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Wilfrid Laurier University
David Smith

Chapter one A Green Alga -using light for both energy and information, structure that allows this is called the eyespot (light sensor) can sense where light is coming from, and will move towards it so it can use it to use light as a source of energy (via chloroplast) The Sun -converts matter into energy (in the form of electromagnetic radiation) Range of electromagnetic spectrum: Gamma, x-ray, ultraviolet, near-infrared, infrared, microwaves, radio waves -shorter the wave length, the higher the energy Longer the wave length, lower the energy “Visible Light 400-700nm” Blue – shorter, Red – Long Different kinds of UV rays What is Light? Electromagnetic radiation that humans can detect with their eyes -a wave of discrete particles called photons Wave length – distance between two successive peaks For light energy to be used, must be absorbed/interact by molecules called pigments See. Fig 1.6 on page 5 Light interacting with matter – some wave lengths are absorbed by pigments, some are reflected, others go straight through. Typically green light is reflected off which why plants appear green is. If you try to grow a plant with only green wave lengths the plant will not grow. Pigment Structure (see slide 6 for visual) Wide variety of different kinds of pigments All have alternating double and single bonds between carbons “Conjugated system” It is the electron that absorbs the light, so the electron is “delocalized” and able to absorb, not held close to molecule Pigments are differentiated because they all absorb different wave lengths of light Color we see are a result of the wave lengths NOT absorbed Absorption of light by chorophyll Ground state, when electron is at more basic energy level When an electron absorbs photon of light, gets “excited” and rises energy levels See figure on page 8, amount of energy in red wave length matches the difference between ground state and energy state one. Save goes for blue photon, blue wave length matches the difference in energy between ground state and energy level 2 because it has more stored energy. -halobacteria also captures light energy  live in very salty waters, absorb different wave lengths and reflect wave length of the pink color retinal pigment in this bacteria absorbs a different wave length, when it receives light it changes its conformation, which changes the conformation of the protein, which pumps protons from the inside of the cell to the outside to cell when enough of this happens it creates a gradient, increase concentration on outside of cell and low concentration on inside of cell; this is a form of potential energy. this potential energy is then used by ATP-ase, when the protons pass through it, energy is used to convert ADP + Pi, into ATP (stored energy) Light as a source of information: Photoreceptors – basic light-sensing system, found almost universally in all organism -a pigment molecule bound to a protein Rhodopsin – most common photoreceptor in nature (basis of vision in animals, also used by other organisms) -highly conserved photoreceptor that consists of a pigment molecule (retinal) bound to a protein (opsin) Bacteriorhodopsin – membrane protein bound to a molecule of retinal, allows halobacteria to use light as a source of energy, and is a protein pump -bacteria rhodopsin is using light as a source of energy, not really a “photoreceptor” -rhodopsin is using light as a source of information -in rhodopsin the conformation change, leads to other cellular changes that will lead to metabolic changes (not pumping protons like in retinal pigment) Eyespot – sensing light without eyes -allows sensing of light direction and intensity, organism responds by phototaxis (process of moving towards or away from source of light to optimise photosynthesis) Photomorphogenesis: Phytochrome is photoreceptor in plants, when it absorbs light it starts a bunch of metabolic processes. plant is grown in the dark, it will grow long skinny and white and have virtually no green *Signal transduction pathway is a result of activation of a photoreceptor What distinguishes the eye of an animal from the eyespot of the green algae C. reinhardtii? Vision  requires a brain to interpret signals sent from eye -> co-evolution (most likely) Simplest eye (ocellus of planaria, flat worm)  senses light direction and intensity Compound eye of a deer fly  each eye is made up of thousands of ommatidium Receives a mosaic image of the world, extraordinarily adept at detecting movement Camera eyes (octopus eye)  eyes with single lenses (same as human eye) (Not going to get tested on structure of eye) Evolution of the eye “Darwin” (summarize) 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 -->watch video on slides small portion of spectrum essential for life  400-700nm Long wavelengths – tend not to reach