Bio 1000 Final Notes PDF

Chapter 1-Light and Life Light serves 2 functions: 1) a source of energy that directly or indirectly sustains virtually all organisms. 2) light provides organisms with info about the physical world that surrounds them - Wavelength: distance between 2 successive peaks - Light: most...

Chapter 1-Light and Life Light serves 2 functions: 1) a source of energy that directly or indirectly sustains virtually all organisms. 2) light provides organisms with info about the physical world that surrounds them - Wavelength: distance between 2 successive peaks - Light: most commonly defined as the portion of the electromagnetic spectrum that humans can detect with their eyes o 400-700nm o Light has no mass o Particle-wave duality: light is a wave of protons  Inverse relationship: the longer then wavelength, the lower the energy of the photons it contains  Photons: stream of energy particles - Although light has no mass, it is still able to interact with matter and cause change o When a photon of light hits an object, the photon has 3 possible fates: 1) reflected off object 2) transmitted through object or 3)absorbed by object - A major class of molecules that are very efficient at absorbing photons are called PIGMENTS o 3 types: 1) chorophyll a (involved in photosynthesis) 2) retinal (involved in vision) and 3)indigo (in jeans) o They can absorb photons easily because: they have a region where carbon atoms are covalently bonded to each other with alternating single and double bonds (conjugated system) which results in the delocalization of electrons…means the electrons are available to interact with a photon of light o Pigments absorb light at different wavelengths  Differs in the amount of excited states a pigment has o Photon absorption is related to the concept of colour  A pigments colour is the result of photons of light that it DOES NOT absorb - The basic light-sensing system is termed the PHOTORECEPTOR. o Most common photoreceptor is rhodopsin (basis of vision in animals) o Each rhodopsin molecule consists of a protein called opsin that binds a single pigment molecule called retinal. Opsins are membrane proteins that span a membrane multiple times and form a complex with the retinal molecule at the centre o Absorption of a photon of light causes the retinal pigment molecule to change shape. This change triggers alterations to the opsin protein which triggers downstream events, including alterations in intracellular ion concentrations and electrical signals. - Eyespot: o In organisms such as plants, algae, and invertebrates o Light sensitive structure o Within chloroplast of the cell o Photoreceptors of the eye spot allow the cell to sense light direction and intensity o Does not play a role in photosynthesis o Light absorption by the eyespot is linked to the swimming response by a signal transduction pathway o In plants: a photoreceptor called phytochrome senses the light environment  Present in the cytosol  Phytochrome becomes active and initiates a signal transduction pathway that reaches the nucleus  Critical for the normal developmental process activated when seedlings are exposed to light - The eye can be defined as the organ animals use to sense light o The process of vision requires not only an eye to focus and absorb incoming light but also a brain or at least a simple nervous system that interprets signals sent from the eye  We see with our brain, not with our eyes o Simplest eye: ocellus  The photoreceptor cell is actually a modified nerve cell that contains thousands of individual photoreceptor molecules  In flatworms o Compound eyes:  Common in insects  Built of hundreds of individual units called OMMATIDIA fitted closely together  Incoming light gets focused onto a bundle of photoreceptor cells by the ommatidia  Brain receives a mosaic image of the world  Good at detecting movement o Single-lens eye:  Most vertebrates including humans  Light enters through the transparent cornea; a lens concentrates the light and focuses it onto a layer of photoreceptor cells at the back of the eye, the retina. The photoreceptor cells of the retina send information to the brain through the optic nerve. - The photoreceptor cells that line the human retina can be damaged by exposure to bright light  o Photo-oxidative damage: the absorption of excess light energy can result in excited electrons reacting with O2, producing what are called reactive oxygen species o Ionizing radiation: photons at these wavelengths are energetic enough to remove an electron from an atom resulting in the formation of ions o Dimers: damage to structure of DNA resulting in change of shape of the double helix and prevents its replication. - Many organisms synthesize melanin, a pigment that strongly absorbs ultraviolet light o Humans synthesize melanin in specialized skin cells called