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Module 1: Biology Notes

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Biological Sciences
Bebhinn Treanor

Module #1: Cell Biology and Metabolism Lecture 2: Biology and the Tree of Life What is biology?  The scientific study of life What is life?  Consist of organized cells  Contain heritable genetic information for reproduction  Show grow  Respond to stimuli  Exhibit homeostasis (regulation)  Harness and utilize energy  Adapt to environmental change – with evolution through natural selection How is ALL life on earth related? 1. The Cell Theory  Cells are the basic units of life  All organisms are composed of cells  All cells come from pre-existing cells 2. The Theory of Evolution by Natural Selection  All species, past and present, trace their ancestry back to a single common ancestor Diversity and Unity of Life through Evolution 1. Diversity of Life- through evolution  Biology uses Charles Darwin’s Theory of Evolution through Natural Selection (1859) as a unifying framework  All organisms capable of reproductions involving duplication of genetic material with potential for errors  Results in biological evolution through Natural Selection  Differences among organisms enable them to: 1.To live in different kinds of environments 2.To adapt to changing environmental conditions 2. Unity of Life- through evolution  Despite the great diversity of life- remarkable unity among all organisms 1.Cells enclosed by lipid bilayer 2.Genetic system based on DNA 3.System of information transfer- DNA to RNA to protein 1 4.System of protein assemble by translation of messenger RNA (mRNA) and transfer RNA (tRNA) using ribosomes 5.ATP molecule of chemical energy 6.Metabolic pathway to generate ATP 7.Proteins as major structural and catalytic molecule Taxonomy- Classification of Life:  System developed by Linnaeus (1735)  Organisms classified on the basis of shared (obvious) features- structure and function  All organisms have a unique 2-part scientific name (italicized) 1. genus name 2. species name What is meant by the “Tree of Life”?  Tree of life- represents the phylogeny of organisms: the genealogical relationship among species with a single ancestral species at its base  still a work in progress- active debate and ongoing research Biology is a DYNMAIC SCIENCE:  taxonomy, genetics, molecular biology, cell biology, systems biology, ecology, biochemistry, physiology, evolutionary biology, phylogeny  biologists closer understand: o how a single cell develops into an organisms o how plants convert sunlight to a chemical energy o how the human brain works o how living organisms interact o how the diversity of life on earth evolved Lecture 3: The Origins & Chemical Building Blocks of Life How did life on Earth originate?  Billion years ago, Earth was a hostile place  Severe volcanic and tectonic activity  Intense ultraviolet energy from the sun  No oxygen existed in the atmosphere until photosynthesis developed in microbes  No life existed Origins of Life on Earth:  Chemical and physical processes on early Earth produced simple cells with the characteristics of living organisms 2  Speculate that life formed in four main stages: 1. Abiotic synthesis of small organic molecules(monomers) 2. Polymerization- joining of monomers into polymers 3. Packaging of these molecules into protobionts (membranes) that maintained distinct internal chemistry 4. System to store information and use it to guide synthesis 1. Abiotic Synthesis:  all life forms composed of macromolecules:  nucleic acids  proteins  lipids  carbohydrates How were these molecules formed in the absence of life?  Three major hypotheses:  Primordial Soup  Deep Sea Vents  Extraterrestrial Origins (Panspermia) Primordial Soup:  Primordial atmosphere o Water vapour o Hydrogen (H 2 o Carbon dioxide (CO 2 o Ammonia (NH ) 3 o Methane (CH )4 o BUT virtually no oxygen (O2) o Miller-Urey experiment = organic compounds (amino acids etc.) Reducing atmosphere + no ozone (Oparin-Haldane Hypothesis) + Cyanide and formaldehyde = ALL the building blocks of complex biological molecules: Amino acids, fatty acids, purine and pyrimidine, sugars and phospholipids Deep-Sea Vents:  Hydrothermal vents = superheated water  Rich in hydrogen, hydrogen sulfide, carbon dioxide and nitrogen  Gases bubble up through chambers creating a geochemical gradient 3 o These catalytic “cells” generated lipids, proteins and nucleotides