earth, also not the right wavelength to excite electrons Shorter wavelengths – do reach earth and can damage biological molecules (damage DNA – skin cancer) -Protective mechanisms to protect us from these damaging wave lengths, (other pigments beta carentine, that absorb shorter wave lengths, melanin serves as a protective mechanism that absorbs damaging wave lengths of light) (plants also have mechanisms that heal damaged cells) (DNA is most susceptible to damage when replicating, so replication typically duplicates in the dark over evolution) (see section 1.5 for more details) Circadian Rhythms we are tired when its dark, not as tired when its bright jet lag (circa) around (dian) day are not direct responses to light, it is not that fact that your body senses light and makes you hungry, it is the fact that your body knows what time it is going to be light, and at that time you get hungry. if you are in the dark for three weeks, eventually your circadian rhythm, will go. oscillate with a period of approximately 24 hours controlled by an internal organism-based clock not just mammals, plants also have circadian clocks. sunflower example, track the light, go to sleep at night time, open up leaves and turn towards the east so when the sun rises it is ready to go Chapter 2  the Cell: An Overview Cell theory All organisms are composed of one or more cells (cells of multicellular organisms can sustain themselves independently under the right conditions) The cell is the basic structural and functional unit of all living organisms (if you break a cell open and isolate the component parts, they can’t survive on their own. Need the cell as a whole unit to function) Cells arise only from the division of pre-existing cells 1600’s -cells first observed in the 1600’s by Robert hooke and anton van leeuwenhoek -hook coined the term “cellulae” -van leeuwenhoek described bacteria and protists as “animalcules” 1800’s Robert Brown – first to observe nucleus Mathias Schleiden – plants are made of cells, and nucleus is important for development Theodor schwann – all animals are made of cells Rudolf Virchow (Robert remak) – cells only arise from pre-existing cells What about Synthetic Cells? -First reported in 2010 - Mycoplasma – small genome was used, chemically synthesised entire genome with a few changes -took a cell of another related bacteria and removed the genome sothey had an empty organism -put synthetic genome and placed it in the empty bacteria of a different kind of bacteria -cell began to “boot up” and metabolize and divide -new cells were distinguishable of mycoplasma, no longer the same as the host bacteria Cell Division: microscopy has been key -most cells are too small to be seen unaided by the human eye Typical animal cell (50-30 micrometers in diameter) Bacterial cells (0.5-5 micrometers in diameter -figure of the scare (fig 2.3) page 27 -purple pages F-7 WHY AREN’T CELLS BIGGER? -Surface area-to-volume ratio -volume determines capacity for chemical activity -surface area determines the amount of transport in and out -double the diameter of the cell, you will increase volume by 8 times, but surface area only increase by 4 times (fig. 2.5 page 29) September 21, 2012 -check page 28 fig 2.4, see what light microscopy is Prokaryotes and Eukaryotes -all forms of life are based on two distinct types of cells: prokaryotic and eukaryotic -prokaryotic cells lack a nucleus (pro  before, evolutionarily earlier form of life, make up two of the domains of life: Bacteria and Archeae) -Eukaryotes (eu  true, yotesnucleus) -share basic features: Plasma membrane Cytoplasm (cyosol, organelles, cytoskeleton) All have ribosomes DNA organized into chromosomes Prokaryotes – circular one chromosome, eukaryotes – have many linear chromosomes Basic cellular processes (electron transport chain, transcription and translation) 3 domains of life: Bacteria, Archaea, Eukarya -look at chart page 481 that compares archaea vs. bacteria and eukarya Prokaryotic Cell Structure: E. Colli -see page 466-470 fig 20.6 for more details on cell wall of prokaryote cells -plasma, cell membrane, and in case of ecolli a capsule -lots of ribosomes in cytoplasm Characteristics of eukaryotic cells are different from prokaryotic cells -separation of DNA and cytosol by nuclear envelope -presence of membrane-bound compartments with specialized functions: mitochondria, chloroplasts, ER, golgi complex etc. -highly specialized motor proteins Page 32 (figure 2.8) “Typical Animal Cell” Page 32 (figure 2.9) “Typical Plant Cell” -90% of volume can be taken up by vacuole in plant cell -plasmadesmata (channels that connent adjacent cells) Eukaryotic Cells -distinguishing feature is the presence of a nucleus -presence of organelles (many are found only in eukaryotes) but prokaryotes can have organelles as well Organelle – a membrane bound compartment in a cell Why are organelles