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GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O THE CELL MODULE 1: BIOLOGY AND ITS THEME PROKARYOTIC E...

GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O THE CELL MODULE 1: BIOLOGY AND ITS THEME PROKARYOTIC EUKARYOTIC EVOLUTION - Simpler and smaller - With membrane - No nucleus or bound organelles Process of change that has transformed membrane-enclosed life on Earth organelles Adaptation is a result of evolution Core theme of Biology Scientific explanation for both the unity DNA and diversity of organisms Each chromosome has 1 DNA with hundreds or thousands of genes BIOLOGY Controls development and maintenance Study of life of organisms ○ Order Each DNA is made up of 2 long chains ○ Evolutionary adaptations arranged in double helix ○ Regulation ○ Reproduction GENE EXPRESSION ○ Response to environment ○ Growth and development Process of converting information from ○ Energy processing gene to cellular product ORGANIZATION! GENOMICS PROTEOMICS Biosphere -> Ecosystem -> Communities -> Population -> Organisms -> Organ -> Tissues -> Study of genes within Study of proteins Cells -> Organelles -> Molecules species encoded by the genomes (proteomes) EMERGENT PROPERTIES HIGH THROUGHPUT TECHNOLOGY Results from arrangement and interaction of parts within a system Tools that can analyze many biological samples very rapidly REDUCTIONISM BIOINFORMATICS Narrowing down complex systems to simpler components to make it more Use of computers to store, organize, and manageable to study analyze the large volumes of data SYSTEMS BIOLOGY ENERGY AND MATTER How parts within a biological system Energy flows within an ecosystem interact with one another (systems & Enters as light, exits as heat function) PAGE 1 GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O INTERACTIONS Interactions between organisms, which may be beneficial or harmful to one or both organisms. ECOLOGICAL INTERACTIONS One benefits, other is Parasitism harmed Mutualism Both benefits One benefits, other is Commensalism unaffected One benefits, other is Predation harmed or killed Competition Both are harmed THREE DOMAINS OF LIFE One is harmed, other 1. Bacteria – Prokaryotic, unicellular Amensalism organisms with no membrane-bound is unaffected nucleus. 2. Archaea – Prokaryotic, unicellular FEEDBACKS organisms that often live in extreme environments. Refers to the processes by which a 3. Eukarya – Organisms with eukaryotic system regulates itself by responding to cells, which have a nucleus and other changes membrane-bound organelles. NEGATIVE POSITIVE THREE MULTICELLULAR KINGDOMS FEEDBACK FEEDBACK - Reduces the - Increases the Within the domain Eukarya, the three reactions within the reactions within the multicellular kingdoms are: body body Ex. Regulation of Ex. breastfeeding 1. Plantae – Includes all multicellular plants blood sugar that produce their own food via photosynthesis. 2. Fungi – Includes multicellular fungi such LEVELS OF CLASSIFICATIONS as mushrooms, which absorb nutrients from organic material. Remember: “Dear King Phillip Came 3. Animalia – Comprises multicellular Over For Good Spaghetti” animals that consume other organisms for energy. PAGE 2 GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O UNITY IN DIVERSITY OF LIFE SPECIALIZATIONS IN ZOOLOGY DNA is universal genetic language Entomology Insects common to all organisms Parasitic worms Helminthology CHARLES DARWIN (helminths) Created “Theory of Natural Selection” Herpetology Amphibians & reptiles Species showed evidence of “descent with modification” from common Ichthyology Fishes ancestors “Natural selection” is the mechanism Mammalogy Mammals behind descent with modification Ornithology Birds ZOOLOGY Protozoology Protozoa Scientific study of animals MODULE 2: THE ANIMAL CELL ANATOMY Structure of organisms and their parts THE FUNDAMENTALS OF LIFE CYTOLOGY 1. All organisms are made up of cells Study of structure, function, and behavior 2. The cell is the simplest collection of of cells matter that can be alive 3. All cells are related by their descent from ECOLOGY earlier cells 4. Cells can differ substantially from one Environment of organisms another, yet they share common features EMBRYOLOGY MICROSCOPE Study of development of an embryo from Light microscope the stage of ovum fertilization