COLEGIO DE SAN SEBASTIAN SABLAYAN, OCCIDENTAL MINDORO COLLEGE DEPARTMENT LEARNING MODULE ON CELL AND MOLECULAR BIOLOGY BACHELOR IN SECONDARY EDUCATION MAJOR IN SCIENCE BSED II MR. DAVE C. PITA JR. INSTRUCTOR SCHOOL YEAR 2020-2021 Avcell has a history; ‘its inherited, it 'grows, divides, an in the em rye of higher animals, the products of division differentiate on. complex lines. Living: cells, moreo transmit all that is involved”; ‘in their complex heredity Me paclarlele Gowlenel Hopkins “More science quotes at Today in Science History” tedayinselcomVISION: Colegio De San Sebastian, a Christian oriented community envisions the total development of its members- spiritually, morally, intellectually and technologically so that they become responsible, innovative, socially committed, locally active and globally competitive individuals MISSION: It aims to provide relevant and quality education and achieve academic excellence through discipline, hard work and critical thinking. It hopes to contribute to the globally ‘community individuals who are willing to LEAD and SERVE for COUNTRY and for GOD. GOALS: Colegio De San Sebastian aims to institutionalize faculty an staff development, upgrade learning facilities and equipment; produce relevant curriculum materials; provide opportunities for holistic development of students and establish linkage with the community. OBJECTIVES: To produce graduates who are Christ- centered, permeated with the gospel of love, Justice, honesty and service; prepared to meet the challenges of a globally competitive world, through hard work, positive attitude, critical thinking and effective decision making. COURSE TITLE: CELL AND MOLECULAR BIOLOGY CREDIT UNITS: 4 COURSE PRE/CO-REQUISITES: None COURSE DESCRIPTION: This course will provide full overview of the world of cell and microbiology. We will first provide the basic components comprised within all living things before moving onto to how ‘organisms’ internal systems work and how they coexist and contend with external elements. Further on in the course, we touch upon more complex subjects such INA and RNA; protein structures; and movement along cellular pathways. And, alas we delve into some of the deeper molecular biological issues, including those of pathogens; formation of cancerous ceils; and, one of today's hot topics-the facts behind the controversial issue of stem cell research. Despite the small size of researchers’ subjects, cell and molecular biology continues to be an area generating sizable interest. Not only are the applications of cell and molecular biology vastly infinite, its basic fundamental principles are critical to daily life. We believe you will gain many valuable nuggets of information from this course and using its basic teachings to better understand the world around you. ‘At the end of this course the students should be able; Understand and utilize the scientific vocabulary used in communicating information in cell and molecular biology 1. Understand and apply general concepts of cell and molecular biology to relevant, ‘specific problems 2. Describe and discuss the properties and biological significance of the major classes of ‘molecules found in living organisms and the relationship between molecular structure and biological function 3. Represent and illustrate the structural organization of genes and the control of gene expression 4. Conceptualize and describe protein structure, folding and sorting 5, Explain the structure of membranes and intracellular compartments and relate these to function. 6, Summarize the processes of energy transduction in cells and explain their significance, 7. Relate how cell movement and cell-cell communication occur and discuss mechanisms of signal transduction ‘8. Outline the processes that control eukaryotic cell cycle and cell death.9. Link the rapid advances in cell and molecular biology to a better understanding of diseases, including cancer. INTRODUCTION: Deoxyribonucleic acid (DNA) is the molecule which carries the genetic instructions for ‘almost every living thing, Its unique chemistry not only allows this information to be copied and passed on to an organism's descendents, it also allows scientists opportunities to investigate and ‘Manipulate an organism at 2 molecular level. As 2 result, molecular biology techniques are at the forefront of most cutting edge scientific research. In this project you will Investigate a number of ‘commonly used molecular biology techniques involving DNA.STRUCTURE AND F OF THE CELL INTRODUCTION TO THE CELL Both living and non-living things are composed of molecules made from chemical elements such Carbon, Hydrogen, Oxygen, and Nitrogen. The organization of these molecules into cells is one feature that distinguishes living things from all other matter. The cell is the smallest unit of matter that can carry on all the processes of life. 1. Every living thing - fiom the tiniest bacterium to the largest whale - is made of one or more cells. 2. Before the C17, no one knew that cells existed, since they are too small to be seen with the naked eye. The invention of the microscope enabled Robert Hooke, (1665) and Anton van Leuwenhock (1675) to see and draw the frst ‘cells’, a word coined by Hooke to describe the cells in a thin slice of cork, which reminded him of the rooms where monks lived. 