important? Compartmentalise the enzymes and proteins, creating chemical gradients, and having the cell more organized Nuclear envelope: -Nuclear envelope (phospholipid bilayer), have pores throughout nucleur envelope to let certain things in and others out. -Ribosomes on nucleus envelope Ribosomes – unifying feature of all cell types (translation) -bacterial, archaeal and eukaryotic are all slightly different -in eukaryotes some are free in cytosol, others are attached to endoplasmic reticulum membranes, still others are found in mitochondria and chloroplasts Three types of ribosomes: 1) found in cytosol or ER 2)found in mitochondria 3) found in chloroplasts Cytosolic ribosomes – not part of the endomembrane system Ribosomes on the Rought ER are part of the endomembrane system Endoplasmic Reticulum (ER) -extensive interconnected network of membranous channels and vesicles Rough ER – ribosome studded, makes proteins that become part of cell membranes or are released (Secreted) from cell Smooth ER – synthesizes lipids and is the site of many other essential cellular functions Endomembrane System -Characteristic feature of eukaryotic cells Nucleus envelop ER Golgi complex Lysosomes/vacuoles Vesicles Plasma membrane Golgi Complex -flattened membranous sacs -chemically modifies proteins made in Rough ER -sorts finished proteins to be secreted from cell or embedded in plasma membrane Ex. Antibodies are made at the ER, than go from ER to golgi, where they get modified and put into vesicles to be secreted out of the cell Vesicular Traffic Diagram pg. 37 fig 2-20 Exocytosis and Endocytosis: Exo – a secretory vesicle fuses with the plasma membrane, releasing the vesicle contents to the cell exterior Endo – materials from the cell exterior are enclosed in a segment of the plasma membrane that pockets inward and pinches off as an endocytic vesicle -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 Other molecules not part of the endomembrane system: Mitochondria – inner-membrane is bigger than outer membrane because of the cristae inside the cell that fold up inside the cell. Chloroplasts – three membranes? -mitochondria and chloroplasts have their own ribosomes; this is because each of these organelles also have their own genome and make SOME of their own proteins. Theory of endosymbiosis (section 3.5 pg 64-65) -Energy-transducing organelles, chloroplasts and mitochondria, thought to have been derived from free-living prokaryotic cells Mitochondria – developed from ingested prokaryotes capable of using oxygen for aerobic respiration (why they still do respiration to this day) Chloroplasts – developed from ingested cyanobacteria (cyanobacteria were photosynthetic) Pg. 65 figure 3.21 has diagram -first nucleus formed, very primitive cell with no organelles engulfed aerobic bacteria, these bacteria continued to live within the cell and became the mitochondria/chloroplast (depending on what type of cell, whether it engulf the aerobic bacteria or the cyanobacteria Evidence to support the endosymbiosis theory: Endo (within) sym (together) biosis (living) Symbiosis: can describe any close and prolonged relationship between individuals of 2 different species Nodulation: bacteria form structures called nodules on plant roots (bacteria fixes nitrogen so plant can form amino acids, plant process sugars which feeds bacteria) – eliminates need for fertilizer -mitochondria and chloroplasts resemble prokaryotes in numerous ways: -are each about the same size and shape as many bacterial cells -contain ribosomes (are more like bacterial ribosomes), possess electron transport chains, and contain their own DNA Morphology (outer membrane) – the outer membrane and inner membrane are very different, because when it was first engulfed the bacteria cell kept its own membrane, and part of the plasma membrane pinched off from the host cell as well. Reproduction (division) Genetic information (structure and organization of genomes) – the chromosome in a chloroplast and mitochondria is circular, like they are in bacteria, uncharacteristic of eukaryotes (where they are linear and straight) Transcription and translation – the transcription and translation that occurs is very similar to that of bacteria Electron transport chain – the electron transport system that occurs in bacteria is almost the exact same that it happens in mitochondria and chloroplast that they do now. Diagram: -started with a prokaryote (22billion years ago) formed a nucleus and a few ER’s. -this eukaryotic cell was very primitive -primitive eukaryote engulfed aerobic bacteria (1,9 billion years ago) -those bacteria through evolution became mitochondria (gave rise to plant cells) -then some of these primitive cells with mitochondria and nucleus and ER then engulphed another kind of bacteria (cyanobacteria) (1.6 billion years ago) -those cyanobacteria then revolutionized into chloroplasts (gave rise