through to ○ Visible light passes through a the fetal stage specimen and then through the glass lenses ○ Lenses refract the light and the OTHERS image is magnified Genetics ○ Can magnify up to about 1,000 Histology times the size of the actual Molecular Biology specimen Parasitology Electron microscope Physiology 1. Scanning Electron Microscope Systematics (SEM) ○ Focus the electron beams on the surface of the PAGE 3 GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O specimen which provides LPO 10 x 10 100 3D image 2. Transmission Electron Microscope HPO 10 x 40 400 (TEM) ○ To study internal Oil Immersion 10 x 100 1000 structures of the cells LIGHT ELECTRON CELL FRACTIONATION MICROSCOPE MICROSCOPE Takes cells apart and separates the major organelles from one another Brightfield Scanning Phase-contrast Enables scientists to determine the Transmission Fluorescence function of each organelles Confocal Deconvolution EUKARYOTIC AND PROKARYOTIC Super-resolution Differential-contr CELLS ast Basic features of all cells Interferential-con 1. Plasma membrane trast 2. Semifluid substance (Cytosol) 3. Chromosomes (carry genes) 4. Ribosomes (make proteins) PARTS OF THE MICROSCOPE PROKARYOTIC CELL EUKARYOTIC CELL No true nucleus With true Lacks nuclear nucleus membrane DNA is Genetic material bounded by is in nucleic nuclear region (nucleoid) No envelope membrane-bou Genetic nd organelles material within Cytoplasm is nucleus bound by Contains plasma cytoplasm with membrane cytosol and membrane- bound organelles PARTS OF ANIMAL CELL: EUKARYOTIC EYEPIECE X TOTAL OBJECTIVE MAGNIFICATION PLASMA MEMBRANE Scanner 10 x 4 40 PAGE 4 GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O Selective barrier that allow a sufficient SMOOTH ER ROUGH ER passage of oxygen, nutrients, and waste to service the volume of every cell Synthesizes Has bound lipids ribosomes, NUCLEUS Metabolized which secrete carbohydrates glycoproteins “Information Central” Detoxifies (proteins Contains most of the cell’s genes drugs and covalently Usually the most conspicuous organelle poisons bonded to Nuclear envelope encloses the nucleus Stores calcium carbohydrates and separates the nucleus from the ions Distributes cytoplasm transport Nuclear membrane is a membrane that vesicles consist of a lipid bilayer (secretory Nucleolus is located within the nucleus, proteins may vary in numbers in a nucleus, and surrounded by the site of ribosomal RNA (rRNA) membranes) synthesis A membrane The pores regulate the entry and exit of factory for the molecules from the nucleus cell Nuclear size of the envelope is lined by nuclear lamina which is composed of proteins and maintains shape of the GOLGI APPARATUS nucleus “The Shipping and Receiving Center” RIBOSOMES Made up of flattened membranous sacs — Cisternae “Protein Factories” Modifies products of the ER Complexes made of ribosomal RNA and Manufactures certain macromolecules protein Sorts and packages materials into Carries out protein synthesis in 2 location: transport vesicles ○ Cytosol (free ribosomes) ○ Outside the endoplasmic LYSOSOMES reticulum or the nuclear envelope (bound ribosome) “Digestive Compartments” A membranous sac of hydrolytic ENDOPLASMIC RETICULUM enzymes that can digest macromolecules “Biosynthetic Factory” Lysosomal enzymes work best in the Accounts for more than half of the total acidic environment inside the lysosome membrane in many eukaryotic cells Hydrolytic enzymes and lysosomal Continuous with the nuclear envelope membranes are made by the RER then 2 distinct regions transferred to the Golgi apparatus for ○ Smooth ER (lacks ribosomes) further processing ○ Rough ER (surface is studded with ribosomes) PAGE 5 GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O VACUOLES ENDOSYMBIONT THEORY Suggests that an early ancestor of “Diverse Maintenance Compartments” eukaryotes engulfed an oxygen-using Large vesicles derived from ER and Golgi non photosynthetic prokaryotic cell apparatus The engulfed cell formed a relationship Perform different functions in different with the host cell, becoming an cells endosymbiont The endosymbionts evolved into TYPES OF VACUOLES mitochondria At least one of these cells may have Formed by taken up a photosynthetic prokaryote, Food vacuole which evolved into a chloroplast phagocytosis Found in many PARTS OF ANIMAL CELL: PROKARYOTIC