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UNIFYING THEMES IN Structure and Function If there is a defect in the structure, the function is affected. BIOLOGY...

UNIFYING THEMES IN Structure and Function If there is a defect in the structure, the function is affected. BIOLOGY Ex. The structure of a hummingbird gives it the ability to rotate its wings to fly backward. ZOOLFUN – Fundamentals of Zoology Instructor: Dr. Frances C. Recuenca The Cell: An Organism’s Basic Unit The lowest level of organization that can perform all OUTLINE activities required for life Two Types: Eukaryotic and Prokaryotic Cells I. Biology ○ In terms of size, eukaryotic cells are bigger A. Biological Organization 1. Emergent Properties ○ Both cells are covered with plasma 2. Structure and Function membrane/cell membrane 3. The Cell: An Organism’s ○ Eukaryotic cells have membrane-enclosed Basic Unit organelles while prokaryotic cells do not B. Themes ○ In terms of the presence of the nucleus, the C. Classifying the Diversity of Life eukaryotic cell has a nucleus, wherein within the 1. 3 Domains of Life nucleus, we can find the DNA. Prokaryotic cells D. Theory of Natural Selection do not have a nucleus but also have DNA. BIOLOGY THEMES Scientific study of life Life’s Processes Involve the Expression and Transmission Bio meaning life of Genetic Information Logos meaning study Life Requires the Transfer and Transformation of Energy Biologists ask questions such as and Matter ○ How does a single cell develop into an From Ecosystems to Molecules, Interactions are Important organism? in Biological Systems ○ How does the human mind work? Genomics: Large sca;e analysis of DNA Sequences ○ How do living things interact in communities? ○ Genome The study of life reveals common themes ○ Genomics Biology is a subject of enormous scope ○ Proteomics There are five unifying themes ○ Proteomes ○ Organization Evolution accounts for the unity and diversity of life ○ Information ○ Core theme ○ Energy and matter ○ Living organisms are modified descendants of ○ Interactions common ancestors ○ Evolution CLASSIFYING THE DIVERSITY OF LIFE BIOLOGICAL ORGANIZATION Approximately 1.8 million species have been identified to New properties emerge at successive levels of biological date, and thousands are more identified each year organization Estimates of the total number of species that actually exist 1. The Biosphere range from 10 million to over 100 million 2. Ecosystems Taxonomy 3. Communities ○ branch of biology that names and classifies 4. Populations species into groups of increasing breadth 5. Organisms 6. Organs and Organ Systems The Three Domains of Life 7. Tissues 8. Cells Organisms are divided into three domains, named 9. Organelles Bacteria, Archaea, and Eukarya 10. Molecules These domains are made up of prokaryotes Archaea thrive in extreme environments Eukarya include all living organisms Emergent Properties ○ Fungi absorb nutrients Result from the arrangement and interaction of parts ○ Animals are heterotrophs within a system ○ Protists are microscopic unicellular organisms Characterize non biological entities as well ○ Ex. a functioning bicycle emerges only when all THEORY OF NATURAL SELECTION of the necessary parts connect in the correct way Charles Darwin published On the Origin of Species by To explore emergent properties, biologists use systems Means of Natural Selection in 1859 biology to analyze the interactions among the parts of a Darwin’s theory explained the duality of unity and diversity biological system Darwin observed that Castilla, Selene Mari D. | 1 ZOOLFUN – UNIFYING THEMES IN BIOLOGY ○ Individuals in a population vary in their traits, which are heritable ○ More offspring are produced than survive, and competition is inevitable ○ Species generally suit their environment Darwin inferred that ○ Natural selection The environment “selects” for the propagation of beneficial traits ○ Natural selection results in the adaptation of organisms to their environment Ex. bat wings are an example of adaptation The Tree of Life ○ Darwin proposed that natural selection could cause an ancestral species to give rise to two more descendent species Castilla, Selene Mari D. | 2 Cell Structure and Function PARTS OF THE CELL ZOOLFUN – Fundamentals of Zoology Instructor: Dr. Frances C. Recuenca Plasma Membrane A selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of OUTLINE every cell Serves as a barrier for external and internal environments. I. The Fundamental Units of Life A. Prokaryotic vs Eukaryotic cells Regulation B. Parts of the Cell ○ Important for the cell to prevent materials from 1. Plasma Membrane stopping in one place (burst) and regulates 2. Nucleus materials to not over exit the cell (shrink). 3. Endomembrane System Maintains normality of cell. 4. Endoplasmic Reticulum Hydrophilic region (water-loving) 5. Ribosomes ○ Mainly consists of phosphate because of 6. Golgi Apparatus 7. Lysosomes phospholipids facing outwards 8. Vacuoles Hydrophobic region (water-fearing) 9. Mitochondria ○ Fatty acids or phospholipids are not attracted to 10. Chloroplast water 11. Peroxisomes Proteins act as channels C. The Cytoskeleton 1. Microtubules 2. Microfilaments Nucleus 3. Intermediate Filaments D. The Extracellular Matrix Information center E. Cell Junctions Contains most of the cell’s genes and is usually the most F. Plasma Membrane conspicuous organelle 1. Functions Easily identifiable and distinct 2. Membrane Nuclear envelope (connected to the rough endoplasmic Carbohydrates reticulum): 3. Permeability 4. Transport Proteins ○ Inner membrane G. Cell Transport ○ Outer membrane 1. Passive Transport ○ Nuclear pores - pathway of the materials, such 2. Active Transport as ribosomal RNA, exiting the nucleus Inside the nucleus ○ Chromatin - consists of the DNA and proteins THE FUNDAMENTAL UNITS OF LIFE ○ Nucleolus - important for the production of All organisms are made up of cells. RNA, particularly the ribosomal RNA Chromosome ○ Has proteins and nucleic acids COMPARING THE PROKARYOTIC AND Chromatin EUKARYOTIC CELLS ○ Has histones that packages DNA ○ Histones are where the dna strands are wound into Prokaryotic Cell Eukaryotic Cell Unicellular Bigger Endomembrane System Smaller More complex Complex and dynamic player in the cell’s compartmental More simple Has organization Does not have any membrane-enclosed organelles organelles Consists of: Does not have a Presence of the ○ Nuclear envelope nucleus nucleus ○ Endoplasmic reticulum Has additional outer Domain Eukarya ○ Golgi apparatus