3, The idea that all living things are made of cells was put forward in about 1840 and in 1855 came ‘Cell Theory’ ~i-e. “cells only come from other cells’ — contradicting the earlier theory of — Repet e “Spontaneous Generation’ tenga mie sono ‘spaces, What ihe cal Be Cell Theory consists of three principles: 1. All living things are composed of one or more cells. ». Cells are the basic units of structure and function in an organism. ¢. Cells come only from the replication of existing cells. | CELL DIVERSITY Not all cells are alike. Even cells within the same organism show enormous diversity in size, shape, and intemal organization. Your body contains around 10” to 10'*cells of around 300 different cat bre, which we broadly classify into 4 groups. CELL SIZE 1. A few types of cells are large enough to be seen by the unaided eye. The human egg (ovum) is. largest cell in the body, and can (just) be seen without the aid of a microscope. 2. Most cells are small for two main reasons: 2). The cell’s nucleus can only control a certain volume of active cytoplasm, b). Cells are limited in size by their surface area to volume ratio. A groupof small cells has larger surface area than a single large cell of the same volume. This is important because the m oxygen, and other materials a cell requires must enter through it surface. As a cell grows larger a some point its surface area becomes too small to allow these materials to enter the cell quickly enough tq meet the cell's need, (= Fick's Law ~ something you need to learn well Rate of diffusion a Surface Area x Concentration Difference DistanceProkaryotes v. Eukaryotes isms whose cells normally contain a nucleus are called Eukaryotes; those (generall ryotess ly smaller) organisms whose cells Inck a nucleus and have no membrane-bound organelles are known as Prokaryotes. ‘A Prokaryoti cell (bacterium) ‘A Bukaryote cell (plans) Prokaryotes Eukaryotes ‘Typical organisms bacteria Protoctista, fungi, plants, animals ' Typielsize | ~ 110 um 10500 pene) eet oe ae Typectuncem Rocedoor” real nucleus with nuclear envelope ! DNA circular (coe DNA) ee (chromosomes) with histone Ribosomes 70S 80S t Asean very few structures highly structured by membranes anda cytoskeleton Cell movement aera made of pagellae and cilia made of tubulin i Mitochondria none 1-100 (though RBC’s have none) i ‘Chloroplasts none in algae and plants single cells, colonies, higher ‘multicellular i Organization usually single cells egansms with specialized cells | Binary fission Mitosis (normal cell replication) Meiosis | Cell division (imple division) (gamete production)THE CELL MEMBRANE 1. A cell cannot survive if itis totally is is a s ly isolated from its environment. is , merrier Separting very cell from its extemal environment. Tepe memset aca 3. Theodl lectively Permeable" ‘membrane regulates what Passes into and out of the cell. Cell membrane is a fluid mosaic of proteins floating in a phospholipid bilayer, . 4. The cell membrane functions like a gate, controlling which molecules can enter and leave the cel 5. ‘The cell membrane controls which substances pass into and out of the cell. Carrier proteins in or on the ‘membrane are specific, only allowing a small group of very similar molecules through. For instance, a- glucose is able to enter, but B — glucose is not. Many ‘molecules cannot 4 cross at all. For this reason, the cell membrane is said to be selectively permeable, 6. The rest of the cell membrane is mostly ‘composed of phospholipid molecules. They have only two fatty acid ‘tails’ as one has been replaced by a phosphate group (making the ‘head’ 7. The head is charged and so polar, the tails are not charged and so are non-polar. Thus the two ends of the phospholipid molecule have different properties in water. ‘The phosphate bead is hydrophyllic and so the head will orient itself so that it is as close as possible to water molecules. The fatty acid tails are hydrophobic and so will tend to orient themselves away from water, 8. So, when in water, phospholipids line up on the surface with their phosphate heads sticking into the water and fatty acid tals pointing up from the surface. 9. Cells are bathed in an aqueous environment and since the inside of a cell is also aqueous, both sides of the cell membrane are surrounded by water molecules. 10. This causes the phospholipids of the cell membrane to form two layers, known as a phospholipid bilayer. In this, the heads face the watery fluids inside and outside the cell, whilst the fatty acid tails are sandwiched inside the bilayer. 11. ‘The cell membrane is constantly being formed and broken down in living cells. CYTOPLASM. 1, Everything within the cell membrane which is not the nucleus is as the cytoplasm. 2. Cytosol is the jelly-like mixture in which the other organelles are suspended, so eytosol + organelles = cytoplasm. 