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Biology 110

198 Pages

Course Code
Matthew Smith

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BIOLOGY: Unifying Life Processes 11/30/2012 10:03:00 PM S.I Sessions Sunday 5-7pm in room 2C15 (arts c wing) Midterm review: Tuesday October 9 , 10pm in room 1E1 (Arts e wing) Peerwise (participation marks) KAKE-ZFDU-JEYA  Create 2 questions for each midterm  Create 3 questions for the final exam  Answer 5 questions before each midterm  Answer 10 questions before the final Life and Light A Green Alga  Using light for both energy and information  Eyespot: light sensor  Moves toward light (not intense)  Moves away light (too intense)  Chloroplast  The Sun  The reason there is life on earth  We are at the optimal distance from the sun (able to use the energy)  Energy comes from the conversion of matter  Produces electromagnetic radiation Electromagnetic Spectrum  Differ in their waves length  The shorter the wave lengths means higher energy  Longer the wave length means lower energy  Gamma Rays (shortest, most energetic)  X rays  Ultraviolet rays (range most radiation reaching the surface of earth)  Near infrared radiation (range most radiation reaching the surface of earth)  Infrared radiation (range of heat escaping from the surface of earth)  Microwaves  Radio waves (the longest, lowest energy wavelength) What is Light?  Electromagnetic radiation that humans can detect with their eyes  Electromagnetic radiation travels in the form of a wave  A wave of discrete particles called photons  Wavelength: distance between 2 successive peaks  To be used, light energy must be absorbed by molecules called pigments  The longer the wavelength, the lower the energy of the photon (red light)  The shorter the wavelength, the higher the energy of the photon (blue light) Light Interacting with Matter  Allows the energy of light to be used by living things  Wavelengths can be reflected, transmitted, absorbed  To be used as a source of energy or information absorption must take place  Absorption of light occurs when the energy of the photon is transferred to an electron within a molecule o This excites the electron, moving it from its ground state to a higher energy level (excited state)  Photon can be absorbed by an electron if the photon’s energy equals the energy difference between the electron’s ground state and an excited state Pigment Structure  Conjugated system o Alternating double/single carbon bonds o Delocalization of e- (not tightly held between one atom to the next) o Electrons that are absorbing the wavelengths of light  More available of absorbing photons of light  Similar between the different molecules o The types of bonds o Have alternating single and double bonds (conjugated system)  Pigments are different colours because they absorb different wavelength of light (transmit different wavelength of light) Absorption of Light by Chlorophyll  Colour is the result of wavelengths of light that are not absorbed by a pigment  Able to absorb red light: the amount of energy matches the differences between 0-1 (must exactly match the difference of energy between the ground state and the next highest energy state)  Which has a longer wavelength? Red or blue light? o Red photons excite electrons to a higher energy state o Blue photons excite electrons to an even higher energy state o RED HAS A LONGER WAVELENGTH: uses less energy  The potential energy of excited electrons with pigment molecules is used in photosynthetic electron transport to synthesize NADPH and ATP  Consumed into the Calvin Cycle to convert carbon dioxide into carbohydrates  Cellular respiration breaks down carbohydrates, releases ATP Light as a Source of Energy: Photosynthesis Sustains Almost All Life  Energy is stored as chemical energy (sugar)  Oxygen goes in  Cellular respiration releases chemical energy from sugar molecules  Released chemical energy is made available for other metabolic processes  Carbon dioxide and water  Photosynthesis captures electromagnetic energy from sunlight (electromagnetic energy in sunlight)  Oxygen is released Halobacteria Also Captures Light Energy  How the bacteria can use light as a source of energy o Do not use light energy to convert carbon dioxide into carbohydrates o Contain a pigment protein complex called bacteriorhodopsin (protein pump) o Captures photons of light that provide the energy supply needed to pump protons out of the cell o Resulting in difference in H+ concentration across the plasma membrane (source of potential energy that is used by the enzyme ATP synthase to generate ATP from ADP)  When absorbs it changes its shape of the pigment molecule (result)  Causes the entire protein to change its shape (protein is being activated: going from resting state to active state)  Once activated: able to transport protons from inside the cell to outside the cell  Creates a concentration gradient (concentration inside will be lower, outside greater: form of potential energy) Light as a Source of Information: Photoreceptors (captures energy as a source of information)  Photoreceptor o Basic light sensing system, found almost universally in all organisms o Serves as a light sensing unit of the eyespot  Rhodopsin o Most common photoreceptor in nature o Basis of vision in animals o Also used by many other organisms o A highly conserved photoreceptor:  Consists of a pigment molecule (retinal) bound to a protein (opsin)  Absorption of a photon of light causes the retinal pigment molecule to change shape  This triggers alternations to the opsin protein, which then triggers downstream events (alternations in intracellular ion concentrations and electrical signals) An Eyespot: Sensing Light Without Eyes  Eyespot: light sensitive structure that is found within the chloroplast of a cell  Play a role in focusing and directing incoming light toward the photoreceptors  Eyespot does not play a role in photosynthesis  Allows the cell to sense light direction and intensity  Cells can respond to light by swimming toward or away from the light source in a process called phototaxis  Phototaxis: allows the cell to stay in the optimum light environment to maximize light capture for photosynthesis  Light absorption by the eyespot is linked to the swimming response by a signal transduction pathway o Light absorption triggers rapid changes in the concentration of ions, which generate electrical events o Change the beating pattern of the flagella used in locomotion Photomorphogenesis  Phytochrome is photoreceptor in plants  Critical for photomorphogensis (plant development, in the light)  Uses the light to trigger other cellular processes  Exposed to wavelengths of red light, becomes active and initiates a signal transduction pathway that reaches the nucleus  Signals actives hundreds of genes (code for proteins) involved in photosynthesis and leaf development  The Eye  What distinguishes the eye of a simple invertebrate from the eyespot of the green algae? o Vision  Requires a brain to interpret signals send from eye  Co evolution (most likely) Ocellus of Planaria  Ocellus o Consists of photoreceptors o Photoreceptors is modified nerve cell that contains thousands of individual photoreceptor molecules o This reaction carries them directly away from the source of light toward darker areas, where the risk of predation is smaller  Planaria o Organ is used to sense light intensity and direction to a light source o Compound eyes and single lenses Compound Eye of a Deer Fly  Brain receives a mosaic image of world  Extraordinarily adept at detecting movement Octopus Eye  Eyes with single lenses - “camera eyes”  Retina  Cornea  Lens  Pupil  Iris Darwin and the Evolution of the Eye  The eye as it exists in humans and other animals did not appear suddenly but evolved over time  Most eyes have fundamental similarities in their underlying developmental program  Similar set of highly conserved genes to orchestrate eye development  Gene Pax6: Master control gene that is almost universally employed for eye formation in animals Evolution of the Eye  Camera eyes evolved by variation and natural selection from a simple, primitive eye  Improved eyes give a huge advantage to