covering (aside from ○ Lysosomes the cell membrane) ○ Vacuoles Cell wall Capsule (not all) ○ Plasma membrane Has a flagellum for locomotion (not all) Endoplasmic Reticulum Domain Archea & Bacteria Extensive network of membrane-bounded tubules and Both have cell membrane, ribosomes, and genetic sacs material (DNA) Membrane separates lumen from cytosol The surface area to volume ratio of a cell is critical Continuous with nuclear envelope Smaller surface area is more efficient Accounts for more than half of the total membrane in many eukaryotic cells Rough ER ○ Has attached ribosomes in its surface Castilla, Selene Mari D. | 1 ZOOLFUN – CELL STRUCTURE AND FUNCTION ○ Only for support Vacuoles ○ Protein synthesis ○ Connected to nuclear envelope Large membrane bound vesicle ○ Adds carbohydrates to proteins to make Diverse maintenance compartments glycoproteins Function ○ Produces new membranes ○ Digestion Smooth ER ○ Storage ○ Does not have ribosomes ○ Waste disposal ○ Synthesizes lipids/fats ○ Water balance ○ Metabolizes carbohydrates ○ Cell growth ○ Detoxification of drugs and poisons ○ Protection ○ Stores calcium ions Types: ER lumen - space between the ER ○ Food vacuoles - for animal cells only Cisternae - foldings of the ER ○ Contractile vacuoles - in primitive organisms Transport vesicle - will deliver products from the smooth Expels excess water to maintain ER and ribosomes to the Golgi apparatus balance ○ Central vacuoles - for plant cells Has organic compounds & water Ribosomes Protein factory Mitochondria Complexes made of ribosomal RNA and protein Not organelles because they do not have their own The site of cellular respiration membrane, only ribosomal RNA. Cellular respiration - the process in which energy Two types: molecules are produced ○ Rough or attached ribosomes - attached to ○ Produces adenosine triphosphate (ATP), an cellular structures energy molecule used in cellular respiration ○ Free ribosomes - ribosomes that are floating Mitochondria has its own ribosomes and DNA different freely from the nucleus Large and small subunit ○ DNA of the nucleus (nuclear DNA or primary Proteins DNA) - has control of everything in the cell ○ Structural support ○ DNA of mitochondria (mitochondrial DNA or ○ Building block for rna secondary DNA) - control only the mitochondria; has no effect on other organelles and other functions of the cell Golgi Apparatus Parts Stacks of flattened membranous sacs ○ Two membranes Shipping and receiving center of proteins Inner membrane Consists of the flattened membranous sacs called Outer membrane cisternae ○ Cristae - increases surface area for the Two faces - polarity production of ATP; foldings of the inner ○ Cis face - receiving side membrane ○ Trans face - shipping side ○ Mitochondrial matrix - contains free ribosomes Functions Mitochondria and chloroplasts change energy from one ○ Modification of proteins, carbohydrates on form to another proteins and phospholipids Produce atp ○ Synthesis of polysaccharides Mitochondrial dna is used for forensic investigation ○ Sorting of Golgi products which is then released It can reproduce to vesicles Bacteria-like behavior It was a separate organism before it became an organelle Lysosomes Chloroplast Digestive compartments Membranous sac of hydrolytic enzymes (lysosomal Light energy to chemical energy enzymes) that can digest macromolecules ○ Hydrolytic enzymes (digestive enzymes) - Peroxisomes highly acidic; its function is to digest macromolecules Specialized metabolic compartments bounded by a single Functions membrane ○ Breakdown of ingested substances, cell Produce hydrogen peroxide and convert it to water macromolecules, and damaged organelles for Hydrogen peroxide - a byproduct of cellular respiration recycling ○ Somewhat toxic to the cell because it can react Two processes to other parts of the cell, such as the DNA and ○ Phagocytosis: lysosome digesting food cell other organelles, which affects the integrity of eating the cell ○ Autophagy: lysosome breaking down damaged ○ To counteract the toxicity, the peroxisome organelles converts hydrogen peroxide to water Some cells can engulf another cell by phagocytosis Functions ○ Formation of food vacuole (fv - same as plasma ○ Contains enzymes that transfer hydrogen atoms membrane, we don’t want it to get mixed up in from substrates to oxygen, producing hydrogen the cytoplasm) peroxide as by-product Autophagy - self eating old or damaged organelles Castilla, Selene Mari D. | 2 ZOOLFUN – CELL STRUCTURE AND FUNCTION Oxidation THE EXTRACELLULAR MATRIX OF ANIMAL Perform reactions with many different functions CELLS How peroxisomes are related to other organelles is still unknown Made of glycoproteins ○ Collagen ○ Fibronectin THE CYTOSKELETON ○ A proteoglycan complex A network of fibers that organizes structures and activities ECM proteins bind to receptor proteins in the plasma in the cell membrane called integrins. nor an organelle Three types of molecular structures: ○ Microtubules (Tubulin Polymers) ○ Microfilaments ○ Intermediate filaments For support and motility, maintaining cell shape Microtubules Also known as tubulin polymers Structure: Hollow tubes Diameter: 25nm with 15-nm lumen = thickest Protein subunits: Tubulin, a dimer consisting of α-tubulin and β-tubulin Main Functions: CELL JUNCTIONS ○ Maintenance of cell shape Neighboring cells in tissues, organs, or organ systems (copression-resisting “girders”) often adhere, interact, and communicate through direct ○ cell motility (as in cilia or flagella) physical contact ○ chromosome movements in cell division Tight junctions ○ organelle movements ○ Prevent fluid from moving across a layer of cells The centrosome has a pair of centrioles, each with Desmosomes nine triplets of microtubules arranged in a ring ○ Cilia and flagella share a common structure Gap junctions ○ A core of microtubules ○ Known as communicating junctions, the provide ○ A basal body that anchors the cilium or a direct channel or cytoplasmic channels flagellum between cells ○ A motor protein called dynein ○ Called gap junctions because of pores a microtubule-based molecular motor These three cell junctions are present or common in that is involved in various biological epithelial tissues. functions, such as axonal transport, mitosis, and cilia/flagella movement. PLASMA MEMBRANE Microfilaments Boundary that separates the living cell from its surrounding Also known as actin filaments Exhibits selective permeability Structure: Two intertwined strands of actin Exhibits fluid mosaic model states that a membrane