melanocytes  Melanin synthesis increases upon skin exposure, which results in the brown colour of a suntan  People with high melanin levels who live in regions that do not receive abundant sunlight are susceptible to vitamin D deficiency  Some ultraviolet radiation is good to synthesize vitamin D - Circadian Rhythms o Circa=around diem=day o Governed by an internal biological clock o Free running: run along time independently of external conditions o A biological clock is built around a small set of so-called clock genes and clock proteins  The expression of these genes and proteins is autoregulatory: they control their own abundance o Presence of biological clock enhances an organism’s ability to survive under ever- changing environments by giving them the ability to anticipate or predict when a change will occur. o Photoperiod: when organisms keep track of the changing seasons in part by being able to measure day length o Suprachiasmatic nucleus (SNC): central clock which regulates the timing of clocks in peripheral tissues  Receives direct light inputs through the optic nerve of the eyes so that it can be reset periodically - Pollination involves the movement of pollen from anthers (male parts) of one flower, to the stigma (female parts) of the same or other flowers to effect fertilization and production of fruit and seeds o Plants that use animals as pollinators must obtain the correct candidates o Bees and some insects can see ultraviolet regions of the electromagnetic spectrum and are particularly attracted to flowers that strongly reflect ultraviolet radiation - Camouflage is used for concealment from either predators or prey o Colour, pattern and behaviour  - The presence of artificial light disrupts the orientation of nocturnal animals - With decreasing light levels, we first lose our ability to see colour, followed by our ability to distinguish shapes o Rod receptors, which do not perceive different colours, are about 100 times as sensitive to light as cone receptors - Bioluminescence: make their own light 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, and when the electron returns to the ground state, the energy is released as a photon of light o Used to attract mate or prey, camouflage and communication o Has not been reported in land plants or higher vertebrates Chapter 2- the cell: an overview - Cell theory o All organisms are composed of one or more cells o The cell is the basic structural and functional unit of all living organisms o Cells arise only from the division of pre-existing cells - If cells are broken open, the property of life is lost - Cells are bounded by the PLASMA MEMBRANE o Bilayer made of lipids with embedded protein molecules o Hydrophobic barrier o Semi permeable…maintains the specialized internal ionic and molecular environments required for cellular life - Central region of the cell o Contains DNA molecules o Genes: segments of DNA that code for individual proteins o Contains proteins that help maintain the DNA structure and enzymes that duplicate DNA and copy its information into RNA - Cytoplasm: o Contains organelles, cytosol and cytoskeleton o Cell’s vital activities occur in the cytoplasm o Organelles: small, organized structures important for cell function o Cytosol: aqueous solution containing ions and various organic molecules o Cytoskeleton: protein-based framework of filamentous structures that, among other things, helps maintain proper cell shape and plays key roles in cell division and chromosome segregation from cell generation to cell generation - Prokaryotic cells: o Three common shapes: spherical, rodlike and spiral o Does not contain a nucleus o Has a nucleoid: DNA-containing central region of the cell that has no boundary membrane separating it from the cytoplasm  o Individual genes in the DNA molecule encode the info required to make proteins.  This info is copied into mRNA (messenger RNA)  Ribosomes: use the info in the mRNA to assemble amino acids into proteins o Contains a cell wall-provides rigidity and protects cell  Cell wall is coated with an external layer of polysaccharides called GLYCOCALYX  When its diffused and loose=slime layer  When its gelatinous and firm=capsule  Helps protect cells from physical damage and desiccation and may enable a cell to attach to a surface o Plasma membrane: contains most of the molecular systems that metabolize food molecules into the chemical energy of ATP o Most cellular functions occur either on the plasma membrane or in the cytoplasm o Flagella: long, threadlike protein fibres that rotate in a socket in the plasma membrane and cell wall to push the cell through a liquid medium o Pili: hair-like shaft of protein extending from cell that helps to attach the cell to surfaces - Eukaryotic cells o Divided into four major groups: protists, fungi, animals and plants o Defined as having