3. Organelles carry out specific functions within the cell. In Eukaryot cells, most organelles are surrounded by a membrane, but in Prokaryotic cells there are no membrane-bound organelles. | FLUID MOSAIC MODEL OF CELL MEMBRANES: | 1, Membrmes am fal nd ar mir viaooes fle vogeabla cil | | 2. The molecules of the cell membrane are always in motion, so the phospholipids are able to drift across the membrane, changing places with their neighbour. 3. Proteins, both in and on the membrane, form a mosaic, floating in amongst the phospholipids. 4, Because of this, scientists call the modern view{of membrane structure the ‘Fluid Mosaic Model’. in the cell membrane is . 1. A variety of Fee protein molecules SS 7 3 3 f ‘are embedded in the basic phospholipid bilayer. i : ‘Some proteins are attached to the surface Saks of the cell ‘membrane on both the internal and ‘external surface. ‘These may be hormone receptors, i ‘enzymes or cell recognition proteins (or antigens) Other proteins are embedded in the i i phospholipid bilayer itself. These are often associated mujuivne with transporting molecules from one side of the membrane to the other and are referred to as carrier proteins. 4, Some of these form channels or pores through which substance on one side of ‘the —H,O (water) + NaCl (salt) So when you feel hyperacidity, taking an antacid such as Kremil S® can neutralize the stomach acidity and makes you feel better. pH scale ‘One way to identify the acidity or basicity (alkalinity) of a solution is the use of pH scale. The pH scale has a range of 0-14. A range of 0-6 in the pH scale indicates that the substance is acidic with pH 0 as the most acidic. Example, gastric juice with pH 1 has ten times more H+ and more acidic than lemon juice with pH 2. A pH of 7 indicates that the substance is neutral such as pure water. A pH of 8 to 14 indicates that substance is a base or alkaline. The higher the pH the more alkaline the substance with pH 14 as the most basic or alkaline, Example, time water with pH 12 has H+ ten times lesser but more alkaline than ammonium hydroxide with pl of II Every substance within the organism and in the environment has specific pH, which should be maintained, Maintaining the pH is very important for normal biochemical reactions. Example, the normal pH of human blood is 7.4. If blood pH will be changed because of certain factors such as emotional stress, it creates an imbalance that may lead to irritation and inflainmation and sets the stage for sickness that eventually can be life-threatening, 33 Acids are substances that increase H atoms when added to water, Bases are substances: that OH atoms when added to water. pH scale is a scale that is numbered 0-14 used to mea- acidity or alkalinity ofa substance.FUNDAMENTALS OF BIOLOGY 1 In the cnvironment, changes in normal pHi of substances have adverse effects, Take for example the effects of acid rain. Normal rainwater has a pH of 5.6. When the pH level goes below 5.6, it is considered acid rain. Acid rain is caused by air pollutants particularly sulfur dioxide and nitrogen oxides released by factories and vehicles. Adverse effects of acid rain‘ include death of plants and some aquatic organisms and corrosion of building materials that cause building structures and historical monuments to weaken and eventually crumble. Dehydration ‘synthesis fetal bases. process by which water Organic Compounds meecules Carbohydrate, lipid, nucleic acid and protein are important organic femoved to | compounds. They are macromolecules composed of many subunits such as form bonds Activity 2.2 helps you understand more the concepts of acids and ee ae simple sugar (carbohydrate), glycerol and fatty acids (lipid), nucleotide joining the | (nucleic acid) and amino acid (protein). These subunits are being joined together together through the process of dehydration synthesis, where water forming | molecules are removed forming a specific complex organic compound. complex However, in order to be used by the cells, these macromolecules are broken compound. | down into simpler units. The breaking down process entails the addition of Hydrolysis | Water molecules, thus the process is called hydrolysis. Each of these organic isa compourids plays important roles essential for survival of living things ess which | A. Carbohydrate ae Carbohygrate is composed of C, H, and O with a general formula are added of Cn(H20)n. lin the formula, the ratio of H to O is 2:1 where there are breaking two atoms of hydrogen for every one atom of oxygen. Carbohydrate ee originates as a product of the process of photosynthesis, so plants and its Compound | products are major source of carbohydrate. This is classified into different into it | types that perform important functions. Basically, this is considered as a chief | source of energy for all organisms. Isomers. ‘Types ‘of Carbohydrate These are compounds | 1, Monosaccharides pl the Monosaccharide (from Greek monos: single, sacchar; sugar) is the same ot | simplest form of carbohydrate. This is just made up of one sugar unit. atoms for | Examples of monosuecharide are glucose, galactose and tructose. These Each sent | three are isomers that is they have the same molecular formula, but Stement but| different structural formula, The ratio of carbon, hydrogen and oxygen