Bio Unit 2 - Ch. 4, 5, 18, & 25

Signal Transduction Allows the Cell to Respond to its Environment

- A cascade of events, one following another, occurs after a receptor is activated by a signal - Often, a soluble second messenger conveys signaling information from the primary messenger (ligand) at the membrane to downstream signaling molecules in the cytoplasm. Cyclic AMP (cAMP) is an important second messenger - Activated enzymes may in turn activate other enzyme in a signal transduction pathway, leading to impressive amplification of a signal - Protein kinases covalently add phosphate groups to target proteins, cAMP binds target proteins noncovalently. Both kinds of binding change the target protein's conformation to expose or hide its active site - Signal transduction can be regulated in several ways. The balance between the activation and inactivation of the molecules involved determines the ultimate cellular response to a signal - The cellular responses to signals may include the opening of ion channels, changes in gene expression, or the alteration of enzyme activities

Active Transport Moves Solutes against Their Concentration Gradients

- Active transport requires the use of chemical energy to move substances across membranes against their concentration gradients. The sodium-potassium (Na+-K+) pump uses energy released from the hydrolysis of ATP - Primary and secondary

Biological Membranes Have a Common Structure and Are Fluid

- Biological membranes that consist of lipids, proteins, and carbohydrates. The fluid mosaic model of membrane structure describes a phospholipid bilayer in which proteins can move about within the plane of the membrane - The two layers of a membrane may have different properties because of their different phospholipid compositions, exposed domains of integral membrane proteins, and peripheral membrane proteins. Transmembrane proteins span the membrane - Cell membrane also has carbs - glycolipid, glycoprotein, proteoglycan

Cells Provide Compartments for Biochemical Reactions

- Cell theory states that the cell is the fundamental unit of biological structure and function - Cells are small because a cell's surface area must be large compared with its volume to accommodate exchanges between the cell and its environment (volume determines the amt of metabolic activity cell carries out per unit of time AND surface area of a cell determines the amount of substances that can enter from outside and waste exit) - All cells are enclosed by a selectively permeable cell membrane that separates their contents from the external environment

The Membrane Plays a Key Role in a Cell's Response to Encironmental Signals

- Cells receive many signals from the physical environment and from other cells. Chemical signals are often at very low concentrations - A signal transduction pathway involves the interaction of a signal (often a chemical ligand) with a receptor; the transduction and amplification of the signal via a series of steps within the cell; and a cellular response. The response may be short term or long term; autocrine, paracrine, and juxtacrine - Cells respond to signals only if they have specific receptor proteins that can be activated by those signals. Many receptors are located at the cell membrane. They include ion channels, protein kinases, and G protein - linked receptors

Changes in Earth's Physical Environment Have Affected the Evolution of Life

- Earth's crust consists of solid plates that float on fluid magna. Continental drift is caused by convection currents in the magma, which move the plates and the continents that lie on top of them - Major physical events, such as continental collisions and volcanic eruptions, have affected Earth's climate, atmosphere, and sea levels. In addition, extraterrestrial events such as meteorite strikes have created sudden and dramatic environmental shifts. All of these changes affected the history of life - Oxygen generating cyanobacteria liberated enough O2 to open the door to oxidation reactions in metabolic pathways. Aerobic prokaryotes were able to harvest more energy than anaerobic organisms and began to proliferate. Increases in atmospheric O2 concentrations supported the evolution of large eukaryotic cells and, eventually, multicellular organisms

Large Molecules Cross Membranes via Vesicles

- Endocytosis is the transport of molecules, large particles, and small cells into eukaryotic cells via the invagination of the cell membrane and the formation of vesicles; phago and pino cytosis - In receptor endocytosis, a specific receptor on the cell membrane binds to a particular macromolecules that is to be transported into the cell - In exocytosis, materials in vesicles are secreted from the cell when the vesicles fuse with the cell membrane

Eukaryotic Calles Have a Nucleus and Other Membrane Bound Compartments

- Eukaryotic cells contain many membrane enclosed organelles that compartmentalize their biochemical functions - The nucleus contains most of the cell's DNA - The endomembrane system - consisting of the nuclear envelope, endoplasmic reticulum, Golgi apparatus, and lysosomes - is a series of interrelated compartments enclosed by membranes. Lysosomes contain many digestive enzymes. - Mitochondria and chloroplasts are semiautonomous organelles that process energy. - A vacuole is prominent in many plant cells. It is a membrane - enclosed compartment full of water and dissolved substances.

Passive Transport across Membranes Requires NO Input of Energy

- Membranes exhibit selective permeability that regulates which substances can pass through them - A substance can diffuse passively across a membrane by one of two processes: simple diffusion through the phospholipid bilayer or facilitated diffusion, either through a channel created by a channel protein or by means of a carrier protein. In both cases, molecules diffuse down their concentration gradients - In osmosis, water diffuses from a region of higher water concentration to a region of lower water concentration, largely through membrane channels called aquaporins. Ions diffuse across membranes through ion channels - Carrier proteins bind to polar molecules such as sugars and amino acids and transport them across the membrane