to plant cells) Semiautonomous – take organelle out of a cell, and it cannot exist on its own. -Chloroplast and mitochondria are different from endomembrane system -Import proteins on separate pathways back and forth, instead of through vesicles like the endomembrane system. Peroxisomes -another type of eukaryotic organelle that is NOT part of the endomembrane system Surrounded by single envelope membrane Do not have their own genome (Because of this, probably did not result from endocytosis) Site of biochemical pathways that generate hydrogen peroxide as a by product Fatty acid metabolism Enzymes that “scavenge” hydrogen peroxide are also abundant (Enzymes that find the h2o2, and engulf and destroy them so it doesn’t damage cell) -example of why organelles are an evolutionary benefit Cytoskeleton -supportive structure Animal and plant cells:  Cytoskeleton consists of three major types  Microtubules  Intermediate filaments  Microfilaments All made of proteins  Tubulin  Intermediate filament proteins  actin -experiment where negative pictures of a man was held up to a plant for a duration of time, while bright light was shone on it -the shadow of the man was visible -different shades of green, is because the chloroplasts moved within the cell to where either the negative was shining light coming through, or where it was blocked Chapter 3 – Defining life and its origins -there is very little difference between the biotic and abiotic worlds at the atomic/chemical level Seven characteristics of life: (see figure 3.2 on page 52 for pretty summary!) -display order, harness and utilize energy, reproduce, respond to stimuli, exhibit homeostasis, growth and development, and evolve. Virus – a protein shell with a nucleic acid inside (DNA or RNA viruses), no nucleus, no organelles, no membranes, but do have some properties of life:  display order, distinct shapes  reproduce (usually using a host cell)  evolve (example SARS, HIV) – the protein coat on virus are constantly changing -although they can’t produce their own proteins, and can’t maintain homeostasis (nothing there except protein and nucleic acid to maintain) -took 500 million years for the earth to cool down enough after big bang before it could even start to support life -was no oxygen in the atmosphere in early earth -lots of water vapor (due to heat), hydrogen sulphate gas, ammonia, methane. Biologically important macromolecules:  nucleic acids (DNA and RNA)  proteins  lipids  carbohydrates -all except lipids are polymers made up from simpler building blocks, and all are made within cells by complex metabolic pathways Formation of biologically important molecules: Oparin-Haldane Hypothesis: -organic molecules that form building blocks of life found have been formed in conditions that prevailed on primitive earth (page 55) -reducing atmosphere that lacked oxygen -allows for synthesis of complex organic molecules -see page 56 for other hypothesis Miller-Urey Apparatus -tested the oparin-haldane hypothesis -stimulated how primitive earth was (boiled water to form water vapor, lots of hydrogen sulphate, ammonia, methane, sparks to stimulate lots of lightning) in an airtight container -let run for a week, and analyses the products, and found amino acids, and lipids, and sugars, and nucleotides which proves previous hypothesis. -possible to produce organic molecules from abiotic conditions Polymers from Monomers -key macromolecules of life, such as proteins and nucleic acids, are polymers that were NOT formed in the Miller- Urey experiment -polymerization reactions may have occurred on solid surfaces. Example: clay (see figure 3.12 page 56-57) Protobionts; The first cells -group of abiotically produced organic molecules that are surrounded by a membrane or membrane like structure (page 57) -can form spontaneously -phosopholipids in solution will spontaneously form a membrane -hydro phobic tails hydrol philic head groups (polar) -primitive cell-like structures -have some of the properties of life -may have been the precursors of the cell The Central Dogma: -information is stored in DNA -the information in DNA is copied into RNA -the information in RNA guides the production of proteins 1979 page 30 -Thomas Cech discovered ribozymes -ribozymes: RNA molecules that catalyze specific reactions Ribozymes are still present in cells today -ribosome is essentially a fancy ribozyme, it’s the RNA in the molecule that performs translation; the rest is just structure RNA is not always straight, it can fold up on itself and take on weird shapes -RNA takes on certain shapes like enzymes do, and can serve as a catalyst -hypothesis was maybe there were RNA molecules in the primitive cell like structure -would have catalysed reactions, and given those cells an advantage... so those cells would live more than other cells with no RNA molecules -DNA and proteins may have evolved after RNA Testing