diferent | which is 1:2:1 is the same for the three monosaccharides, but the arrange- structural arrangements are different. Chemical formula for monosaccharides ment of is C,H, molecules. eeMODULE 4~ Understanding Cells: The Building Pieces of Lite Glucose This is the most common monosaccharide. Glucose is the only form ‘of stigar used by the body to provide energy to fuel all cellular processes. ‘Therefore, complex carbohydrates and even other monosaccharides must be converted into glucose units. Glucose is a significant component of blood and its level'should be kept relatively constant for proper functioning of the body. b. Galactose Galactose is obiained from milk. It is also found in the human body. At certain times, galactose is converted by the liver into glucose to provide ‘energy for the body when glucose level is low. Aside from it being a source of energy, galactose is an important component that serves as a marker that can help in identifying blood types. For example, blood type B has an additional galactose compared to blood type O. cc. Fructose This sugar is basically found in fruits, honey, and com syrups. This is considered as the sweetest among the sugar. In pure crystalline, form, fructose has applications in commercial food industry. Its uses include being, food sweetener, flavour enhancer, and increases shelf life of frozen fruits and sweet food products. When taken in, fructose is converted into glucose by the liver. 2. Disaccharides Two monosaccharides joined together form a disaccharide Formation of charides is made possible through removal of a water molecule between two monosaccharides through dehydration synthesis. Thus, the chemical formula of disaccharides is C,,H,,0,,. The bond that joins simple sugars to form a disaccharide or polysaccharide is called glycosidic bond. However, for a disaccharide to serve as fuel for cellular activities, it must be broken down info its monosaccharide units through the process of hydrolysis a. Sucrose This is commonly knows combination of glucose and fructose, Sucrose is considered as an excellent natural preservative and is an indispensable ingredient in many jarred food products such as jams and jellies, Naturally they ean be found in sugar cane, maple syrup and beet. table sugar. This is formed through 4. Lactose Lactose is a disaccharide formed by'combining glucose and galactose. This is referred to as milk sugar because this is most notably 35FUNDAMENTALS OF BIOLOGY 1 pn found in milk and other milk products. This is the first carbohydrate that newborn mammals, who are dependent on milk, consume in considerably tau amounts, Mattose This is also referred to as malt sugar or beer sugar. This is composed of two glucose units joined by glycosidic bond. Maltose is the disaccharide that is produced when mouth enzyme amylase breaks down starch found in the food we eat. Another enzyme called maltase found in the body breaks down maltose into glucose units. Maltose is also used in commercial alcohol production. Through the anaerobic process of fermentation, maltose and other sugar are converted by yeast cells into alcohol. 3. Oligosaccharides Oligosa charides (from Greek word oligos meaning "few" and sacchar "sugar") are composed of repeating units of galactose. glucose and fructose. They are found in plant foods such as onions, beans, legumes, wheat, and asparagus. These are often found as components of glycoproteins or glycolipids found in the cell membrane of animal cells often serving as chemical markers important for cell-to-cell reco} 4, Polysaccharides Just like oligosaccharides, polysaccharides are made up of repeating units joined together by glycosidic bonds. However, polysaccharides are longer and more complex made up of more than ten monosaccharide units. These can be classified as structural or storage polysaccharides, Structural polysaccharides are components of structural parts of living things such as the cell wall of plants and shells of animals. Cellulose and chitin are structural polysaccharides. The second group of polysaccharides is called storage polysaccharides for they serve as storage of energy, examples of which are starch and glycogen. a. Cellulose Cellulose provides support and protection to the cell walls of plants and other organisms such as bacteria. This is considered to be the most abundant organic molecule on earth. Normally, animals cannot digest lulose. However, some animals particularly ruminants (v.g., goat, sheep and cattle) and termites, can digest cellulose with the help of symbiotic inicroorganisms that live in their intestines such as the protozoan Trichonympha canpanula, Humans cannot digest cellulose because the enzyme necded for digesting it is absent. However, cellulose is recommended to be part of daily diet because it is a source of roughage or dietary fiber, Which aids in proper disposal of feces,MODULE A.