is a Diameter: 7nm - thinnest fluid structure with a “mosaic” of various proteins Protein subunits: Actin embedded in it Main Functions: Phospholipid layer - Main component of the cell ○ Maintenance of cell shape (tension-bearing membrane elements) ○ Hydrophobic - Lipid ○ changes in cell shape ○ Hydrophilic - Phosphate Cellular membranes are fluid mosaics of lipids and ○ muscle contraction proteins ○ cytoplasmic streaming in plant cells ○ Phospholipids - most abundant ○ cell motility (as in amoeboid movement by Amphiphatic - containing extending pseudopodia) hydrophobic and hydrophilic regions ○ division of animal cells Membrane Proteins and Their Functions Intermediate Filaments Proteins determine most of the membrane’s specific Structure: Fibrous proteins coiled into cables functions Diameter: 8-12 nm - middle range Peripheral proteins - on the surface of the membrane Protein subunits: One of several different proteins (such Integral proteins - penetrate the hydrophobic core as keratins) Main Functions: Six Major Functions of Membrane Proteins ○ Maintenance of the cell shape (tension-bearing elements) Transport ○ anchorage of nucleus and certain other Enzymatic activity organelles Signal transduction cell-cell recognition ○ formation of nuclear lamina Intercellular joining Attachment to the cytoskeleton and ECM Castilla, Selene Mari D. | 3 ZOOLFUN – CELL STRUCTURE AND FUNCTION ○ Water always moves to the hypertonic areas The Role of Membrane Carbohydrates in Cell-Cell Recognition ○ Isotonic solution no water goes inside or outside, Glycolipids - membrane carbohydrates that are normal covalently bonded to lipids Iso - same Glycoproteins - membrane carbohydrates that are Equal solutes and water molecules covalently bonded to proteins ○ Hypertonic solution lose water, shriveled Synthesis and Sidedness of Membranes Hyper - more More solute, less water molecules Membranes have distinct inside and outside faces that why water moves out of the cell The asymmetrical distribution of proteins, lipids, and to balance water molecules outside associated carbohydrates in the plasma membrane is the cell determined when the membrane is built by the ER and ○ Hypotonic solution golgi apparatus gain water, lysed Hypo - less Permeability of the Lipid Bilayer Less solute, more water molecules so water moves into the cell Membrane structure results in selective permeability ○ Hypertonic or hypotonic environments Hydrophilic molecules including ions and polar molecules create osmotic problems for organisms do not cross the membrane easily ○ Osmoregulation, the control of solute Hydrophobic (nonpolar) molecules, such as concentrations and water balance, is a hydrocarbons, can dissolve in the lipid bilayer and pass necessary adaptation for life in such through the membrane rapidly environments ○ The protist Paramecium, which is hypertonic to Transport Proteins its pond water environment, has a contractile vacuole that acts as a pump Allow passage of hydrophilic substances across the 2. Facilitated diffusion membrane Transport proteins speed the passive movement of Channel proteins - hydrophilic channel molecules across the plasma membrane ○ Aquaporins - facilitate the passage of water ○ Channel proteins provide corridors that allow a Carrier proteins - bind to molecules and change shape to specific molecule or ion to cross the membrane shuttle them across the membrane Aquaporins - facilitate diffusion of water CELL TRANSPORT Ion channels - facilitate diffusion of ions Some ion channels, called “gated channels”, open or close in response to a stimulus. Active Transport Uses energy to move solutes against their gradients Moves substances against their concentration gradients Requires energy, usually in the form of ATP Performed by specific proteins embedded in the membranes The sodium-potassium pump is one type of active transport system How ion pumps maintain membrane potential ○ Membrane potential is the voltage difference across a membrane ○ Voltage is created by differences in the Passive Transport distribution of positive and negative ions across 1. Diffusion of a substance across a membrane with no a membrane energy investment ○ Two combined forces, collectively called the Diffusion is the tendency for molecules to spread out electrochemical gradient, drive the diffusion of evenly into the available space ions across a membrane At dynamic equilibrium, as many molecules cross the A chemical force (the ion’s membrane in one direction as in the other concentration gradient) Osmosis An electrical force (the effect of the ○ Diffusion of water across a selectively membrane potential on the ion’s permeable membrane movement) ○ Water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration until the solute concentration is equal on both sides. Water balance of cells without cell walls ○ Tonicity - ability of surrounding solution to cause a cell to gain or lose water (ECF) Castilla, Selene Mari D. | 4  C6H12O6+6O2 → 6CO2+6H2O + Energy (ATP + heat) Cell Respiration ZOOLFUN – Fundamentals of Zoology ReDox Reactions Instructor: Dr. Frances C. Recuenca Oxidation and Reduction The transfer of electrons during chemical reactions releases energy stored in organic molecules OUTLINE This released energy is ultimately used to synthesize ATP Principle of Redox I. Cellular Respiration ○ Chemical reactions that transfer electrons A. Catabolic Pathways and Production of ATP between reactants are called 1. ReDox Reactions oxidation-reduction reactions, or redox 2. Oxidation of Organic reactions Fuel Molecules ○ In oxidation, a substance loses electrons, or is 3. Stepwise Energy oxidized Harvest eg. Glucose is "burned" to CO2 and B. The Stages of Cellular Respiration 1. Glycolysis H20 after extracting its electrons. 