organism Small Portion of Spectrum Essential for Life -> 400 to 700 nm  Longer wavelengths o Tend not to reach Earth’s surface o Also not the right wavelength to excite electrons  Shorter wavelengths o Do reach Earth, and can damage biological molecules o Photosystems involved in photosynthesis o Damage to DNA -> skin cancer o Protective mechanisms Using Light to Tell Time: Circadian Rhythms  Oscillate with a period of approximately 24 hours  Controlled by an internal (endogenous) organism based clock Life in the Dark- Blind Mole Rat  Functionally blind, yet are descended from ancestors that had functional eyes  Photoreceptors are still functional Readings  1.7 the role of light in behaviour and ecology “the bluest fruit” o leads to unique colourations that may serve to attract members of the same species o bright colouration is thought to serve a valuable role in communication o Electus parrot: female is more brightly coloured o An exception to the general rule that the male is usually more brightly coloured o European barn swallow: more colourful males are more likely to find a mate o Penguins: both male and females are more likely to find a mate o Bright colours means health  Based on understanding of the pigments used for ornamentation  Beta carotene  Obtain from what they eat and circulate the blood stream before being deposited in feathers  Play a role in breaking down potentially harmful reactive oxygen species  Melanin based pigments are also found in darker and brown colourations of birds o Attract pollinators  The movement of pollen from the anthers (male parts) of one flower to the stigma (female parts) if the same or other flowers to effect fertilization and production of fruits and seeds  Protein rich pollen, sugar rich nectar waxes or resins found in the flower  Must attract the correct candidates to ensure efficient pollination  Co evolution refers to the fact that over evolutionary time, a change in one species triggers change in others  The food reward has become an important part of the pollinators diet o Camouflage  Concealment from either predators or prey  1.8 life in the dark o Decreasing light levels, we first lose our ability to see colour, followed by shapes o Rod photoreceptors which do not perceive different colours are 100 times as sensitive o Larger eyes are able to collect more photons o Many of the animals have become adapted to these environments o The photoreceptors of the eye remain functional even though the image forming part of the brain is dramatically reduces o The maintenance of photoreceptors allows for the proper setting of biological clocks necessary for the regulation of circadian rhythms  1.9 bioluminescence o Able to make their own light o Process of light absorption by a pigment: the energy of a photon is transferred to an electron, raising it from the ground state to an excited state o Essentially the same process in reverse o Chemical energy in the form of ATP is used to excite an electron in a substrate molecule from the ground state to a higher excited state o The electron returns to the ground state, the energy is released as a photon of light The Cell 11/30/2012 10:03:00 PM The Cell Theory  All organisms are composed of one or more cells  The cell is the basic structural and functional unit of all living organisms  Cells arise only from the division of pre existing cells (cell division) o Cell division is driven by the genetic information within the cell  Cells first observed in the 1600’s by Robert Hooke and Anton van Leeuwenhoek o Hooke coined the term “cellulae” gives us the word cell o Van Leeuwenhoek describe bacteria and protists as “animalcules”  1800’s o Robert Brown: first to observe the nucleus o Mathias Schleiden: plants are made of cells, and nucleus is important for development o Theordor Schwann: all animals are made of cells o Rudolf Virchow (Robert Remak): cells only arise pre existing cells Synthetic Cells  First reported in 2012  Working with bacteria: micro plasma  Chemically synthesized the genome  Had other bacteria cells and took out DNA  Took the synthetic genome into the empty cell  Genome starting to produce protein, and divide  New daughter cells had same characteristics as the micro plasma Basic Features of Cell Structure and Function  Contain highly organized systems of molecules o Including nucleic acids, DNA and RNA o Hereditary information o Direct the manufacture of cellular molecules  Cells use chemical molecules or light as energy sources  Respond to changes in their external environment by alternating their internal reactions  Cells duplicate and pass on their hereditary information as part of cellular reproduction  Unicellular (protists: amoebas, yeast) o Functionally independent organism capable of carrying out all activities necessary for its life  Multicellular organism o Divided among varying numbers of specialized cells o Potentially capable of surviving by themselves if placed in a chemical medium that can sustain them o If broken, are unable to grow, reproduce to outside stimuli in a coordinated, potentially independent fashion Cell Diversity: Microscopy Has Been Key  Most cells are too small to be seen unaided by the human eye o Typical animal cell: 5-30 um in diameter o Bacterial cells: Approx. 0.5-5 um in diameter  Microscopy o A technique for producing visible images of objects, biological or otherwise that are too small to be seen by the human eye o Light Microscopy  Use light to illuminate the specimen o Electron Microscopes  Use electrons to illuminate the specimen o Magnification  The ratio of the object as viewed to its real size o Resolution  Is the minimum distance by which two points in the specimen can be separated and still be seen as two points  Depends primarily on the wavelength of light or electrons used to illuminate the specimen: the shorter the wavelength, the better the resolution Units of Measure Important in the Study of Molecules and Cells  Last one should be “nm”  After nano o Pico = 10 power of -12 o Femto = 10 power of -15 Scale in Biology Scale of Plant, Animal, and Bacterial Cells  Micrometers (um) or 10 power -6 meters - Light microscopy range Scale of Macromolecules  Nanometers (nm) or 10 power -9 meters o Electron microscopy o Why Aren’t Cells Bigger?  Surface area to volume ratio  Volume determines capacity for chemical activity o Chemical activity requires energy, produce at the end (bi products, potentially harmful) o Cells need to get rid of waste and bringing energy / nutrients in happens at surface of the cell  Surface area determines the amount of transport in and out  When volume increases by 8 times, the surface area increases by 4 times o Volume is increasing faster than the surface area  Past a certain point, increasing the diameter of a cell gives a surface area that is insufficient to maintain an adequate nutrient  Some cells increase their ability to exchange materials with their surroundings by flattening or by developing surface folds or extensions that increase their surface area  Difference between Florence and Confocal o Can look at slices in cell in Confocal  Electron o Use beams of electrons o Can see more detail o Transition  Take a section of sample, stain it (lipids or proteins) able to see the scale of how things are arranged and structure (internal) o Scanning  Looking at surfaces of cells  Detailed structures that are on surface Prokaryotes and Eukaryotes  All forms of life are based on 1 distinct types of cells o Prokaryotic and Eukaryotic  Prokaryotic cells lack a nucleus o “pro” before, evolutionarily earlier form of life o Make up two of the domains of life: bacteria & archaea o Nucleotide  DNA containing central region of the cell  No boundary membrane separating it from the cytoplasm o A typical human cell has about 10 times the diameter and over 8000 times the volume of an average prokaryotic cell o Spherical rod like shape o Genetic material of archaea and bacteria is located in the nucleotide: in an electron microscope, that region of the cell is seen to contain a highly folded mass of DNA o Individual genes in the DNA molecule encode the information required to make proteins  This information is copied into a type of