RNA World hypothesis: -david bartel’s laboratory in MIT -trying to create, in vitro a ribozyme that is capable of catalyzing the addition of ribonucleotides to an existing strand of RNA -employed “in vitro evolution” started with a set of millions-billions of different large RNA molecules -selected the ribozymes with the best activity, randomly mutated the sequences, and repeated at least 18 times Protein s and DNA -proteins became dominant structural and functional macromolecule of all cells -proteins are made up of 20 different amino acids, and only 4 nucleotides that make up RNA -proteins are more complex and can catalyze more enzymes -ribozymes are generally slow, and can only catalyze a small number in comparison to proteins -DNA is double stranded and more stable than RNA and thus evolved as better repository of genetic information. -RNA is very unstable, when isolation it from a cell has to take a ton of precautions. -the sequence of DNA has a second strand to fix if it is damaged, RNA only has one strand Energy-Harnessing Reaction Pathways -early metabolism (metabolic pathways require energy) was probably based on simple oxidation-reduction reactions Our cells -oxidize food molecules (energy, electrons) -use energy to reduce other molecules -multi-step process Oxidation-reduction reaction -reduced compound A (extra energy in form of electrons) -compound A is oxidized losing electrons -oxidized compound A Development of intermediate carriers ATP (Adenosine Triphosphate) – became coupling agent that links energy-releasing reactions to those requiring energy (page 60) -every organism uses ATP as energy carrier Earlist forms of life (section 3.4) -earliest forms of life were most likely simple prokaryotes -earliest fossil evidence 3.4billion years ago -indirect evidence (carbon isotope ratios) 3.9 billion years ago EARLY prokaryotes -heterotrophs (as opposed to autotrophs) anaerobic respiration to extract energy -first autotrophs performed anoxygenic photosynthesis (used H2S instead of H20) -early earth, reducing earth so almost no oxygen in atmosphere Heterotrophs – the don’t make their own food, acquires energy from outside sources -FIRST LIFE FORM THAT EVOLVED ON PRIMITIVE EARTH = ANAEROBIC HETEROTROPHIC ORGANISM Oxygenation of the atmosphere -atmospheric oxygen began increasing approx. 2.5 billion years ago -due to cyanobacteria that evolved the ability to use h20 instead of h2s as the source of electrons (oxygenic photosynthesis) Solar Power Sea Slug -a heterotrophic organism acquires ability to be autotrophic -extracts chloroplasts from algae & uses them to produce food Section 3.4e: LUCA Sections 3.5e, 3.5f: Multicellularity Order of development of organisms 1) Heterotrophic anaerobic organisms 2) Anoxygenic photosynthetic organism 3) Oxygenic photosynthetic organism After midterm Chapter 4 Energy and Enzymes -life requires temperatures that are relatively cold (below 100 degrees Celsius) -without enzymes to speed up rates of chemical reactions, life as we know it could not exist -phosphatase enzymes remove phosphate groups from proteins in  10ms -the uncatalyzed reaction would take  1 trillion years! Energy  the capacity to do work  Kinetic Energy: energy of motion  Potential Energy: Stored energy  Energy may be converted readily from one form to another Thermodynamics  Study of energy and its transformations  Closed systems: exchanges energy but not matter with surrounding  Open systems: exchanges energy and matter with surroundings  Isolated system: exchanges nothing with its surroundings Laws of Thermodynamics: 1. Energy can be transformed but not created or destroyed (conservation of energy), total amount of energy in a system + surroundings remains constant 2. Each time energy is transformed, some is lost (unavailable to do work), can never have 100% efficiency. The unused energy that is released increases disorder of the system or the surroundings. Ex. Only 30% of energy is gas in converted into mechanical energy. Ex. Only 40% of energy in glucose is converted to ATP. Total disorder of a system and its surroundings always increases. Entropy – measure of disorder. More disorder, Higher Entropy. Life is highly ordered, which suggests that it goes against the second law of thermodynamics. Living things bring in energy and matter to generate order out of disorder. Total disorder of a system and its surroundings always increase Why do we need to eat?  