~ Understanding Cells. The Building Pieces of Lite Snes ia Uo b. Chitin Chitin is a principal component of exoskeletons of animals like crustaceans and motluses, and ccll walls of certain fungi. This provides strength and protection to organisms. Chitin is characterized as flexible and strong material, thus it is used in making surgical threads. tt is also biodegradable that it wears away as the wound heals. In industrial use, chitin acts as binders in dyes, fabries and adhesives. It is also applied to strengthen paper materials. c. Starch Starch is a storage polysaccharide in plants found in forms of amylase and amylopectin. Starch can be derived from foods such as potatoes, wheat, bread, pasta, rice and other bread produets d. Glycogen Tn animals, carbohydrate is primarily stored in the liver and muscle as glycogen. This is sometimes referred as animal starch. When needed. alycogen is converted to glucose units to provide needed energy. B. Lipids Lipids arc a complex diverse group of naturally occurring organic compounds. They share a common characteristic of being insoluble in water ut soluble in nonpolar organic solvents such as ether, chloroform, acetone and benzene. Their low solubility to water is attributed to the absence of polar groups. 1, Fats Fats are a subgroup of lipids. A fat molecule is composed of one lycerol and three fatty acids; hence this is also called as trigiyeeride. | Giyeerol and fatty acids are joined together by ester bonds formed through dehydration synthesis. Fats are deposited in the adipose tissues. There are significant uses of fats in the organism's body. One is a being a source ef energy. During low blood glucose level, fats are broken down into glycerol and fatty acids by hydrolysis. The glycerol is converted to glucose by the liver and is used as energy. Compared to the same amount of carbohydrates, fats can give twice as much energy. Fats surrounding intemal organs act as cushions protecting them from shocks andl injuries. They also act as insulators protecting animals from extreme cold Fats can be classified as saturated or unsaturated. Saturated fats have single bonds formed between carbon atoms. These fats have hydrocarbon chains that are fairly straight and are packed closely together, making them solid at room temperature. Major sources of saturated fats are animal food-based proclucts. Lard, butter and margarine are common sourcs of saturated fats. SoFUNDAMENTALS OF BIOLOGY 1 On the other hand, unsaturated fats have double bonds between carbon atoms. Wherever there is a double bond, the carbon atom bonds only with one hydrogen atom and a bend or "kink" is formed in the hydrocarbon tail. Because of the double bonds, unsaturated fats cannot pack closely together making them liquid at room temperature. Oils coming from plants like corn oil and palm oil are examples of unsaturated fats. Eating foods that are rich in fats are found to be unhealthy. This is link to the build up of fat deposits in the coronary heart artery leading to cardiovascular diseases. 2. Piospholipids Phospholipids are a subgroup of lipid, which is a major structural component of all cell membranes. In the cell membrane, there are two layers of these phospholipids in which the hydrophilic ("water-loving”") heads interact with water and the hydrophobic ("“water-hating) tails are directed away from the watery environment of the cells. Phospholipids are made up of glycerol, two fatty acids and a phosphate group (instead af another fatty acid). The two fatty acids are found in the hydrocarbon tails making them hydrophobic. The phosphate groups are found in the head region making it hydrophilic interacting with the watery environment surrounding the cells. Examples of phospholipids include lecithins and cephalins. 3. Sphingolipids These comprise a class of lipids that contain. the organic amino aicohol sphingosine. Sphingolipids are located mainly in the cell membrane of mammalian cells. They serve as structural components as well as adhesion sites for proteins from extracellular tissue. 4, Waxes Waxes are simple lipids consisting of a long-chain alcohol and a fatty acid joined by ester bonds. Naturally, waxes are found as coatings on leaves and stems. They prevent excessive amounts of water loss that cenable:plants to resist drought. Waxes also. provide protection for plants from disease and insects. Animals also have wax such as beeswax, which is an abdominal secretion of bees used form the hive cells. In other insects, waxes cover their body surfaces that restrict movement of water across cuticle and prevent drying, ids Steroids are another major class of lipids. A steroid molecule s structure that is entirely different from other classes of lipids. This is composed of a ring system structure where a variety of funetional groups can be attached. But just like other lipids steroids contains a large number of 5. Ster contain ss LTMODULE 2- Understanding Goll The Busing Prec of alo : 39 cambon-hydrogen at sex hormones, and nis making then non-polar, Steroids inelude cholesterst \renocorticaid hormones. aly a, Cholesterol y Cholesterol 1s an essential component of animal cell membranes Aside from bYing a structural component, this also regulates membra | | ey i | Auidity over range of physiological temperatures, especially whe exposed (0 cok! temperature. Within the eet! membrane, cholesteral also plays significant roles in intracelfutar transport, endocytosis, cell