Major Events in the Evolution of Life Can be Read in the Fossil Record

- Paleontologists use fossils and evidence of geological changes to determine what Earth and its biota may have looked like at different times - Before the Phanerozoic, life was almost completely confined to the oceans. Multicellular life diversified extensively during the Cambrian explosion, a prime example of an evolutionary radiation - The periods of the Paleozoic era were each characterized by the diversification of specific groups of organisms. During the Mesozoic era, distinct terrestrial biotas evolved on each continent - Five episodes of mass extinction punctuated the history of life in the Paleozoic and Mesozoic eras - The Cenozoic era is divided into the Tertiary and Quaternary periods, which in turn are subdivides into epochs. This era saw the emergence of the modern biotas as mammals radiated extensively and flowering plants became dominant - The tree of life can be used to reconstruct the timing of evolutionary events

Plants Acquire Mineral Nutrients from the Soil

- Plants are photosynthetic autotrophs that require water and certain mineral nutrients to survive. They obtain most of these mineral nutrients as ions from the soil solution. - The essential elements for plants include six macronutrients and several micronutrients. Plants that lack a particular nutrient show characteristic deficiency symptoms. - The essential elements were discovered by growing plants hydroponically in solutions that lacked individual elements - Soils supply plants with mechanical support, water and dissolved ions, air, and the services of other organisms - Protons take the place of mineral nutrient cations bound to clay particles in soil in a process called ion exchange - Farmers may use shifting agriculture or fertilizer to make up for nutrient deficiencies in soil

Prokaryotic Cells Do Not Have a Nucleus

- Prokaryotic cells usually have no internal compartments, but have a nucleoid containing DNA, and a cytoplasm containing cytosol, ribosomes (the sites of protein synthesis), proteins, and small molecules. Many have an extracellular cell wall. - Some prokaryotes have folded membranes, for example photosynthetic membranes, and some have flagella for motility

Soil Organisms Contribute to Plant Nutrition

- Signaling molecules called strigolactones induce the hyphae of arbuscular mycorrhizal fungi to invade root cortical cells and form arbuscules, which serve as sites of nutrient exchange between fungus and plant - Legumes signal nitrogen fixing bacteria (rhizobia) to form bacteroids within nodules that form on their roots - In nitrogen fixation, nitrogen gas is reduced to ammonia in a reaction catalyzed by nitrogenase - Carnivorous plants supplement their nutrient supplies by trapping and digesting arthropods. Parasitic plants obtain minerals, water, or products of photosynthesis from other plants

The Cytoskeleton Provides Strength and Movement

- The microfilaments, intermediate filaments, and microtubules of the cytoskeleton provide the cell with shape, strength, and movement - Microfilaments and microtubules have dynamic instability and can grow or shrink in length rapidly - Cilia and flagella are microtubule lined extensions of the cell membrane that produce movements of cells or their surrounding fluid medium - Motor proteins move cellular components, such as vesicles, around the cell by walking them along the microtubules - Biologists establish cause and effect relationships by manipulating biological systems

Extracellular Structures Provide Support and Protection for Cells and Tissues

- The plant cell wall consists principally of cellulose. Cell walls are pierced by plasmodesmata that join the cytoplasms of adjacent cells - In animals, the extracellular matrix consists of different kinds of proteins, including collagen and proteoglycans. Integrins connect the cell cytoplasm with the extracellular matrix - Specialized cell junctions connect cells in animal tissues. These include tight junctions, desmosomes, and gap junctions. Gap junctions are involved in intercellular communications

Events in Earth's History Can Be Dated

- The relative ages of organisms can be determines by the dating of fossils and the strata of sedimentary rocks in which they are found - Radiometric dating techniques use variety of radioisotopes with different half-lives to date events in the remote past - Georgists divide the history of life into eons, eras, and periods based on major different in the fossil assemblages found in successive strata

Solutes are Transported in the Phloem by Pressure Flow

- Translocation is the movement of the products of photosynthesis, as well as some other small molecules, through sieve tubes in the phloem. The solutes move from source to sinks - Translocation is explained by the pressure flow model: the difference in solute potential between sources and sinks creates a difference in pressure potential that pushes phloem sap along the sieve tubes

Water and Solutes Are Transported in the Xylem by Transpiration - Cohesion - Tension

- Water moves through biological membranes by osmosis, always moving toward regions with a more negative water potential. The water potential of a cell or solution is the sum of its solute potential and its pressure potential - The physical structure of many plants is maintained by the positive pressure potential of their cells (turgor pressure); if the pressure potential drops, the plant wilts - Water moves into root cells by osmosis through aquaporins. Mineral ions move into root cells through ion channels, by facilitated diffusion, and by secondary active transport - Water and ions may pass from the soil into the root by way of the apoplast or the symplast, but they must pass through the symplast to cross the endodermis and enter the xylem. The Casparian strip in the endodermis blocks further movement of water and ions through the apoplast - Water is transported in the xylem by the transpiration - cohesion - tension mechanism. Evaporation from the leaf produces tension in the mesophyll, which pulls a column of water held together by cohesion up through the xylem from the root - Stomata allow a balance between water retention and CO2 uptake. Their opening and closing is regulated by guard cells

All biological systems from cells and organisms to populations, communities and ecosystems are affected by complex biotic and abiotic interactions involving exchange of matter and free energy.

A cell is a living unit greater than the sum of its parts.