Average person consumes 1500 kcal/day  A significant portion of this energy is used to maintain order in our cells  We eat food to maintain low entropy Spontaneous Reactions  occur without an input of energy from the surroundings -removed of phosphate from an ATP molecule (occurs spontaneously but would take a trillion years if not for a catalyst, rust accumulating on a nail, a match) – not always fast -reactions tend to be spontaneous if products have less potential energy than reactants Enthalpy (H): Potential energy in a system -reactions also tend to be spontaneous when products are less ordered than reactants Entropy (S): amount of randomness or disorder -we eat to maintain low entropy Endothermic Reactions  Reactions that absorb energy  Will feel cold to the touch  Products have more potential energy than reactants  How can melting of ice be a spontaneous reaction if it is endothermic? Melting of ice ICNREASES entropy, ice is a more ordered form than liquid water  Solid  liquid  gas  Not only energy decides of if something is spontaneous, also entropy Exothermic Reactions  Reactions that release energy  Products have less potential energy than the reactants  Ex. Burning of natural gas (methane) a spontaneous, exothermic reaction  Will generally feel warm to the touch Free Energy (Delta G) -energy available to do work G = H – T S G – Change in free energy (Gibbs free energy) H – Change in enthalpy T – Absolute temperate (degree Kelvin) S – Change in entropy -as reaction goes to completion it is influenced by two factors (change in energy and entropy) -if there is a big loss of energy, H will be negative, and reaction will be spontaneous -for a spontaneous reaction, G<0 Chemical Reactions and Equilibrium -equilibrium is maximum stability -equilibrium point is reacted when reactants are converted to products and products are converted back to reactants at equal rates G = 0 Equilibrium in Living Systems -living systems are open -G of life always negative as organisms continually take in energy rich molecules (or light, if photosynthetic) and continually use them to do work -organisms reach equilibrium only when they die (change in G = 0) Metabolic Pathways and Reactions Exergonic reaction – where G is negative because products contain less free energy than reactants – energy is released – reaction proceeds spontaneously Endergonic reactions - where G is positive because products contain more free energy than reactants – not spontaneous, proceeds only have energy supplied by exergonic reaction Free Energy Summary -free energy changes when the potential energy and or 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 and require an input of energy to proceed Metabolic Pathways Metabolic pathway – series of sequential reactions in which products of one reaction are used immediately as reactants for the next reaction in the series Catabolic pathway – energy is released by breakdown of complex molecules to simpler compounds ex. Respiration Anabolic pathway – consumes energy to build complicated molecules from simpler ones (Anabolic steroids) – adenine di-phosphate to adenine triphosphate, or photosynthesis *things may have an overall spontaneous status, but doesn’t actually occur spontaneous because some steps require input of some energy 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? It is the removal of the terminal phosphate to make an ADP and energy. This is an exergonic reaction that releases energy, that energy can then be used to drive endergonic reactions. The exergonic reaction can be coupled to make otherwise endergonic reactions proceed spontaneously. Coupling reactions require enzymes.  Most of potential energy stored in ATP that is available to drive cellular reactions is found in the bonds between the phosphate groups ATP/ADP Cycle -exergonic catabolic reactions supply energy for endergonic reaction producing ATP from ADP +P, exergonic reaction hydrolyzing ATP provides energy for endergonic reactions in the cell Enzymes -just because a reaction is spontaneous does not mean that is proceeds rapidly -enzymes are a special group of proteins that can alter the speed of a reaction Activation Energy  Initial input of energy to start a reaction even if it is spontaneous  Activation energy EAinitial energy investment required to start a reaction  Molecules that gain necessary activation energy occupy the transition state Biological Catalysts  Catalyst: chemical agent that speeds up the rate of reaction without itself taking part in the reaction  Enzymes: are biological catalysts that increase the rate of a reaction by lowering activation energy of a reaction  Enzymes do not change the delta G of the reaction (the energy released by the reaction) Enzyme Specificity  Active sit of enzyme combines briefly with reactants (substrates)  Enzyme is released unchanged, although may change in the middle of the process  Enzyme is much bigger than substrate and very complex  Substrate binds to specific location (binding site or active site)  Binding site determined by the conformation of both the enzyme and substrate  May be multiple binding sites, but only one active site  Enzyme slightly changes conformation upon binding of the substrate Catalytic Cycle of Enzymes 1. Substrate, lactose, binds to the enzyme beta-galactosidase forming an enzyme substrate complex. Transition