2. Citric Acid Cycle ○ In reduction, a substance gains electrons, or is 3. Oxidative reduced (the amount of positive charge is Phosphorylation reduced) 4. Chemiosmosis eg. The e from glucose are 5. Accounting of ATP transferred to e carriers like NAD+ and Production FAD. Reduced forms are NADH and 6. Anaerobic Respiration FADH2. ○ The electron donor is called the reducing agent CELLULAR RESPIRATION ○ The electron receptor is called the oxidizing Life is work agent ○ Living cells require energy from outside sources ○ Some redox reactions do not transfer electrons ○ Some animals, such as the giraffe, obtain but change the electron sharing in covalent energy by eating plants, and some animals feed bonds on other organisms that eat plants An example is the reaction between Energy flows into an ecosystem as sunlight and leaves as methane and O2 heat Photosynthesis generates O2 and organic molecules, which are used in cellular respiration Oxidation of Organic Fuel Molecules During Cellular Respiration Cells use chemical energy stored in organic molecules to generate ATP, which powers work During cellular respiration, the fuel (such as glucose) is Catabolic pathways yield energy by oxidizing organic oxidized, and O2 is reduced fuels ○ Catabolic pathways release stored energy by breaking down complex molecules ○ Electron transfer plays a major role in these pathways Note: electron carriers NADH and FADH2 donate their ○ These processes are central to cellular electrons to O2. respiration Stepwise Energy Harvest via NAD+ and the CATABOLIC PATHWAYS AND PRODUCTION ETC OF ATP In cellular respiration, glucose and other organic The breakdown of organic molecules is exergonic molecules are broken down in a series of steps Fermentation is a partial degradation of sugars that Electrons from organic compounds are usually first occurs without O2 transferred to NAD+, a coenzyme Aerobic respiration consumes organic molecules and O2 As an electron acceptor, NAD+ functions as an oxidizing yields ATP agent during cellular respiration ○ With oxygen Each NADH (the reduced form of NAD+) represents Anaerobic respiration is similar to aerobic respiration but stored energy that is tapped to synthesize ATP consumes compounds other than O2 NADH passes the electrons to the electron transport ○ Without oxygen chain * From glycolysis, ATP and NADH are produced, NADH Unlike an uncontrolled reaction, the electron transport needs to release its electrons to continue the pathway. chain passes electrons in a series of steps instead of one Cellular respiration includes both aerobic and explosive reaction anaerobic respiration but is often used to refer to aerobic O2 pulls electrons down the chain in an energy-yielding respiration tumble Although carbohydrates, fats, and proteins are all The energy yielded is used to regenerate ATP consumed as fuel, it is helpful to trace cellular respiration with the sugar glucose Castilla, Selene Mari D. | 1 ZOOLFUN – CELLULAR RESPIRATION NADH does not transfer its e- directly to O2. This needs a series of carriers to prevent this explosive reaction. THE STAGES OF CELLULAR RESPIRATION Harvesting of energy from glucose has three stages ○ Glycolysis breaks down glucose into two molecules of pyruvate ○ The citric acid cycle completes the breakdown of glucose Pyruvate oxidation + citric acid cycle ○ Oxidative phosphorylation accounts for most of the ATP synthesis Electron transport chain and chemiosmosis After pyruvate is oxidized, the citric acid cycle Glycolysis completes the energy-yielding oxidation of organic Glycolysis harvests chemical energy by oxidizing molecules glucose to pyruvate In the presence of O2, pyruvate enters the mitochondrion Glycolysis ("sugar splitting") breaks down glucose into (in eukaryotic cells) where the oxidation of glucose is two molecules of pyruvate completed Glycolysis occurs in the cytoplasm and has two major phases ○ Energy investment phase The cell actually spends ATP. ○ Energy payoff phase When ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released from the oxidation of glucose. Glycolysis occurs whether or not O2 is present Oxidation of Pyruvate to Acetyl CoA Before the citric acid cycle can begin, pyruvate must be converted to acetyl Coenzyme A (acetyl CoA), which links glycolysis to the citric acid cycle This step is carried out by a multienzyme complex that catalyzes three reactions Castilla, Selene Mari D. | 2 ZOOLFUN – CELLULAR RESPIRATION Citric Acid Cycle The citric acid cycle, also called the Krebs cycle, completes the breakdown of pyruvate to CO2 The cycle oxidizes organic fuel derived from pyruvate, generating 1 ATP, 3 NADH, and 1 FADH, per turn For each molecule of glucose degraded to CO2 and water by respiration, the cell makes up to 32 molecules of ATP During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis Following glycolysis and the citric acid cycle, NADH and FADH account for most of the energy extracted from food These two electron carriers donate electrons to the electron transport chain, which powers ATP synthesis via oxidative phosphorylation The Pathway of Electron Transport The electron transport chain is in the inner membrane (cristae) of the mitochondrion Most of the chain's components are proteins, which exist in multiprotein complexes The carriers alternate reduced and oxidized states as they accept and donate electrons Electrons drop in free energy as they go down the chain The citric acid cycle has eight steps, each catalyzed by a and are finally passed to O2, forming H2O specific enzyme Electrons are transferred from NADH or FADH, to the The acetyl group of acetyl CoA joins the cycle by electron transport chain combining with oxaloacetate, forming citrate Electrons are passed through a number of proteins The next seven steps decompose the citrate back to including cytochromes (each with an iron atom) to O2 oxaloacetate, making the process a cycle The electron transport chain generates no ATP directly The NADH and FADH, produced by the cycle relay It breaks the large free-energy drop from food to O2 into electrons extracted from food to the electron transport smaller steps that release energy in manageable amounts chain Chemiosmosis The Energy-Coupling Mechanism Electron transfer in the electron transport chain causes proteins to pump H+ from the mitochondrial matrix to the intermembrane space H+ then moves back across the membrane, passing through the protein complex, ATP synthase ATP synthase uses the exergonic flow of Ht to drive phosphorylation of ATP This is an example of chemiosmosis, the use of energy in a H+ gradient to drive cellular work Oxidative Phosphorylation The process that generates most of the ATP is called oxidative phosphorylation because it is powered by redox reactions Oxidative phosphorylation accounts for almost 90% of the ATP generated by cellular respiration A smaller amount of ATP is formed in glycolysis and the citric acid cycle by substrate-level phosphorylation Castilla, Selene Mari D. | 3 ZOOLFUN – CELLULAR RESPIRATION Alcohol fermentation by yeast is used in brewing, winemaking, and baking Accounting of ATP Production by Cellular Respiration Protein complex of electron carriers During cellular respiration, most energy flows in this In lactic acid fermentation, pyruvate is reduced by NADH, sequence: forming lactate as an