they are soluble in nonpolar organic
solvents such as ether, acetone, chloroform, benzene and CCl4.
4. Lipids are said to be HYROPHOBIC meaning “water-fearing”, or have large hydrophobic regions.
5. Lipids are water insoluble.
*Biological Roles of Lipids:
1. Dietary Constituents
2. Thermal Insulators
3. Nonpolar Lipids as Electrical Insulators
4. Cellular Constituents
FATTY ACIDS - Fatty acids are the building blocks of lipids. These are molecules characterized by the presence of a carboxyl group attached to a
long hydrocarbon chain. These are carboxylic acids with long, hydrophobic carbon chains containing an even number of carbon atoms.
 Saturated Fatty Acids have only single bonds in the hydrocarbon. Animal fats are a source of saturated fatty acids.
*Some of the most commonly occurring saturated fatty acids include:
Butyric (butanoic acid): CH3(CH2)2COOH or C4:0
Caproic (hexanoic acid): CH3(CH2)4COOH or C6:0
Caprylic (octanoic acid): CH3(CH2)6COOH or C8:0
Capric (decanoic acid): CH3(CH2)8COOH or C10:0
Lauric (dodecanoic acid): CH3(CH2)10COOH or C12:0
Myristic (tetradecanoic acid): CH3(CH2)12COOH or C14:0
Palmitic (hexadecanoic acid): CH3(CH2)14COOH or C16:0
Stearic (octadecanoic acid): CH3(CH2)16COOH or C18:0
Arachidic (eicosanoic acid): CH3(CH2)18COOH or C20:0
Behenic (docosanoic acid): CH3(CH2)20COOH or C22:0
 Unsaturated Fatty Acids have at least one C=C double bond in the chain. A fatty acid with one double bond is called
monounsaturated. If it contains two or more double bonds, we say that the fatty acid is polyunsaturated. Plants are the sources of
unsaturated fatty acids.
Examples are:
Oleic CH3(CH2)7CH=CH(CH2)7COOH
Linoleic CH3(CH2)4(CH=CHCH2)2(CH2)6COOH
Linolenic CH3CH2(CH=CHCH2)3(CH2)6COOH
Arachidonic CH3(CH2)4(CH=CHCH2)4(CH2)2COOH
 Essential fatty acids are unsaturated fatty acids which cannot be synthesized by the body. Essential molecules are molecules that our
body needs but unable to synthesize. Linoleic acid is an essential fatty acid. They can be synthesized. Nonessential fatty acids can be
made by the human body and so do not need to be obtained from diet alone. These are made from carbohydrates and proteins or
from other fatty acids. Fatty acids are an important source of energy.
*While carbohydrates or proteins only provide 4 kcal/g of energy, fatty acids provide more than twice the energy per unit weight of 9 kcal/g.

*Classification of Lipids:
1. Simple Lipids - are esters of fatty acids with various alcohols. They are called simple because no additional functional groups were attached
to the lipids.
 Triglycerides - are esters of fatty acids and glycerol and often called triacylglycerol. Esters are formed by splitting out a molecule of
water between an alcohol and an acid. Glycerol or 1, 2,3-propanetriol is an important trihydroxy alcohol, a syrupy liquid with a sweet
warm taste. Short-chain unsaturated triglycerides are liquids at room temperature. Long-chain saturated triglycerides are solids at
room temperature.
Fat is a mixture of triglycerides containing a high proportion of long chain, saturated fatty acids.
Oil is a mixture of triglycerides with high proportion of long chain unsaturated fatty acids or short-chain, saturated fatty acids.
*Physical Properties of fats and oil:
- White or yellow solids and liquids
- Odorless and tasteless
- Insoluble in water but soluble in organic liquids such as ether, acetone and benzene.
- Not diffuse through membrane
- Lighter than water and have a greasy feeling
- Form a temporary emulsion when shaken with water.
- Emulsified by bile in the body before they can be digested.

*Uses of fats in the body:

1. Fats are important food source for humans and normally account for about 25.50% of our caloric intake.
2. Fats are the most concentrated source of energy, producing more energy per gram than either carbohydrates or protein.
3. Fats supply about 40 KJ of energy per gram (9Kcal/g), more than twice the amount obtained from carbohydrates or proteins.
4. Fats also serve as a reserve supply of food and energy for the body.
5. Fats also serve as a protector for the vital organs.
6. Fats act as heat insulators, helping to keep the body warm in cold weather.
7. Fats act as vehicles for the fat-soluble vitamins A, D, E, and K.