state is reached tightest binding but least stable 2. Beta-Galactosidase catalyzes the breakage of the bond between the two sugars of lactose and the products are released 3. Enzyme can catalyze another reaction Enzyme Cofactors  Enzyme cofactors – inorganic ions or organic non-protein groups necessary for catalysis to occur  Cofactors – metallic ions (Mg2+, Fe2+, Cu2+,Zn2+)  Coenzymes – organic cofactors such as vitamins Transition State  During catalysis the substrate and active site form an intermediate transition state  Enzymes facilitate the formation of the transition state via 3 major mechanisms: o Bringing the reacting molecules into close proximity o Exposing the reactant molecules to altered environments that promote their interactions o Changing the shape of a substrate molecule Formation of Transition State  Bringing the reacting molecules together reacting molecules can assume the transition state only when they collide; binding to an enzymes active site brings the reactants together in the right orientation for a catalyst to occur  Exposing the reactant molecule to altered charge environments that promote catalysis. In some systems the active sit of the enzyme may contain ionic groups whose positive or negative charges alter the substrate in a way that favours catalysis.  Changing the shape of a substrate molecule (distort or strain substrate molecules) Enzyme and Substrate Concentrations  In presence of excess substrate, rate of catalysis is proportional to amount of enzyme  At constant, moderate amount of enzyme -Low substrate concentrations reaction rates are slow  enzymes and substrate collide infrequently  High substrate concentrations (enzymes become saturated with reactants, rate of reaction levels off)  Excess substrate: linear line  Enzyme concentration is kept constant Enzyme Inhibition  Enzyme inhibitors are non-substrate molecules that can bind to an enzyme and decrease its activity  Two classes  Differ in how strongly they bind -Reversible: weak -Irreversible: strong Covalent bonds Highly toxic (e.g. cyanide), can be drugs or antibiotics as well, and cell can inhibit itself by regulating its own enzyme activity Competitive Inhibitors  Substrate is unable to bind when inhibitor is bound to active site  Competitive inhibitor molecule resembles substrate and completes for active site Non-competitive Inhibitors  Substrate cannot bind  Non-competitive inhibitor binds at a site other than the active site, causing the enzymes shape to change so that substrate cannot bind to active site. Enzyme Regulation  A futile cycle occurs when two metabolic pathways run simultaneously in opposite directions and have no overall effect other than wasting energy  Enzyme activity is often regulated to meet the needs for reaction products  Allosteric regulation and feedback inhibition are important examples Allosteric Regulation  Occurs with reversible binding of a regulatory molecule to the allosteric site, a location on the enzyme outside the active site  Look at figures on page 87 Fig. 4.21 for activation and inhibition examples o High-affinity state (Active form); enzyme binds to substrate strongly o Low-affinity state (inactive form); enzyme binds to substrate weakly or not at all Feedback Inhibition  Product of enzyme-catalyzed pathway acts as a regulator of the reaction  Helps conserve cellular resources  Mechanism is allosteric regulation  Is a reversible reaction  Enzyme A  Enzyme B  Enzyme C, have too much C, so C tells A to stop making B, to stop making C. Covalent Modification  Pg. 88, example phosphorylation Temperature and pH effects  Typically each enzyme has an optimal temperature and pH where it operates at peak efficiency  At temperature and pH values above and below optimum, reaction rates fall off Effects of pH  Most enzymes have a pH optimum near the pH of a cellular contents, about pH 7 (neutral)  Enzymes secreted from cells may have pH optima farther from neutrality  digestive enzymes - acidic  Changes in pH affect the charged side groups in the amino acids of the enzyme Effects of Temperature  Two distinct effects o As temperature rises, the rate of reactions increases o High temperatures effect proteins, including enzymes, by denaturing (takes away 3D conformation) them, and reducing the rate of reactions Chapter Five Cell Membranes and Signalling The Importance of Selectively Permeable Membranes  Cells and organelles need barrier to separate internal and external contents  Barrier must have following qualities o Impermeable to most molecules and ions o Ability to exchange molecules/ions between compartments o Insoluble in water o Permeable to water  water can move across membrane Functions of membranes 1. Boundary and permeability barrier 2. Organization and localization of function 3. Transport processes 4. Signal detection 5. Cell-to-cell interactions and communication What is a cell membrane?  