Extracellular Components

Cell Wall Extracellular structure that distinguishes plant cells from animal cells Also found in prokaryotes, fungi, and some protists (similar function, different structure) ECM Surrounds animal cells Composed of proteins and polysaccharides Secreted locally and assembled into an organized meshwork in close association with the surface of the cell that produced them. Functions of the ECM: Mechanical support - between cells in a tissue Cell signaling - within tissues Wound healing - pathway for cellular migration Regulation of cell activities Embryonic development Intercellular Junctions Types of intercellular junctions - Allows cells in tissues, organs, or organ systems to adhere, interact, and communicate through direct physical contact Plasmodesmata in Plant Cells Channels that perforate plant cell walls Allow water and small solutes (and sometimes proteins and RNA) to pass from cell to cell Tight Junctions, Desmosomes, and Gap Junctions in Animal Cells Tight junctions, membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid Desmosomes (anchoring junctions) fasten cells to underlying connective tissue into strong sheets Gap junctions (communicating junctions) provide cytoplasmic channels between adjacent cells

Regulating Transpiration

Consequence of photosynthesis (?) Stomata allow gas exchange, transpiration Stomata regulation Result of turgor, osmotic balance, active transport Guard cell structure Potassium & water balance

Structural Network

Cytoskeleton Network of fibers extending throughout the cytoplasm Organizes the cell's structures and activities, anchoring many organelles Composed of three types of molecular structures: Microtubules - hollow tubes with walls that consist of 13 columns of tubulin molecules; maintenance of cell shape, motility, chromosome movements in division, organelle movements Microfilaments - two intertwined strands of actin; maintenance of cell shape, changes in cell shape, muscle contraction, cytoplasmic streaming, cell motility, division Intermediate filaments - fibrous proteins supercoiled into thicker cables; maintain cell shape, anchor nucleus and other organelles, formation of nuclear lamina Centrosomes and Centrioles Centrosome - "microtubule-organizing center" Animal cells - centrosome has a pair of centrioles Cilia and Flagella Locomotion appendages of some cell types Differ in number, size, & beating patterns Dynein proteins move flagella and cilia:

Organisms must exchange matter with the environment to grow, reproduce and maintain organization.

Essential knowledge 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization. b. Surface area-to-volume ratios affect a biological system's ability to obtain necessary resources or eliminate waste products. Evidence of student learning is a demonstrated understanding of each of the following: 1. As cells increase in volume, the relative surface area decreases and demand for material resources increases; more cellular structures are necessary to adequately exchange materials and energy with the environment. These limitations restrict cell size. To foster student understanding of this concept, instructors can choose an example such as: • Root hairs • Cells of the alveoli • Cells of the villi • Microvilli 2. The surface area of the plasma membrane must be large enough to adequately exchange materials; smaller cells have a more favorable surface area-to-volume ratio for exchange of materials with the environment. Exchange OF Matter - Gas exchange, metabolism, plasma membrane osmosis endo/exocytosis and diffusion - affecting factors are surface area, enzymes, gradient

Membrane Potential

Facilitates movement of positively charged ions into cells. Ion movement is "passive" but is a consequence of the active movement of H+ through the proton pump that maintains the membrane potential. Proton pump actively moves many minerals into cells in quantities higher than what is found in the environment. Contratransport Negative ion movement is coupled to H+ flow along the H+ gradient. Negative charges are attracted to the H+ and can be moved against their gradient Also used to move neutral solutes such as sucrose against a gradient

Osmosis & Water Potential

In cells, water moves from areas of low solute concentration to areas of high solute concentration during osmosis. In plants, bacteria, and fungi, however, the cell wall exerts a force on the internal environment of the cell and affects the net flow of water through the cell membrane. The effects of solute concentration and the pressure provided by the cell wall are incorporated into a quantity called water potential (ψ ). Osmosis moves water from areas of high water potential to areas of low water potential.

Studying Cells

Microscopes - visualize cell structure Cell culture - cell function Cell Fractionation and centrifugation The following videos explain cell fractionation and centrifugation Cell fractionation (requires Adobe Flash) Subcellular Fractionation The cell fractionation example you watched in the animation was specific to prokaryotic cells, but the same procedure may be applied to eukaryotic cells. Because of the size difference and increased intricacy of the cells, usually cell fractionation of eukaryotic cells requires additional rounds of centrifugation or additional analysis of the supernatant. Prokaryotic Cells - Plasma membrane, ribosomes, 1-10 um Eukaryotic Cells - Plasma membrane, cytosol with organelles, ribosomes, nucleus, internal membranes, 10-100 um

Mitochondria and Chloroplasts

Mitochondria and chloroplasts CONVERT energy from one form to another Not part of the endomembrane system Have a double membrane Have proteins made by free ribosomes Contain their own DNA Mitochondria Have a smooth outer membrane and an inner membrane folded into cristae The inner membrane creates two compartments: intermembrane space and mitochondrial matrix Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix Cristae present a large surface area for enzymes that synthesize ATP Plastids Chloroplasts contain pigments (chlorophyll and others) & enzymes plus other molecules that function in photosynthesis found in leaves and other green organs of plants and in algae Two compartment types: -Thylakoids, membranous sacs, stacked to form a granum -Stroma, the internal fluid Chromoplasts store pigments, basis for color in leaves, flowers, fruit Leucoplasts store starch (location?)