 Waxes - are esters made up of long chain fatty acids and long chain alcohols and are considered the hardest of the lipids. Beeswax is
used in polishes and pharmaceutical products. Carnauba wax from a Brazilian palm tree is used in polishes and floor waxes. Lanolin
from lamb’s wool is for skin ointments. Spermaceti from sperm whale are used for cosmetics and candles.
*Physical properties of waxes:
- Insoluble in water, nonreactive and flexible
- Have higher boiling points than fats
- Wax molecules makes was solid
- The size of the wax molecules contain carbon chains

2. Complex Lipids - are esters of fatty acids containing groups in addition to an alcohol and a fatty acid. Include the phospholipids, sphingolipids
and glycolipids.
 Phospholipids - a group of compounds that yield one or more fatty acid molecules, a phosphate group, and usually a nitrogenous base
upon hydrolysis. This is a class of waxy solids that form part of the structure of cell membrane.
 Sphingolipids - are lipids with the alcohol components as sphingosine instead of glycerol. These are also common membrane
components. Sphingomyelins are the most common sphingolipids which are largely found in the brain and nerve tissues. They form
part of the myelin sheath, the protective coating of the nerves.
 Glycolipids - are lipids/ substances that yield sphingosine or glycerol, a fatty acid and a carbohydrate upon hydrolysis. They are
sphingolipids or phospholipids that contain a carbohydrate group. The two classes; Cerebrosides may contain either D- glucose or D-
galactose and are found in high concentrations in the brain and nerve cells especially the myelin sheath. Gangliosides resemble
cerebrosides in structure but contain complex oligosaccharides instead of a simple monosaccharide.

3. Derived Lipids - These include fatty acids, glycerol, steroids, other alcohols, fatty aldehydes, and ketone bodies, hydrocarbons, lipid-soluble
vitamins, and hormones.
Steroids are the most important derived lipids. These are compounds that have the steroid nucleus, which consists of four fused
carbocyclic rings. This nucleus contains 17 carbon atoms in one five-membered and three six-membered rings.
Cholesterol is the most abundant and the most important steroid in the body. It serves as a plasma membrane component in all animal cells. It
serves as a raw material for the synthesis of other steroids such as sex and other adrenocorticoid hormones and bile salts.
Atherosclerosis is a metabolic disease that leads to the deposits of cholesterol and other lipids on the arteries' inner walls.
*Reaction of lipids:
1. Hydrolysis. Superheated steam, hot mineral acids and specific enzymes hydrolyze fats to produce glycerol and fatty acids.
2. Formation of Acrolein. The glycerol produced during hydrolysis of fats is converted to acrolein upon heating.
3. Halogenation. The C-C double bonds in an unsaturated fatty acid react with molecular iodine in a halogenation reaction. This is
useful in laboratory tool in determining the degree of unsaturation in fats.
4. Hydrogenation. This is the process of adding hydrogen to C-C double bonds of the fatty acid. This converts oils to fats by
converting double bonds to single bonds.
5. Hydrolysis and Oxidation. The oxidation of the hydrolyzed fatty acids causes the distinct disagreeable odor and taste of rancid
butter. In other words, rancid butter has undergone hydrolysis and oxidation.
6. Saponification. This is the base-catalyzed hydrolysis of fats and oils producing glycerol and a mixture of fatty acid salts called
soaps.

3. PROTEINS - Proteins are nitrogenous organic compounds of high molecular weight present in every cell. The name was actually derived
from the Greek word proteios, which means "holding first place."
*Function of Proteins:
1. Structure and Support. Keratin is the protein found in the outer layers of skin and makes skin a strong protective layer to the outside world.
It is also the structural protein that makes hair, horns, and nails. Collagen forms the bone matrix and makes up a large proportion of the
ligaments, tendons, and skin.
2. Catalysis. All the countless chemical reactions that take place in living organisms are catalyzed by proteins called enzymes. Digestive enzymes
are proteins that drive digestion by speeding up chemical reactions. They are responsible for breaking down food molecules into smaller, water-
soluble molecules. Some examples of digestive proteins include amylase, the enzyme in saliva that breaks down starch into soluble sugars,
lipase that breaks down fats and other lipids, and pepsin that breaks down proteins in food.
3. Movement. Muscles are made up of protein molecules called myosin, dynein and actin. Myosin is the protein found in muscle and causes the
contraction of muscle fibers in muscles. Dynein provides the power that drives flagella - the long, thin structures attached to the outside of
certain cells, such as sperm cells, and are responsible for their mobility.
4. Transport. Hemoglobin is the protein in blood that binds to oxygen so that oxygen can be transported around the body.
5. Hormones. Insulin lowers blood glucose level and promotes glucose storage as glycogen and fat. Glucagon increases blood glucose level. The
human growth hormone is a protein that regulates the development of the body.
6. Protection. When proteins from outside sources or other foreign substance enters the body, the body makes its own proteins called
antibodies to counteract the foreign protein.
7. Storage. Ferritin, a protein in the liver that stores iron.
8. Regulation. Some proteins control the expression of genes, thereby regulating the kind of proteins synthesized in a particular cell. Proteins
also regulate the concentration of acids and bases in the blood and other bodily fluids.