Extraterrestrial Origins (Panspermia)  More than 500 meteorites impact Earth each year  Many are carbonaceous chondrites = rich in organic molecules  Murchison meteorite (1969) o Amino acids: glycine, glutamic acid and alanine o Purines and pyrimidines 2. Polymerization:  key chemical components of life are polymers: o nucleic acids: polymers of nucleotides o proteins: polymers of amino acids o carbohydrates: polymers of simple sugars  Clay hypothesis: o Charged layered structure of class allows for molecular adhesion forces to bring monomers together to form short polymers o Clays can store potential energy- used in energy- requiring polymerization reactions 3. Appearance of Protobionts:  Protobiont: group of abiotically produced organic molecules surrounded by a membrane o unique internal chemistry and concentration of molecules  lab experiments show they can be spontaneously generated  may be similar to liposome- lipid vesicle with lipid bilayer similar to cell membrane  capable of simple reproductions and metabolism The central dogma:  each step requires ENZYMES = proteins So how did such a system evolve? 4. Systems to store information and use it to guide synthesis:  RNA molecules can function as enzymes ; ribosomes  Catalytic properties due to folding = specifically for substrate  Early life may have existed in an “RNA world” o RNA o RNA to protein o DNA to RNA to Protein 4 So why don’t we still live in an “RNA world”?  DNA is better at information storage than RNA o More structurally complex – double stranded and contains sugar deoxy-ribose o Chemically more stable o Base uracil replaces with thymine- DNA repair o Double-stranded – DNA repair  Proteins are better catalysts than RNA o Rate of catalysts 10-100 times greater o Variety of proteins -22 different amino acids into proteins BUT only combination of 4 nucleotides in RNA o Amino acids can interact chemically – bonding arrangement not possible between nucleotides How did life on evolve on Earth?  Early protobionts used molecules present in the environment for growth and replication  Heterotrophs (other feeding) – organisms that obtain carbon from organic molecules- likely via anaerobic respiration and fermentation  Produced CO 2  Autotrophs (self feeding) emerged , which are organisms that obtain carbon from inorgranic molecules (often C2 )  Anoxygenic photosynthesis  Evolution of oxygenic photosynthesis – cyanobacteria use water as electron donor – produce O 2 Primoridial heterotrophs did not survive the change in the environment and those that did evolved the capacity for aerobic respiration What types of cells on found on Earth?  Cell =basic unit of life’s organization  Prokaryotes – lack membrane enclosed organelles ( no nucleus which contains DNA)  Eukaryotes – have membrane enclosed organelles Cell types are distinguished by the Presence/Absence of Internal Membrane bound compartments:  Modern classifications based on: o Obvious similarities o Evolutionary relationships  Bacteria and Achaea are common ancestors of all organisms  Prokaryotes: bacteria and Achaea  Eukaryotes: Eukarya (protists, plantae, fungi, animalia) 5 Lecture 4: Prokaryotes (domain bacteria and domain archaea)  Thrive almost everywhere including extreme habitats too hostile for most organism, remarkable diversity  Appear simple in structure compared to eukaryotic cells  Have the greatest metabolic diversity of all organisms  Classified into two domains that differ in structure, physiology, and biochemistry: 1. Bacteria  Most familiar to use  Some responsible for disease  Some essential for health  Many important for food productions (yogurt, cheese) 2. Archaea  Not well known- only discovered about 40 years ago  Share some cellular features with bacteria, some with eukaryotes and some unique  Many live in very extreme conditions that no other organisms can survive Prokaryotic Morphology:  Are unicellular  Three common cell shapes: o Sphere (coccus) o Rod (bacillus) o Spiral (spirillus)  Are very small o Diameters in the range of 1 to 10 um Prokaryotic Cell Structure:  External: o Cell wall o Cell membrane o Capsule o Pili o Flagella  Internal: o DNA packed into area called nucleoid o Plasmids o Ribosomes o Lack internal membrane bound organelles o Semblance of cytoskeleton 6 Bacterial Cell Wall  Cell wall maintains the shape of the cell, affords protection, and prevents bursting in a hypotonic environment  Most bacterial cell walls contain peptidoglycan