Module I General Zoology - Introductory Lessons to Zoology PDF

MODULE I Lesson 1 Zoology as a Science Lesson 2 Characteristics of Life Lesson 3 Origin and Chemistry of Life Lesson 4 Cell Structures and Functions Module I ...

MODULE I Lesson 1 Zoology as a Science Lesson 2 Characteristics of Life Lesson 3 Origin and Chemistry of Life Lesson 4 Cell Structures and Functions Module I  2 MODULE I INTRODUCTORY LESSONS TO ZOOLOGY  INTRODUCTION Zoology is also known as animal science and is a study devoted to studying animal life. This course covers areas ranging from the structural and functional components of organisms to the cellular, even molecular, unit of life. The study of zoology also tackles how animals are formed and what traits are being passed through generations. Also, interactions with an animal to their environment, as well as the significance of their behaviors are studied. Zoology is both analytical and descriptive. Module 1 is set for five weeks, bearing 3 hours per week, covering 15 hours for the lecture. OBJECTIVES After studying the module, you should be able to: 1. Discuss the definition and importance of zoology 2. Explain the importance of the process of the scientific method 3. Inculcate the different tenets of the nature of science 4. Distinguish the sub-disciplines of zoology 5. Discuss the different properties of life 6. Describe the components of the biological hierarchy structure 7. Enumerate the four unifying principles of modern science 8. Enumerate and discuss the general properties of living 9. Describe and cite examples of the four biomolecules 10. Enumerate the different cell structures and functions  DIRECTIONS/ MODULE ORGANIZER There are four main lessons in this module. Read each lesson carefully, then answer the exercises/activities to determine how much you have benefited from it. Work on these exercises reliably and submit your output to your tutor or the CAS office. In case you encounter difficulty, discuss this with your tutor during the face-to-face meeting. If not, contact your instructor at the CAS office. Good luck and happy reading!!! Module I  3 Module I  4 Lesson 1  Zoology as a Science Learning Objective for Lesson I: 1. Discuss the definition and importance of zoology 2. Explain the importance of the process of the scientific method 3. Inculcate the different tenets of the nature of science 4. Distinguish the sub-disciplines of zoology Zoology Zoology is also known as animal science, is a study devoted to studying animal life. This course covers areas ranging from the structural and functional components of organisms to the cellular, even molecular, unit of life. The study of zoology also tackles the development of animals and what traits remain through generations. Also, interactions with an animal to their environment and the significance of their behaviors are studied. Zoology is both analytical and descriptive. Historically, zoology requires efforts to analyze and classify zoons (animals). Aristotle, a Greek philosopher, devised a classification system recognizing similarities in diverse organisms by grouping them base on habitat and modes of reproduction. Carolus Linnaeus dominated the 12th century by devising a nomenclature system for classifying animals based on their morphological anatomy through the binomial system, establishing taxonomy based on their genus and species. In the current period, zoology offers a wide range and is evolved into an interdisciplinary field to offer various techniques and knowledge. Zoology not only study animals, but it also studies how to classify and explore anatomy and physiology. Principle of Science  Tenets of the Nature of Science - Science is guided by natural law (natural phenomena) - Body of knowledge, collected through scientific inquiry - Develop hypotheses/ explanations - Science is testable - Design and conduct experiments - Systematic observation and relevant evidence - The conclusions of science are durable yet tentative Module I  5 - People contribute to science - Scientific knowledge relied heavily on but not entirely to skepticism, rational ideas, experiments, and observations - There is no single way to deal with science, no universal scientific method - Scientific knowledge is creative, imaginative, and inferential and subject to change The scientific method is summarized through the following series of steps: 1. Observation 2. Problem/ Questions 3. Hypothesis Formation 4. Empirical Test- Experimentation; Controlled Experiments Include 2 Groups - Test/ Experiment Group Module I  6 - Control Group 5. Conclusions- accept or reject your hypothesis 6. Publications 7. Cycle to create new experiments and discoveries Zoology- is the scientific study of animal life. - It encompasses all aspects of scientific knowledge about animals, like embryonic development, evolution, behavior, ecological distribution, and classification. - They are broken down into many branches because there are many different ways to study animals. Zoology- according to the animals being studied Entomology- insects Paleontology- fossils Lepidopterology- butterflies/moths Herpetology- reptiles/amphibians Myrmecology- ants Ichthyology- fishes Coleopterology- beetles Malacology- mollusks Ornithology- birds Conchology- shells Mammalogy- mammals Zoology- according to what aspect of scientific knowledge is being studied. Invertebrate zoology- the study of animals without backbones Anatomy- internal structure and relationship between body parts Morphology- structure, and forms of organisms Physiology- a function of body parts and body as a whole Cytology- The study of cells Histology- the microscopic structure of tissues and cells Development- the transformation from single fertilized egg to complex multicellular adult Taxonomy- identification/ phylogeny/ classification Genetics- heredity, and variations Ecology- interactions among organisms and their environment Ethology- animal behavior Helminthology – parasitic worms Evolution- the historical transformation from simple forms of the past to the complex form of the present/ origin Primatology- the study of primates Zoogeography- distribution of animals Sociobiology- ecology, evolution, and behavior of social animals 2 Major Theories that guide Zoological Research 1) Theory of Evolution- Charles Darwin - Fossils record supports Darwin - All organisms rise and develop through Natural Selection from Adaptations - Individual’s ability to compete, survive and reproduce Module I  7 2) The Chromosomal Theory of Inheritance- Theodore Boveri and Walter Sutton 1. Genes are found at specific locations in the chromosomes, and they passed from one generation to the next. 2. Chromosomes contain the genes, and they are replicated and passed to produce offspring. 3. Chromosomes are present as pairs in diploid cells. 4. Chromosomes segregate and assort independently. THINK! 1. Enumerate the different sub disciplines of zoology. 2. Explain the importance of studying zoology BRAIN EXERCISE! Match the following animals or process (from Column A) to the discipline (Column B) they are studies. Write your answers on the space provided before each item. Column A Column B. ___1. owls a. Herpetology ___2. Stone imprints b. Ornithology ___3. clownfish b. Primatology ___4. bees a. Helminthology ___5. octopus b. Ichthyology ___6. Inherited traits a. Paleontology ___7. tapeworm b. Entomology ___8. Homeostasis a. Genetics Module I  8 Lesson 2  Characteristics of Life Learning Objectives:  Describe the characteristics shared by all living organisms  Order the level of organization of living things From the most prominent animals like the blue whale down to the smallest bacterium are made of cells possess features for reproduction to increase in the future generations. Without such characteristics, there is no life. CHARACTERISTICS OF LIFE Zoology examines the function, structure, origin, growth, distribution, evolution, and interactions of the animals. They are aligned with the four unifying principles of modern biology: evolution, genetics, cell theory, and homeostasis. All life forms can be guided through the principles mentioned. An individual living creature is called an organism, and all organisms share the same characteristics: 1. Made up of specific molecules - Carbohydrates - Lipids - Proteins - Nucleic Acid (DNA and RNA) 2. Hierarchical Organizations 3. Reproduce 4. Genetic Code 5. Develop 6. Interact with Development 7. Movement GENERAL PROPERTIES OF LIVING SYSTEM 1. Chemical Uniqueness- organisms exhibit a unique and highly complex molecular organizations 2. Complexity and Hierarchical Organization o In a living system there exist a hierarchy of levels includes:  Macromolecules, cells, tissues, organ, organ system, species/organisms, population Module I  9 o In multicellular organisms, similar cells form tissues. Tissues, in turn, collaborate to form organs (body structures with a distinct function). Organisms work together to form organ systems. Unicellular organisms are also complex such that they are made up of molecules from atoms, which in turn make up organelles and other inclusions. Hierarchy of Biological Structure Organisms Organ System Organs Tissues Cells Nuclei, Mitochondria, Chloroplasts Multienzymes complexes, ribosomes, chromosomes, membranes, structural elements, contractile system Proteins Nucleic Polysaccharide Phospholipids Acids s 20 Amino Nucleotides Sugars Palmitate, other Acids fatty acids, Glucose glycerol, choline CO2, H2O, N2 3. Reproduction- living systems can reproduce themselves. At each level living forms reproduce: o Unicellular organisms reproduce by doubling their DNA by equally dividing the cell to form two new cells o Multicellular organisms produce through specializes germline cells o Genes are replicated to produce new genes. o Cells divide, producing new cells. o Organisms reproduce, either sexually or asexually, to produce new organisms. o Populations may fragment to yield new populations. o Genes ensure offsprings of the same species given with similar size, shape, and characteristics Module I  10 4. Possession of Genetic Program- a genetic program provides: o Nucleic Acids: polymers built of repeated units called nucleotides (A, T, C, and G). - Nucleic Acid= DNA- Deoxyribonucleic Acid 1.7-1.8 approximately strand o DNA: long, linear, chain of nucleotides containing genetic information- the double helix o Genetic Code: correspondence between base sequences in DNA and the sequence of amino acids in a protein. o Information flow- replication, transcription, and translation WATSON AND CRICK AND ROSALYN FRANKLIN- the double helix  Nucleotides 1. Phosphate 2. Sugar- deoxyribose 3. Nitrogenous Base (A) Adenine= (T) Thymine (C) Cytosine= (G) Guanine 5. Metabolism- Living organisms maintain themselves by acquiring nutrients from their environments - Some total of all chemicals reactions occurring within the organisms.  Metabolic processes include:  Digestion  Energy Production (Respiration)  Destructive (catabolic) and Constructive (anabolic) reactions 6. Development- there are always stages. - All organisms pass through a characteristics life cycle. - The progress that an organism undergoes from its origin to its final adult form. - Transformation 7. Environmental Interaction- the ability to response - All animals interact with their environments. o Ecology- is the study of organismal interaction with an environment. o All organisms respond to environmental stimuli 8. Locomotion or Movement: o Movements at the level of cells are required for: Reproduction, Growth, and Responses to stimuli. o On a larger scale: Entire populations or species may disperse from one location or another over time. Module I  11 o Organisms respond to stimuli. Most animal movement depends on contractile proteins which can change shape to contract and relax (e.g., cilia and flagella, pseudopods) o Animals move for a variety of reasons: finding mate, escape predators, create habitats and for many, it is essential for survival o Other locomotory modes include: self-propelled movements (swimming, walking, running, flying, and gliding), passive locomotion dependent on the environment (kiting for spiders, sailing for jellyfishes, phoresis or riding other animals, and rolling for some beetles) THINK! 1. What are the different properties of life? Identify one organism and explain in detail its properties. 2. What are the four unifying principles that form the foundation of modern biology? 3. Identify three of the seven characteristics of living things. Module I  12 Lesson 3  Origin and Chemistry of Life Learning Objectives for Lesson 4 1. Enumerate and discuss the general properties of living 2. Describe and cite examples of the four biomolecules The Chemistry of Life: Macromolecules Within cells, small organic molecules are linked to form larger molecules, which may comprise thousands of covalently bonded atoms weighing hundreds of thousands of daltons. The macromolecules have four significant classes. These are carbohydrates, lipids, proteins, and nucleic acids connected the most common elements Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur (CHNOPS) Organic Compounds - compounds that contain CARBON are called organic - Diverse and varied structural organization of carbon atoms, there is a unique variation in the biological system. Biomolecules- molecules of life - Provide the structural framework for all living things, and the mechanisms needed to perform various biological processes. Macromolecules These are large organic molecules, also known as called polymers (repeated units), made up of smaller building blocks called monomers. Polymerization is the process of linking monomers to form polymers. The chemical processes that cells use to make and break polymers are similar for all macromolecules. o Dehydration or condensation reaction allows monomers to connect by covalent bonds to form through the loss of a water molecule. When bonds form between two monomers, each monomer contributes to the lost water molecule. One monomer provides its hydrogen (—H) while the other renders a hydroxyl group (—OH) at the expense of energy aided by enzymes. o Hydrolysis disassembles the covalent bonds connecting monomers in a polymer; this is the reverse of the dehydration process. Here, the addition of water molecules breaks the bonds. A hydrogen atom joins to one monomer, and a hydroxyl Module I  13 group joins to the adjacent monomer. Food consumed undergoes hydrolysis acted upon by many enzymes to break down specific polymers resulting in the absorption of monomers in the bloodstream. Then, the somatic (body cells) make use of the dehydration reaction process to assemble the monomers to new polymers that carry out functions specific to the individual cell types. In the figure below, you can find the synthesis (dehydration) and breakdown (hydrolysis) of polymers An enormous variety of polymers are put together from a small set of monomers. o One cell comprises of thousands of different kinds of macromolecules that vary among cells of the same individual and unrelated individuals of a species, and even more between species. o Various combinations of the 40–50 typical monomers and some others that occur rarely make it diverse. o The monomers can be attached in many combinations. MONOMERS POLYMERS Amino Acids Polypeptide – Protein Simple Sugars Polysaccharide – Carbohydrates Nucleotide Polynucleotides – Nucleic acids Fatty Acids + Glycerol Lipids THINK! 1. What are the four main classes of large biological molecules? 2. Suppose you eat a serving of green beans. What reactions must occur for the amino acid monomers in the protein of the beans to be converted to proteins in your body? Module I  14 1. CARBOHYDRATES: Carbohydrates serve as fuel and building material. Carbohydrates include sugars and polymers.  The simplest carbohydrates the simple sugars or monosaccharides.  Disaccharides, also known as double sugars, comprises of two monosaccharides joined by a condensation reaction.  Polysaccharides are polymers of many monosaccharides.  