freshwater protists; Contractile vacuole pump excess water out of cells ENDOMEMBRANE SYSTEM Found in many mature Regulates protein traffic and performs Central vacuole plant cells; hold organic metabolic functions in the cell compounds and water Made up of: ○ Nuclear envelope ○ Endoplasmic reticulum MITOCHONDRIA AND CHLOROPLAST ○ Golgi apparatus Both change energy from one form to ○ Lysosomes another ○ Vacuoles 1. Mitochondria ○ Plasma membrane ○ Sites of cellular respiration (metabolic process that uses PEROXISOMES oxygen to generate ATP) ○ “Chemical Energy Conversion” Specialized metabolic compartments ○ They have smooth outer Produce hydrogen peroxide and membrane and an inner convert to water membrane folded into cristae Its relationship with other organelles is ○ Inner membrane creates 2 still unknown compartments: Intermembrane space and Mitochondrial matrix CYTOSKELETON 2. Chloroplast ○ Found in plants and algae Network of fibers that organizes ○ Site of photosynthesis structures and activities in the cell Mitochondria and chloroplasts have Help support the cell and maintain its some similarities with the bacteria shape ○ Enveloped by a double 3 structures: membrane ○ Microtubules ○ Contain free ribosomes and ★ Thickest of the 3 circular DNA molecules components ○ Grow and reproduce somewhat ★ Hollow tubes independently in cells PAGE 6 GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O ★ Maintains the cell shape ○ Intermediate filaments ★ Cell motility ★ Fibers with diameters in a ★ Chromosome movement middle range in cell division ★ Fibrous proteins coiled ★ Organelle movements into cables ★ Maintenance of cell shape ★ Anchorage of nucleus and CILIA AND FLAGELLA some other organelles Microtubules control the beating of ★ Formation of nuclear flagella and cilia, lamina microtubule-containing extensions that project from some cells. Cilia and flagella differ in their beating EXTRACELLULAR MATRIX OF ANIMAL patterns. CELLS Common structure: ○ A core of microtubules sheathed by the plasma membrane ○ A basal body that anchors the cilium or flagellum ○ A motor protein called dynein, which drives the bending movements of a cilium or flagellum Animal cells lack cell walls but are covered by an elaborate extracellular matrix The ECM is made up of glycoproteins such as collagen, proteoglycans, and fibronectin ECM proteins bind to receptor proteins in the plasma membrane ○ Integrins CELL JUNCTIONS Tight Junctions: Member of neighboring cells are pressed together, preventing ○ Microfilaments leakage of extracellular fluid ★ Actin filaments Desmosomes: Called as “Anchoring ★ Thinnest junctions” and fasten cells together into ★ Maintenance of cell shape strong sheets ★ Changes in cell shape Gap Junctions: Called as ★ Muscle contraction “Communicating junctions” and provide ★ Cell motility cytoplasmic channels between adjacent ★ Division of animal cells cells PAGE 7 GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O CROSS SECTION OF STOMACH CROSS SECTION OF FROG OVARY ANIMAL CELL STRUCTURE HUMAN CHEEK CELLS FROG’S BLOOD SMEAR PAGE 8 GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O CROSS SECTION OF FROG’S TESTIS FLUID MOSAIC MODEL A membrane that is a fluid structure with a “mosaic” of various proteins embedded in it ○ Proteins are not randomly distributed in the membrane Phospholipids in the plasma membrane can move within the bilayer Most lipids, and some proteins, drift laterally Rarely would a lipid flip-flop transversely across the membrane MODULE 3: MEMBRANE TRANSPORT PHOSPHOLIPID Proteins determine most of the PLASMA MEMBRANE membrane’s specific functions 1. Peripheral protein - bound to the Boundary that separates the living cell surface of the membrane from its surroundings 2. Integral protein - penetrate the Exhibits selective permeability (allows hydrophobic core: some substance to cross the membrane a. Transmembrane protein - more easily than other substance) integral proteins that span Cell membranes are fluid mosaics of the membrane lipids and proteins MAJOR FUNCTIONS OF MEMBRANE PROTEINS PHOSPHOLIPID Most abundant lipid in the plasma membrane Amphipathic molecules (contains both hydrophilic (the head) and hydrophobic (the tail) regions) A phospholipid bilayer can exist as a stable boundary between 2 aqueous compartments PAGE 9 GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O