RNA molecule (messenger RNA)  Ribosomes use the information in the mRNA to assemble amino acids into proteins  Form a combination of ribosomal RNA (rRNA) and protein molecules o Cell wall provides rigidity, protects the cell from physical damage o Plasma membrane  Transporting materials into and out of the cell  Contains most of the molecular systems that metabolize food molecules into the chemical energy of ATP  In photosynthetic bacteria, the molecules that absorb light energy and convert it to chemical energy are also associated with the plasma membrane o Internal membranes  Cellular functions occur either on the plasma membrane or cytoplasm  Some archaea and bacteria have ore extensive internal membrane structures  Photosynthetic bacteria have complex layers of intracellular membranes formed by invaginations of the plasma membrane o Prokaryotic Cytoskeletons  Play important roles in creating and maintaining the proper shape of cells (in cell division) o Flagella  Bacteria and archaea can move through liquids and across wet surfaces  Threadlike protein fibres which extend from the cell surface  Bacterial flagellum rotates in a socket in the plasma membrane and cell wall to push the cell through a liquid medium o Pili  Hair like shafts of protein  Extending from their cell walls  Attaching the cell to surfaces or other cells  Sex pilus attaches one bacterium to another during mating  Eukaryotes o “eu” - true, “karyon” - nucleus o Plants, animals, fungi, algae, protozoa o Contains extensive membrane systems that form organelles with their own distinct environments and specialized functions o Cytoplasm surrounding nucleus  Specialized to carry out one or more major functions of energy metabolism and molecular synthesis, storage and transport o The nucleus is separated from the cytoplasm by the nuclear envelope  Consists of 2 membranes (one layered just inside the other and separated by a narrow space)  Embedded in the nuclear envelope are many hundreds of nuclear pore complexes  Nuclear pore complexes is formed from many proteins called the nucleoporins  It exchanges components between the nucleus and cytoplasm and prevents the transport of material not meant to cross the nuclear membrane o A channel through the nuclear pore complex  A path for the assisted exchange of large molecules such as proteins and RNA molecules with the cytoplasm  Whereas small molecules pass by without assistance o Enzymes for replicating and repairing DNA must be imported into the nucleus to carry out their functions o Proteins to be imported into the nucleus are distinguished from those that function in the cytosol by the presence of a short amino acid sequence called a nuclear localization signal o A specific protein in the cytosol recognizes and binds to the signal and moves the protein containing it to the nuclear pore complex, where it is transported through the pore into the nucleus o Nucleus contains one or more nucleoli  Form around the genes coding for the rRNA molecules of ribosomes  The information in rRNA genes is copied into rRNA molecules, which combine with proteins to form ribosomal subunits  Subunits then leave the nucleoli and exit the nucleus through the nuclear pore complexes to enter the cytoplasm, where they join on mRNAs to form complete ribosomes  Share basic features o Plasma membrane  Separating the cell from the external environment  Proteins act as receptors; they recognize and bind specific signal molecules in the cellular environment and trigger internal responses  Proteins recognize and adhere to molecules on the surface of other cells  Proteins are markers in the immune system  The immune system can identify cells without those markers as being foreign and most like; pathogens (disease causing organism or virus) o Cytoplasm (everything inside the plasma membrane) o Within the cytoplasm:  Synthesis and assembly of most of the molecules required for growth and reproduction and the conversion of chemical and light energy into forms that can be used by cells  Conducts stimulatory signals from the outside into the cell interior and carries out chemical reactions that respond to these signals  Cytosol  Fluid matrix that makes up the internal part  Participates in energy metabolism and molecular synthesis and performs specialized functions in support and motility  Organelles (eukaryotes vs. prokaryotes)  Floating around within cytosol  Some bacteria have certain types of organelles  Why are they important in Eukaryotic cells:  Eukaryotic cells are considered to be more evolutionarily advanced is because they have all these organelles.  Organelles allow for specific biochemical pathways to be concentrated (enzymes of the pathway, substrates that feed it are concentrated - there are more of them causing more efficiency)  Segregated (no biochemical pathways competing with each other, the product of one pathway can inhibit another pathway)  Cytoskeleton  Filaments of protein that gives the cell structure  Helps maintain proper cell shape and plays key roles in cell division and chromosome segregation from cell generation to cell generation o DNA organized into chromosomes  Structure of chromosomes is different between eukaryotes and prokaryotes o Basic processes  Electron transport chain  Generating ATP  Eukaryote cell occurs in mitochondria  Prokaryote cell occurs in plasma membrane  Transcription and translation  Characteristics of Eukaryotic Cells are different from Prokaryotic cells o Separation of DNA and cytosol by nuclear envelope o Presence of membrane bound compartments with specialized functions: mitochondria, chloroplasts, ER, Golgi complex o Highly specialized motor proteins 3 Domains of Life  2 of the 3 domains of life are prokaryote cell (bacteria and archaea)  Archaea are more closely related to eukaryote (evolutionary) even though they are prokaryotes Prokaryotic Cell Structure: E. Coli Animal Cell Plant Cell Characteristics Bacteria Archaea Eukarya DNA Single, circular iSingle, circular Multiple linear arrangement most, but some molecules linear and or multiple Chromosomal Prokaryotic Five eukaryotic Five eukaryotic proteins histonlike histones histones proteins Genes arranges Yes Yes No in operons Nuclear envelope No No Yes Mitochondria No No Yes Chloroplast No No Yes Peptidoglycan in Present Absent, some have Absent cell wall pseudopeptidoglycan Membrane lipids Unbranched, Branched, linked by Unbranched, linked by ester ester linkage, may linked by ester linkages have polar heads on linkages both ends RNA polymerase Limited Multiple types Multiple types variations Ribosomal Prokaryotic Some prokaryotic, Eukaryotic proteins some eukaryotic First amino acid Formylmethonine Methionine Methionine placed in proteins Aminoacyl-tRNA Prokaryotic Eukaryotic Eukaryotic synthetizes Cell division Prokaryotic Prokaryotic Eukaryotic proteins Proteins of Prokaryotic Prokaryotic Eukaryotic energy metabolism Nucleus is Defining Feature of Eukaryotic Cells  Envelope that surrounds the nucleus are 2 different membranes (outer and inner)  2 membranes are connected (folds)  Nuclear pore complex (the green) regulate what can get into (protein) the nucleus or leave the nucleus (RNA)  Ribosomes on outer surface on nuclear envelope Ribosomes  Unifying feature of all cell types (translation) - responsible for translating proteins o Bacterial, archaeal and eukaryotic are all slightly different  In Eukaryotes, some are free in cytosol, others are attached to endoplasmic reticulum membranes o Still others are found in mitochondria and chloroplasts  Have ribosomes because they have their own genomes (genes need to be transcribed and translated into proteins, need ribosomes)  Ribosomes found in mitochondria and chloroplast are different then in cytosol or ER  In animal cell, 2 different types of ribosomes in 3 different locations  In plant cell, 3 different types of ribosomes (eukaryotic type, mitochondria, chloroplast) 4 locations Endoplasmic Reticulum (ER)  Extensive interconnected network of membranous channels and vesicles  Many different subtypes of ER (have different functions)  Rough ER o Ribosome studded o Make proteins that become part of cell membranes or are released (secreted) from