Monosaccharides have molecular formulas of multiple units of CH2O. (e.g., glucose has the formula C6H12O6). They consist of a carbonyl group (>C=O) and multiple hydroxyl groups (—OH). o The sugar is either an aldose or a ketose depending on the carbonyl group's position. o o Most names for sugars end in -ose. Module I  15 o The structural isomers are glucose, an aldose, fructose, and ketose o The number of carbons in the carbon skeletons classifies the Monosaccharides. o Glucose along with other six-carbon sugars is called hexoses. o Five-carbon backbones are pentoses, and three- carbon sugars are trioses. o Monosaccharides, mainly glucose, are a significant fuel for cellular work. Also, they function as raw materials for the integration of other monomers, such as fatty acids and amino acids. o Monosaccharides can form wings in aqueous solutions. o Glycosidic linkages allow two monosaccharides to merge to form a disaccharide via dehydration reaction. For example, (1)Maltose is formed by joining two molecules of glucose, (2) Sucrose is formed by joining glucose and fructose, and (3) Lactose is formed by joining galactose and glucose. o Polysaccharides are the polymers of sugars that have structural and storage roles. o They are polymers of hundreds to thousands of monosaccharides joined by glycosidic linkages. o Polysaccharides serve as building blocks for the cell or the whole organism. Module I  16 o Some polysaccharides have a purpose for storage and are hydrolyzed as sugars are needed. 1. Starch, a storage polysaccharide, is composed entirely of glucose enjoined by 1–4 linkages attached to numbers 1-4 carbon) between the glucose molecules. 2. Amylose, the purest form of starch, is unbranched whereas Amylopectin is branched. Branching created complexity. When animals feed on plants with these structures, they have to have digestive enzymes to hydrolyze starch into simple sugars called glucose. Animals store this glucose in the form of polysaccharide glycogen. Vertebrates store its supply of glycogen in the liver and muscles. 3. Cellulose is a major component of the tight plant walls. Billions of cellulose are produced by plants annually and are the most abundant organic content on the Earth. Cellulose is also a polymer of glucose but differs on the glycosidic linkages by the structural ring of glucose. Two rings differ in terms of the attached hydroxyl group to Carbon number 1—beta glucose for the above attachment, and alpha glucose fo the below attachment in the plane ring. Module I  17 o Starch is a polysaccharide of alpha-glucose monomer. Cellulose, in contrast, is a polysaccharide made of beta-glucose monomers. o The glycosidic bond difference makes the two molecules have a distinct 3D shape. o On the other hand, polymers with alpha glucose form helical structures and polymers with beta glucose form vertical structures. Vertical structures allow hydrogen (H) atoms form a bond with the hydroxyl (OH) of other strands o Enzymes capable of hydrolyzing and digesting starch the alpha linkages cannot do the same with the beta linkages in cellulose. (e.g., human food containing cellulose pass through the digestive tract as an insoluble fiber whereas herbivores symbiotic with microbes that have cellulase enzyme access the energy in the plants. Aside from herbivores, some fungi can also digest the cellulose. 4. Chitin is an essential polysaccharide found in the exoskeletons of most arthropods (crustaceans, spiders, and insects). They are also in the cell walls of many fungi. This structure is similar to cellulose but has additional nitrogen on the appendages of each glucose. They are structurally leathery but can be hardened with the addition of CACO3. Module I  18 2. LIPIDS- or fats are organic compounds comprising of carbon, hydrogen, and oxygen. Lipids are essential structural components of all cells, especially the cell membranes. Lipids also represent an essential energy reserve molecule. Lipids offer twice as much energy as carbohydrates. Three essential lipids in the body are Triglycerides, Phospholipids, and Cholesterol. o Lipids are unique to other biomolecules, do not form polymers, and that they all have little to no water affinity due to the immense hydrocarbon which forms nonpolar covalent bonds. Despite this, they serve diverse forms and functions. 1. Fats store large quantities of energy.  They form large molecules assembled from smaller molecules by dehydration reactions even without struct polymerization.  There are two small units for fat - glycerol and fatty acids. Module I  19 o Glycerol contains a hydroxyl group attached to each three-carbon alcohol. o Fatty acid (FAs) comprises of 16-18 long carbons attached with a carboxyl group o The hydrophobic property is attributed to the many nonpolar C—H bonds in the long hydrocarbon skeleton. o Triacylglycerol or triglyceride in fat has three fatty acids joined to Glycerol by an ester linkage. The three fatty acids in fat may be the same or different. They may have variations in the number of carbons and the locations of double bonds. o Saturated fatty acid are FAs saturated with hydrogens at all possible position because it lacks carbon-carbon double bonds. This forms a straight chain. Most animal fats like lards are examples of this, and they are solid at room temperature. A diet with high saturated fatty acid contributes to plague deposits-causing atherosclerosis. o An unsaturated fatty acid is FAs that have one or more carbon-carbon double bonds formed due to the removal of H atoms from the carbon skeleton. This forms a kink to areas with double bonds. Plants (peanut butter, margarine, and hydrogenated vegetable oils) and fishes have this kind of fat and are liquids at room temperature. Kinks from the double bonds prevent tight packing, thus, prevents it from solidification. Hydrogenating unsaturated fatty acids produces saturated FAs and unsaturated FAs with trans double bonds. The latter is worse and contributes more to atherosclerosis 2. One of the significant functions of fats is energy storage. o Fat stores twice as much energy than a polysaccharide like starch. Due to the immobility of plant, they function even with bulky energy and only makes use of their oil for compact storage or dispersal. o Animals carry their stored energy and therefore needs bulkier storage deposited in long-term energy reserve that can swell and shrink such as the adipose cell (adipocytes) that does not only store but also cushions vital organs like the kidney, and adds an insulator function within the subcutaneous especially in marine animals. 3. Phospholipids make up the cell membranes. o Attached to the two FAs are Glycerol and a phosphate group at the third position. The latter bears the negative charge. Module I  20 o Smaller groups of phosphate groups make up various phospholipids. These phospholipids have a complex interaction with water. The tails are hydrophobic, and the head is hydrophilic due to the attached phosphate group. They self assemble when added to water with tails pointing towards the interior are arranged at the surface of the cell as a bilayer. Hydrophilic heads on the outside of the bilayer are in contact with the aqueous solution. The hydrophobic tails point on the interior of the bilayer. This interaction provides a barrier between the cell and its external environment 4. Steroids are formed by the addition of cholesterol and certain hormones o Steroids are lipids with four fused rings on its carbon skeleton o They vary depending on the functional groups in its rings o Cholesterol, an animal cell membrane component, is a vital precursor where all steroids are synthesized. Many of the steroids are hormones such as a vertebrate sex hormone THINK! 1. Compare the structures of phospholipid and otriglycerides. Where do you find them? 2. Are sex hormones considered as lipids? 3. PROTEINS Proteins have diverse structures, resulting in a broader range of functions. They make up about 15% of the cells  Have many functions in the cell:  Structural Signaling  Enzymes Receptors  Transport Gene Regulation  Motor Special Functions Module I  21  Storage o Proteins constitute for 50% of the dry mass in cells. They are versatile in almost everything that an organism does. The Protein functions are (1) structural support, (2) storage, (3) transport, (4) cellular signaling, (5) movement, and (6) defense from foreign substances. o Proteins serve an essential role, such as enzymes that function as catalysts in cells—they regulating metabolism by accelerating chemical reactions selectively without being disbursed. o They have the most complex structure of the 3D shape of conformation deduced from the same set of 20 amino acid monomers. o Polypeptides are the polymers of proteins. Module I  22 1. Proteins are made of amino acids o Amino acids are molecules that possess carboxyl and amino groups with an asymmetric center of carbon atom called the alpha carbon. Four components attach to it: an amino group, a hydrogen atom, a carboxyl group, and a variable side chain (R group). o Sidechains (R Groups) characterize the different amino acids. It may be an H atom (glycine) or a carbon skeleton with a diverse functional group (glutamine). The properties, physical and chemical, deters the characteristic of particular amino acids Module I  23 The negative charge of some acidic R groups is due to the presence of a carboxyl group. In contrast, primary R groups are positive in charge due to the attached amino acid.  