o Polymer of modified sugars cross linked by short polypeptides o Related molecule in archaea, but different molecular components and bonding structure  Some bacterial cell walls contain outer membrane o Contains lipopolysaccharide (LPS)  Differences in cell structure used to classify bacteria The Gram Stain – Classifying Bacteria  Classification based on reaction Gram stain procedure  Differences in cell wall composition : peptidoglycan  Cells stained with crystal violet, then idodine (crystal-violet idodine =purple  Cells rinsed with ethanol, counterstained with safranin (pink o Gram positive (purple) o Gram negative (pink)  Not useful for identifying archaea- variable response to gram stain Sticky capsule protects many prokaryotic cells:  Layer that lies outside the cell wall  Consists of polysaccharides  Protects bacteria from external environment o Desiccation o Extreme temperatures o Invading viruses o Antibiotics  Considered a virulence factor – helps to evade detection by immune cells Pili and Fimbriae:  Pilius (singular)- a hair like appendage found on the surface of many bacteria (latin for hair)  Aids to attachment of bacteria to host surfaces o Required for colonization during infection o Required to initiate formation of a biolfilm  Conjugative (sex)- pili allow transfer of plasmids (DNA) between bacteria o one method for horizontal gene transfer (HGT) 7 Flagella: a Sensory and Locomotive Organelle  a flagellum (singular) – a cell surface appendage (latin for whip)  primary role in locomotion  also sensory organelle – sensitive to external environment (chemicals and temperature)  prokaryotic and eukaryotic flagella differ in protein compositions, structure and mechanism of propulsion Prokaryotic Genome:  majority of genomes consist of a ring of DNA o single, circular DNA molecule= chromosome o packed into nucleoid region o no nucleolus o no nuclear membrane o small genome ( ~1/1000 size of genome of average eukaryote)  may also have similar rings of DNA – plasmids o provide resistance to antibiotics o replicate independently of the chromosome o can be transferred between bacteria via pili Prokaryotic Ribosomes:  smaller than eukaryotic ribosomes  protein synthesis similar to eukaryotes  archaeal ribosomes share some similarities with eukaryotic ribosomes o bacteria ribosomes sensitive to antibiotics, archaeal and eukaryotic ribosomes are not Prokaryotes Reproduce by Binary Fission:  asexual reproduction  produces exact copies of parent  can result in rapid population growth 1. Replication 2. Segregation 3. Cytokinesis Mechanisms Promoting Genetic Diversity in Prokaryotes: 1. Rapid Reproduction and Mutation:  New mutations, even if rare, can increase genetic diversity quickly in species with short generation times 8 -7  Example: a spontaneous mutation is given E.coli gene ~1/10,000,000 (1x10 ) per cell divisions – but 2x10 new E.coli each day in intestine = 2000 bacteria that have a mutation in that gene o Consider all 4,300 E. Coli genes = 9 million per day per host 2. Genetic Recombination: (combing of DNA from two sources)  Conjugation: DNA transferred from on prokaryotic cell to another via pilus  Transformations: uptake of foreign DNA from surroundings  Transduction: bacteriophages (viruses that infect bacteria) carry prokaryotic gene from one host cell to another Metabolic Diversity of Prokaryotes:  Autotrophs- self feeling ; obtain energy from inorganic carbon  Heterotrophs- other feeding; obtain energy from organic carbon o Organisms grouped according to source of carbon But organisms also grouped according to source of energy:  Phototrophs: o Use lights as energy source o Photoautotrophs and photoheterotrohs  Chemotrohps o Oxidize inorganic or organic substances o Chemoautotrophs and chemoheterotrophs Domain Bacteria – 6 important Examples: 1. Proteobacteria:  Highly diverse gram negative  Purple in colour from type of chlorophyll  Photoautotrophs (purple sulfur) or photoheterotroph (purple non sulfur)  Do no release O 2s a product 2. Green Bacteria:  Highly diverse gram negative  Named for green chlorophyll (not the same as in plants)  Photoautotrophs or photoheterotrophs  Usually found in hot springs  Do not release O2as a product 3. Cyanobacteria:  Gram negative aerobic photosynthetic organism  Carry out photosynthesis using the same pathways and same chlorophyll as eukaryotic algae and plants  Responsible for oxygen based life on earth 9 4. Gram –positive