cell o Proteins made on ribosomes attached to the ER enter the ER lumen, where they fold into their final form o Chemical modifications of these proteins  Addition of carbohydrate groups to produce glycoproteins, occur in the lumen  Smooth ER o Synthesizes lipids and is the site of many other essential cellular functions o Contains enzymes that convert drugs, poisons and toxic byproducts of cellular metabolism into substances that can be tolerated or more easily removed from the body The ER Endomembrane System  Characteristic feature of eukaryotic cells o Nuclear envelope o ER o Golgi complex o Lysosomes/Vacuoles o Vesicles o Plasma Membrane Golgi Complex  Flattened membranous sacs  Chemically modifies proteins made in rough ER (antibodies proteins) o Removing segments of the amino acid chain, adding small functional groups, or adding lipid or carbohydrate units  Regulates the movement of several types of proteins o Some are secreted from the cell o Others become embedded in the plasma membrane as integral membrane proteins, and yet others are placed in lysosomes  Sorts finished proteins to be secreted from cell or embedded in plasma membrane  Located near concentrations of rough ER membranes, between the ER and the plasma membrane  Secretory vesicles o Release their contents to the exterior by exocytosis o Endocytosis, which brings molecules into the cell from the exterior Vesicular Traffic  All connected by vesicular traffic  1) Proteins made by ER ribosomes enter ER membranes or the place inside ER o Chemical modification of some proteins begin o Membrane lipids are also made in the ER  2) Vesicles bud from the ER membrane and then transport unfinished proteins and lipids to the Golgi complex  3)Protein and lipid modification is completed in the Golgi complex and products are sorted into vesicles that bud from the complex  4) Secretory vesicles budding from the Golgi membranes transport finished products to the plasma membrane o the products are released by exocytosis o other vesicles remain in storage in the cytoplasm  5) Lysosomes budding from the Golgi membranes contain hydrolytic enzymes that digest damaged organelles or the contents of endocytic vesicles that fuse with them o Endocytic vesicles form at the plasma membrane and move into the cytoplasm Exocytosis and Endocytosis  Vesicles are responsible for transporting materials between compartments of the endomembrane system  Also used for secretion to cell exterior, and bringing molecules into the cell  Exocytosis o Secretory vesicles, release their contents to the exterior o Secretory vesicle fuses with the plasma membrane and spills the vesicle contents to the outside o Including molecules such as hormones, neurotransmitters, waste products, toxic substances and enzymes  Endocytosis o Brings molecules into the cell from the exterior o Plasma membrane forms a pocket, which bulges inward and pinches off into the cytoplasm as an endocytic vesicle o Carried to the Golgi complex or to other destinations such as lysosomes in animal cells o Sorted and placed into vesicles for routing to other locations What About Other Types of Organelles?  Mitochondria o Membrane bound organelles in which cellular respiration occurs  Cellular respiration is the process by which energy rich molecules such as sugars, fats, and other fuels are broken down to water and carbon dioxide by mitochondrial reaction, with the release of energy o Generate most of the ATP of the cell o Outer mitochondrial membrane is smooth and covers the outside of the organelle o The surface area of the inner mitochondrial membrane is expanded by folds called cristae o The ATP generating reactions of mitochondria occur in the cristae and matrix o Mitochondrial matrix also contains DNA and ribosomes that resemble the equivalent structures in bacteria  Chloroplasts  Similarities o Both surrounded by 2 distinct membranes (outer, inner) o Mitochondria: Folded o Chloroplast: Also folded but not part of the membrane (3 membranes) o Both have DNA o Chloroplast: harnessing energy and storing for sugars o Mitochondria: taking sugar and forming it into ATP o Both have their own ribosomes Theory of Endosymbiosis Sections 3.5 a,b,c (page 64-66)  Energy transducing organelles, chloroplasts and mitochondria, thought to have been derived from free living prokaryotic cells o Chloroplast and mitochondria were though to originally been bacteria cells  Mitochondria developed from ingested prokaryotes capable of using oxygen for aerobic respiration o Thought to have come from bacteria cells o One cell ingested a bacteria cell, that bacteria was already using oxygen for aerobic respiration  Chloroplasts developed from ingested cyanobacteria o Thought came from a photosynthesizing cyanobacteria Endosymbiont Hypothesis  Original prokaryotic host cell o DNA o Nucleus formed  Multiple ingestion of the plasma membrane o Aerobic bacteria is ingested o Has own plasma membrane, then ingested  Plasma membrane is folded  Cell inside cell, 2 membranes  Inner membrane of chloroplast and bacteria are very similar  Outer membrane of chloroplast and bacteria are very different o Endosymbiosis event: became dependent on one another  The bacteria became mitochondria o Eukaryotic cell o ER and nuclear envelope form from the plasma membrane invaginations (not part of Endosymbiont hypothesis)  Eukaryotic Cells (plants, some protists) o Photosynthetic bacteria was ingested o Became chloroplast o Mitochondria  Eukaryotic Cells (animals, fungi, some protists) o Cells without mitochondria Evidence to Support Endosymbiosis Theory  Mitochondria and chloroplasts resemble prokaryotes in numerous ways o Morphology (outer membrane) o Reproduction (division)  Chloroplast and mitochondria are constantly dividing within a cell (daughter cells)  So there is the right number of mitochondria and chloroplast  Processes of division between chloroplast and mitochondria is most similar to bacteria division o Genetic information  Structure and organization of genomes  Prokaryotes (circular genomes) Eukaryotes (linear genomes)  Structure of chloroplast and mitochondria genomes are more similar to prokaryotic genomes  Genes are regulated and organized in particular ways o Transcription and Translation  Genes in chloroplast and mitochondria must be transcribed and translated (on ribosomes)  More similar to bacteria cells  Look at ribosomes of mitochondria, look very different to the ribosomes on cytoplasm and ER but almost the same as bacteria cell o Electron Transport  Almost the same in the bacteria cell Horizontal Gene Transfer  Nuclear genome o Integration of gene into nuclear genome  Gene Transfer + Protein synthesis and import - Chloroplast genome o Chloroplast, to nucleus, back to chloroplast  Chloroplast o 3000 different proteins (coding proteins that are still needed in the chloroplast)  Chloroplast genome - Chloroplast encoded proteins  Chloroplast genome  Nuclear genome  Nuclear encoded proteins  The 2 genomes are maintained separately from each other o Gene transfer events are happening but maintained separately (never mix)  Purpose of gene transfer o Gene regulation o Better to have things in the nucleus Endosymbiosis  Is endosymbiosis something that happened only twice? o No o Those are the 2 most important endosymbiosis events that lead to mitochondria and chloroplast o A cell that already had mitochondria and chloroplast engulfed more bacteria cells o Interaction or relationship between two organisms Peroxisomes  Another type of eukaryotic organelle that is NOT part of the endomembrane system (similar to chloroplast and mitochondria due to not being apart of endomembrane system) o Surrounded by single envelope membrane (chloroplast and mitochondria are surrounded by 2 membrane) o Do not have their own genome (chloroplast and mitochondria have their own genome)  Site of biochemical pathway(s) that generate hydrogen peroxide as a by product o Fatty acid metabolism o Too must hydrogen peroxide can damage DNA and lipids in the cell but it is produced as a by product as a pathway  Enzymes that “scavenge” H2O2 are also abundant  Make the by product not harmful (concentrates and segregates) Chloroplasts Move in Response to