All amino acids have amino and carboxyl groups. The terms acidic and basic refers only to the groups attached in the R groups.  Peptide bonds are the resulting covalent bond from a dehydration reaction that removes the hydroxyl group from one amino acid of the carboxyl end and hydrogen from the amino group of another.  When the course is repeated, it creates a polypeptide chain that has an amino acid with a free amino group (the N- terminus) on one end and an amino acid with an open carboxyl group (the C-terminus) on the other. The range in size is vast from little to thousands, and each has its unique linear sequence that can be determined Frederick Sanger of Cambridge University determined the amino acid sequence of insulin in the 1950s by using enzymes that are protein- digesting, along with other catalysts, to hydrolyze insulin using chromatography that breaks down polypeptides. He used a chemical method and searched for overlapping regions. He was able to reconstruct the deconstructed insulin completely, given that a polypeptide can be sequenced. 2. Protein function is deterred by conformation  Functional protein has one or more polypeptides that have unique shapes such as twisted, folded, and coiled—the order of amino acids that control the three-dimensional conformation of the protein. The conformity, in turn, determines the function.  In a cell synthesis, the polypeptide chain folds continuously to assume conformational function for that protein. The folding depends on the sequence of amino acid reinforced by a variety of bonds between parts of the chain. Most protein shapes are globular, and others are fibrous. Module I  24 The ability to recognize and bind is the function of the protein  In almost every case, the role of a protein depends on its ability to identify and bind to some other molecule. e.g., the antibody binds to a specific substance. An enzyme acknowledges and binds to particular substrates to come up with a chemical reaction. Endorphins, a natural signal molecule bind to specific receptor proteins on the brain surface to induce euphoria and pain reliever). Other molecules that mimic endorphins such as morphine, heroin, and opiate can bind to the brain’s endorphin receptors due to the similarity in shape.  Three levels of structure are categorized on the organization of folding single polypeptides— primary, secondary, and tertiary structures. The quaternary structure arises when two or more polypeptides join to form a protein. 1. The primary structure of a protein is from the unique sequence of its amino acids. Slight changes in this affect the conformation and ability to function For example, a substitution of one amino acid (Val) for the normal one (GLN) at a specific position in the primary structure of hemoglobin can cause sickle-cell disease. This inherited blood disorder clogs capillaries. Module I  25 2. Secondary structure. Most proteins have parts of their polypeptide chains repeatedly folded and coiled as a result of the hydrogen bonding of repeating constituents. Hydrogen bonds are weak, but collectively, they stabilize the structure of the protein. Coils (an alpha helix) or folds (beta-pleated sheets) are the features of secondary structures 3. Tertiary structures are determined by interactions between various R groups, which include (a) hydrogen bonds between polar areas, (b) ionic bonds between charged R groups, and (c) hydrophobic interactions inclusive of the Van der Waals interactions. The interactions between the three are weak. Disulfide bridges, on the other hand, are strong covalent bonds formed between the sulfhydryl groups (SH) of two cysteine monomers act to screw parts of the protein. 4. Quaternary structure is the aggregations of two or more subunits of polypeptides. (1) Collagen, an excellent example of quaternary, is a fibrous protein of three polypeptides that are supercoiled.  The complexity of the structure provides structural strength for collagen’s role as a connective tissue (2) Hemoglobin is also a quaternary structure with globular protein  It consists of 2 alpha- and 2 beta-chains that consist mainly of alpha-helical secondary structure. Each subunit of the polypeptide has a non-peptide heme constituting iron atom that binds oxygen. Module I  26 In a given amino acid sequence, a polypeptide chain can spontaneously automatically arrange itself to a 3D shape determined and conserved by the interactions responsible for the secondary structure and the tertiary structure. The process of folding takes place as the protein is being synthesized within the cell. Protein conformation may depend on the circumstances of the environment of the protein. o Denaturation of protein is possible through alterations in pH, temperature, and salt concentration. Denaturation disrupts bondings of hydrogen, ionic, and disulfide bridges that provide tensile strength to maintain the shape’s integrity. o When transferred on an organic solvent, proteins denature. The hydrophobic region tumbles facing toward the solvent when it refolds. Denaturation can also be caused by heat, disrupting weak interactions that stabilize conformation. An example of this is the fatality of extreme fevers caused by denatured blood proteins attributed to high body temperature. Only a few denatured proteins can revert to its functional shape. o Despite having fixed configurations, it is still challenging to identify proteins due to varying appearance in intermediate stages before maturation. o Protein foldings are assisted by chaperone proteins, chaperonins by segregating and protecting during folding of the polypeptide. Module I  27 o X-ray crystallography is used at present to determine the configuration of proteins. This skill can also determine the location of atoms to be able to build a replica using computer simulation. Non-usage of protein is also possible with a nuclear magnetic response (NMR). THINK! 1. Can denatured proteins still serve their function normally? 2. Which part of a polypeptide chain participates in bonds 4. NUCLEIC holding secondary and tertiary structure ACID Stores and transmits hereditary information (gene). Gene is the unit of inheritance that programs the amino acid sequence of a polypeptide. The gene comprises of DNA (deoxyribonucleic acid), a polymer known as nucleic acid. There are two types of Nucleic acids: (1) ribonucleic acid (RNA) and (2) deoxyribonucleic acid (DNA). These two permits living organisms to reproduce their complex components from generation to generation. In a eukaryotic cell, DNA in the nucleus programs protein production in the cytoplasm by dictating synthesis of messenger RNA (mRNA). The cell nucleus is actually much larger relative to the other elements of the figure below. 1. DNA provides its directions for replication and directs RNA synthesis and further controls protein synthesis. Organisms inherit DNA from their parents. The DNA is extensively long, comprising of hundreds to thousands of genes. Before cells divide for the reproduction phase, the DNA is copied, and the copies are passed to the next generations of cells. Module I  28 o Proteins are responsible for executing the instructions contained in DNA that encode the information that programs cell activities. o All genes along a DNA molecule lead the synthesis of a specific type of messenger RNA (mRNA) molecule. o The mRNA molecule works together with the cell’s protein-synthesizing machinery to steer the ordering of amino acids in a polypeptide. o The genetic information flows from DNA -> RNA -> protein. o Protein synthesis happens on ribosomes, a cellular structures o In eukaryotic organisms, DNA is situated in the nucleus. However, most ribosomes are located in the cytoplasm. mRNA serves as an intermediary that hastens the transfer of directions and information from the nucleus to the cytoplasm. o Prokaryotes have no nuclei but make use of RNA as an intermediary to transmit messages from DNA to its ribosomes.  