Lectures 2&3 BIO131 Summer PDF

Because learning changes everything.® Chapter 4 Lecture Outline See separate PowerPoint slides for all figures and tables pre-inserted into PowerPoint without notes and animations. © 2020 McGraw-Hill Education. All rights reserved. Authorized only for instructor use in the cla...

Because learning changes everything.® Chapter 4 Lecture Outline See separate PowerPoint slides for all figures and tables pre-inserted into PowerPoint without notes and animations. © 2020 McGraw-Hill Education. All rights reserved. Authorized only for instructor use in the classroom. No reproduction or further distribution permitted without the prior written consent of McGraw-Hill Education.  General Features of Cells Key Concepts: Origin of Living Cells on Earth Overview of Cell Structure The Cytosol The Nucleus and Endomembrane System Semiautonomous Organelles Protein Sorting to Organelles Systems Biology of Cells: A Summary © McGraw-Hill Education 2  Origin of life – four overlapping stages Nucleotides and amino acids produced prior to the existence of cells Nucleotides and amino acids became polymerized to form DNA, RNA and proteins Polymers became enclosed in membranes Polymers enclosed in membranes acquired cellular properties © McGraw-Hill Education 3  Stage 1: Origin of organic molecules Conditions on primitive Earth may have been more conducive to spontaneous formation of organic molecules Prebiotic or abiotic synthesis Little free oxygen gas Formed prebiotic soup Several hypotheses on where and how organic molecules originated © McGraw-Hill Education 4  Origin of organic molecules 1 Reducing atmosphere hypothesis Based on geological data Atmosphere rich in water vapor, H2, CH4, NH3 (and little O2) Stanley Miller used a chamber apparatus to simulate this atmosphere and bolts of lightning Formed precursors, amino acids, sugars and nitrogenous bases First attempt to apply scientific experiments to understand origin of life Since 1950s, ideas about early Earth atmosphere changed Still, similar results © McGraw-Hill Education 5 © McGraw-Hill Education 6  Origin of organic molecules 2 Extraterrestrial hypothesis Meteorites brought organic carbon to Earth Includes amino acids and nucleic acid bases Opponents argue that most of this would be destroyed in the intense heating and collision Deep-sea vent hypothesis Biologically important molecules may have been formed in the temperature gradient between extremely hot vent water and cold ocean water Supported by experiments Complex biological communities found here that derive energy from chemicals in the vent (not the sun) © McGraw-Hill Education 7  a) Deep-sea vent hypothesis © McGraw-Hill Education 8  b) A deep-sea vent community © McGraw-Hill Education b: ©CSSF/Neptune Canada 9  Stage 2: Organic polymers Experimentally, prebiotic synthesis of polymers not possible in aqueous solutions Hydrolysis competes with polymerization Experiments have shown formation of nucleic acid polymers and polypeptides on clay surface © McGraw-Hill Education 10  Stage 3: Formation of boundaries Protobiont An aggregate of prebiotically produced molecules and macromolecules Have acquired a boundary, such as a lipid bilayer, that allow it to maintain an internal chemical environment distinct from that of its surroundings © McGraw-Hill Education 11  Formation of boundaries Four characteristics of a protobiont: Boundary separated external environment from internal contents Polymers inside the protobiont contained information Polymers inside the protobiont had catalytic function Protobionts capable of self-replication © McGraw-Hill Education 12  Living cells may have evolved from Coacervates Droplets that form spontaneously from the association of charged polymers Enzymes trapped inside can perform primitive metabolic functions Liposomes Vesicles surrounded by a lipid layer Clay can catalyze formation of liposomes that grow and divide Can enclose RNA © McGraw-Hill Education 13 © McGraw-Hill Education a: Source: A. l. Oparin. From The Origin of Life, New York: Dover, 1952; b: ©Mary Kraft 14  Stage 4: RNA world Majority of scientists favor RNA as the first macromolecule of protobionts Three key RNA functions: Ability to store information Capacity for self-replication Enzymatic function (ribozymes) DNA and proteins cannot do all 3 functions © McGraw-Hill Education 15  Chemical selection A chemical within a mixture has special properties that cause it to increase in number compared to other chemicals in the mixture Hypothetical scenario with two steps: One of the RNA molecules mutates and has enzymatic ability to attach nucleotides together Advantage of faster replication Second mutation produces enzymatic ability to synthesize nucleotides No reliance on prebiotic synthesis © McGraw-Hill Education 16  1a Mutation: A mutation provides an RNA molecule with the 2a Mutation: A second mutation provides an RNA catalytic ability to synthesize new RNA molecules using molecule with the ability to catalyze a step in the pre-existing RNA molecules as templates. synthesis of ribonucleotides. 2b Chemical selection: The second mutation is also favored, so after many generations, the protobionts have 2 catalytic functions— self-replication and ribonucleotide synthesis. 1b Chemical selection: The amount of this mutant RNA with catalytic function increases because it can self-replicate faster. © McGraw-Hill Education 17  Advantages of DNA / RNA / protein world Information storage DNA would have relieved RNA of informational role and allowed RNA to do other functions DNA is less likely to suffer mutations Metabolism and other cellular functions Proteins have a greater catalytic potential and efficiency Proteins can perform other tasks – cytoskeleton, transport, etc. © McGraw-Hill Education 18  Cell theory All living organisms are composed of one or more cells Cells are the smallest units of life New cells come only from pre-existing cells by cell division © McGraw-Hill Education 19  Overview of Cell Structure Two categories of life: Prokaryotes Simple cell structure No nucleus Eukaryotes More complex cells DNA enclosed within membrane-bound nucleus Internal membranes form organelles © McGraw-Hill Education 20  Prokaryotic cells Two categories of prokaryotes: Bacteria Small cells, 1 micrometer to 10 micrometer in diameter Very abundant in environment and our bodies Vast majority are not harmful to humans Some species cause disease Archaea Also small cells, 1 micrometer to 10 micrometer in diameter Less common Often found in extreme environments © McGraw-Hill Education 21  Typical bacterial cell Inside the plasma membrane: Cytoplasm – contained within plasma membrane Nucleoid region – where DNA is located Ribosomes – synthesize proteins Outside the plasma membrane: Cell wall – provides support and protection Glycocalyx – traps water, gives protection, help evade immune system Appendages – pilli (attachment), flagella (movement) © McGraw-Hill Education 22  A Diagram of a typical rod-shaped bacterium A colorized TEM of Escherichia coli © McGraw-Hill Education b: ©Dennis Kunkel Microscopy, Inc./Phototake 23  Eukaryotic cells DNA is housed inside membrane-bound nucleus Compartmentalized functions Organelles Membrane-bound compartments Each has a unique structure and function Variety Shape, size, and organization of cells vary considerably Differences between species Differences between specialized cell types © McGraw-Hill Education 24  Animal cell Access the text alternative for slide images. © McGraw-Hill Education 25  Cell morphology Size and shape of eukaryotic cells show great variation Even cells that share the same genome can have very different morphologies © McGraw-Hill Education a: ©Ed Reschke/Getty Images; b: ©Eye of Science/Science Source 26  Plant cell Access the text alternative for slide images. © McGraw-Hill Education 27  The Proteome Largely Determines the Characteristics of a Cell 1 How does a single organism produce different types of cells? The DNA is identical in each cell of an organism However, the cells have different proteomes © McGraw-Hill Education a: ©Ed Reschke/Getty Images; b: ©Eye of Science/Science Source 28  The Proteome Largely Determines the Characteristics of a Cell 2 The DNA in different cells is identical — but they have different proteomes Structure determines function Protein profile varies based on: Which proteins are expressed Levels of expression Which subtypes of proteins are expressed post-translational modifications Relevant to disease: proteomes of healthy cells are different