The tendency for molecules to spread CELL TO CELL RECOGNITION out evenly into the available space PERMEABILITY OF THE LIPID BILAYER Hydrophobic: can dissolve in the lipid bilayer and pass through the membrane rapidly Hydrophilic: includes ions and polar molecules that do not pass the membrane easily TRANSPORT PROTEINS Allows the passage of hydrophilic PASSIVE TRANSPORT substance across the membrane ○ Channel proteins Substances diffuse down their ★ With hydrophilic channel concentration gradient that certain molecules can No work must be done to move the use as a tunnel substances down the gradient ★ Passive transport ★ Aquaporins - facilitate the passage of water OSMOSIS ○ Carrier proteins Diffusion of water across the selectively ★ Bind to molecules and permeable membrane from the region of change shape to shuttle lower solute concentration to the them across the regions of higher solute concentration membrane until the concentration is equal on both ★ Active transport sides DIFFUSION WATER BALANCE OF CELLS WITHOUT Movement of molecules from an area of CELL WALLS higher concentration to an area of Tonicity: Ability of a surrounding solution lower concentration without any energy to cause a cell to gain or lose water investment PAGE GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA 10  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O ○ Isotonic solution: Solute PASSIVE TRANSPORT concentration is the same as inside the cell. There is no net Transport proteins speed up the passive movement of water across the movement of molecules across the membrane. plasma membrane ○ Hypertonic solution: Solute ○ Carrier proteins: Undergo subtle concentration is greater outside change in shape that translocates the cell. The cell loses water and the solute-binding site across the becomes shriveled. membrane ○ Hypotonic solution: Solute ○ Channel proteins: Provide concentration is less than the corridors to allow specific inside of a cell. The cell gains molecules to cross the membrane water and may swell or burst. ○ Aquaporin: Facilitate diffusion of water ○ Ion channel: Facilitate diffusion of ions. Some are known as gated channels (they open and close in response to a stimulus) ACTIVE TRANSPORT Moves substances against their concentration gradient Requires energy, usually in the form of ATP Performed by specific proteins embedded in the plasma membrane OSMOREGULATION Allows cells to maintain concentration Control of solute concentrations and gradients that differ than their water balance surroundings Examples of saltwater osmoregulators, Sodium-potassium pump is one type of for instance, include fish that do so by the active transport gaining water and salts from drinking seawater. To osmoregulate, the saltwater fish will filter excess salt ions across their gills and through the kidneys, and a small amount of water is also excreted in the urine. PAGE 11 GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O MEMBRANE POTENTIAL Voltage difference across a membrane ○ Created by differences in the distribution of positive and negative ions across a membrane ELECTROCHEMICAL GRADIENT 2 combined forces Drive the diffusion of ions across a membrane Chemical force ○ Ion’s concentration gradient BULK TRANSPORT Electrical force Movement of proteins or ○ Effect of membrane potential on macromolecules into and out of the cell the ion’s movement Requires energy 2 types: ELECTROGENIC PUMP ○ Exocytosis ★ Transport vesicles migrate A transport protein that generates to the membrane, fuse it, voltage across the membrane and release their contents Sodium-potassium pump: Major outside the cell electronic pump for animal cells ★ Many secretory cells use Proton pump: Major electrogenic pump exocytosis to export their for plants, fungi, and bacteria products Help store energy that can be used for ○ Endocytosis cellular work ★ Cells take in macromolecules by COTRANSPORT forming vesicles from plasma membrane Coupled transport by a membrane protein TYPES OF ENDOCYTOSIS Occurs when active transport of a solute indirectly drives transport of other Cellular eating substances Cell engulfs a particle in a vacuole Phagocytosis The vacuole fuses with a lysosome to digest the particle Cellular drinking Pinocytosis Molecules PAGE GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA 12  