Each nucleic acids are made of nucleotide monomers that bear three parts: (1) a nitrogenous base, (2) a pentose sugar, and (3) a phosphate group. 1. Nitrogenous Base  It is made of rings of carbon and nitrogen—two types of base: pyrimidines and purines. 1.a. Pyrimidines comprise of a single six-membered ring. Module I  29  The three different kinds of pyrimidines are thymine (T), cytosine (C), and uracil (U). 1.b. Purines contains a six-membered ring attached to a five- membered ring.  The two kinds of purines are adenine (A) and guanine (G). 2. Pentose Sugar The pentose fused to the nitrogen base is ribose in the nucleotides of RNA and deoxyribose in DNA. The difference between the sugars is the lack of oxygen atom on carbon-2 in deoxyribose. The sugar atoms possess a prime after the number to differentiate them due to the numbering of atoms in both the nitrogenous base and the sugar. Thus, carbon-2 in the sugar ring is the 2’ carbon, and the carbon that sticks up from the ring is the 5’ carbon. The addition of a pentose to a nitrogenous base is called nucleoside, whereas the addition of a phosphate group makes a nucleotide, otherwise known as nucleoside monophosphate. 3. Phosphate Group Covalent bonds join polynucleotides called phosphodiester linkages to synthesize adjacent nucleotides that form between the hydroxyl (—OH_ group on the 3’ (3 prime) of one nucleotide and the phosphate on the 5’ (5 prime) carbon of the next. This bonding creates a continuous repeating backbone of the sugar- phosphate units, with appendages comprising of the nitrogenous bases. The polymer has a distinct two free ends. One end has a hydroxyl group on a 3’ carbon; this is the 3’ end. The other end has a phosphate attached to a 5’ carbon; this is the 5’ end.  The sequence of bases in both DNA and mRNA polymer is unique for each gene. The base combinations are virtually limitless because genes have hundreds to thousands of nucleotides long. Further, the 3D function and conformation are determined by the primary structure of the protein based on the linear order of bases in a gene that specifies the amino acids. The DNA double helix replication is the basis of inheritance Module I  30  An RNA molecule has a single polynucleotide chain.  DNA molecules contain two polynucleotide strands that spiral around an invisible axis to form a double helix (proposed in 1953 by James Watson and Francis Crick as the structure of DNA).  Located on the outside of the helix are the sugar-phosphate backbones of the two polynucleotides. The arrangement is antiparallel, where two backbones run in opposite 5’ -> 3’ directions from each other.  Hydrogen bonds connect pairs of nitrogenous bases per strand to the polynucleotide chains.  The majority of DNA molecules have almost millions of base pairs, but due to their shapes, there is limited compatibility.  The pairing is always: Adenine (A) with thymine (T) and cytosine (C) with guanine (G).  The sequence on the opposite strand is easily identified, given this rule on base-pairing given one strand. With this, the two strands are complementary.  Before cell Choices. Multiple division Select occurs, theonebestfull strand answer serves on the spaceas a template to order nucleotides provided before the item numbers.to form a new complementary strand resulting in two identical copies of the original double- stranded DNA ____1. molecule Which further of the following dispersed is not to the daughter cells. a polymer? The entire processB)ensures A) glucose starch a full set of genetic C) cellulose information that is D) chitin conveyed whenever ____2. What is theachemical cell reproduces. mechanism by which cells make polymers from monomers? THINK! A) phosphodiester linkages B) hydrolysis C) In a DNA, a region alongD)one dehydration reactions the formation strand hasof disulfide bridgesof a sequence ____3. Which of the following polymers contain nitrogenous bases: 5'-TAGGCCT-3'. Write down the nitrogen? A) starch B) glycogen C) cellulose D) chitin strand ____4. Theand its complementary molecular strand formula for glucose is C6stating thewould H12O6. What 5' and 3' ends of the complementary strand. be the molecular formula for a molecule made by linking three glucose molecules together by dehydration reactions? Exercise A) C18H36O18 B) C18H30O15 C) C6H10O5 D) C18H10O15 ____5. Amylase enzymes can break glycosidic linkages between glucose monomers if the monomers are the alpjha form. Which of the following could amylase break down? A) glycogen B) cellulose C) chitin D) A and B only ____6.What does the term ʺinsoluble fiberʺ refer to on food packages? A) cellulose B) polypeptides C) starch D) amylopectin ____7. What is a triacylglycerol? A) a protein with tertiary structure B) a lipid made with three fatty acids and glycerol C) a lipid that makes up much of the plasma membrane D) a molecule formed from three alcohols by dehydration reactions ____8. Which of the following is true regarding saturated fatty acids? A) They are the predominant fatty acid in corn oil. B) They have double bonds between carbon atoms of the fatty acids. C) They are the principal molecules in lard and butter. D) They are usually liquid at room temperature. ____9. Large organic molecules are usually assembled by polymerization of a few kinds of simple subunits. Which of the following is an exception to this statement? Module I A) a steroid B) cellulose C) DNA D) an enzyme ____10. Why are human sex hormones considered to be lipids? A) They are essential components of cell membranes.  31 Lesson 4  Cell Structure and Functions Cells Cells are the basic unit of life. The cell is a model of “Emergent Properties,” where organelles alone can do nothing, but if all of them are put together inside a cell membrane, “life” emerges. Cytology is the study of cells, and cytologists are persons who work and study the cells. Cytology joined with the study of molecules and chemical processes in biochemistry produce essential bade for modern cell biology. The following are valid to all living organisms: o All organisms are built from cells. o Many organisms are single-celled (unicellular). o The cell is the basic unit for both the structure and function even in multicellular organisms o The cell is the simplest pool of matter that can live. o Their descent from earlier cells relates to all cells. The Classical Cell Theory states, that: 1. All organisms are composed of one or more cells 2. Cells are the basic unit of structure and function in organisms. 3. All cells comr from preexisting (other) cells Modern Cell Theory states, that: 1. All living things are made up of cells. 2. Cells are the basic units of structure and function in living things. 3. Living things come only from other living cells. 4. The cell contains hereditary information which is passed on from cell during cell division 5. All cells are basically the same in chemical composition. 6. All energy flow (metabolism & biochemistry) of life occurs within the cells. Cells are characterized by having a small size so that they can exchange materials with their surroundings. The smaller the cell, the more surface area per volume is covered. If the surface area to volume ratio is too small, the rate of chemical exchange decreases, and eventually, the cell will die. Module I  32 Therefore, in order to buil larger organisms, they must be built up from small cell subunits. Two Cell Types Prokaryotic cells (eubacteria and archaea) Prokaryotic organisms existed before the evolution of the nucleus and nuclear membrane. The cell before lacks membrane-bound organelles or compartmentalization. They are also tiny compared to the eukaryotic cells. It is believed that the first prokaryotic cells came into existence about 3. 