Origin of Matter

Nuclear fusion reactions in stars When stars exploded atoms were blown into interstellar space forming molecules Dust particles gathered into enormous clouds that have been visualized by the Hubble Telescope in extraordinary detail. Where does matter come from?All atoms heavier that hydrogen and helium, including the elements important in living systems (carbon, oxygen, nitrogen, phosphorus and sulfur) are produced are produced in stars by nuclear fusion reactions. The atoms are then blown out into interstellar space toward the end of a star's lifetime when the star explodes as a nova or, more rarely, a supernova. The atoms then form molecules and dust particles and gather into the enormous clouds that have been visualized by the Hubble Telescope in extraordinary detail. The dust particles, composed largely of silicate minerals, are called interstellar grains. The grains are coated thin layers of ice and frozen gases like carbon dioxide, carbon monoxide, ammonia and methanol, as well as a variety of more complex organic compounds. The last point is among the most significant new discoveries about the interstellar medium. That is, organic compounds composed of carbon and the other biogenic elements are not limited to the Earth and its neighboring planets in our solar system, but are present wherever stardust gathers into interstellar clouds. We live in an organic universe. No new elements have been created since Earth formed. This means that all the atoms in you and your world, other than hydrogen and helium, were once inside a star, long ago.

Cell Membranes

One universal feature of all cells is an outer limiting membrane called the plasma membrane. In addition, all eukaryotic cells contain elaborate systems of internal membranes which set up various membrane-enclosed compartments within the cell. Selectively Permeable Cell membranes are selectively permeable due to their structure. a. Cell membranes separate the internal environment of the cell from the external environment. b. Selective permeability is a direct consequence of membrane structure, as described by the fluid mosaic model. 1. Cell membranes consist of a structural framework of phospholipid molecules, embedded proteins, cholesterol, glycoproteins and glycolipids. 2. Phospholipids give the membrane both hydrophilic and hydrophobic properties. The hydrophilic phosphate portions of the phospholipids are oriented toward the aqueous external or internal environments, while the hydrophobic fatty acid portions face each other within the interior of the membrane itself. 3. Embedded proteins can be hydrophilic, with charged and polar side groups, or hydrophobic, with nonpolar side groups. 4. Small, uncharged polar molecules and small nonpolar molecules, such as N2, freely pass across the membrane. Hydrophilic substances such as large polar molecules and ions move across the membrane through embedded channel and transport proteins. Water moves across membranes and through channel proteins called aquaporins. c. Cell walls provide a structural boundary, as well as a permeability barrier for some substances to the internal environments. 1. Plant cell walls are made of cellulose and are external to the cell membrane. 2. Other examples are cells walls of prokaryotes and fungi.

Getting Through Cell Membrane

Passive Transport Simple diffusion diffusion of nonpolar, hydrophobic molecules lipids high → low concentration gradient Facilitated transport diffusion of polar, hydrophilic molecules through a protein channel high → low concentration gradient Active transport diffusion against concentration gradient low → high uses a protein pump requires ATP Variation in molecular units provides cells with a wider range of functions. Large Molecules Moving large molecules into & out of cell through vesicles & vacuoles endocytosis phagocytosis = "cellular eating" pinocytosis = "cellular drinking" exocytosis Endocytosis Phagocytosis - fuse with lysosome for digestion Pinocytosis - non-specific process Receptor-Mediated Endocytosis - triggered by molecule signal Exocytosis

Fluid Mosaic

Phospholipids Fatty acid tails Phosphate group Arrangement-bilayer Membrane Lipids Composition of lipids varies Affects flexibility Membrane must be fluid & flexible about as fluid/viscous as thick salad oil % unsaturated fatty acids in phospholipids keep membrane less viscous cold-adapted organisms, like winter wheat increase % in autumn Cholesterol in membrane Membrane Proteins Proteins determine membrane's specific functions Membrane proteins: peripheral proteins - loosely bound to surface of membrane -cell surface identity marker (antigens) integral proteins - penetrate lipid bilayer, usually across whole membrane transmembrane protein - transport proteins - channels, permeases (pumps) Proteins Domains Anchor Molecule Within membrane Nonpolar/hydrophobic amino acids anchors protein into membrane On outer surfaces of membrane Polar/hydrophilic amino acids extend into extracellular fluid & into cytosol Signal transduction - transmitting a signal from outside the cell to the cell nucleus, like receiving a hormone which triggers a receptor on the inside of the cell that then signals to the nucleus that a protein must be made. Membrane Carbohydrates Play a key role in cell-cell recognition ability of a cell to distinguish one cell from another important in organ & tissue development basis for rejection of foreign cells by immune system The four human blood groups (A, B, AB, and O) differ in the external carbohydrates on red blood cells. MEMBRANE IS A COLLAGE OF PROTEINS & OTHER MOLECULES EMBEDDED IN THE FLUID MATRIX OF THE LIPID BILAYER. The carbohydrates are not inserted into the membrane -- they are too hydrophilic for that. They are attached to embedded proteins -- glycoproteins..

Transpiration & Water Transport in Plants resource acquisition

Photosynthesis requires an input of light, carbon dioxide and water. In primitive plants, such as mosses and liverworts, as well as photosynthetic protists and prokaryotes, these nutrients can be obtained via simple diffusion. As the complexity of plants increased evolution has favored specific structures and processes to better absorb these nutrients from the environment. These more complex plants possess roots for absorbing water, vascular systems for transporting water, and leaves for absorbing photons and carbon dioxide. The earliest plants were aquatic, and either filamentous or laminar (sheetlike), so that most cells came into contact with their environmental medium. Water and needed nutrients were readily available to individual cells. The move to land and differentiation of the plant body into tissues and organs with different functions, required systems to transport needed materials to cells in different parts of the plant from the region where they were obtained. Vascular tissue is the tissue that transports water and nutrients throughout the plant.