Bacteria:  Primarily chemoheterotrophs  Many pathogenic species o Bacillus anthracis- causes anthrax o Staphylococcus – causes food poisoning, pneumonia, meningitis o Streptococcus- causes strep throat, pneumonia, necrotizing fascititus  Beneficial species: o Lactobacillus- uses lactic acid fermentation to produce pickles, yogurt etc 5. Spirochetes:  Gram negative  Helically spiralled flagella- move in corkscrew pattern  Some harmless (in human mouth)  Some pathogenic (causes syphilis) 6. Chlamydias:  Gram negative  Cell walls with membrane outside  Lack peptidoglycans  Chlamydia trachomatis –common sexually transmitted infection Domain Archaea- Three major Groups: 1. Euryarchaeota:  Methanogens: generate methane, live in low oxygen environments (swamps, large intestine)  Halophiles: “salt loving”: aerobic chemoheterotrophs- energy from sugars, alcohols, amino acids  Extreme Thermophiles: “hot loving”: live in hydrothermal vents, hot springs – can tolerate temperature between 70 C -95 C 2. Crenatchaeota:  Extreme Thermophiles o o  Psychrophiles: “cold Loving” – thrive between -10 C to -20 C  Mesophiles: many plankton in cool marine waters 3. Korarchaeota:  Recognized only by sequence in DNA samples  Nothing known about physiology Prokaryotes have both harmful and beneficial effect on human health: Harmful Effects:  Prokaryotes cause about half of all human diseases  Between 2-3 million people a year dies of tuberculosis caused by the bacillus Mycobacterium tuberculosis 10 BUT, only a small fraction of bacteria are pathogenic  Cause disease by secreting toxins  Exotoxins: leak from or are secreated (are proteins)  Endotoxins: the lipid A portion of LPS (outer membrane of all gram negative bacteria) Characteristics of Bacterial Endotoxins and Exotoxins: Property Endotoxin Exotoxin Chemical nature Lipopolysaccharide Protein Reltionship to cell Part of outer membrane Extracellular, diffusible Denaturing by boiling No Usually Antigenic Yes Yes Potency Relatively low Relatively high Enzymatic Activity No Often Beneficial Health Effect of Prokaryotes on Human Health  Bacteria cover every inch of the human body o Estimated 1 trillion bacteria, or 100,00 per square cm of skin o Trillions more tucked away in your gut, nasal passage, hair and eyelashes  Humans consist of ~10 quadrillion cells but host ~100 quadrillion bacterial cells Human Microbiome Project (HMP)- aims to characterize the microbial communities at different sites in the human body and analyze their role in health and disease Bacteria and Archaea play important roles in biogeochemical cycles:  Biogeochemical cycles- pathway by which a chemical element moves through an ecosystem  Nitrogen: component of proteins and nucleotides o Most organisms cannot use atmospheric nitrogen because they cannot break the strong triple bonds o Some bacteria and archaea can do this because of Nitrogen Fixation +  N2is reduced to ammonia (NH )3then ionized to ammonium (NH ) 4  Only mechanism of replenishing nitrogen source = all organisms rely on nitrogen fixed by bacteria and archaea Lecture 5: Eukaryotic Cells  Two major characteristics distinguish them from prokaryotes 1. Separation of DNA and cytoplasm by nuclear envelope 2. Presence of membrane bound compartments with specialized metabolic and synthetic functions 11  most widely held hypothesis: derived from infolding of the plasma membrane The theory of Endosymbiosis: 1. Morphology: o Bacterium, mitochondrion, chloroplast 2. Reproduction: o A cell cannot synthesize a mitochondrion or a chloroplast o Derived only from pre-existing mitochondrion and chloroplasts o Divide by binary fission 3. Genetic Information: o Contain their own DNA-circular 4. Transcription and Translation: o Contain complete machinery for transcription and translation- ribosomes similar to bacterial ribosomes 5. Electron Transport: o Have electron transport chains (ETCs) similar to prokaryotic cells o Used to generate chemical energy o In prokaryotes, ETC in plasma membrane- swallowed up - inner member 6. Sequence Analysis: o Ribosomal RNA sequencing firmly establishes mitochondria and chloroplasts belong on the bacterial tree of life o Chloroplast RNA most similar to cyanobacteria o Mitochondrial RNA most similar to proteobacteria Endosymbiosis and Horizontal Gene Transfer:  Typical bacterium has ~3000 genes BUT human mitochondrial genome has only 37 What happened to the other genes? 