end product, with no release of CO2. glucose → NADH → electron transport chain → Lactic acid fermentation by some fungi and bacteria is proton-motive force → ATP used to make cheese and yogurt About 34% of the energy in a glucose molecule is Human muscle cells used lactic acid fermentation to transferred to ATP during cellular respiration, making generate ATP when O2 is scarce. about 32 ATP There are several reasons why the number of ATP is not known exactly Anaerobic Respiration Fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen Most cellular respiration requires O2 to produce ATP Without O2, the electron transport chain will cease to operate In that case, glycolysis couples with anaerobic respiration or fermentation to produce ATP Anaerobic respiration uses an electron transport chain with a final electron acceptor other than O2, for example sulfate Fermentation uses substrate-level phosphorylation instead of an electron transport chain to generate ATP. In alcohol fermentation, pyruvate is converted to ethanol in two steps ○ The first step releases CO2 ○ The second step produces ethanol Castilla, Selene Mari D. | 4  Cytokinesis MITOSIS AND CELL CYCLE ○ The cell divides into two daughter cells, genetically identical to each other and to the ZOOLFUN – Fundamentals of Zoology parent cell. Instructor: Dr. Frances C. Recuenca The daughter cells may go on to divide, repeating the cycle. OUTLINE I. Cell Division A. Key Roles of Cell Division 1. Identical Daughter Cells B. Cellular Organization of The Genetic Material C. Distribution of Chromosomes During Eukaryotic Cell Division D. Eukaryotic Cell Division E. Phases of The Cell Cycle 1. Interphase 2. Mitosis F. Mitosis 1. Mitotic Spindle 2. Anaphase CELLULAR ORGANIZATION OF THE 3. Cytokinesis GENETIC MATERIAL G. Binary Fission In Bacteria All the DNA in a cell constitutes the cell’s genome 1. The Evolution of Mitosis H. The Cell Cycle Control System A genome can consist of a single DNA molecule (common 1. The Cell Cycle Clock in prokaryotic cells) or a number of DNA molecules 2. Internal and External (common in eukaryotic cells) Signals at The DNA molecules in a cell are packaged into chromosomes Checkpoints The DNA molecule of a chromosome carries several 3. Loss of Cell Cycle hundred to a few thousand genes Control In Cancer Cells Eukaryotic chromosomes consists of chromatin, a complex DNA and protein that condenses during cell division CELL DIVISION Every eukaryotic species has a characteristic number of Most cell division results in genetecially identical daughter chromosomes in each cell nucleus cells Somatic cells (nonreproductive cells) have two sets of The ability of organisms to produce more of their own kind chromosomes is the one characteristic that distinguishes living things Gametes (reproductive cells: sperm and egg) have half as from non living matter many chromosomes as somatic cells The continuity of life is based on the reproduction of cells, or cell division DISTRIBUTION OF CHROMOSOMES DURING EUKARYOTIC CELL DIVISION KEY ROLES OF CELL DIVISION In preparation for cell division, DNA is replicated and the Cell division plays several important roles in life chromosomes condense Single-celled organisms give rise to new organisms Each duplicated chromosome has two sister chromatids through cell division (joined copies of the original chromosome), attached along Multicellular eukaryotes undergo embryonic development their lengths by cohesins through cell division The centromere is the narrow “waist” of the duplicated Cell division continues to function in renewal and repair in chromosome, where the two chromatids are most closely fully grown multicellular eukaryotes attached A crucial function of most cell division is the distribution of identical genetic material to the two daughter cells Cell division is remarkably accurate in passing DNA from one generation to the next Identical Daughter Cells Interphase During cell division, the two sister chromatids of each ○ The cell grows; in preparation for cell division, duplicated chromosome separate and move into two the chromosomes are duplicated, with the nuclei genetic material (DNA) copied precisely Once separated, the chromatids are called chromosomes Mitosis ○ The chromosome copies are separated from each other and moved to opposite ends of the cell Castilla, Selene Mari D. | 1 ZOOLFUN – MITOSIS AND CELL CYCLE Mitosis Conventionally broken down into five stages ○ Prophase ○ Prometaphase ○ Metaphase ○ Anaphase ○ Telophase EUKARYOTIC CELL DIVISION Consists of ○ Mitosis - the division of genetic material in the nucleus ○ Cytokinesis - the division of the cytoplasm Gametes are produced by a variation of cell division called meiosis Meiosis yields nonidentical daughter cells that have half as many chromosomes as the parent cell PHASES OF THE CELL CYCLE The mitotic phase alternates with interphase in the cell cycle In 1882, the German anatomist Walther Flemming developed dyes to observe chromosomes during mitosis and cytokinesis During the period between one cell division and the next, many critical events occur The cell cycle consists of ○ Mitotic (M) phase - mitosis and cytokinesis ○ Interphase - cell growth and copying of chromosomes in preparation for cell division MITOSIS The Mitotic Spindle: A Closer Look The mitotic spindle is a structure made of microtubules that controls chromosome movement during mitosis In animal cells, assembly of spindle microtubules begins in the centrosome, a type of microtubule-organizing center The centrosome replicates during interphase, forming two centrosomes that migrate to opposite ends of the cell during prophase and prometaphase By the end of prometaphase, the two centrosomes are at opposite end of the cell An aster (a radial array of short microtubules) extends from each centrosome Interphase The spindle includes the centrosomes, the spindle microtubules, and the asters About 90% of the cell cycle Each sister chromatid has a kinetochore Can be divided into three phases A kinetochore is a protein complex associated with ○ G1 phase - first gap centromeres ○ S phase - synthesis During prometaphase, some spindle microtubules ○ G2 phase - second gap (kinetochore microtubules) attach to the kinetochores The cell grows uring all three phases, but chromosomes At metaphase, the chromosomes are all lined up at the are duplicated only during the S phase metaphase plate, an imaginary plane midway between the spindle’s two poles Castilla, Selene Mari D. | 2 ZOOLFUN – MITOSIS AND CELL CYCLE Anaphase In anaphase, the