5 BYA. The oldest prokaryotic fossils are stromatolites (bacterial mounds) in Shark Bay, Australia. Eukaryotic cells (“Eu” means “true”) Eukaryotic cells evolved latter in the evolution of the nucleus. All organisms, other than eubacteria and archaea, are composed of eukaryotic cells. These cells have a membrane-bound nucleus and membrane-bound organelles, otherwise known as compartmentalized. Endosymbiosis The proponent for endosymbiosis or endosymbiotic hypothesis, Lynn Margulis, hypothesized in 1960 that prokaryotes once started to live in symbiotic relationships with smaller prokaryotes thriving inside bigger prokaryotes. This relationship provided the symbionts an advantage to survival over other prokaryotes that eventually evolved into eukaryotic cells. Smaller organisms gain protection, while larger ones obtained faster motility and energy production. Through time, the DNA segments “swapped” to make a permanent existence, referred to as genetic annealing. The smaller prokaryotes in time became the organelles within larger prokaryotes. Evidence for this hypothesis is found in mitochondria and chloroplasts: 1. Mitochondria and chloroplasts have their single circular chromosome similar to Bacteria. 2. Mitochondria and chloroplasts have ribosomes like those found in Bacteria. Module I  33 3. Mitochondria and chloroplasts are capable of reproducing on their own inside the more giant eukaryotic cells through a process similar to binary fission. 4. Mitochondria and chloroplasts possess a double phospholipid bilayer cell membrane. This is possible evidence of the phagocytosis and pinocytosis of the original symbionts. Microscope Biologists and zoologists use skills and knowledge in biochemistry in studying cells, and most in handling microscopes of varying magnification and resolving power. The discovery and early study of cells progressed simultaneously with the invention of microscopes in 1590 and improved further in the 17th century. Antoine van Leeuwenhoek made his own microscope to observe minute things. Englishman Robert Hooke was the first to use the term “cell” and confirmed the findings of Leeuwenhoek. In 1830s, Matthias Schleiden, a German microscopist found that plants are made of cells. Similarly, Theodore Schwann found that animals are also made of cells. Rudolf Virchow of Germany came to the conclusion that cells come only from preexisting cells. Modern scanning (SEM) and transmission electron microscopes (TEM) allowed scientists to further determine the structure of cells at the level of the organelle. A. Light Microscopy B. Electron Microscopy Module I  34 Cellular Organelles and Their Functions Major organelles can be separated through the process of fractionation driven by an ultracentrifuge, the machine can split organielles by spinning up to 130, 000 rpm and applying 1,000,000 times gravity. This process separates pieces according to their mass, massive pieces are called pellets and lighter pieces remains as supernatant. Cell fractionation prepares isolates of specific cellular components. In this section, we are going to discuss in detail the different parts and components of a typical animal cell. Module I  35 The Major components of cells are (1) plasma membrane, (2) cytosol, (3) hereditary information. Size and complexity differs in prokaryotic and eukaryotic cells. Smaller cells are compartmentalized within bigger organelles. A plasma membrane surrounds all cells and encloses the cell contents. Structurally, it is made of a double layer of phospholipids and proteins. Cytosol is the semifluid substance within the membrane that contains the organelles. All cells hold chromosomes bearing genes in the form of deoxyribonucleic acid (DNA). They have ribosomes, tiny organelles producing proteins using the instructions coded in genes. The location of chromosome is the major difference between prokaryotic and eukaryotic cells. In eukaryotic cells, the chromosomes are enclosed in a membrane-enclosed organelle, the nucleus whereas in prokaryotic cells, the DNA is in the form of nucleoid with no membrane separating it from the rest of the cellular components. In eukaryote cells, the membranous nuclear envelope contains the chromosomes. The cystoplasm is the region between the plasma membrane and the nucleus. The cytoplasm holds all the material within the plasma membrane of a prokaryotic cell. Within the cytoplasm of a eukaryotic cell, there are various membrane-bound organelles of specialized form and function, they are also known as compartmentalized. These compartments or membrane-bound organelles are absent in prokaryotes. As to the size, eukaryotic cells are generally much bigger than prokaryotic cells. This sets them apart due to the logistics of carrying out metabolism that set limits on cell size. 1. Plasma Membrane The plasma membrane acts as a semi- permeable membrane or a selective barrier that permits the passage of oxygen, nutrients, and wastes for the entire volume of the cell. The volume of cytoplasm limits the need for this exchange. Internal membranes compartmentalize the functions of various organelles in eukaryotic cell. A eukaryotic cell has extensive and complex in-house membranes that partition the cell into smaller compartments. These membranes participate in the efficiency of metabolism, as many enzymes are assembled into membranes that provide different local environments that facilitate specific metabolic Module I  36 functions, permitting several incompatible processes to go on instantaneously in a cell. The general structure of a biological membrane is a double layer of phospholipids. Phospholipids are polar (has hydrophyil head and a hydrophobic tail) and actively interacts with water. Other lipids and diverse proteins are embedded either in lipid bilayer or attached to its extracellular matrix (ECM). Each type of membrane has a unique combination of proteins and lipids with definite functions. 2. Nucleus and Nuclear envelope The nucleus holds most of the genes in a eukaryotic cell. Extra genes are positioned in mitochondria and chloroplasts (for plant cells). The nucleus is disjointed from the cytoplasm by a perforated dual membrane, called the nuclear envelope. At the brim of each pore, the inner and outer membranes of the nuclear envelope are merged to form an unceasing membrane. Each pore lines up a protein structure called a pore complex that regulates the channel of certain large macromolecules and particles. The nuclear lamina lines the nuclear side of the envelope made of the network of protein filaments that sustains the shape of the nucleus. Also, nuclear matrix, a framework of fibers, extends through the nuclear interior. Eukaryotic species has a specific number of chromosomes. A regular human cell (somatic) has 46 chromosomes. A human sex cell or gametes (egg or sperm) has only 23 chromosomes. Module I  37 Chromatin is a fibrous material of complex proteins and DNA that makes up each chromosome. When cell divides, the chromatin fibers prepare to coil up and condense turning into thick and recognizable chromosomes. The nucleolus located within the nucleus is a region of densely stained fibers and granules adjoining chromatin that synthesizes and manufactures through assembling with proteins from the cytoplasm to form the ribosomal subunits. These subunits then pass through the nucleopores down to the cytoplasm where they fuse to become ribosomes. From that, the nucleus directs protein synthesis by creating messenger RNA (mRNA) that travels to cytoplasm through nucleopores and fuses with ribosomes to translate its genetic code into the primary structure of specific polypeptides. 3. Ribosomes Ribosomes that contain rRNA (ribosomal RNA) and proteins, are the organelles that perform protein synthesis. The amount of ribosome and prominence of nucleoli play a factor such that these kinds of cell types are capable of synthesizing large quantities of proteins (e.g., pancreas cells). Some ribosomes outside the nucleus are called the free ribosomes. These ribosomes are suspended in the cytoplasm and synthesize proteins that function within it. Additional ribosome are attached to the outside of the endoplasmic reticulum or nuclear envelope are identified as bound ribosomes that synthesize proteins either included in membranes or exported from the cell. Ribosomes are able to shift between roles subject on the polypeptides they are synthesizing. 