signalling and Nerve conduction, Within cells, cholesterol serves as precursor molecule several biochemical pathways. In the liver, cholesterol is converted to bile, weal ‘which is then stored in the gallbladder. The bile salts in the gall blaler two witubilize fats in the digestive tract and aid in the intestinal absorption of Fit sods | locus as well the fLaaluble vitamins A, D, FE, and &, Cholesterol is sod | an important precursor moteeute for the synthesis of Vitamin Band the up | steroid hormones, adrenal gland, hormones ‘and sex hormones, wy | The intakes of saturated fats contribute much to the inercase in em — | jogd! cholesterol. High blood cholesterol is offen pointed out as the reason oF ‘sit | atherosclerosis ia which fat deposits form plaques on the arterial wall ells. | Causing narrowing of arteries, thus impeding normal blood Movs. | b. Sex hormones “Another group of steroids are sex hgrmones, These include the mle nino | hormone testosterone and female hormones ~ progesterone and wee | estrogen, Testosterone is produced in the testes and is responsible for the sion development of male primary and secondary sex characteristics. Progesterone and estrogen control the ovulation cycle of women | | station during pregnancy and embryogenesis of j wotes the development of female secondary seaual nda | characteristics. sucly as breast enlargen and is also involved in the son | thickening OF the ¢} | ¢. Adrenucarticoid hormones ou) “These are produced in the adrenal glands, Adrenocorticond honmones is an | nelude aldosterone and cortisol Aldoesterone regulates the reabsorption of — | sediune and chloride ions in the kidney tubules, Cortisol increases glucose sabia and glycogen concentrations in the body. | , Nucleic acids cule | Nucleic acids are complex macromolecules which store This | information that determine the type and structure of all specific proteins ean found in an organism's body. These macromolecules were first disvovered by ber of | Friedrich Micscher, Nucleic avids are polymers made up of monomers | called nucleotide, Lach nucleotide is composed of three components which40 FUNDAMENTALS OF BIOLOGY 1 are covalently bounded together. These include @ phosplite molecule, a carbon sugar (pentose). and @ nitsogen-containing base. Phosphate and sat molecules form the backbone of the nucleotide. The sugar molecule is then attached to a specific nitrogen base. Nucleotides are linked together by phosphodiester bonus to form the polymer nucleic acids. ‘A nucleotide Figure 2.1. Composition of Nucleotide’ ‘There are five common hitrogen bases. These are adenine (A), cytosine (C), guanine (G), thymine (7), and uracil (U). These bases act like genetic alphabets on which the structure and type of each protein is based. ‘A. G, C ate found in DNA and RNA. Tis only found in DNA while U is only found in RNA. U replaces T in pairing with A in the RNA molecule, Nitrogen bases are further grouped into pyrimidine and purine buses. Pyrimi- dine bases are composed of one six-sided ring while purine bases have two rings- a six-sided ring fused to a five-sided ring, Purine bases are larger than pyrimidine bases. A and G are purine bases, while C, T, and U are pyrimi- dine Furthermore, each nitrogen base has a complementary base pair, a fixed and expected counterpart of the other. A pyrimidine base is always paired with a purine base (vice versa). A is always paired with T in the DNA molecule and paired with U in the RNA molecule. G is always paired with C There are two types of nucleic acids which are all made up of nucleotides, These are basically named according to the type of sugar found in each nucleic acid. Deoxyribonucleic acid (DNA) contains deoxyribose while ribonucleic acid (RNA) contains ribose sugar: DNA DNA is the genetic material that is transmitted from the parents to the offsprings from generation to generation. It contains all the genetic information that programs all cellu nism. DNA is located i activities and characterizes each de the nucleus of a cell. This is often orA) like sed. vis cule, two than rimi- air, @ ways nthe vaired up of found ribose nts to cenetic seach often MODULE 4 ~ Understanding Colls; The Building Pieces of Life ee Pe CC referred as the blueprint of life. Just like the blueprint of a building or house, whatever is specilied in the blueprint, it is what the building or house will be made up of. DNA is the organism's blueprint that contains genet instructions thar determine all cellular components and activities and characteristics of organisms as a whole. It contains coded set of instructions about when and what type ancl amount of proteins to be made. DNA segments carrying specilie genctic information are called genes. Gene's tmessage to the cell is encoded in its specific sequence of the Tour DNA bases. Specific sequence of bases determines specific gene, The sequcit and type of bases along a gene specifies the amino acid sequoie® ofa particular protein, protein conformation and function. defective gene nay indicate that there is something wrong in the DNA molecule such as wrong base pairing. ‘The DNA structure was discovered by Nobel Prize winners