Water loss & plant cells

Plants are 80-90% water (wet weight). Soil and atmosphere usually contain a much lower proportion of water Most plants present large surface areas to their surroundings (?) Adaptations Stomata - Vacuoles (turgor) Cuticle - dead cells & tissues

Oparin-Haldane Theory

Primitive atmosphere Source of carbon for life Site of prebiotic evolution Mechanism Oparin Reducing, composed of methane, ammonia, hydrogen and water vapor Methane Atmosphere, then oceans Spontaneous appearance of coacervates followed by evolution to cell-like state Haldane Reducing, composed of carbon dioxide, ammonia and water vapor Carbon dioxide Atmosphere, then oceans Synthesis of increasingly complex organic molecules in presence of ultraviolet light

The Cell Membrane & Cell Transport Movement across the Cell Membrane -Growth and dynamic homeostasis are maintained by the constant movement of molecules across membranes.

Process of diffusion Diffusion - 2nd Law of Thermodynamics governs biological systems - universe tends towards disorder (entropy) - Move from HIGH to LOW concentration "passive transport" no energy needed Diffusion across cell membrane - Cell membrane is the boundary between inside & outside...separates cell from its environment IN: food, carbohydrates, sugars, proteins, amino acids, lipids, salts, O2, H2O OUT: waste, ammonia, salts,CO2, H2O, products Diffusion through phospholipid bilayer: Lipids & other nonpolar molecules get through directly. Can't get through = polar molecules, H2O, ions, salts, ammonia, large molecules, starches, proteins Channels through cell membrane Membrane becomes semi-permeable with protein channels specific channels allow specific material across cell membrane Things that determine rate of diffusion: The steepness of the concentration gradient. The bigger the difference between the two sides of the membrane the quicker the rate of diffusion. Temperature. Higher temperatures give molecules or ions more kinetic energy. Molecules move around faster, so diffusion is faster. The surface area. The greater the surface area the faster the diffusion can take place. This is because the more molecules or ions can cross the membrane at any one moment. The type of molecule or ion diffusing. Large molecules need more energy to get them to move so they tend to diffuse more slowly. Non-polar molecules diffuse more easily than polar molecules because they are soluble in the non polar phospholipid tails. Facilitated Diffusion: Diffusion through protein channels channels move specific molecules across cell membrane no energy needed Each transport protein is specific as to the substances that it will translocate (move). For example, the glucose transport protein in the liver will carry glucose from the blood to the cytoplasm, but not fructose, its structural isomer. Some transport proteins have a hydrophilic channel that certain molecules or ions can use as a tunnel through the membrane -- simply provide corridors allowing a specific molecule or ion to cross the membrane. These channel proteins allow fast transport. For example, water channel proteins, aquaporins, facilitate massive amounts of diffusion. Active Transport Cells may need to move molecules against concentration gradient Protein changes shape to transport solutes from one side of membrane to other protein "pump" "costs" energy = ATP Some transport proteins do not provide channels but appear to actually translocate the solute-binding site and solute across the membrane as the protein changes shape. These shape changes could be triggered by the binding and release of the transported molecule. This is model for active transport.

Endomembrane System

Regulates protein traffic and performs metabolic functions in the cell. These components are either continuous or connected via transfer by vesicles. The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells. The ER membrane is continuous with the nuclear envelope. The Golgi consists of flattened membranous sacs called cisternae Lysosomes contain hydrolytic enzymes that can digest macromolecules, cellular components, other cells. Perform autophagy. Vacuoles - food vacuoles, contractile vacuoles, central vacuoles Cooperative interactions within organisms promote efficiency in the use of energy and matter.

Solute Potential

Solute potential is dependent upon type and concentration of solute. Its value can be determined using the following equation: ψs = -iCRT i =# of particles/ions in one molecule of solute after dissociation C = molar concentration (M) R = pressure constant (0.0831 L bar/mol K or 0.0083 L MPa/mol K) T = temperature (K)

Deep-Sea Hydrothermal Vents

Some deep-sea hydrothermal vents discharge copious amounts of hydrogen, hydrogen sulfide, and carbon dioxide at temperatures around 100°C. (These are not "black smokers".) These gases bubble up through chambers rich in iron sulfides (FeS, FeS2). These can catalyze the formation of simple organic molecules like acetate. (And life today depends on enzymes that have Fe and S atoms in their active sites.) Discovery of vents Deep-sea vents are a better location for the origins of life. Deep under the ocean's surface, these rocky chimneys spew out superheated water and hydrogen-rich gases. Their rocky structures contain a labyrinth of small compartments that could have concentrated life's building blocks into dense crowds, and minerals that would have catalyzed their get-togethers. Far away from visions of languid soups, these churning environments are the current best guess for the site of life's hatchery.