1. Some genes lost  Redundant with nuclear genes 2. Some Genes relocated to nucleus (HGT)  Centralize genetic information  90% of proteins required for mitochondrial and chloroplast function are encoded by genes found in the nucleus Why do both mitochondria and chloroplasts still retain a genome? 1. Gene transfer not yet complete 2. Retained genes encode for protein involved in electron transport chain (ETC)- tight regulation may be difficult if genes are in the nucleus 12 The nucleus:  DNA organized into chromosomes = single DNA molecule + proteins (chromatin)  Nucleolus site of rRNA synthesis  Nuclear envelop is a double membrane  Pore complex regulates entry and exit (RNA, proteins, macromolecules) Surface of the nuclear envelope:  Inner membrane  Outer membrane  Inner pore Ribosome: Protein Factories:  Free ribosomes in cytosol: proteins which function in the cytosol  Ribosomes bound to ER  Protein are destined for: o Insertion in membranes o Packaging in organelles (ex: lysosomes) o Export from the cell (secretion) The Endoplasmic Reticulum:  “little net”  Interconnected network of membranous channels and vesicles called cisternae  Cisternae formed by a single membrane – enclosed space called the ER lumen  Consists of the rough ER and smooth ER The Rough ER:  Ribosomes stud membrane surfaces facing cytoplasm  Proteins enter the lumen where they are chemically modified (ex: glycosylated)  Proteins then delivered to other regions of the cell within small vesicles The Smooth ER:  Synthesizes lipids  Detoxifies drugs and poisons  Stores calcium ions The Glogi Complex:  Proteins enter via vesicles at the cis face and exit via the trans face  Modifies ER products 13  Manufactures certain macromolecules  Sorts and packages for transport Lysosomes:  Membranous sac of hydrolytic enzymes  Digest macromolecules (and lots of other stuff)  Acidic pH Phagocytosis: process in which some types of cells engulf bacteria or other cellular debris to break them down 1. Lobes begin to surround prey 2. Lobes close around prey 3. Prey is enclosed in endocytic vesicle that sinks into cytoplasm Mitochondria:  Site of cellular respiration  ATP-generating reaction occur in the cristae and matrix Lecture 6: Eukaryotic Cells II The cytoskeleton:  Three main types of fibers: o Microtubules o Intermediate filaments o Microfilaments Microtubules:  Tubulin= dimer of alpha tubulin and beta tubulin  Hollow tube; wall consists of 13 columns of tubulin  Functions: o Maintain cell shape o Cell motility o Chromosome movement during cell division o Organelle movement Intermediate Filaments:  Fibrous proteins coiled, then supercoiled into thick cables  Functions: o Maintain cell shape o Anchorage of nucleus and some other organelles 14 o Formation of nuclear lamina Microfilaments:  Two intertwined strands of actin- each a polymer of actin subunits  Functions: o Maintenance of cell shape o Changes in cell shape o Cell motility o Cell division o Muscle contraction Centrioles:  Comprise part of the microtubule organizing center (MTOC)  Involved in microtubule “spindle” organization during cell division  Flagella and cilia arise from centrioles  Made up of 9 sets of three (triplet) molecules Flagella and Cilia:  Motile structure extending from cell surface  Similar in structure except cilia usually shorter and often numerous on cells  Dynein motor proteins slide the microtubules over each other to produce movements  Flagella moves in s-waves : propels a cell through watery medium (ex: sperm cell)  Cilia beat in oarlike stroke: moves fluids over cell surface (Ex: airway epithelial cell) Plant Cell Wall and Plasmodesmata:  Cell walls support and protect  Composed of cellulose fibres, embedded in branched carbohydrate network  Perforated by small channels (plasmodestmata) – all ions and small molecules to move between cells  Some cells of fungi and algal protists have cell walls Chloroplast:  Site of photosynthesis  Molecules in the thylakoid membrane absorb light energy (light reactions)  Enzymes in the stroma use this energy to make carbohydrates Central Vacoule:  Large vesicles- perform specialized functions =organelle  90% of the cell volume may be occupied by one or more central vacuoles 15  Surrounded by a tonoplast (membrane) – contains transport proteins to move material in and out  Storage function: o Salts o Sugars o Pigments o Waste products Animal vs. Plant Cell: Animal Cell Plant Cell Lysosomes Choloroplasts Centrosome (with centrioles) Central vacuole Flagella (present in some plant sperm) Cell wall Plasmodesmata Lecture 7: Cell Membranes Why are membranes important for living organisms?  