AMINO ACIDS: THE BUILDING BLOCKS OF PROTEINS

Amino acids ( α-amino carboxylic acid) are a group of organic molecules known to be the basic building blocks of proteins. Amino acids are
organic compounds that are composed mainly of hydrogen, carbon, oxygen, and nitrogen. These amino acids are linked together in long chains
called polypeptides to form the vast assortment of proteins found in all living cells.
Two groups; The α-amino group and the α-carboxyl. The α-carbon, carboxyl, and amino groups are common to almost all amino acids, so the R-
group is the only unique feature in each amino acid. As the amino group is attached to the first or α-carbon atom attached to the carboxyl
group, the amino acids in proteins are called alpha (α) amino acids.
 Neutral when their molecules have the same number of amino and carboxyl groups.
 Acidic when their molecules have more carboxyl groups than amino groups
 Basic when their molecules have more amino groups than carboxyl groups.

Amino acids are joined together to form proteins by Peptide bonds. Peptide bonds are amide bonds, which are covalent bonds created by the
reaction between the amino group (-NH2) of one amino acid and the carboxylic group (-COOH) of the second. The amino group and carboxyl
group bond together through a peptide bond, and a water molecule is produced as a byproduct. As there is loss of water, the process is called a
dehydration synthesis, or a condensation reaction that involves dehydration.
Dipeptides are two amino acids joined together by a peptide bond.
Tripeptides are made up of three amino acids joined together by a peptide bond.
Polypeptides contain up to 40-50 amino acid units in a chain.
Proteins consist of more than fifty amino acids.

Naming of Polypeptides:
The amino group end is called the N-terminal residue, and the other end. The N-terminal residue is the first amino acid in the chain with a free
amino group, glycine. The C-terminal residue is the one at the last of the chain, that is, cysteine, as it has a free carboxyl group.

*Four levels of organization in Protein Structure:

1. Primary Structure of Proteins
The primary structure is the specific sequence of amino acids or the order that they are bonded together. This consists of the linear sequence of
amino acids that make up the chain. It is established by the number, kind, and sequence of amino acid units composing the polypeptide chain
and making up the molecule.

2. Secondary Structure of Proteins

Secondary structure can be characterized as a regular 3-dimensional structure held together by hydrogen bonding between the oxygen of the
C=O and the hydrogen of the N-H groups in the polypeptide chains.
a. α-helix - a single protein chain that twists in such a manner that its shape resembles a right-handed coiled spring that is, a helix . The shape of
the helix is maintained by the numerous intermolecular hydrogen bonds that exist between the backbone C=O and H-N groups.
b. β-Pleated Sheet - a secondary structure in which the backbone of two protein chains in the same or different molecules is held together by
the hydrogen bonds. It is a sheet-like arrangement in which two or more extended polypeptide chains are aligned side by side.

Collagen is one of the most plentiful naturally occurring proteins. It provides

strength and elasticity as it is the structural proteins of connective tissues like the bone, cartilage, tendon, blood vessels, and skin. It provides
structure to our bodies, protecting and supporting the softer tissues and connecting them with the skeleton.
3. Tertiary Structure - refers to the distinctive and characterized conformation or shape of the protein molecule. This over-all three-dimensional
conformation is held together by a variety of interactions between amino acid side chains. This is the basis of protein grouping.
 Hydrogen bonds are formed between a highly electronegative oxygen atom or a nitrogen atom and a hydrogen atom attached to
another oxygen atom or a nitrogen atom, such as those found in polar amino acid side chains.
 Ionic bonds result from electrostatic attractions between positively and negatively charged side chains of amino acids.
 Disulfide bridges are very strong covalent bonds found between cysteine residues that are in close proximity in space.
 Hydrophobic interactions are non-covalent bonds are the most important factor and driving force in the formation of the tertiary
structure.
Fibrous proteins are insoluble in water, have long and narrow shapes, and are used mainly for structure purposes. Considered as fibrous
proteins are the α-keratins found in hair, feathers, horn, and hooves; fibroin, the silk protein; and collagen, the most abundant protein in
the animal kingdom. Collagen is the structural protein of connective tissues such as bones, cartilage, tendon, and skin, providing strength
and elasticity. Globular proteins are more or less soluble in water, round or spherical, and used mainly for non-structural purposes.
4. Quaternary Structure - is produced and stabilized by the same kinds of interactions that produce and maintain the tertiary structure.
When a protein contains more than one polypeptide chain, each chain is called a subunit.