Light  Took a leaf  Took a negative, and put it in front of the leaf  Put light on negative - through the leaf  Took negative away and took picture  Chloroplasts in the cell move according to how much light is there  All the chloroplasts go to the top surface of the cell (try to capture light)  Regions of the leaf where there is a lot of light (migrate to the sides of the cell) leaving most of the cell free of chloroplast (instead of dark green, look white)  Movement moves along the cytoskeleton 2.3(f) Cytoskeleton  Supportive structure  Important for cell movement  Animal cells o Built from microtubules, intermediate filaments and microfilaments  Plant cells o Built from microtubules and microfilaments  Characteristic shape and internal organization of each type of cell is maintained in part by its cytoskeleton  The interconnected system of protein fibers and tubes that extends throughout the cytoplasm  Reinforces the plasma membrane and functions in movement, both of structures within the cell and of the cell as a whole  Highly developed in animals, in which it gills and supports the cytoplasm from the plasma membrane to the nuclear envelope  Even though present in plants, the fibers are less prominent  Cytoskeleton in animal cells contains structural elements of three major types (all made up of proteins) o Microtubules (tubulin) o Intermediate filaments o Microfilaments  Microtubules are the largest cytoskeletal elements, and microfilaments are the smallest  Each cytoskeletal element is assembled from proteins microtubules from tubulins, intermediate filaments from a large and varied group of intermediate filament proteins and microfilaments from actins  Keratins of animal hair, nails and claws contain a common form of intermediate filament proteins known as cytokeratin  Microtubules o Microscope tubes o They function much like the tubes used by human engineers to construct supportive structures o A filament is a linear polymer of tubulin dimers o Organized head to tail in each filament, giving the microtubule a polarity, meaning that the two ends are different o Microtubules are dynamic structures, changing their lengths as required by their functions (seen readily in animal calls that are changing shape) o Change length by the addition or removal of tubulin structures also formed microtubules called the centrioles o Provide tracks along which vesicles move from the cell interior to the plasma membrane and in the reverse direction o Separating and moving chromosomes during cell division, determining the orientation for growth of the new cell wall during plant cell division, maintaining the shape of animal cells and moving animal cells themselves o Animal cells movement  Generated y motor proteins that push or pull against micro muscles produce body movements by acting on bones of the skeleton  One end is firmly fixed to a cell structure (vesicle)  Other end has reactive groups that “walk” along another microtubule by making an attachment, forcefully swiveling a short distance  Releasing ATP supplies the energy for the walking movements  Motor proteins that walk along microfilaments are called myosins  Walk along microtubules are called dyneins and kinesins  Intermediate Filaments o These fibers occur singly, in parallel bundles and in interlinked networks, either alone or in combination with microtubules, microfilaments or both o Only found in multicellular organisms o Microtubules and microfilaments are the same in all tissues, intermediate filaments are tissue specific in their protein composition o They all play similar roles in the cell, providing structural support in many cells and tissues  Microfilaments o Consist of 2 polymers of actin subunits wound around each other in a long helical spiral o Occur in almost all eukaryotic cells and are involved in many processes including a number of structural and locomotors functions o Actively flowing motion of cytoplasm called cytoplasmic streaming, which can transport nutrients, proteins and organelles in both animal and plant cells and which is responsible for amoeboid movement 2.3 Flagella and Cilia: Differences between prokaryotes and eukaryotes  Elongated, slender motile structures that extend from the cell surface  They are identical in structure except that cilia are usually shorter than flagella and occur on cells in great numbers  The whiplike or oarlike movements of a flagellum propel a cell through a watery medium, and cilia move fluids over the cell surface  A bundle of microtubules extends form the base to the tip of a flagellum or cilium  Arise from the centrioles  During the formation of flagellum or cilium, a centriole moves to a position just under the plasma membrane  When developed its complete as the basal body of the structure  Found in protozoa, algae and many times of animal cells have flagella  Cilia covering cells that line the air passages of the lungs sweep out mucus containing bacteria, dust particles, and other contaminants  Purpose of the eukaryotic flagellum is the same as the prokaryotic flagella, the genes that encode the components of the flagellar apparatus of the cells are different 2.4 Plant Vacuoles and Cell Walls  Vacuoles o Central vacuoles are large vesicles identified as distinct organelles of plant cells because they perform specialized functions unique to plants o Pressure within the central vacuole supports the cell o Membrane that surrounds the central vacuole, the tonoplast, contains transport proteins that move substances into and out of the central vacuole o Store salts, organic acids, sugars, storage proteins, pigments, and in some cells waste products o Enzymes capable of breaking down biological molecules are present in some central vacuoles, giving them some of the properties of lysosomes  Cell Walls o Cell walls of plants are extracellular structures because they are located outside the plasma membrane o Provide support to individual cells, contain the pressure produced in the central vacuole and protect cells against invading bacteria and fungi o Consist of cellulose fibres, which give tensile strength to the walls, embedded in a network of highly branched carbohydrates o Cell walls also surround the cells of fungi and algal protists 2.5 Animal Cell Surface  Cell adhesion molecules bind cells together  More complex cell junctions seal the spaces between cells and provide communication between cells  Extracellular matrix supports and protects cells and provides mechanical linkages, such as those between muscles and bone Defining Life and its Origins 11/30/2012 10:03:00 PM  Very little difference between biotic (alive) and abiotic (not alive) worlds at the atomic/chemical level  If were to look at the atomic composition of living and non living things there is very little difference  Made up of the same elements (carbon, oxygen, nitrogen)  Relative amounts are not the same, but they are all still there The Characteristics of Life are Emergent  Reflects a remarkable complexity resulting from a hierarchy of interactions that begins with atoms and progresses through molecules to macromolecules and cells  May continue upward in complexity and include organelles, tissues, and organs  The seven properties of life are called emergent because they come about, or emerge from many simpler interactions that, in themselves, do not have the properties found at a higher levels  Ability to harness and utilize energy  Ability emerges from the interactions of all three of these part of a metabolic process The Seven Characteristics of Life  Small number of biological systems that straddle the line between the biotic and abiotic worlds  Display order o All forms of life including this flower are arranged in a highly ordered manner, with the cell being the fundamental unit of life  Harness and Utilize energy o Like this hummingbird, all forms of life acquire energy from the environment and use it to maintain their highly ordered state  Reproduce o All organisms have the ability to make some of their own kind. Here, some of the bacteria have just divided into major daughter cells  Respond to stimuli o Organisms can make adjustments to their structure, function, and behaviour in response to changes to the external environment o A plant can adjust the size of the pores (stomata) on the surface of its leaves to regulate gas exchange  Exhibit Homeostasis o Organisms are able to regulate their internal environment such that conditions remain relatively constant o Sweating is one way in which the body attempts to remove heat and thereby maintain a constant temperature  Growth and development o All organisms increase their size by increasing the size and number of cells o Many organisms also change over time  Evolve o Populations of living organisms change over the course of generations to become better adapted to their environment o The snowy owl illustrates this Is a Virus Alive?  