Separate cell interior from external environment  Enclose organelles inside cells- concentrate molecules  Makes cells and organelles selectively permeable Singer-Nicolson Fluid Mosaic Model (1972):  Plasma membrane composed of a phospholipid bilayer in which relatively disperse membrane protein could freely diffuse  Phospholipid structure: polar hydrophilic head and non-polar hydrophobic tail (1 fatty acid= nd singles bonds, 2 fatty acid = carbon double bond = kink in the chain)  Head: Polar unit, phosphate group, glycerol, Tail: fatty acid chains Frye-Edidin Experiment: Membrane bilayer is fluid  Fused the Human cell and mouse cell (cell fusion)  Membrane protein segregated: human/mouse hybrid cell  Eventually membrane proteins mixed - proves that bilayer is fluid like olive oil Phopholipids self assemble in aqueous environment:  When a phospholipid is added to an aqueous solution, phospholipids self assemble into either a micelle, liposome or a bilayer – depending on the phospholipid concentration  Hydrophobic effect – due to spontaneity o Tendency of polar molecules like water to exclude hydrophobic molecules (fatty acids) 16 Membrane Fluidity is dependent on fatty acid composition and temperature:  All fatty acids initially synthesized as saturated molecules  Desaturases remove two hydrogen atoms from neighbouring carbon atoms – introduce double bond  Saturated hydrocarbon tail = viscous (tightly packed)  Unsaturated hydrocarbon tail = fluid (loosely packed due to double bond kink) Organisms can regulate fatty acid saturation:  Bacteria, archaea, protists, and plants can thrive at temperature at which the plasma membrane would solidify  Able to regulate the proportion of unsaturated fatty acids- desaturase transcript (removes two H to produce a carbon double bond) – every double bond is the result of one desaturase  Decrease growth temperature – increase desaturase mRNA- increase unsaturated fatty acids (organisms can maintain proper membrane fluidity by regulating the amount of unsaturated fatty acid incorporation into their membranes) Sterols influence membrane fluidity:  Acts as membrane buffers o At high temperatures: help restrain movement of lipids , reduce fluidity of membrane o At low temperature: disrupt fatty acid association by occupying space between lipid molecules (slowing the transition of the non-fluid gel state) Plasma membrane proteins: 1. Integral membrane proteins (transmembrane proteins)  Proteins embedded in the phospholipid bilayer  Traverse lipid bilayer  Distinct domains : extracellular, transmembrane (TM), intracellular (cytoplasmic)  TM domain o Stretch of 17-20 non-polar hydrophobic amino acids o Formation of alpha helix 2. Peripheral membrane proteins  Positioned on membrane surface – do not interact with hydrophobic core  Held to membrane by interacting with integral membrane proteins or lipids Functions of membrane proteins: 1. Transport – hydrophilic channel 2. Enzymatic activity – enzymes are membrane proteins 3. Signal transduction – receptor proteins that bind and trigger changes leading to transduction 4. Attachment – proteins exposed to internal/external membrane surfaces act as attachment 17 Transport across the plasma membrane:  Hydrophobic nature restricts free movement of molecules  O2can diffuse, but many others – ions, charged molecules, and macromolecules cannot 1. Passive membrane transport  Simple  Facilitated 2. Active membrane transport  Primary  Secondary  Passive membrane transport:  Movement of a substance across a membrane without expending energy; ATP  Diffusion: net movement of a substance from an area of higher concentration to an area of lower concentration  rate of diffusion depends on concentration gradient o the larger the gradient, the fast the rate of diffusion  Simple Diffusion:  Movement of molecules across a membrane without involvement of a transporter  Rate depends on molecular size and lipid solubility  Practically impermeable to charged molecules (Cl, K, Na)  Osmosis: the diffusion of water across a selectively permeable membrane from a solution of lesser solute concentration to a solution of greater solution concentration  2 M sucrose solution: o In distilled water = expands (hyptonic conditions) o In 10 M Sucrose solution = contracts (hypertonic conditions) o In 2 M sucrose solution = holds