4. Endomembrane System Majority of the internal membranes of an organelle in a eukaryotic cell are part of the endomembrane system. They are diverse in structure and in function and are either directly continuous or connected via transfer of vesicles, sacs of membrane. The endomembrane system comprises of the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane. Module I  38 4.a. Endoplasmic Reticulum Half of the membranes in a eukaryotic cell is accounted for the endoplasmic reticulum (ER). This membranous structure has membranous tubules and internal, fluid-filled spaces called cisternae. The endoplasmic reticulum is continuous with the nuclear membrane, and the cisternal space of the ER is continuous with the space between the two membranes of the nuclear envelope. There are two regions of endoplasmic reticulum that differ in structure and function. a. Smooth ER appears smooth because it lacks ribosomes. b. Rough ER appears rough because bound ribosomes cling to the outside, including the outside of the nuclear envelope. The smooth ER is abundant in enzymes and plays a role in a variety of metabolic courses including the synthesize lipids (oils, phospholipids, and steroids), and sex hormones of vertebrates and adrenal steroids. In theliver, smooth ER enzymes aids in detoxifying poisons and drugs like alcohol.Repeated use of these drugs leads to the propagation of smooth ER in liver cells, increasing the rate of detoxification. Smooth ER also stores calcium ions. Muscle cells (myocytes) have a specialized smooth ER that drives calcium ions from the cytosol and stores them in the cisternal space. Rough ER (RER) is particularly rich in cells that secrete proteins. As a polypeptide is manufactured on a ribosome attached to RER, it is pinned to the cisternal space through a pore made by a protein complex in the ER membrane.From the cisternal space, new proteins are folded into its natural conformation. Glycoproteins, secretory proteins, which a carbohydrate attaches. Secretory proteins are wrapped in transport vesicles that carry them to their next stage. In addition, RER is a membrane factory that directly synthesizes membrane. The enzymes in the RER synthesizes phospholipids from its precursors in the cytosol. As it expands, membrane can be transferred as a transport vesicle to other parts of the endomembrane system. Module I  39 4.b The Golgi apparatus or the Golgi bodies The Golgi Apparatus or the Golgi bodies are responsible for shipping and receiving the cell products. Many transport vesicles from the ER travels to Golgi apparatus (GA)to modify their contents. The Golgi is the core for warehousing, manufacturing, sorting, and shipping. Aside from these, it functions in cells extensively for secretion, Structurally, the Golgi apparatus comprises of cisternae, a flattened membranous sac. The membrane on the cisternae separates its internal space from the cytosol. There are two sided of the GA, the cis and the trans. The cis side is situated near the ER and it receives material by melding with the transport vesicles from the ER. The trans side, buds off vesicles travelling different cell locations. The GA is capable of manufacturing its own macromolecules (e.g., pectin and noncellulose polysaccharides). It progresses from the cis to the trans face, transporting and modifying their cargo as they move on the two sides. Also, the GA sorts and packages materials into transport vesicles. Identification tags are further added to products to aid in sorting (acts like a ZIP code for mailing products) 4.c. Lysosomes Lysosomes are membrane-bound sac of hydrolytic enzymes which animal cells use to digest macromolecules and are also known as digestive compartments. The enzymes of lysosomes can hydrolyze all macromolecules (polysaccharides, proteins, fats, and nucleic acids). These enzymes works at pH 5. Rupture of a few lysosomes has little to no impact on the cell because the lysosomal enzymes are not very active at the neutral pH but immense rupture of many lysosomes can abolish a cell through autodigestion. Inner proteins located on the Module I  40 surface of the lysosomal membrane are safe from digestion by their 3D conformations that protect vulnerable bonds from any form of hydrolysis. The lysosomes carry out intracellular digestion in a variety of circumstances (e.g., Amoebas engulf small organisms through phagocytosis). When polymers are digested, monomers passes to the cytosol and convert nutrients for the cell. Lysosomes play a role in recycling of the cell’s macromolecules. The recycling or autophagy, renews the cell. During the process of autophagy, a damaged organelle becomes surrounded by membrane and lysosome fuses with the resulting vesicle that digests the macromolecules and returning the organic monomers to the cytosol for reuse. They also have critical yet essential roles in programmed destructions of cells that plays a role in development (e.g., the hands of human embryos are webbed. The lysosomes digests the cells in the tissue in the middle of the fingers. This is called programmed cell death, PCD, or apoptosis). 4.d Vacuoles Vesicles (smaller compartments) and vacuoles (larger versions) are membrane-bound sacs with varied functions in cellular maintenance.  The food vacuoles are formed by phagocytosis and fuse with lysosomes.  Contractile vacuoles, pumps water out of the cell to maintain the appropriate concentration of salts.  large central vacuole is found in mature plant cells. In plants, central vacuole is surrounded by a membrane called the tonoplast that is selective in its transport of solutes. The central vacuole mainly functions for stockpiling (proteins, organic ions), Module I  41 pigment holding area, storing defensive compounds (mechanism against herbivore) 5. Mitochondria Mitochondria and chloroplasts can convert energy to forms that cells can use for work. Mitochondria are the spots of cellular respiration, In the process,it generates ATP from the catabolism of fats,sugars, and other fuels using oxygen. In plants and fungi, chloroplasts are the sites of photosynthesis. The chloroplasts convert solar energy (sun) to chemical energy and manufacture new organic compounds such as sugars from water (H2O) and carbon dioxide (CO2). Though mitochondria and chloroplasts has membranes separating their innermost space from the cytosol, they are not part of the endomembrane system. Their membranes are made from free ribosomes within themselves and not made by the ER. The two organelles also have tehri DNA in small quantities that directs the active ynthesis of polypeptides. They can also reproduce and grow as semiautonomous organelles. Mitochondria is found in almost all eukaryotic cells and are correlated with aerobic metabolic avtivities. Mitochondria are dynamic. They move, alter shape, and divide by pinching in two. It moves along the tracks of the cytoskeleton. They have infoldings in the innermembrane and a smooth outer membrane. Its inner membrane divide a mitochondrion into two internal compartments: an intermembrane space and an inner membrane. (a) The intermembrane space is a narrow section in between the inner and outer membranes. (b)The inner membrane envelopes the mitochondrial matrix, a fluid- filled space that bears ribosomes, enzymes, and DNA. It is also in the mitochondrial matrix where the metabolic steps of cellular respiration are catalyzed by enzymes. The presence of folds, or cristae, increases the surface area for enzymes that synthesizes ATP. 6. Peroxisome Module I  42 Peroxisomes are bound by a single membrane and do not form an endomembrane rather the incorporation of proteins and lipids from the cytosol. Also, they fragment in two when they reach a certain size. Enzymes from peroxisomes transfer hydrogen from various substrates to oxygen. It can generate as an intemediate product hydrogen peroxide (H2O2) when performing different metabolic functions. The enzymes in peroxisome can also degrade the H2O2 to water. Aside from the H2O2, it breaks fatty acids to smaller molecules needed in mitochondira for cellular respiration. In livers, peroxisome functions as detoxifier of alcohol. Glyoxysomes are specialized peroxisomes that convert the fatty acids in seeds to sugars capable of photosynthesis. 7. Cytoskeleton The cytoskeleton is a fibrous network extending throughout the cytoplasm. The cytoskeleton provides motility, support, and regulation.  The cytoskeleton maintains cell shape and provides mechanical support.  