James Watson and Francis Crick in 1953. DNA is composed of two long helical strands of nucleotides forming double helix, Phosphate and sugar backbones are located outside of the double helix exposed to water and other substances while the base paits lie inside within the middie. In the DSA Trolecule, coniplementary base pairs are joined by hydrogen bonds that clilfe ve number for each type of base pair. Base pair A and T is always joined ty two hydroyen bonds while G and C base pair is held together by three hydrogen bonds, Thus, G-C base pair is more stable than A-T. Fifty years after the discovery of the double helix, the Human Genome Project was completed in 2003 reporting that there are around 3.2 billion base pairs in the human genome. Figure 2.2. DNA double helix ig sya tar Yar Haran Gaane Rta nts) at Genes are segments of DNA that carry genetic informa- tion.FUNDAMENTALS OF BIOLOGY 1 RNA Ribonucleic acid (RNA) is another type of nucleic acid. It is named after the ribose sugar found in the molecule’s backbone. Just like DNA, RNA has a sugar-phosphate backbone with nucleotide bases attached to it There are other characteristics of RNA that are different from DNA molecule, These are described in the following table. ‘Table 2. Differences between RNA and DN. Element RNA DNA location in the cell | nucleus and cytoplasm} — Nucleus no. of strand single-stranded base pairs, CGAT RNA molecules are also important nucleic acids performing vital role in the cells. They can move around the cells of living organisms and thus, serve as a sort of genetic messenger, relaying the information stored in the cell's DNA out from the nucleus to the ribosome where it is used to help make proteins. How RNA is synthesized was discovered in 1959 by Nobel Prize winner Severo Ochoa. here are three types. of RNA named after the functions they perform in relation to protein synthesis. The first is messenger RNA or mRNA. This transmits genetic instructions coded in the DNA inside the nucleus to the cytoplasm particularly in the ribosome where it is translated into amino acids to produce proteins. ‘The second type of RNA is transfer RNA ({RNA). This is found in the cytoplasm of the cell. Most often this is referred to as an “amino acid escort” because it covalently attaches amino acids to the ribosome facilitat- ing, protein synthesis. Transfer RNA transfates the codon of mRNA into amino acids. The third type is ribosomal RNA (rRNA). This does not contain genetic information, however, rRNA is a major component of the ribosome, It is the protein factory of the cell, Ribosomal RNA molecules are abundant in the cytoplasm. These combine with protein to form ribosome D. Proteins Proteins are a vital organic substance in the organism's body. These come from the Greck word proteios, which means “primary.” Such name is appropriate, for all gells need protein in carrying out cellular processes. Proteins are considered as the most abundant and most complex, yet functionally versatile among the organic macromolecules. Proteins are made of monomers of amino acids that are joined together by peptide bondsof bie MODULE Q = Undeistanding Coils: The Bulkina Pr formed through dehydration synthesis, ‘There are venty dif acids. All of these amino acids have th une amino group (-NIL) and carboxyl group (COOL, but different side chain group (represented by 1) The peptide bon! is formed between the amino group of one amino acid and the carboxy! proup of another amino acid, Differences in the side chain group identify specific amino avid and give their different individual properties. For example lyeine, the simplest among the amino acid, has only fone hydrogen atom attached to its side chain, while aking (C1) has 3 erent amine R (side-chain group) WN - € - COOH amino (group) Hi (caboxyl group) Figure 2.3. The Composition of Amino acid ‘Amino acids can be ctassitied into essential or nonessential amino mino acids are thase that are not naturally produced by the Is these amino acids are obtained through consumption of foods rich in protein. Thus, protein rich foods should be part of our daily diet to ensure the steady supply of essential amino acids. Essential amino acids include isoleucine, leucine, lyeine, methionine, phenylalanine, threonine, tryptophan, and valine. The remaining twelve amino acids- alanine, arginine, asparagine, aspartic acid, eysteine, glutamic acid, glutamine, glycine, histidine, proline, serine, and tyrosine - are classified as honessential amino acids. These are amino acids that can be naturally produced in our body, Each protein has specific sequence, types or number of amino acids. A slight change in the sequence, number or type of amino acid. changes the structure of the protein which in turn changes ity ability to function. If this happens, mutation in the protein. structure will take place resulting to. manifestation of certain serious medical conditions. An example of this is sickle cell anemia that results from a single incorrect amino acid in the peptide chain of 146 amino acids of hemoglobin, The single amino acid error results to a serious medical condition in which the red blood cells become