from those of cancerous cells © McGraw-Hill Education 29  Cell surface area and volume As cells get larger, the surface area-to-volume ratio gets smaller. This affects cell function Radius (micrometer): 1 10 100 Surface area ( micrometer 2 ) 12.6 Approximately 1,260 Approximately 124,600 ( A = 4πr 2 ) : Volume ( micrometer )3 4.2 Approximately 4,200 Approximately 4,200,000 ( V = 4 πr : 3 3 ) Surface area/volume ratio: 3.0 : 1 0.3 : 1 0.03 : 1 © McGraw-Hill Education 30  The Cytosol Region of a eukaryotic cell that is outside the cell organelles but inside the plasma membrane Cytoplasm includes everything inside the plasma membrane Cytosol Endomembrane system Semiautonomous organelles © McGraw-Hill Education 31  Figure 4.13 © McGraw-Hill Education 32  Molecular synthesis and breakdown Sum of all chemical reactions by cells Catabolism Breakdown of a molecule into smaller components Anabolism Synthesis of cellular molecules and macromolecules Cytosol is central coordinating region for metabolic activities of eukaryotic cells © McGraw-Hill Education 33  Cytoskeleton Network of three types of protein filaments Microtubules Long, hollow cylindrical structures Dynamic instability Intermediate filaments Intermediate in size Form twisted, ropelike structure Actin filaments Also known as microfilaments Long, thin fibers © McGraw-Hill Education 34  Motor Proteins Use ATP as a source of energy for movement Three domains— the head, hinge, and tail Walking analogy The ground is the cytoskeletal filament, your leg is the head of the motor protein, and your hip is the hinge Three kinds of movements Motor protein carries cargo along the filament Motor protein remains in place, the filament moves Motor protein and filament both restrained – action of the motor protein exerts a force that bends the filament © McGraw-Hill Education 35  Access the text alternative for slide images. © McGraw-Hill Education 36  Flagella and cilia Flagella Usually longer than cilia Present singly or in pairs 9 + 2 microtubule array Cilia Often shorter than flagella Tend to cover all or part of the cell surface Also a 9 + 2 microtubule array Movement involves the propagation of a bend, beginning at the base and moving toward the tip © McGraw-Hill Education 37 © McGraw-Hill Education b: Courtesy of Dr. Barbara Surek, Culture Collection of Algae at the University of Cologne (CCAC); c: ©SPL/Science Source 38  The Nucleus and Endomembrane System Network of membranes enclosing the nucleus, endoplasmic reticulum, Golgi apparatus, lysosomes, and vacuoles Also includes plasma membrane May be directly connected to each other or pass materials via vesicles © McGraw-Hill Education 39  Figure 4.18 © McGraw-Hill Education 40  Nuclear envelope Double-membrane structure enclosing nucleus Outer membrane of the nuclear envelope is continuous with the ER membrane Nuclear pores provide passageways Materials within the nucleus are not part of the endomembrane system © McGraw-Hill Education 41  Figure 4.19 © McGraw-Hill Education (top right, middle right): ©Don W. Fawcett/Science Source 42  Nucleus Chromosomes Composed of DNA and proteins = chromatin Nuclear matrix Filamentous network Organizes chromosomes Ribosome assembly occurs in the nucleolus © McGraw-Hill Education 43  Endoplasmic reticulum Network of membranes that form flattened, fluid-filled tubules or cisternae ER membrane encloses a single compartment called the ER lumen Rough endoplasmic reticulum (rough ER) Studded with ribosomes Involved in protein synthesis and sorting Smooth endoplasmic reticulum (smooth ER) Lacks ribosomes Detoxification, carbohydrate metabolism, calcium balance, synthesis, and modification of lipids © McGraw-Hill Education 44 © McGraw-Hill Education (right): ©Dennis Kunkel Microscopy, Inc./Phototake 45  Golgi apparatus Also called the Golgi body, Golgi complex, or simply Golgi Stack of flattened, membrane-bounded compartments Vesicles transport materials between stacks Three overlapping functions Secretion, processing, and protein sorting © McGraw-Hill Education 46 © McGraw-Hill Education 47  Secreted Proteins Move Sequentially Through Organelles of the Endomembrane System George Palade used pulse-chase experiments to trace path of radioactive proteins Studied pancreatic cells – primary function is protein secretion Dark spots in TEM images revealed radioactive proteins First evidence that secreted proteins are synthesized into rough ER and move through a series of compartments before secretion © McGraw-Hill Education 48  Figure 4.23 through Step 2 HYPOTHESIS Proteins that are to be secreted follow a particular intracellular pathway. KEY MATERIALS Male guinea pigs. 1. Inject guinea pigs with a radioactive amino acid, éë 3 H ùû – leucine. After 3 minutes, inject them with nonlabeled leucine, which is called a chase. 