Miller - Urey

Stanley Miller, a graduate student in biochemistry, built the apparatus shown here. He filled it with water (H2O), methane (CH4) , ammonia (NH3) and hydrogen (H2) but no oxygen He hypothesized that this mixture resembled the atmosphere of the early earth. (Some are not so sure.) The mixture was kept circulating by continuously boiling and then condensing the water. The gases passed through a chamber containing two electrodes with a spark passing between them. At the end of a week, Miller used paper chromatography to show that the flask now contained several amino acids as well as some other organic molecules. In the years since Miller's work, many variants of his procedure have been tried. Virtually all the small molecules that are associated with life have been formed: 17 of the 20 amino acids used in protein synthesis, and all the purines and pyrimidines used in nucleic acid synthesis. But abiotic synthesis of ribose — and thus of nucleotides — has been much more difficult. However, success in synthesizing pyrimidine ribonucleotides under conditions that might have existed in the early earth was reported in the 14 May 2009 issue of Nature. One difficulty with the primeval soup theory is that it is now thought that the atmosphere of the early earth was not rich in methane and ammonia — essential ingredients in Miller's experiments.

Basis of Biological Function: A Tour of a Cell 2 Types of Cells

The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells Protists, fungi, animals, and plants (Domain Eukarya) all consist of eukaryotic cells Eukaryotic cells maintain internal membranes that partition the cell into specialized regions. These internal membranes compartmentalize their functions. a. Internal membranes facilitate cellular processes by minimizing competing interactions and by increasing surface area where reactions can occur. b. Membranes and membrane-bound organelles in eukaryotic cells localize (compartmentalize) intracellular metabolic processes and specific enzymatic reactions. [See also 4.A.2] To foster student understanding of this concept, instructors can choose an illustrative example, such as: • ER, Mitochondria, Chloroplasts, Golgi, Nuclear envelope

Nucleus and Ribosomes

The eukaryotic cell's genetic instructions are housed in the nucleus and carried out by the ribosomes The nucleus contains most of the DNA in a eukaryotic cell Ribosomes use the information from the DNA to make proteins Consists of ribosomal RNA and Protein Bound Ribosomes (ER, Nuclear Envelope) Free Ribosomes

Emergence of Organic Molecules

There are several hypotheses about the natural origin of life on Earth, each with supporting scientific evidence. Scientific evidence from many different disciplines supports models of the origin of life. Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.

How Water Moves

Transpiration-Tension-Cohesion Theory Water lost through transpiration creates negative water potential in mesophyll cells Negative water potential exerts a "pull" on water in xylem creating strong tension Cohesive property of water creates column of water that is literally pulled up through the xylem of the plant. Adhesion, cohesion, & transpiration create force strong enough to move water against forces of gravity

Osmosis is diffusion of water

Water is very important to life, so we talk about water separately Diffusion of water from high concentration of water to low concentration of water across a semi-permeable membrane Concentration of Water Direction of osmosis is determined by comparing total solute concentrations Hypertonic - more solute, less water Hypotonic - less solute, more water Isotonic - equal solute, equal water Hypotonic to hypertonic Managing Water Balance Cell survival depends on balancing water uptake & loss Isotonic animal cell immersed in mild salt solution example: blood cells in blood plasma problem: none no net movement of water flows across membrane equally, in both directions volume of cell is stable Hypotonic a cell in fresh water example: Paramecium problem: gains water, swells & can burst water continually enters Paramecium cell solution: contractile vacuole pumps water out of cell ATP plant cells turgid Hypertonic a cell in salt water example: shellfish problem: lose water & die solution: take up water or pump out salt plant cells plasmolysis = wilt Water Regulation - Unicellular - Contractile vacuole in Paramecium Water Regulation - Multicellular - Osmoregulation Water balance systems are based on three processes: Diffusion Osmosis Active transport Osmoregulation processes often tied to excretion Multicellular organisms use transport tissues or organ systems to control water loss and excretion

Water Potential and Water Movement in Plants

Water moves from a greater to a lesser water potential (ψ) - process? Relative water potential in plants - as move from soil, to roots to stem to leaves water potential becomes more and more negative When the water potential inside the cell is higher than the environment, water will leave cells and plasmolysis results. Mechanisms of Movement Root pressure Capillarity Adhesion/cohesion

Water Potiential

Water potential is calculated using the following equation: ψw = ψp + ψs Water Potential = Pressure Potential + Solute Potential Water potential is measured in megapascals (MPa) or bar. 1 MPa = 10 bar Note: Animal cells do not have cell walls so pressure potential = zero

Origin of Oceans

Where did the water come from? Two sources (hypotheses): condensation following the outgassing of water vapor from the surface of the planet delivered by impacting comets. Isotope commonly found in comets, deuterium, not found in Earth's oceans - impact on comet source hypothesis? Study carried out by scientists at the California Institute of Technology, the results of which were published in March 1999, suggests that most of Earth's water probably did not have a cometary origin. Using Caltech's Owens Valley Radio Observatory (OVRO) Millimeter Array, cosmochemist Geoff Blake and his team found that Comet Hale-Bopp contains substantial amounts of heavy water, which is rich in the hydrogen isotope deuterium. If Hale-Bopp is typical in this respect and if cometary collisions were a major source of terrestrial oceans, it suggests that Earth's ocean water should be similarly rich in deuterium, whereas in fact it is not