shape (isotonic conditions)  Facilitated diffusion:  Diffusion of molecules across a membrane through the aid of a transporter  Carried out by transmembrane proteins  Channel Proteins:  Form hydrophilic pathways in the membrane  Molecules are shielded from hydrophobic core of bilayer  Transport of water and ions –aquaporin and voltage-gated channel Both integral membrane proteins  Aquaporin: o Channel is very narrow- single file movement of water o Channel is highly specific o Does not allow diffusion of ions o Positive charges in centre thought to repel transport of protons o Nobel Prize winning discovery- Peter Agre (2003) 18 +  Voltage-gated channel (K ): o Critical for movement of most ions, Na , K , Ca , Cl 2 o Opening and closing- changes in 3D structure of protein o Nerve conduction and muscle contraction o Normal voltage = gate closed o Voltage change = gate opens  Carrier Proteins: o Binding site exposed to region of higher concentration (passageway through bilayer) o Each carrier proteins binds to a specific molecule and transports it across the membrane o Conformation change in carrier protein- binding site exposed to area of lower concentration o Solute molecule released and carrier protein returns to conformation in step #1 Transport Kinetics:  rate of facilitated diffusion depends on: 1. size of the concentration gradient 2. number of channel/carrier proteins in membrane  Active Membrane Transport: 1. Transport of molecules across a membrane across concentration gradient- requires energy 2. Solute move from are of low concentration to an area of high concentration 3. About 25% of a cells ATP requirement are for active transport  Three main functions: 1. Uptake for essential nutrients 2. Removal of secretory or waste materials 3. Maintenance of intracellular concentration of ions  Two main classes: 1. Primary active transport 2. Secondary active transport  Primary Active transport:  The same protein that transports a substance also hydrolyses ATP to power transport directly  A+L primary active transport pumps move positively charged ions  H pumps: push hydrogen ions from cytoplasm to cell exterior- generate membrane potential, keep lysosomal pH low 2+  Ca pumps: pushes calcium ions from the cytoplasm to the cell exterior and from the cytosol into ER- universally used regulatory mechanism for cellular activities  Na /K pumps: pushes 3 sodium ions out and 2 potassium ions in – creates membrane potential (voltage across a membrane as a result of the difference in charge and unequal distribution of ions)(plasma membrane in animal cells) 19  Secondary Active Transport:  Transport proteins use ion concentration gradient (from primary active transport) to drive transport of a different molecule o Symport: transported solute moves in the same direction as the gradient of the driving ion (cotransport) o Antiport: transported solute moves in the direction opposite to the gradient of the driving ion (exchange diffusion) Exocytosis transport material out of the cell:  Secretory vesicle move through cytoplasm and contact plasma membrane  Vesicle fuses with plasma membrane  Proteins inside vesicle are released to the cell exterior; proteins in vesicle membrane become part of plasma membrane Endocytosis transports material into the cell: 1. Bulk (fluid)-phase endocytosis (pinocytosis)  Solute molecules and water molecules are outside the plasma membrane  Membrane pockets inward, enclosing solute molecules and water molecules  Pocket pinches off as endocytic vesicle 2. Receptor-mediated endocytosis:  Substances attach too membrane receptors  Membrane pockets inward  Pocket pinches off as endocytic vesicle Membrane proteins function in intercellular joining:  Anchoring junction: adjoining cells adhere at a mass of proteins anchored beneath their plasma membrane by many intermediate filaments or microfilaments of the cytoskeleton (“welding”)  Tight junction: form between adjacent cells by fusion of plasma membrane proteins on their outer surface – proteins make a seal tight enough to prevent leaks of ions/ molecules between cells  Gap junction: cylindrical arrays of proteins form direct channels that allow small molecules and ions to flow between the cytoplasm of adjacent cells Membrane proteins respond to environmental stimuli:  Reception: o The binding of a signal molecule with a specific receptor of target cells  Signalling Cascade:
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