2. At various times after the second injection, remove samples of pancreatic cells. Access the text alternative for slide images. © McGraw-Hill Education 49  Figure 4.23: Steps 3 to 5 3. Stain the sample with osmium tetroxide, which is a heavy metal that binds to membranes. 4. Cut thin sections of the samples, and place a thin layer of radiation-sensitive emulsion over the sample. Allow time for radioactive emission from radiolabeled proteins to precipitate silver atoms in the emulsion. Wash away unprecipitated silver atoms. 5. Observe the sample under a transmission electron microscope. © McGraw-Hill Education 50  Figure 4.23 Steps 6 to 8 6. THE DATA Schematic drawings of transmission electron micrographs 7. CONCLUSION To be secreted, proteins move from the ER to the Golgi to secretory vesicles and then to the plasma membrane, where they are released to the outside of the cell. 8. SOURCE Caro, L.G., and Palade, G.E. 1964. Protein synthesis, storage, and discharge in the pancreatic exocrine cell. An autoradiographic study. Journal of Cell Biology 20: 473 to 495. © McGraw-Hill Education 51  Lysosomes Contain acid hydrolases that perform hydrolysis Many different types of acid hydrolases to break down proteins, carbohydrates, nucleic acids, and lipids Autophagy Recycling of worn-out organelles through endocytosis © McGraw-Hill Education 52  Vacuoles Functions are extremely varied, and they differ among cell types and environmental conditions Central vacuoles in plants for storage and support Contractile vacuoles in protists for expelling excess water Phagocytic vacuoles in protists and white blood cells for degradation © McGraw-Hill Education 53 © McGraw-Hill Education a: ©Biophoto Associates/Science Source; b: Courtesy of Dr. Peter Luykx, Biology, University of Miami; c: ©Dr. David Patterson/Science Source 54  Peroxisomes Catalyze certain reactions that break down molecules by removing hydrogen or adding oxygen Hydrogen peroxide (H2O2) is a byproduct Catalase breaks down dangerous H2O2 into water and oxygen © McGraw-Hill Education 55  Plasma membrane Boundary between the cell and the extracellular environment. The cell membrane is flexible and allows a unicellular organism to move Functions Membrane transport in and out of cell, with selective permeability Cell signaling using receptors Cell adhesion © McGraw-Hill Education 56  The Fluid Mosaic Model of the cell membrane extracellular fluid (outside) carbohydrate receptor protein glycoprotein phospholipid protein recognition protein binding bilayer site transport cholesterol phospholipid pore protein protein filaments cytosol (inside) © McGraw-Hill Education Membrane components: Lipid bilayer extracellular fluid (watery environment) phospholipid hydrophilic heads hydrophobic tails bilayer hydrophilic heads cytosol (watery environment) © McGraw-Hill Education  Figure 4.26 Cell adhesion: Proteins in the plasma membranes of adjacent cells hold the cells together. Membrane transport: Proteins in the plasma membrane allow the transport of substances into and out of cells. Cell signaling: An extracellular signal binds to a receptor in the plasma membrane that activates a signal transduction pathway, leading to a cellular response. © McGraw-Hill Education 59  Semiautonomous organelles Mitochondria and chloroplasts Grow and divide to reproduce themselves They are not completely autonomous because they depend on the cell for synthesis of internal components © McGraw-Hill Education 60 © McGraw-Hill Education 61  Mitochondria Primary role is to make ATP Outer and inner membrane Intermembrane space and mitochondrial matrix Also involved in the synthesis, modification, and breakdown of several types of cellular molecules © McGraw-Hill Education 62 © McGraw-Hill Education ©Don W. Fawcett/Science Source 63  Chloroplasts Photosynthesis Capture light energy and use some of that energy to synthesize organic molecules such as glucose Found in nearly all species of plants and algae Outer and inner membrane Intermembrane space Thylakoid membrane © McGraw-Hill Education 64 © McGraw-Hill Education ©Dr. Jeremy Burgess/Science Source 65  Chloroplasts and mitochondria Contain their own DNA, divide by binary fission 1. Mitochondrial genome replicates. 