sickle-shaped cells, blocking, capillaries resulting to disruption of the normal blood flow to various organs. Levels of Protein Structure ‘The function of the protein depends on its specific conformation. Proteins exhibit the idea that form fits its function. Usually the more complex the conformation of the protein, the more complex is its funetion in the organism's body. Protein structure has four different levels. These are Primary, seconduiry, tertiary and quarternary structures. Primary structure of 43 Bssential amino acids are amino acids that are not naturally produced by the body and thus, must be obtained from protein rich | foods Non: essential amino acids are amino acids that naturally produced in levels needed by the body. Mutation is an alteration or change in the natural composi- tion or structure of DNA.FUNDAMENTALS OF BIOLOGY 1 r Denaturation is the process in which the natural conformation or structure of protein is changed or altered because of certain « factors. the protein is described by a precise and unique sequence of wmmino ids. ‘The secondary structure is protein segments of polypeptide chain that are repeatedly coiled or folded in specifie pattern such as alpha helix or pleated sheet. ‘Tertiary steucture is composed of irregular contortions that results from bonding between side chains (R groups). Quaternary structure the overall protein structure resulting from the aggregation of different polypeptide subunits, These structures can be changed by denaturation as brought about by factors such as radiation. temperature, e normal substance concentrations within or .¢ a protein loses its conformation it will ical capacity: proce: chemicals, and changes in thi outside the cell environment. On never be recovered and thurs loses its normal biolo Functions of Proteins Proteins provide many significant functions i are classified according to the vital roles they perfor body. in all living things. These 1m within the organism's Antibodies - These defend the organism from disease-causing and viruses and invading foreign molecules. These agents such as bacteria found in blood or other bodily jnclude the gamma globulin proteins that are fluids of vertebrates. Enzymes ~ These hasten or speed up all cellular and chemical reactions, in the organism's body. Examples are amylase and lipase which hasten digestion of starch and fats, respectively. Hormones ~ They act as chemical messengers sending regulatory signals among cells. Example is growth hormone, which regulates cellular growth sind division. Another is follicle-stimulating hormone in females, which stimulatcs the release of estrogens from the ovarian follicle. Menibrane transport proteins - These facilitate the transport of substances across biological membrane. Aquaporins that allow water molecules to pass through the cell membrane are examples of membrane transport proteins. Morile proteins - These enable cells to move. Example is the dyein which cts on the microtubules causing whipping movements of sperm tails. Receptor proteins ~ These serve as binding sites found outside cell surfaces or within the cells. Attachment of signal molecules to these binding sites Wiggers series of reactions that are important for cellular communication arid signal transduetion. Regulatory proteins ~ These control many cellular and body processes such as regulating the expression of a gene.MODULE 2 ~ Understanding Cells: The Building Pieces of Life ee =—_ Storage protein - These function as reserves of amino by organisms. Ovalbumin, the main protein in egy white is a storage protein Structural proteins - These serve as part of a cellular structure ats well as other structural parts of organisms. These include microtubules and microfilaments inside the cell: keratin in hairs and nails; and collagen in the connective tissues. Activity 2.3 will belp you identify the organic compounds which are found in common foods eaten by people everyday. Laboratory Activities Activity 2.1 Water for Life Objectives: 1. Identify properties of water. 2. Explain the importance of the different properties of water to organisms and the environment What are necded? Tap watery Ice cubes, Acetone, Ethyl alcohol, lee, Graduated cylinder, Small beakers What to do? 1. Put § ml of water, acetone, and alcohol in three separate containers, Observe the volume of the three liquids afier 20 minutes. Compare their volumes. Note: While waiting for 20 minutes, you may proceed to procedure no. 2 ‘After 20 minutes go back to your set ups in procedure no. a. Is there a difference in the volume after 20 minutes? If there is a difference, expldin what could be the reason for such difference? b. What property of water is exhibited in this activity? Describe a situation that illustrates the importance of this property of water to life 2, Put an ice cube into a glass of water. Observe your set-up. a. Did the ice cube sink or float? Explain the reason for your observation. b. What property of water is exhibited in this set-up? Explain the ecological importance of this property of water and give an example, €. Describe two other properties of water and explain their importance to organisms. 45