Virus o Display many of the properties of life, including the ability to reproduce and evolve over time o Characteristics of life that a virus has are based on its ability to infect cells o Although viruses contain nucleic acids (DNA and RNA), they lack the cellular machinery and metabolism to use that genetic information to synthesize their own proteins o To make proteins, they have to infect living cells and essentially hijack their translational machinery and metabolism in order to reproduce Timeline for the Evolution of Major Forms of Life History of Earth Early Earth Earth Lies Within the Habitable Zone Around the Sun  All components of the solar system were formed ay the same time by the gravitational condensation of matter present in an interstellar cloud, which initially consisted mostly of hydrogen  Intense heat and pressure generated in the central region of the cloud formed the Sun, where as the reminder of the spiraling dust and gas condensed into the planets  Over time, Earth radiated away some of its heat and surface layers cooled and solidified into the rocks of the crust  Within the solar system, there is currently no conclusive evidence that a planet other than Earth harbors life  Unlike the other planets, Earth is situated at a position where heat from the Sun allows for surface temperatures to be within a range that allows water to exist in a liquid state Biological Important Macromolecules  4 major types of macromolecules important for all forms of life o Nucleic acids (DNA and RNA) o Proteins o Lipids o Carbohydrates  Except lipids are polymers made up from simpler building blocks, and are all made within cells by complex metabolic pathways Primordial Earth: Formation of Biologically Important Molecules (hypothesis 1)  PAGE 56  Oparin Haldane hypothesis o Early atmosphere was a reducing atmosphere because of the presence of large concentrations of molecules such as hydrogen, methane and ammonia o These molecules contain an abundance of electrons and hydrogen and would have entered into reactions with one another that would have yielded larger and more complex organic molecules o Organic molecules that have formed building blocks of life could have been formed given conditions that prevailed on primitive Earth (page 27) o Reducing atmosphere that lacked oxygen o H2S, CO2, NH3, CH4, H2O (vapor) o Allows for synthesis of complex organic molecules o Today’s atmosphere is classified as an oxidizing atmosphere o Oxygen is a particularly strong oxidizing molecule and would itself accept the electrons from organic molecules and be reduced to water o Lack of oxygen in the primordial atmosphere also meant that there was no ozone layer, which developed after oxygen levels in the atmosphere began to increase o Without the ozone layer, energetic ultraviolet light was able to reach the lower atmosphere, and along with abundant lightning, provided the energy needed to drive the formation of biologically important molecules  Miller Urey Apparatus o Created a laboratory stimulation of the reducing atmosphere believed to have existed on early Earth o Placed components of a reducing atmosphere-hydrogen, methane, ammonia, and water vapor in a closed apparatus and exposed the gases to an energy source in the form of continuously sparking electrodes o Water vapor was added to the “atmosphere” o Large assortment of organic compounds including urea; amino acids; and lactic, formic and acetic acids after condensing the atmosphere into a liquid o Stimulate conditions on primordial Earth o Abiotic synthesis of biologically important compounds  Is it possible to form these molecules abiotily?  Urea, amino acids o Adding HCN and CH20  Fatty acids, purines and pyrimidine, sugars, and phosplipid  Hypothesis 2: Deep Sea Vents o Complex organic molecules necessary for life could have originated on the ocean floor at the site of deep sea (hydrothermal) vents  Hypothesis 3: Extraterrestrial Origins o Came from space o Contains an assortment of biologically important molecules including a range of amino acids Polymers from Monomers: Macromolecules (proteins, carbohydrates, lipids, nucleic acids)  Primordial Earth contained very little oxygen and because of this, complex organic molecules could have existed for much longer than would be possible in todays oxygen rich world  Amino acids and nucleotides are monomers o Simpler and easier to synthesize than the key chemical components of life  Nucleic acids and proteins are polymers o Macromolecules formed from the bonding together of individual monomers  The synthesis of proteins and nucleic acids requires protein based catalysts called enzymes o Results in macromolecules that often consist of hundreds to many thousands of monomers linked together  Key macromolecules of life, such as proteins and nucleic acids are polymers that are not formed by the Miller Urey experiment  Polymerization reactions may have occurs on solid surfaces (page 56-57) o Example: Clay o Could have provided the type of environment necessary for polymerization to occur o Consists of very thin layers of minerals separated by layers of water only a few nanometers think o The layered structure of clay is also charged, allowing for molecular adhesion forces to bring monomers together in precise orientations that could more readily lead to polymer formation o Store the potential energy Key Attributes of a Modern Cell  A membrane defined compartment – the cell  A system to store genetic information and use it to guide the synthesis for specific proteins  Energy transforming pathways to bring in energy from the surroundings and harness it to sustain life Protobionts: The First Cell  Formation of a membrane defined compartment  Allow for primitive metabolic reactions to take place in an environment that is distinctly different than the external surroundings o The concentration of key molecules could be higher and greater complexity could be maintained in a closed space  Group of abiolotically produced organic molecules that are surrounded by a membrane or membrane like structure (page 57) o Can form spontaneously  Without any input of energy, given the conditions on primordial Earth  Hydrophobic tails (attract to one another), hydrophilic heads: when there is a bunch of phospholipids form spontaneously o Primitive cell like structures o Some properties of life o May have been precursors of cells Vesicles from Phospholipids Pathway of Information Flow: The Central Dogma  DNA (information is stored in DNA) - RNA (information in DNA is copied into RNA) - Protein (information in RNA guides the production of proteins) Ribozymes  Ribozymes: RNA molecules that catalyze specific reactions  DNA and proteins may have evolved after RNA  How did such a system evolve when the products of the process, proteins, are required to catalyze each step of the process? o RNA molecules that could themselves act as catalysts o Can catalyze reactions on the precursor RNA molecules that lead to their own synthesis as well as n unrelated RNA molecules o Single stranded molecules can fold into very specific shapes based on intermolecular hydrogen bonding or base pairing o Function is very common to proteins, especially enzymes where precise three dimensional shape is critical for reacting with substrate molecules Testing the “RNA World” Hypothesis  David Bartel’s laboratory at MIT o hQp://  Trying to create, from scratch a ribozyme that is capable of catalyzing the addition of ribonucleotides to an existing strand of RNA o Looking