2. Mitochondrion begins to divide by binary fission. 3. Binary fission is completed. b) Transmission electron micrograph of the process a) Binary fission of mitochondria © McGraw-Hill Education b: ©Don W. Fawcett/Science Source 66  Endosymbiosis of chloroplast and mitochondrion Modern mitochondria were derived from purple bacteria, also called α - proteobacteria Similarly, chloroplasts were derived from cyanobacteria (a photosynthetic blue- green bacteria) © McGraw-Hill Education 67  Protein sorting Eukaryotic proteins are sorted to the right destination Remain in cytosol Cotranslational sorting Post-translational sorting © McGraw-Hill Education 68  Systems biology of cells Systems Biology – the study of how new properties of life arise from complex interactions of its components “Emergent properties” The cells is viewed in terms of functional connections (not just individual molecules) Eukaryotic cells have dynamic organization The nucleus, cytosol, endomembrane system and semiautonomous organelles work together © McGraw-Hill Education 69  The Venn diagram comparing plant and animal cells. Chloroplast Ribosome Cell wall Mitochondria Animal Cytoplasm Plant Cell Cell Cell membrane Vacuole Nucleus © McGraw-Hill Education  Table 4.2 A Comparison of Cell Complexity Among Bacterial, Animal, and Plant Cells Copyright © McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. Structures Bacteria Animal cells Plant cells Extracellular structures Cell wall* Present Absent Present Flagella/cilia Flagella sometimes present Cilia or flagella present on certain cell Rarely presentϮ types Plasma membrane Present Present Present Interior structures Cytoplasm Usually a single compartment inside Composed of membrane-bound Composed of membrane-bound organelles the plasma membrane organelles that are surrounded by the that are surrounded by the cytosol cytosol Ribosomes Present Present Present Chromosomes Typically one circular chromosome Multiple linear chromosomes in the Multiple linear chromosomes in the nucleus, per nucleoid; a nucleoid is not a nucleus, which is surrounded by a double which is surrounded by a double membrane. membrane-bound compartment. membrane. Mitochondria also have Mitochondria and chloroplasts also have chromosomes. chromosomes. Endomembrane system Absent Present Present Mitochondria Absent Present Present Chloroplasts Absent Absent Present *Note that the biochemical composition of bacterial cell walls is very different from plant cell walls. ϮSome plant species produce sperm cells with flagella, but flowering plants produce sperm within pollen grains that lack flagella. © McGraw-Hill Education 71  Nucleus Endomembrane system Location of most of the genome 1. Nuclear envelope Gene expression and regulation Double membrane that surrounds the nucleus Organization and protection of 2. Endoplasmic reticulum chromosomes via the nuclear matrix Protein secretion and sorting Site for ribosome subunit assembly Glycosylation Lipid synthesis Metabolic functions and accumulation of Ca 2+ 3. Golgi apparatus Protein secretion and sorting Glycosylation 4. Lysosome/vacuoles Degradation of organic molecules Storage of organic molecules Accumulation of water (plant vacuoles) 5. Peroxisomes Breakdown of toxic molecules such as H2O2 Breakdown and synthesis of organic molecules 6. Plasma membrane Uptake and excretion of ions and molecules Cell signaling Cell adhesion Semiautonomous organelles Cytosol 1. Mitochondria Coordination of responses to the Synthesis of ATP environment Synthesis and modification of other Coordination of metabolism organic molecules Synthesis of the proteome Production of heat Organization and movement via 2. Chloroplasts (plants and algae) cytoskeleton and motor proteins Photosynthesis © McGraw-Hill Education 72