Universal Ancestor

an ancestor that was universal to all living (extant) life an organism that possessed all of the basic molecular characteristics shared by all extant organisms DNA-based genotype Three-nucleotide codons using the code still employed today A lipid-based separator between cytoplasm and the extracellular environment RNA-based ribosomes, mRNA, tRNA, etc. Protein-based phenotype Universal Tree Phylogeny of all cellular life based on sequence comparisons of rRNA Divides cellular life into three types Bacteria (Eubacteria) Archaea (Archaeobacteria) Eucarya (Eukaryotes) Three types of life each holds similar degrees of genetic variation By far and away the majority of genetic variation found among extant organisms is found among the unicellular organisms (protists and prokaryotes) Each cellular form of life is called a domain Domain Bacteria Domain Archaea Domain Eukarya 1-10 µm 1-10 µm 10-100 µm Cell wall of peptidoglycan Cell wall various Cell wall of cellulose or chitin No introns in chromosomes Some introns present Introns present Membranes based on fatty acids Membranes based on isoprenes Membranes based on fatty acids No membrane-bounded organelles Membrane-bounded organelles Membrane-bounded organelles 4-subunit RNA polymerase Many-subunit RNA polymerase Many-subunit RNA polymerase

Four Conditions Required forChemical Evolution

Absence of Oxygen in the atmosphere - O2 would have broken down any large organic molecules by accepting electrons. High energy input - at that point in time, the sun was producing massive amounts of ultraviolet radiation Micromolecules- the inorganic molecules had to be in the atmosphere and primitive oceans Time - adequate time had to pass to give the molecules a chance to form, react, and reform.

To account for the origin of life on our earth several problems must be solved:

Creation of the organic molecules that define life, e.g. amino acids, nucleotides (abiogenesis/chemical evolution); Assembly of these into macromolecules, e.g. proteins and nucleic acids, — a process requiring catalysts; Self-replication of these macromolecules; How these were assembled into a system delimited from its surroundings (i.e., a cell).

Logic of the Origin of Life (synopsis & supplemental discussion)

Large volumes Lots of experiments (quantitatively speaking) Diverse environments Lots of experiments (qualitatively speaking) Lots of time As much as 100s of millions of years (lots of experiments) Potential for experiments to build upon each other Reducing atmosphere Modern O2 levels not present (not even close) O2 makes organic molecules unstable Organic molecules Presence inferred (e.g., meteorites and comets indicated organic molecules in space) Presence can be addressed experimentally (the Miller-Urey experiment) Energy Volcanoes (and other geothermal phenomena such as deep-sea vents) Lightning Energy in space brought to earth as chemicals in meteors Sun (UV, IR, and visual spectrums) Logic of self-replication & natural selection Chemicals that are stable and can duplicate themselves naturally increase in abundance Someday we will even know/understand the plausible chemistry No competition Unlike today, there was no competition from super-sophisticated modern organisms (e.g., bacteria)

The Beginning

Many scientists have provided evidence of an event called the "Big Bang". This theory states . . . . . The early universe was almost completely composed of hydrogen (H2) and helium (He). None of the heavier elements (above helium) existed at the dawn of the universe. What is the origin of all the other elements? Of matter? Every piece of matter in the universe came from this one point ... this one explosion. Since everything is made of matter, this means that the material that makes up everything in the universe came from this one point in time.

Extracellular components and connections between cells help coordinate cellular activities

Most cells synthesize and secrete materials that are external to the plasma membrane These extracellular structures include: Cell walls of plants The extracellular matrix (ECM) of animal cells Intercellular junctions

Plant Transport

Movement of water, gases and solutes into and out of individual cells throughout the plant and from the environment into the plant (generally from soil into roots) Localized transport of materials from cell to cell in tissue regions, such as loading solutes into phloem sieve tubes Long distance transport of water and solutes through the vascular tissues of the plant Plasma membrane - selectively permeable. Direction of water movement dependent on the diffusion gradient. Small transport proteins, called aquaporins, facilitate the diffusion of water. Most solutes rely on transport proteins or protein transport channels for facilitated diffusion. Plant Cells and Active Transport - Proton pump to move H+ out of the cell creating a proton gradient that is one source of potential energy (for hydrogen to diffuse back into the cell) Membrane potential

BASIS OF BIOLOGICAL FUNCTION Membranes and Proteins

Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. Properties (of living things) : Evolved programs; Chemical properties; Regulatory mechanisms; Organization; Limited order of magnitude; Life cycle; Open systems. Capacities (of living things) : Evolution Self-replication Growth & differentiation (via a genetic program) Metabolism (binding & releasing of energy) Self-regulation, to keep the complex system in steady state (homeostasis, feedback) Response to stimuli from environment (through perception & sense organs) Change @ two levels (genotype & phenotype) Cell Theory What does it state? Basic structural & functional unit of living things Activity of an organism depends on individual & collective activities of its cells Biochemical activities of cells dictated by subcellular structures - principle of complementarity Continuity of life has cellular basis What interpretation does the perspective of evolution provide for the cell theory? All organisms are composed of cells. Cells are the smallest living things. Cells arise only from pre-existing cells. *** All cells today represent a continuous line of descent from the first living cells. Cell Theory came about through the work of seventeenth century scientists who had invented fairly primitive microscopes. Antonie van Leeuwenhoek made his own microscopes and observed many types of tiny things. Englishman Robert Hooke was the first to use the term "cell" and confirmed Leeuwenhoek's findings. Rudulf Virchow of Germany came to the conclusion that cells come only from preexisting cells. All of these scientists contributed to the Cell Theory. Modern scanning and transmission electron microscopes have allowed scientists to determine the structure of cells at the level of the organelle. As a professor, Schleiden began investigating of the nature of plants. Unlike his contemporaries who simply classified plants according to their physical characteristics, Schleiden studied them with a microscope. As a result, Schleiden was the first person to recognize the importance of cells in plants, first discovered by Robert Hooke in 1655. Schleiden observed that all plants seemed to be composed of cells, and he proposed that these cells were the most basic unit of life in the plants. He proposed that plant growth took place by the generation of new cells, which, he argued, would propagate or 'crystallize' from buds on the nucleus of old cells. Although later work would show his proposal regarding the budding of the cell nucleus was not completely correct, his theories that the cell was the common structural unit to all plants, and that growth occurred by the addition of new cells, attracted significant attention. A year after Schleiden published his cellular theory of plants in Beiträge zur Phytogenesis (Contributions of Phytogenesis) in 1838, his friend and collaborator Theodor Schwann made similar observations in animals. Together, Schleiden and Schwann unified botany and zoology under a common theory that the cell is the basic structural unit of living organisms, both animal and plant. As a result, the two are considered the founders of modern cell theory. Muller's Lab