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O ○ In any species, the number of A dissolved in and T bases are equal and the droplets are number of G and C bases are also taken up when equal extracellular fluid is “gulped” into tiny vesicles JAMES WATSON & FRANCIS CRICK Binding of Introduced the double-helical model ligand to structure based on Rosalin Franklin’s receptor triggers x-ray crystallography of the DNA vesicle molecule. formation Determined that adenine (A) is paired Receptor-mediated only with thymine (T), and guanine (G) Ligand is any endocytosis only with cytosine (C) molecule that binds specifically to a receptor site THEREFORE! of another The Watson-Crick model explains the molecule Chargaff’s rule; in any organism, the amount A=T, and G=C BASE PAIRING 2 strands of DNA are complementary ○ Each strand acts as a template for building a new strand in replication ○ Parent molecule unwinds and makes 2 new daughter strands Watson and Crick’s semiconservative model of replication predicts that when a double helix replicates, each daughter MODULE 4: INTRODUCTION TO molecule will have one old strand and GENETICS one newly made strand. DEOXYRIBONUCLEIC ACID Genetic material Polymer of nucleotides Each consists of: Nitrogenous base, sugar, phosphate group ERWIN CHARGAFF Reported that DNA composition varies from one species to another Made Chargaff’s rule: PAGE GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA 13  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O Bind to and stabilize single-stranded DNA REPLICATION DNA Replication begins at particular sites called origins of replication, where the TOPOISOMERASE two DNA strands are separated, opening up a replication “bubble” Corrects “overwinding” ahead of Replications proceed in both directions replication forks by breaking, swiveling, from each origin, until the entire and rejoining DNA strands molecule is copied. REPLICATION FORK Y-shaped region at the end of each replication bubble where new DNA ANTIPARALLEL ELONGATION strands elongating The antiparallel structure of the double helix affects the replication HELICASE DNA polymerases only add nucleotides to the free 3’ end of a growing strand. Enzymes that untwist the double helix Newly formed strand can only elongate at the replication fork in the 5’ to 3’ direction SINGLE-STRAND BINDING PROTEINS PAGE GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA 14  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O OKAZAKI FRAGMENTS Segments formed from the lagging strand Later on joined by the DNA ligase TELOMERES Special nucleotide sequences found at the eukaryotic chromosomal DNA ends Do not prevent shortening of DNA molecules Postpone the erosion of genes near the DNA molecules It has been proposed that the shortening of telomeres is connected to aging REPLICATING THE ENDS OF DNA MOLECULES Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes The usual replication machinery provides no way to complete the 5’ ends, so repeated rounds of replication produce shorter DNA molecules with uneven ends. PAGE GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA 15  GENERAL BIOLOGY 2 ZOOLOGY ANDREA NICOLE T. MADOLORA I STEM 12-O CELL DIVISION G1 CYCLE The ability of the organisms to produce Increases cell growth more of its own kind best distinguishes Increase in number of cytoplasmic the living things from nonliving things structure Continuity of life based on the ○ Mitochondria number and reproduction of cells cytoskeletal structure Doubling in number of centrosomes UNICELLULAR MULTICELLULAR Preparation for mitosis ORGANISMS ORGANISMS Some cells carry the destined cell Division of one Depends on cell S PHASE cell reproduces division for the whole development, DNA synthesis organism growth, and repair G2 CYCLE Biochemical preparation for the onset of MITOSIS AND MEIOSIS mitosis MITOSIS MEIOSIS G0 CYCLE Normal stage Division of Produces genetic material gametes Will not go to mitosis in the nucleus Yields Nerve cells, heart muscle cells Cytokinesis non-identical (Division of the daughter cells cytoplasm) that have half as many chromosomes as the parent cell CELL CYCLE Consists of Mitotic phase (10%) and Interphase (90%) Interphase has 3 subphases: G1 (first gap), S phase (synthesis), and G2 (second gap) PAGE GENERAL BIOLOGY 2 (LABORATORY AND LECTURE) - ANMADOLORA 16