for storage molecule, and one that can replicate itself  Used “IN Vitro Evolution” method: Started with a set of millions-billions of different large RNA molecules o Selected the ribozymes with the best activity, randomly mutated the sequences, and repeated at least 18 times o Random sequences of RNA molecules o Trying to replicate the macromolecules that were formed o Took billions of these molecules, and looked for which of the RNA molecules are able to self replicate o Once found the RNA molecules, mutated the sequences: then looked for mutated molecules that can self replicate themselves (continued the process) o Ribosomes: protein and RNA - translation: how RNA is translated into protein  Within the particle of a ribosome, it is a ribozyme that is at work Scenario for Evolution of Flow of Information  RNA was catalytic and stored information  RNA was able to produce protein (RNA molecule converts mRNA into protein) Proteins are more efficient to catalyze these reactions faster (more complex then the nucleotides that build RNA)- faster and more  DNA evolved from the conversion of RNA into DNA (reverse transcription) DNA is a better information storage molecule then RNA Proteins and DNA  The evolution of DNA would have reduced the rate of chemical and mutational damage to the genetic material  Proteins become dominant structural and functional macromolecule of all cells o Greater diversity o Much higher rate of catalysis  DNA is more stable than RNA and thus evolved as better repository of genetic information  Once DNA copies were made, selection may have favored DNA, as it is a much better way to store information than RNA o Each DNA strand is chemically more stable, and less likely to degrade, than a strand of RNA o The base uracil found in RNA is not found in DNA  It has been replaced by thymine  This may be because the conversion of cytosine to uracil is a common mutation in DNA  By utilizing thymine in DNA< any uracil is easily recognized as a damaged cytosine that needs to be repaired o DNA is double stranded, so in the case of a mutation to one of the strands, the information contained on the complementary strand can be used to correctly repair the damaged strand  Gives the cell a way to maintain the sequence of genes  RNA does not have this due to being single stranded Energy Harnessing Reaction Pathways  Early metabolism was probably based on simple oxidation reduction reactions o Metabolic pathways require energy  Our cells o Oxidize food molecules - Energy (electrons)  Energy to drive metabolism comes from food molecules  The energy is extracted from the food molecules by oxidization  The energy is being extracted from the food molecules -  energy is in the form of electrons o Use energy to reduce other molecules  Energy is used to reduce other molecules in order to drive the metabolic processes (synthesize) o Multi step process  Respiration: extracting the energy from food molecules  Complicated process  Primitive Cells o One step process Energy Harnessing Reaction Pathways  Oxidation reduction reactions OIL RIG (Oxidation Is Loss Reduction Is Gain)  Diagram: Compound A is the food molecule, Compound B is something that needs to be reduced in order to be useful o Molecule A goes from being reduced to being oxidized o Molecule B goes from being oxidized to being reduced o Some energy is always lost during this process - drive other metabolic processes  Development of intermediate carriers o Energy is released and needs to be used o If its not used, its lost  ATP (adenosine triphosphate) became coupling agent that links energy releasing reactions to those requiring energy (page 60) o Energy through these multi step processes is captured into ATP which will link to other metabolic processes to be used in a different time and place o Energy currency of a cell - all cells use this The Earliest Evidence of Life is found in Fossils  Stromatolies o A type of layered rock that is formed when microorganisms bind particles of sediment together, forming thin sheets o Found in habitats characterized by warm shallow water  Early photosynthetic organisms would have had the ability to take carbon dioxide from the atmosphere and use it to synthesize various organic molecules The First Cells Relied on Anaerobic Metabolism  Earliest forms of life were simple prokaryotes o Earliest fossil evidence was about 3.5 billion years ago o Indirect evidence (carbon isotope ratios): about 3.9 BYA  Early Prokaryotes: Heterotrophs o Anaerobic respiration to extract energy (absence of oxygen) o Organisms that require their energy and nutrients from outside sources o Obtain carbon from organic molecules o Example: Humans o Must have relied on anaerobic (without energy) forms of respiration and fermentative pathways to extract energy from organic molecules  Autotrophs o Can synthesize own food o Obtain carbon from the environment in an inorganic form o Plants and other photosynthetic organisms o First autotrophs performed anoxygenic photosynthesis used H2S instead of H2O  Were not producing oxygen because they did not use water, used hydrogen sulfide and iron instead  Water creates oxygen so there was no oxygenic photosynthesize Solar Powered Sea Slug  A heterotrophic organism acquires ability to be autotrophic o Extracts chloroplasts from algae and uses them to produce food Oxygenation of the Atmosphere: Where did the oxygen come from?  Atmosphere oxygen began increasing approx.. 2.5 BYA  Due to cyanobacteria that evolved the ability to use H2O instead of H2S as the source of electrons  The O2 in the atmosphere comes from a type of photosynthesis that oxidizes water o Used water (has oxygen) instead of hydrogen sulfide - produce oxygen and release it into atmosphere o Oxygen levels increased rapidly in the atmosphere  This adaptation was a huge evolutionary advantage to cyanobacteria  Water was more abundant, new organisms allowed the organisms to periphilate  On abiotic Earth, polymerization of organic molecules may have involved clay surfaces  Oxygenic photosynthesis o Oxidation of water releases not only electrons, which can be used for photosynthetic electron transport, but also molecule oxygen o Initially free oxygen was incorporated into mineral deposits including iron o Oxygen started to accumulate in the atmosphere o Photosynthesis that relies on the oxidation water meant that cyanobacteria could thrive almost anywhere on the planet where there was sunlight Section 3.4e: LUCA  Archaea, bacteria, Eukarya  Share a similar cell architecture o Including the lack of a nucleus they are often referred to as prokaryotes  Molecular evidence indicates that archaea are more closely related to eukaryotes than to bacteria  All forms currently on Earth share a remarkable set of common attributes o Cells made of lipid molecules brought together forming a bilayer o A genetic system based on DNA o A system of information transfer - DNA to RNA to protein o A system of protein assembly from a pool of amino acids by translation using messenger RNA (mRNA) and transfer RNA (tRNA) using ribosomes o Reliance on proteins as the major structural and catalytic molecule o Use of ATP as the molecule of chemical energy o The breakdown of glucose by the metabolic pathway of glycolysis to generate ATP Section 3.5e, 3.5f: Multicellularity Solving an Energy Crisis May Led to Eukaryotes (e)  Compared to eukaryotes; archaea and bacteria show remarkable biochemical flexibility, being able to use an assortment of molecule as sources of energy and carbon and thrive in harsh environments uninhabitable to eukaryotes  Prokaryotic cells are simple  Increased complexity requires increased energy, and while eukaryotic cells can generate huge amounts of it, prokaryotic cells cannot  Mitochondria, like their aerobic progenitor bacteria, undergo aerobic respiration, which generates much greater amounts of ATP from the breakdown of organic molecules than pathways of anaerobic metabolism  Typical aerobic bacterium relies on its plasma membrane for many functions, including nutrient and waste transport and energy production, a typical eukaryotic cell contains hundreds of mitochondria  Cells could become larger as now there was enough energy