What is Known

Root Water moves into root from soil via diffusion Path of water & dissolved solutes: Soil interior cells of root xylem (upward movement) Leaf Water diffuses out of plant via transpiration through stomata Transpiration loss is significant

Early Earth

Studies of volcanos suggest the early atmosphere of Earth was composed of a mix of chemical compounds. Atmosphere contained practically no oxygen, as this gas is not expelled during volcanic eruptions. Mildly reducing atmosphere of carbon monoxide (CO), carbon dioxide (CO2), water vapor (H2O), hydrogen sulfide (H2S), methane (CH4), and ammonia (NH3). Oxygen gas first entered the atmosphere as a byproduct of photosynthesis. Initial oxygen production reacted with iron, producing banded iron formations. These geological formations have been used to date the evolution of photosynthesis to approximately 2.45 billion years ago.

The Murchison Meteorites

The Murchison Meteorite & the ALH84001 meteorite Both contained a variety of organic molecules including: Purines and pyrimidines Amino acids ALH84001 - Evidence that its interior never rose about 40° C during its fiery trip through the earth's atmosphere. Live bacteria could easily survive such a trip. Organic molecules in interstellar space Astronomers, using infrared spectroscopy, have identified a variety of organic molecules in interstellar space. The Murchison Meteorite Representative amino acids found in the Murchison meteorite. Six of the amino acids (blue) are found in all living things, but the others (yellow) are not normally found in living matter here on earth. The same amino acids are produced in discharge experiments like Miller's. Glycine Glutamic acid Alanine Isovaline Valine Norvaline Proline N-methylalanine Aspartic acid N-ethylglycine This meteorite, that fell near Murchison, Australia on 28 September 1969, turned out to contain a variety of organic molecules including: purines and pyrimidines polyols — compounds with hydroxyl groups on a backbone of 3 to 6 carbons such as glycerol and glyceric acid. Sugars are polyols. the amino acids listed in this table. The amino acids and their relative proportions were quite similar to the products formed in Miller's experiments. The question is: were these molecules simply terrestrial contaminants that got into the meteorite after it fell to earth? Probably not: Some of the samples were collected on the same day it fell and subsequently handled with great care to avoid contamination. The polyols contained the isotopes carbon-13 and hydrogen-2 (deuterium) in greater amounts than found here on earth. The samples lacked certain amino acids that are found in all earthly proteins. Only L amino acids occur in earthly proteins, but the amino acids in the meteorite contain both D and L forms (although L forms were slightly more prevalent). The ALH84001 meteorite This meteorite arrived here from Mars. It contained a variety of organic molecules. Furthermore, there is evidence that its interior never rose about 40° C during its fiery trip through the earth's atmosphere. Live bacteria could easily survive such a trip. Organic molecules in interstellar space Astronomers, using infrared spectroscopy, have identified a variety of organic molecules in interstellar space, including methane (CH4), methanol (CH3OH), formaldehyde (HCHO), cyanoacetylene (HC3N) (which in spark-discharge experiments is a precursor to the pyrimidine cytosine). polycyclic aromatic hydrocarbons as well as such inorganic building blocks as carbon dioxide (CO2), carbon monoxide (CO), ammonia (NH3), hydrogen sulfide (H2S), and hydrogen cyanide (HCN). Laboratory Synthesis of Organic Molecules Under Conditions Mimicking Outer Space There have been several reports of producing amino acids and other organic molecules by taking a mixture of molecules known to be present in interstellar space such as: ammonia (NH3) carbon monoxide (CO) , methanol (CH3OH) and , water (H2O) , hydrogen cyanide (HCN) and exposing it to a temperature close to that of space (near absolute zero) intense ultraviolet (uv) radiation. Whether or not the molecules that formed terrestrial life arrived here from space, there is little doubt that organic matter continuously rains down on the earth (estimated at 30 tons per day).

Abiotic Synthesis of Organic Molecules

Three scenarios were synthesized from inorganic compounds in the atmosphere — the "primordial soup" theory; rained down on earth from outer space; were synthesized at hydrothermal vents on the ocean floor. What IS Chemical Evolution? (stated clearly)

Aquaporins

Water moves rapidly into & out of cells evidence that there were water channels