A permeability barrier than consists of; o Phospholipids, glycolipids o Sterols (cholesterol – animals) (ergosterols - fungi) (phytosterols -plants) Mosaic Model  Proof in example about mice and human cells:  Membrane proteins labeled with red or green,  Mixed under cell fusion  Part of cell looked red, part looked green  Tracked under microscope for 40 minutes and membrane mixed over  Proved that membrane wasn’t rigid, it was a fluid structure Cell Chemistry Review  Water molecules are polar  Polarity – is an uneven distribution of charge in molecule  Electronegative – oxygen atom associates with electropositive hydrogen atoms of adjacent water molecules to form hydrogen bonds  Hydrogen bonds are also important in DNA and proteins  A solvent is a fluid in which another substance, called a solute can be dissolved  Polar/charged molecules form hydrogen/ion bonds with water molecules  Hydrophilic (wave loving) sugars, DNA, RNA, organic acids, and some amino acids  Hydrophobic (water fearing) do not dissolve in water, lipids (hydrocarbons), some amino acids (those in integral membrane proteins that associate with lipids) Hydrophobic molecules  No polar regions  Do not interact electrostatically with water  Disrupt hydrogen –bonded structure of water  Tend to coalesce with each other in water  Water molecules tend to exclude molecules that disrupt hydrogen bonding  Hydrophobic interactions are a major driving force in folding of molecules (like proteins), assembly of cellular structures, and membrane organization. Phospholipids are Amphipathic (part that is polar, part is non-polar) Polar head – hydrophilic 2 non-polar hydrocarbon tails – hydrophobic Membrane Fluidity  Fluidity of lipid bilayer dependent on how densely individual phospholipid molecules can pack together  Influenced by two major factors o Composition of the lipid molecules (degree of unsaturation of fatty acid tails, sterols) o Temperature Packing of Membrane Lipids 1. Phospholipids composed of saturated fatty acids a. Each carbon is bound to max number of hydrogen’s (all single bonds between C’s) b. Straight shape, tighter packing c. More viscous/gel like 2. Phospholipids composed of unsaturated fatty acids a. Double-bonds between carbons introduce kinks (bends in the conformation) b. Less dense packing c. More fluid Temperature  If temperature drops low enough, phospholipid molecules become closely packed, and membrane forms highly viscous semisolid gel  At low temps  enzymes and proteins cannot function if fluidity is not maintained  At high temps  too fluid, get leakage Adjusting fatty acid composition  Proper fluidity can be maintained over a broad range of temperatures by adjusting fatty acid composition of the phospholipids, done by the cell. As temperatures get colder, organisms can increase number of unsaturated fatty acids  Desaturases: enzymes that produce unsaturated fatty acids during fatty acid synthesis: introduce double bonds into fatty acids  Regulation of desaturases allows for organisms to closely regulate amount of unsaturated fatty acids and membrane fluidity Desaturases  Are enzymes that introduce double bonds  As the temperature increases, the amount of desaturases being produced decreases (measured by looking at % of transcription)  Amount of desaturases produced below 30 degrees starts increasing to increase fluidity Sterols are membrane buffers  Example: cholesterol, essential part of membrane  Structure 4 ring structure is hydrophobic, hydrophilic is very small; just a hydroxide group  Help to maintain proper membrane fluidity at both high and low temperatures  Without cholesterol, membranes would become too viscous at temperatures that are not particularly low  At high temperatures there is normally too much motion, so cholesterol restrains movement at high temperatures  At low temperatures there is too much rigidity, so It prevents fatty acids from interacting with each other and not getting too close Membrane Proteins; key functions of membrane proteins  Transport of specific ions or molecules across membrane  Enzyme activity, some membrane proteins are enzymes anchored in membrane  Signal transduction that sense hormones or food or viruses and lead to cellular response  Attachment/recognition for attaching to cytoskeleton Integral Membrane Proteins  Proteins embedded in phospholipid bilayer  Composed of predominantly nonpolar amino acids often coiled into alpha helices  Most integral proteins are trans-membrane proteins, are on both sides of the membrane (go through) Trans-membrane proteins  Nonpolar amino acids are hydrophobic  Tend to be in trans-membrane portion Peripheral Membrane Proteins  On surface of membrane  Do not interact with hydrophobic core  associate with membrane surface through non-covalent bonds (ionic and hydrogen bonds)  Most on cytoplasmic side of me
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