PROTEIN DENATURATION - the disruption of the secondary, tertiary and quaternary structure of the native protein resulting in the alterations
of the physical, chemical and biological characteristics of the physical, chemical and biological characteristics of the protein by a variety of
agents such as heat, organic compounds, pH changes, and heavy metal ions.
ENZYMES: BIOLOGICAL CATALYSTS
Enzymes are a biological polymers (mainly proteins) that catalyze biochemical reactions. Ribozymes are molecules of ribonucleic acid
which catalyze reactions in one of their own bonds or among other RNAs.
*Properties of Enzymes:
- Enzymes are larger than their substrates and their size vary, which range from sixty-two amino acid residues to an average of two thousand
five hundred residues present within fatty acid synthase.
- They required only in small amounts.
- Nearly all enzymes are proteins, although a few catalytically active RNA molecules have been identified.
- Enzyme catalyzed reactions usually take place under relatively mild conditions.
- Enzymes are highly specific with respect to the substrates on which they act and the products that they form.
- Enzyme activity can be regulated, varying in response to the concentration of substrates or other molecules.
- They function under strict conditions of temperature and pH in the body.

ENZYME STRUCTURES
 Holoenzyme - consisting of the apoenzyme and the co-factors/co-enzymes.
 Apoenzyme - the protein part of the enzyme without the co-factors/co-enzymes.
Co-factors are non-protein inorganic substances that associate with enzymes. These could be prosthetic groups or metal ions.
Prosthetic groups are cofactors tightly bound to an enzyme at all times. Metal ions are required by certain enzymes at the active site
to form coordinate bonds during catalysis. Zn2+ is a metal ion cofactor used by a number of enzymes.
Co-enzymes are non-protein organic molecules that are mostly derivatives of vitamins. These are bound to an enzyme only during
catalysis and is detached from the enzyme at all other times.
 Isoenzymes - are different forms of an enzyme, which catalyze the same reaction, but which exhibit different physical or kinetic
properties. These types of enzymes are usually derived from different genes and often occur in different tissues of the body.
CLASSIFICATION OF ENZYMES
1. Oxidoreductases. Oxidoreductases catalyze oxidation-reduction reactions where electrons (hydride OH- or H+ atoms) are transferred. The
most common name used for these type of enzymes is dehydrogenase and sometimes reductase is used. An oxidase is referred to when
the oxygen atom is the acceptor.
2. Transferases. Transferases catalyze group transfer reactions (from donor to the acceptor). The donor is a cofactor that is charged with the
group about to be transferred.
3. Hydrolases. Hydrolases catalyze reactions that involve hydrolysis. It usually involves the transfer of functional groups to water.
4. Lyases. Lyases catalyze reactions where functional groups are added to break double bonds in molecules or the reverse where double
bonds are formed by the removal of functional groups.
5. Isomerases. Isomerases catalyze reactions that transfer functional groups within a molecule so that isomeric forms are produced. These
enzymes allow for structural or geometric changes within a compound. They function by moving chemical group inside same substrate.
6. Ligases. Ligases are involved in catalysis where two substrates are ligated and the formation of carbon-carbon, carbon-sulfide, carbon
nitrogen, and carbon-oxygen bonds due to condensation reactions.
Significance of Enzymes:
- They are crucial for normal metabolism of living systems.
- Enzymes are used to treat enzyme related disorders and also used assist in important metabolic processes.
- Enzymes may also assist in drug delivery, especially in cases that the patient lacks enzymes to activate or metabolize the drug.
- Enzymes may also aid in the detection and diagnosis of diseases. Products of enzymatic action may be used as medecines.
Industrial applications of Enzymes include:
1. Amylase, lactases, cellulases are used to break complex sugars into simple sugars.
2. Pectinase-like enzymes, which act on hard pectin is used in fruit juice manufacture.
3. Lipase enzymes act on lipids to break them in fatty acids and glycerol. Lipases are used to remove stains of grease, oils, butter.
4. Enzymes are used in detergents and washing soaps.
5. Protease enzymes are used to remove stains of protein nature like blood, sweat etc.