cohesins are cleavaged by an enzyme called separase Sister chromatids separate and move along the kinetochore microtubules towards opposite ends of the cell The microtubules shorten by depolymerizing at their kinetochore ends Results of a clever experiment suggest that motor proteins on kinetochores “walk” the chromosomes along the microtubules during anaphase The depolymerization of the microtubules at the BINARY FISSION IN BACTERIA kinetochore ends occurs after the motor proteins have passed Prokaryotes (bacteria and archaea) reproduce by a type of This is called the “Pac-man” mechanism cell division called binary fission In binary fission, the chromosome replicates (beginning at the origin of replication), and the two daughter chromosomes actively move apart The plasma membrane pinches inward, dividing the cell into two How bacterial chromosomes move and their location established are active areas of research Other research shows that chromosomes are “reeled in” by motor proteins at the spindle poles Microtubules depolymerize after they pass by the motor proteins at the poles The general consensus is that both mechanisms are used Nonkinetochore microtubules from opposite poles overlap and push against each other, elongating the cell At the end of anaphase, duplicate groups of chromosomes have arrived at opposite ends of the elongated cell Cytokinesis begins during anaphase or telophase, and the spindle eventually disassembles Cytokinesis In animal cells, cytokinesis occurs by a process known as cleavage The first sign of cleavage is the appearance of a cleavage The Evolution of Mitosis furrow, a shallow groove in the cell surface near the old Because prokaryotes evolved before eukaryotes, mitosis metaphase plate probably evolved from binary fission In plant cells, a cell plate forms during cytokinesis Certain unicellular eukaryotes exhibit types of cell division that seem intermediate between binary fission and mitosis Castilla, Selene Mari D. | 3 ZOOLFUN – MITOSIS AND CELL CYCLE THE CELL CYCLE CONTROL SYSTEM The eukaryotic cell cycle is regulated by a molecular control system The frequency of cell division varies with the type of cell These differences result from regulation at the molecular level Cancer cells manage to escape the usual controls on the cell cycle The cell cycle appears to be driven by specific signaling molecules present in the cytoplasm Some evidence for this hypothesis comes from experiments in which cultured mammalian cells at different phases of the cell cycle were fused to form a single cell Internal and External Signals at the with two nuclei Checkpoints Signals in the cytoplasm of the fused cell caused both Many signals registered at checkpoints come from cellular nuclei to enter the same phase of the cell cycle surveillance mechanisms within the cell Checkpoints also register signals from outside the cell Three important checkpoints are those in the G1, G2, and M phases For many cells, the G1 checkpoint seems to be the most important If a cell receives a go-ahead signal at the G1 checkpoint, it will usually complete the S, G2, and M phases and divide If the cell does not receive the go-ahead signal, it will exit the cycle, switching into a nondividing state called the G0 phase The sequenial events of the cell cycle are directed by a distinct cell cycle control system The cell cycle control system is regulated by both internal and external controls The clock has specific checkpoints where the cell cycle stops until a go-ahead signal is received An example of an internal signal is that cells will not begin The Cell Cycle Clock anaphase until all chromosomes are properly attached to the spindle at the metaphase plate Two types of regulatory proteins are involved in cell cycle This mechanism ensures that daughter cells have the control: cyclins and cyclin-dependent kinases (Cdks) correct number of chromosomes Cyclins are named for their cyclically fluctuating External factors, both chemical and physical influence cell concentrations in the cell division The activity of a Cdk rises and falls with changes in Growth factors are released by certain cells and concentration of its cyclin partner stimulate other cells to divide Cdks must be attached to a cyclin to be active Platelet-driven growth factor (PDGF) is made by blood cell MPF (maturation-promoting factor) is a cyclin-Cdk ragments called platelets complex that triggers a cell’s passage past the G2 PDGF is required for the dividion of cultured fibroblasts checkpoint into the M phase Peaks of MPF activity correspond to the peaks of cyclin concentration MPF acts both as a kinase and indirectly through activating other kinases Castilla, Selene Mari D. | 4 ZOOLFUN – MITOSIS AND CELL CYCLE In density-dependent inhibition, crowded cells will stop dividing Most animal cells also exhibit anchorage dependence - to divide, they must be attached to a substratum Density-dependent inhibition and anchorage dependence check the growth of cells at an optimal density Cancer cells exhibit neither type of regulation of their division Loss of Cell Cycle Control in Cancer Cells Cancer cells do not heed the normal sugnals that regulate the cell cycle They do not stop dividing when growth factors are depleted Cancer cells do not need growth factors to grow and divide: ○ They make their own growth factor ○ They may convey a growth factor’s signal without the presence of the growth factor ○ They may have an abnormal cell cycle control system Cells that acquire the ability to divide indefinitely have undergone transformation Cancer cells that are not eliminated by the immune system form tumors, masses of abnormal cell within otherwise normal tissue If abnormal cells remain only at the original site, the lump is called a benign tumor Most benign tumors do not cause serious problems (depending on their location) Malignant tumors invade surrounding tissues and can undergo metastasis, the spread of cancer cells to other parts of the body, where they may form additional tumors Locallized tumors may be treated with high-energy radiation, which damages the DNA in the cancer cells The majority of cancer cells have lost the ability to repair DNA damage Castilla, Selene Mari D. | 5 PRINCIPLES OF GENETICS ZOOLFUN – Fundamentals of Zoology Instructor: Dr. Frances C. Recuenca OUTLINE I. Genetics A. Meiosis B. The Law of Segregation 1. Mendel’s Model C. The Law of Independent Assortment 1. Rules of Probability 2. Inheritance Patterns D. Degrees of Dominance Mendel’s Model 1. Relationship between dominance and Mendel developed a hypothesis to explain the 3:1 phenotype inheritance pattern he observed in F2 offspring. 