The cytoskeleton provides anchorage for the components of the cytosol.  The cytoskeleton is dynamic. It can dismantle and reassemble to modify the shape of the cell.  The cytoskeleton makes the cells motile by changing its location and creating movements in some parts of the cell by interacting with motor proteins (cilia, flagella)  The cytoskeleton controls the plasma membrane to form food vacuoles for the period of phagocytosis.  Cytoskeleton are also found in plants that allows cytoplasmic streaming There are three types of fibers constituting the cytoskeleton: microtubules, microfilaments, and intermediate filaments. The structure and function are summarized on the table below Module I  43 1. Microtubules, the thickest fibers, are made the globular protein tubulin. In each tubulin, it consists of two subunits of dimer. The shape of microtubule can vary in length by the addition or removal of the tubulin dimers. The main function of the microtubulin is to create the shape and to support the cell in carrying organelles to their destination. They are also present in cell division as they are the ones responsible for separating the chromosomes. In most cells, they grow out from the centrosomes near nucleus. Another characteristic is that resist compression to the cell. In an animal cells the centrosome has a pair of centrioles, each centriole bears nine triplets of microtubules arranged in the form of a ring. Before the cell divides, the centrioles replicate. A specialized arrangement of microtubules is accountable for the beating and propelling of cilia and flagella (most unicellular eukaryotic organisms). All cilia and flagella have a “9 + 2” arrangement taken from the nine doublets of microtubules arranged in a ring around a pair at their center. The bending of these locomotory parts are driven by the dynein or the arms of a motor protein. The conformation pf dynein may change with the addition or removal of a phosphate group Cilia and flagella have the same ultrastructure but varies as to their movements. a. Flagella have an undulatory movement that creates force in the same direction as its axis. b. Cilia move more like paddles with alternating power that creates force perpendicular to its axis. Module I  44 2. Microfilaments In muscle cells, actin filaments are arranged parallel to one another. Myosin or the thicker filaments are motor proteins that intertwine with the thinner actin fibers. When the myosin and actin walk along each other, they shorten the cell. A constricting belt of microfilaments divides the cytoplasm of animal cells during cell division. Localized contractions also drives amoeboid movement, similarly, cellular extensions like pseudopodia, extend and contract through the reversible assembly and contraction of actin subunits into microfilaments. 3. Intermediate filaments Intermediate are larger than microfilaments and smaller than microtubules. They form a diverse class of cytoskeletal units, built from keratin, a family of. They are specialized for bearing tension and responsible for permanent fittings of the cytoskeleton that microtubules and microfilaments. Their main function is to reinforce cell shape and fix the organelle location. 8. Extracellular components or Extracellular Matrix (ECM) Despite having no cell walls, animal cells have an intricate extracellular matrix (ECM) that functions in movement, regulation, adhesion and support. The ECM primary constituents are glycoproteins (collagen fibers) embedded in a network of proteoglycans and glycoprotein. In most cells, the ECM has fibronectins connected to integrins, an intrinsic membrane proteins. The interconnections made by the fibronectin-integrin connection permits the integration of changes in and out of the cell. ECM also regulates cell behavior by the combination of chemical and mechanical signaling pathways. 9. Intercellular Junction Module I  45 Neighboring cells in higher levels (tissues, organs, or organ systems) often stick to, interact, and communicate through direct contact via the intercellular junction. Water and small solutes pass freely from cell to cell and in some, proteins and RNA can be exchanged through either of the three intercellular links in animal cells: tight junctions, desmosomes, and gap junctions. a. In tight junctions, continuous membranes of adjacent cells are fused creating a belt that prevents leakage of extracellular fluid. b. Desmosomes, also known as anchoring junctions, fasten cells together like rivets. Intermediate filaments of keratin reinforce desmosomes. C. Gap junctions, also known as communicating junctions provide cytoplasmic channels between adjacent cells. Special membrane proteins border these pores. small molecules such as mino acids, ions, and sugar can pass (e.g., in developing embryos, gap junctions facilitate chemical communication during development). Multiple Choices. Select the best answer on the space Self- before the item numbers. provided Review ____1. All of the following are part of a prokaryotic cell except A) DNA. B) a cell wall. C) ribosomes. D) an endoplasmic reticulum. ____2. The nuclear lamina is an array of filaments on the inner side of the nuclear membrane. If a method were found that could cause the lamina to fall into disarray, what would you expect to be the most likely consequence? A) the loss of all nuclear function B) the inability of the cell to withstand enzymatic digestion C) a change in the shape of the nucleus D) failure of chromosomes to carry genetic information ____3. Under which of the following conditions would you expect to find a cell with a predominance of free ribosomes? A) a cell that is secreting proteins B) a cell that is producing cytoplasmic enzymes C) a cell that is constructing its cell wall or extracellular matrix D) a cell that is digesting food particles ____4. In animal cells, hydrolytic enzymes are packaged to prevent general destruction of cellular components. Which of the following Module organelles I functions in this compartmentalization? A) chloroplast B) lysosome C) central vacuole D) peroxisome ___5. The liver is involved in detoxification of many poisons and drugs. Which of the following structures is primarily involved in this  46  MODULE SUMMARY In module I, you have gained information on the following topics and concepts: Lesson 1 the basic concepts and tenets incorporated in the principles of studying zoology, the flow of scientific method, testing out hypotheses, as well as studying the sub-disciplines of zoology. Lesson 2 general properties of living system and the hierarchical organizations highlighting the characteristics of life Lesson 3 origin and chemistry of life by introducing the four major biomolecules and dissecting its components as to structural and functional parts. Lesson 4. Cell structures and functions were discussed in detail highlighting major features that are specific to animal cells. Congratulations! You have just studied Module I. now you are ready to evaluate how much you have benefited from your reading by answering the summative test. Good Luck!!!  SUMMATIVE TEST 1. Think of one problem in animal science. Create a brief discussion on how you would tackle the problem using the scientific method. 2. What are the different levels of organizations of living things? Give an example per order 3. Discuss exhaustively the composition, structure, and function of the four biomolecules. 4. Discuss the advantage of using light microscopy over electron microscopy (SEM and TEM). References Alberts, B.A., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Watson, J. (2015). Molecular biology of the cell. New York: Garland Publishing, Inc. Module I  47 Campbell, N.A, Reece JB, Urry LA, Cain ML, Wasserman SA, Minorsky PV, Jackson RB. (2010). Biology. 9th ed. Singapore: Pearson Education and South-Asia Pte Ltd. https://www.ck12.org/biology/Characteristics-of-Life/lesson/ Characteristics-of-Life-Advanced-BIO-ADV/ https://courses.lumenlearning.com/suny-wmopen-biology1/chapter/ the-characteristics-of-life/#:~:text=All%20living%20organisms %20share%20several,characteristics%20serve%20to%20define %20life. https://biocyclopedia.com/index/general_zoology/ general_properties_of_living_systems.php https://www.bioexplorer.net/divisions_of_biology/zoology/ Module I