to support a greater volume o More complex The Evolution of Multicellular Eukaryotes Led to Increased Specialization (f)  Evidence appears in the fossil record  Group of individual cells of a species came together to form a colony, or a single cell divided and the resulting 2 cells remained together  All cells are structurally and functionally autonomous (independent)  Key trait of more advanced multicellular organisms o Division of labour  Cells were not functionally identical and thus usually not structurally similar o Harvesting energy o Specific role in the motility of the organism  Cells cooperate with one another for the benefit of the entire organism  A cell colony is a group of cells that are one type; there is no specialization in cell structure of function  Volvox consists of a sphere of 2 to 3 thousand small, flagellated  Chlamydomonas like cells that provide the individual Volvox with the ability to move Energy and Enzymes 11/30/2012 10:03:00 PM Why it Matters  Life requires temperatures that are relatively cold (below 100 degrees) o At the low temperatures, the chemical reactions would be very slow o Speed up reactions by adding heat into the system  Without enzymes to speed up rates of chemical reactions, life as we know it could not exist o Speed up rate of reactions  Phosphatase enzymes removes a phosphate from a protein in - 10 ms  The uncatalyzed reaction would take - 1 trillion years Energy  The capacity to do work o Kinetic energy: energy of motion o Potential energy: stored energy  Energy may be converted readily from one form to another Thermodynamics  Study of energy and its transformations  Closed system o Exchanges energy but no matter with surroundings o A pot of water boiling on the stove  If put lid on the pot, then none of the steam can leave (energy escaping from the pot, but no exchange with matter)  Open system o Exchanges energy and matter with surroundings o All organisms are opened systems  Isolated System o Does not exchange matter or energy with its surroundings o Insolated thermos  Put hot liquid in, it will maintain all the energy inside  No exchange of energy or matter with its surroundings Closed and Open Systems  Isolated system  Closed system  Open system First Law of Thermodynamics  Energy can be transformed but not created or destroyed o Conservation of energy  Total amount of energy in a system and its surrounds remains constant Energy Transformations: Waterfall 1. A water molecule sitting at the top of a waterfall has a defined amount of potential energy 2. As the molecule falls, some of this stored energy is converted to kinetic energy (the energy of motion) 3. When the molecule strikes the rocks below, its energy of motion is converted to thermal, mechanical and sound energy a. The molecules potential energy is now much lower b. The change in potential energy has been transformed into an equal amount of mechanical energy, heat and sound Second Law of Thermodynamics  Each time energy is transformed, some is lost (is unavailable to do work) o Can never have 100% efficiency o The unused energy that is released increases disorder  Energy and disorder are linked o Only 30% of energy in gas is converted into mechanical energy  Lots of energy is being lost  Example: car o Only 40% of the energy in glucose is converted to ATP  Respiration  During this conversion, most of the energy is lost (given off in different forms)  Total disorder of a system and its surroundings always increases (page 74) o Always increasing in disorder  Entropy o Is a measure of disorder Life and The Second Law of Thermodynamics  Life is highly ordered, which suggests that it goes against the second law of thermodynamics o Always must consider the organism and their surroundings  Living things bring in energy and matter to generate order out of disorder o In the process of maintaining order, the chemical reactions (chemical order) that are taking place are contributing to the disorder of its surroundings o Example: Disorder can be in forms of heat Why Do We Need to Eat?  Average person consumes 1500 kal/day  A significant portion of this energy is used to maintain  We eat food to maintain low entropy o Organisms maintain low entropy at the expense of increase entropy of their surroundings Thermodynamics in the Living Cell  Link between energy and entropy  Same amount of energy in both Energy Content and Entropy Contribute to Making Reaction Spontaneous  Spontaneous reactions - occur without an input of energy form the surroundings  Reactions tend to be spontaneous if products have less potential energy than reactant o Enthalpy (H) - potential energy in a system  Reactions tend to be spontaneous when products are less ordered than reactants o Entropy (S) - amount of randomness or disorder Potential Energy of Products and Reactants  Endothermic reactions o Reactions that absorb energy  Products have more potential energy than reactants  Exothermic reactions o Reactions that release energy  Products have less potential energy than the reactants  Example: burning of natural gas (methane) o CH4 + 2O2 - CO2 +2H2O o An exothermic reaction A Spontaneous Endothermic Reaction  How can melting of ice be a spontaneous reaction if its endothermic  Melting of ice increases entropy  Phase changes result in an increase in entropy o Solid - liquid - gas Free Energy (ΔG)  Energy available to do work  ΔG = ΔH – TΔS  Δ (delta) = change (final state – initial state)  ΔG = change in free energy (Gibbs Free Energy)  ΔH = change in enthalpy
 T = absolute temperature (degree Kelvin)
  ΔS = change in entropy  A reaction goes to completion, it is influenced by 2 factors o Changes in energy content: ΔH o Changes in entropy: ΔS  For spontaneous reaction, ΔG < 0 Chemical Reactions and Equilibrium  Equilibrium o Maximum stability o Point is reached when reactants are converted to products and products are converted back to reactants o The rate of the forward and reverse reactions are equal  Equal rates - ΔG = 0  Conversion of glucose 1-phosphate to glucose 6-phosphate Equilibrium in Living Systems  Living systems are open  ΔG of life always negative as organisms continually take in energy rich molecules - or like, if photosynthetic o Continually use them to do work  Organisms reach equilibrium - ΔG = 0 only when they die Metabolic Pathways and Reactions  Two groups of reactions o Exergonic reaction  Where ΔG is negative  Products contain less energy than reactants o Endergonic reaction  Where ΔG is positive  Products contain more free energy than reactants Exergonic and Endergonic Reactions  Exergonic reaction o Free energy is released o The products have less free energy than was present in the reactants o Reaction proceeds spontaneously o Negative ΔG  Endergonic reaction o Free energy is gained o Products have more free energy than was present in reactants o Not spontaneous o Proceeds only if energy is supplied by an exergonic reaction o Positive ΔG - subtract a small number from big number, will still have a big number Free Energy Summary  Free energy changes when the potential energy and entropy of substances changes  Chemical reactions run in the direction that lowers the free energy of the system  Exergonic reactions are spontaneous and release free energy  Endergonic reactions are nonspontaneous are require an input of energy to proceed Metabolic Pathways and Reactions  Metabolic pathway o Series of sequential reactions in which products of one reaction are used immediately as reactants for the next reaction in the series  Catabolic pathway o Energy is released by breakdown of complex molecules to simpler compounds  Anabolic pathway o Consumes energy to build complicated and molecule from simpler ones Catabolic and Anabolic Pathways Example Catabolic Pathway: cellular respiration ( break down of glucose ), ATP - ADP Example Anabolic Pathway: photosynthesis ATP  ATP- adenosine triphosphate  ATP hydrolysis releases free energy that can be used as a source of energy for the cell  What kind of reaction is the hydrolysis of ATP? ATP and Energy Coupling  Hydrolysis of ATP o Exergonic reaction o Coupled to make endergonic reactions - proceed
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