2. Frequency of Dominant Alleles 3. Multiple Alleles 4. Pleiotropy 5. Polygenic Inheritance 6. A Mendelian View of Heredity and Variation 7. Pedigree Analysis 8. Recessively Inherited Disorders 9. Dominantly Inherited Disorders 10. Multifactorial Disorders GENETICS Four related concepts make up this model the “blending” hypothesis is the idea that genetic First, alternative versions of genes account for variations material from the two parents blend together (e.g. blue in inherited characters -> alleles and yellow make green) Second, for each character, an organism inherits two the “particulate” hypothesis is the idea that parents alleles, one from each parent pass on discrete heritable units (genes) ○ locus - location in chromosome where you find Mendel documented a particulate mechanism through his the gene experiments with garden peas. peas were available to Third, if the two alleles in a locus differ, then one (the Mendel in many different varieties. dominant allele) determines the organism’s appearance, Mendel used the scientific approach to identify two laws of and the other (the recessive allele) has no noticeable inheritance effect on the appearance. ○ law of segregation Fourth, (the law of segregation) the two alleles for a ○ law of independent assortment heritable character separate during gamete formation and a heritable feature that varies among individuals (such as end up in different gametes flower color) is called a character ○ thus, an egg or a sperm gets only one of the two each variant for a character, such as purple or white color alleles that are present in the organism for flowers, is called a trait ○ this segregation of alleles corresponds to the distribution of homologous chromosomes to different gametes in meiosis MEIOSIS Useful genetic vocabulary Most cell division results in daughter cells with identical ○ organism with two identical alleles - genetic information, DNA. The exception is meiosis, a homozygous special type of division that can produce sperm and egg ○ organism that has two different alleles - cells. heterozygous ○ heterozygotes are not true-breeding THE LAW OF SEGREGATION mated two contrasting, true-breeding varieties, a process THE LAW OF INDEPENDENT ASSORTMENT called hybridization Mendel identified his second law of inheritance by what mendel called a “heritable factor” is what we now following two characters at the same time call a gene crossing two true-breeding parents differing in two F1 that is not seen - the property is not lost, it is not just characters produces dihybrids in the F1 generation, both evident are heterozygous in both characters Castilla, Selene Mari D. | 1 ZOOLFUN – PRINCIPLES OF GENETICS a dihybrid cross, which is a cross between F1 dihybrids, Multiple Alleles can determine whether two characters are transmitted to offspring as a package or independently Most genes exist in populations in more than two allelic characters are independent of each other forms Ex: the four phenotypes of the ABO blood group in humans are determined by three alleles Rules of Probability probability laws govern mendelian inheritance mendel’s laws of segregation and independent assortment reflect the rules of probability when tossing a coin, the outcomes of one toss has no impact on the outcome of the next toss multiplication and addition rules appied to monohybrid crosses solving complex genetics problems with the rules of probability we can apply the multiplication and addition rules to predict the outcomes of crosses involving multiple Pleiotropy characters a multicharacter cross is equivalent to two or more Most genes have multiple phenotypic effects, a property independent monohybrid cross occurring simultaneously called pleiotropy in calculating the chances for various genotypes, each Ex. sickle-cell disease character is considered separately, then the individual ○ In homozygous individuals, all hemoglobin is probabilities are multiplied abnormal Symptoms include physical weakness, pain, organ damage, and Inheritance Patterns paralysis inheritance patterns are often more complex than ○ Heterozygotes are usually healthy but may predicted by simple mendelian genetics suffer some symptoms the relationship between phenotype and genotype is rarely Heterozygotes are less susceptible to as simple as in the pea plant characters Mendel studied the malaria parasite (an advantage) many heritable characters are not determined by only one gene with two alleles however, the basic principles of segregation and independent assortment apply even to more complex patterns of inheritance DEGREES OF DOMINANCE Complete dominance - occurs when phenotypes of the heterozygote and dominant homozygote are identical Polygenic Inheritance Incomplete dominance - the phenotype of F1 hybrids is somewhere between the phenotypes of the two parental An additive effect of two or more genes on a single varieties phenotype Codominance - the two dominant alleles affect the Skin color in humans is an exmaple phenotype in separate, distinguishable ways Relationship between dominance and phenotype a dominant allele does not subdue a recessive allele; alleles don't interact that way alleles are simply variations in a gene’s nucleotide sequence for any character, dominance/recessiveness relationships of alleles depend on the level at which we examine the phenotype Frequency of Dominant Alleles Dominant alleles are not necessarily more ommon in populations than recessive alleles A Mendelian View of Heredity and Variation Ex: one baby ot of 400 in the US is born with extra fingers An organism’s phenotype includes all its physical or toes appearance, internal anatomy, physiology, and behavior The alleles for this unusual trait is dominant to the allele An organism’s phenotype reflects its overall genotype and for the more common trait of five digits per appendage unique environmental history In this example, the recessive allele is far more prevalent Many human traits follow Mendelian patterns of than the population’s dominant allele inheritance Castilla, Selene Mari D. | 2 ZOOLFUN – PRINCIPLES OF GENETICS Pedigree Analysis A pedigree is a family tree that describes the inter-relationships of parents and children across generations Inheritance patterns of particular traits can be traced and described using pedigrees Pedigrees can also be used to make predictions about future offspring Recessively Inherited Disorders Many genetic disorders are inherited