4. NUCLEIC ACIDS - Nucleic acids, namely the deoxyribonucleic acids (DNA) and ribonucleic acids (RNA), are mainly involved in heredity and its
expression.
One’s whole genetic make-up is called the genome - It is the collective body of genetic information that is present in a species or a living
organism. The genome is organized into chromosomes - These are threadlike structures that carry the genes. The gene is the basic physical and
functional unit of heredity. It is made up of DNA and act as instructions to make proteins.
Nucleotides are the basic building block of nucleic acids. A nucleotide consists of three groups;
(a) five – carbon sugar deoxyribose (for DNA) or ribose (for RNA)
(b) one phosphate is esterified at the 5’ position of the sugar ring
(c) one nitrogenous base is attached at the 1’ site.

*There are two types of nitrogenous bases based on the number or rings in their structures.
Pyrimidines contain a single ring. These are thymine (T) for DNA or uracil (U) for RNA and cytosine (C).
Purines contain two rings. Guanine (G) and adenine (A) are purines.
The nucleotides are then joined together still by condensation reactions covalently bonding the phosphate of one nucleotide and the sugar of
another, resulting in phosphodiester linkages. This creates the polynucleotides of RNAs and DNAs, where the sugar and phosphate group are
collectively called the sugar-phosphate backbone of the polynucleotides strands.

*Deoxyribonucleic Acid (DNA) Structure/ Ribonucleic Acid (RNA) Structure

The structure of DNA that we know today is based from the Watson-Crick Proposal on DNA Structure, by American biologist James
Watson and English physicist Francis Crick.
DNA Structure is the long double stranded. RNA Structure are shorter and single stranded

1. The molecule is composed of two chains of nucleotides. a. Messenger RNA (mRNA) copy portions of
2. The two chains spiral around each other to form a pair of right-handed helices. genetic code through the process called
3. The two chains comprising one double helix run in opposite directions; that is, they are transcription, and transports these copies to
antiparallel. ribosomes, which are the cellular factories that
4. The –sugar–phosphate–sugar–phosphate– backbone of each strand is located on the facilitate the production of proteins from this
outside of the molecule with the two sets of bases projecting toward the center. code, a process called translation.
5. The bases occupy planes that are approximately perpendicular to the long axis of the
molecule and are, therefore, stacked one on top of another like a pile of plates. b. Transfer RNA (tRNA) are responsible for
6. The two strands are held together by hydrogen bonds between each base of one bringing amino acids, basic protein building
strand and an associated base on the other strand. blocks, to these protein factories, in response
7. The distance from the phosphorus atom of the backbone to the center of axis is 1 nm. to the coded instructions introduced by the
8. A pyrimidine in one chain is always paired with a purine in the other chain mRNA (translation).
9. Adenine was the only purine structurally capable of bonding to thymine and that c. Ribosomal RNA (rRNA) is a component of the
guanine was the only purine capable of bonding to cytosine. ribosome factory itself, without which, protein
10. The spaces between adjacent turns of the helix form two grooves of different width— production would not occur.
a wider major groove and a narrower minor groove—that spiral around the outer surface
of the double helix.
11. The double helix makes one complete turn every 10 residues.
12. The nucleotide sequences of the two strands are always fixed relative to one another.
Summary of Differences between DNA and RNA:
Comparison DNA RNA
Name DeoxyriboNucleic Acid RiboNucleic Acid
Long-term storage of genetic information; RNA converts the genetic information contained within DNA
Function transmission of genetic information to make other to a format used to build proteins, and then moves it to
cells and new organisms. ribosomal protein factories.
DNA is found in the nucleus, with a small amount of RNA forms in the nucleolus, and then moves to specialised
Location DNA also present in mitochondria. regions of the cytoplasm depending on the type of RNA
formed.
B-form double helix. DNA is a double-stranded A-form helix. RNA usually is a single-strand helix consisting
Structural Features molecule with paired long chains of nucleotides. of shorter chains of nucleotides.
Composition of deoxyribose sugar-phosphate backbone ribose sugar-phosphate backbone
Bases and Sugars adenine, guanine, cytosine, thymine bases adenine, guanine, cytosine, uracil bases
Propagation DNA is self-replicating. RNA is synthesized from DNA on an as-needed basis.
AT (adenine-thymine) AU (adenine-uracil)
Base Pairing GC (guanine-cytosine) GC (guanine-cytosine)
The C-H bonds in DNA make it fairly stable, plus the The O-H bond RNA’s ribose makes the molecule more
body destroys enzymes that would attack DNA. The reactive than DNA. RNA is not stable under alkaline
Reactivity small grooves in the helix also serve as protection, conditions, plus the large grooves in the molecule make it
providing minimal space for enzymes to attach. susceptible to enzyme attack. RNA is constantly produced,
used, degraded, and recycled.