in a recessive manner Range from relatively mild to life-threatening Show up only in individuals homozygous for the allele Carriers are heterozygous individuals who carry the recessive allele but a phenotypically normal Albinism is a recessive contusion characterized by a lack of pigmentation in skin and hair Dominantly Inherited Disorders Some human disorders are caused by dominant alleles Dominant alleles that cause a lethal disease are rare and arise by mutation Achondroplasia is a form of dwarfism caused by a rare dominant allele Multifactorial Disorders Many diseases, such as heart disease, diabetes, alcoholism, mental illnesses, and cancer have both genetic and environmental components No matter what our genotype our lifestyle has a tremendous effect on phenotype Castilla, Selene Mari D. | 3 MOLECULAR BASIS OF INHERITANCE ZOOLFUN – Fundamentals of Zoology Instructor: Dr. Frances C. Recuenca OUTLINE I. Molecular basis of Inheritance A. DNA 1. Primary structure 2. Secondary structure B. DNA Replication 1. Base Pairing to a DNA REPLICATION Template Strand 2. DNA Replication Process by which DNA makes identical copies of itself 3. Key Players 4. Antiparallel Elongation Base Pairing to a Template Strand 5. Replicating the Ends of Basic principle DNA Since the complementray DNA strands act as template for 6. Telomeres 7. Steps in DNA building a new strand in replication Replication The parent molecule unwinds, and two new daughter C. Central Dogma of Molecular strands are built based on base-pairing rules Biology Watson’s and Crick’s semiconservative model of 1. Basic Principles replication predicts that when a double helix replicates, 2. Transcription each daughter molecule will have one old strand and 3. Translation 4. Summary one newly made strand MOLECULAR BASIS OF INHERITANCE DNA A polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group. DNA Replication Chargaff’s rules ○ By Erwin Chargaff High fidelity process - needs to be true and original ○ The number of A and T bases is equal and the ○ Sensing proper geometry of the correct base number of G and C bases is equal pairs In 1953, James Watson and Francis Crick introduced a ○ Slowing down catalysis in case of a mismatch double-helical model structure based on Rosalind ○ Partitioning of the mismatch primer to Franklin’s X-ray crystallography of the DNA molecule exonuclase active sites Watson and Crick determined that Adenine (A) paired only Replication begins at particular sites called origins of with thymine (T) and guanine (G) paired only with cytosine replication, where the two DNA strands are separated, (C) opening up a replication “bubble” The Watson-Crick model explains Chargaff’s rules: in any A eukaryotic chromosome may have hundreds or even organism, the amount of A = T and G = C thousands of origins of replication Replication proceeds in bith directions from each origin, until the entire molecule is copied Primary Structure RNA primer - initiate synthesis of DNA polynucleotide Alternating sugar-phosphate backbone Different nitrogenous bases Phosphoester linkage between nucleotides ○ ‘5 phosphate group of one nucleotide and ○ 3’ -OH group of another nucleotide One end free -OH group at 3’C (3’ end) and free phosphate group at 5’C (5’ end) Secondary Structure 2 polynucleotide strands coiled around each other in double helix 2 strands are complimentary due to specific base pairing Purine - pyrimidine 2 strands run in opposite direction - antiparallel Castilla, Selene Mari D. | 1 ZOOLFUN – MOLECULAR BASIS OF INHERITANCE Key Players Protein Function Replication fork - a Y-shaped region at the end of each Helicase Unwinds parental double helix at replication replication bubble where new DNA are elongating forks Helicases - enzymes that untwist the double helix at the replication forks Single-strand Binds to and stabilizes single-stranded DNA Single-strand binding proteins bind to and stabilize binding protein until it is used as a template single-stranded DNA Topoisomerase - corrects “overwinding” ahead of Topoisomerase Relieves overwinding strain ahead of replication forks by breakin, swiveling, and rejoining DNA replication forks by breaking, swiveling, and strands rejoining DNA strands RNA primer - initiate synthesis of DNA polynucleotide Primase Synthesizes an RNA primer at 5’ end of leading strand and at 5’ end of each Okazaki fragment of lagging strand DNA pol III Using parental DNA as a template, synthesizes new DNA strand by adding nucleotides to an RNA primer or a pre-existing DNA strand DNA pol I Removes RNA nucleotides of primer from 5’ end and replaces them with DNA nucleotides Antiparallel Elongation The antiparallel structure of the double helix affects DNA ligase Joins Okazaki fragments of lagging strand; replication on leading strand, joins 3’ end of DNA that DNA polymerases add nucleotides only to the free 3’ end replaces primer to rest of leading strand of a growing strand; therefore, a new DNA strand can DNA elongate only in the 5’ to 3’ direction Leading strand - to the direction of fork, synthesize 5’ to Replicating the Ends of DNA Molecules 3’ Lagging strand - 5’ to 3’, away from the fokrk, DNA polymerase creates problems for the linear DNA of synthesized discontinuously, as a series of segments eukaryotic chromosomes Okazaki fragments - segments of the lagging strand The usual replication machinery provides no way to complete the 5’ ends, so repeated rounds of replication produce shorter DNA molecules with uneven ends This is not a problems for prokaryotes, most of which have circular chromosomes Telomeres Special nucleotide sequences at the eukaryotic chromosomal DNA ends Do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules It has been proposed that the shortening of telomeres is connected to aging Telomerase enzyme - catalyzes lengthening of telomeres Steps in DNA Replication 1. Separation of DNA strands 2. Formation of replication fork 3. Binding of RNA primer 4. Chain elongation 5. Excision of RNA primer & replacement by DNA CENTRAL DOGMA OF MOLECULAR BIOLOGY Basic Principles of Transcription and Translation Genes provide the instructions for making specific proteins ○ RNA is the nucleic acid bridge between the DNA and protein synthesis ○ RNA is chemically similar to DNA except: It contains ribose instead of deoxyribose as its sugar Castilla, Selene Mari D. | 2 ZOOLFUN – MOLECULAR BASIS OF INHERITANCE Has the nitrogenous base uracil rather than thymine An RNA molecule usually consist of a single strand Transcription Synthesis of RNA using information fr