cells where DNA is contained within a membrane-bound compartment called the nucleus o Cytosol: participates in energy metabolism and molecular synthesis and performs specialized functions in support and motility o The nucleus is separated from the cytoplasm by the NUCLEAR ENVELOPE, which consists of 2 membranes, one layered just inside the other and separated by a narrow space (lamins are found on the inner surface) o Embedded in the nuclear envelope are many hundreds of nuclear pore complexes  Large, cylindrical structure formed of many types of proteins called the nucleoporins  Exchanges components between the nucleus and cytoplasm and prevents the transport of material not meant to cross the nuclear membrane  Nuclear pore: path for the assisted exchange of large molecules such as proteins and RNA molecules  Some proteins need to be imported into the nucleus  These are distinguished by the presence of a special, short amino acid sequence called a nuclear localization signal  Nucleoplasm: liquid or semi-liquid substance within the nucleus   Chromatin: takes up most of the space in the nucleus-combination of DNA and proteins o Each individual DNA molecule with its associated proteins is a EUKARYOTIC CHROMOSOME  Chromatin: refers to any collection of eukaryotic DNA molecules with their associated proteins  Chromosome: refers to a one complete DNA molecule with its associated proteins o Nucleoli: mass of small fibres and granules  Froma round the genes coding for the rRNA molecules of ribosomes o Ribosomes:  Eukaryotic ribosomes are larger than prokaryotic  They use info in mRNA to assemble amino acids into proteins  Many ribosomes are attached to membranes  Most are attached to the ER o Endomembrane system  Collection of interrelated membranous sacs that divide the cell into functional and structural compartments  Includes nuclear envelope, endoplasmic reticulum and golgi complex  Synthesis and modification of proteins and their transport into membranes and organelles, synthesis of lipids, detoxification of some toxins  Membranes of the system are connected either directly (physically) or indirectly (vesicles)  Vesicles: small membrane-bound compartments that transfer substances between parts of the system o Endoplasmic reticulum:  Extensive interconnected network of membranous channels and vesicles called CISTERNAE  Each cisternae is formed by a single membrane that surrounds an enclosed space called the ER lumen.  2 ER: rough and smooth  Rough: many ribosomes that stud its outer surface 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 occur in the lumen o Proteins are then delivered to other regions of the cell  o For most proteins made on the rough ER, the next destination is the Golgi complex, which packages and sorts them to delivery to their final destinations.  Smooth: membranes have no ribosomes attached to their surfaces o Has various functions in the cytoplasm o Synthesis of lipids and break down of toxins  Rough and smooth ER are often connected  The relative proportions of rough and smooth ER reflect cellular activities in protein and lipid synthesis o Golgi complex  Consists of a stack of flattened, membranous sacs known as cisternae  Not interconnected  Receives proteins that were in the ER and transported in vesicles. When vesicels contact the CIS face of the complex (side facing the nucleus), they fuse with the golgi membrane and release their contents directly into the cisternal.  Here they are chemically modified  The modified proteins are transported within the Golgi to the TRANS face of the complex (faces the plasma membrane), where they are sorted into vesicles that bud off the margins of the Golgi  Membrane of a vesicle that fuses with the plasma membrane becomes part of the membrane….used to expand the surface of the cell during cell growth.  Used in exocytosis o Lysosomes  Small, membrane-bound vesicles that contain more than 30 hydrolytic enzymes for the digestion of many complex molecules, including proteins, lipids, nucleic acids and polysaccharides  Found in animals but not plants  Central vacuole is the equivalent in plants  Assume variety of sizes and shapes  Are formed from the Golgi complex  Very acidic compared to pH of cytosol….this difference reduces the risk to the viability of the cell should the enzymes be released from the vesicle  Can digest several types of materials  Autophagy: digest organelles that are not functioning correctly  Phagocytosis: process in which some types of cells engulf bacteria or other cellular debris to break them down  Phagocytes use this (white blood cells)   Lysosomal storage disease: hydrolytic enzymes normally found in lysosome is absent  Result: substrate of that enzyme accumulates in the lysosomes and eventually interferes with normal cellular activities o Mitochondria  Membrane-bound organelles in which cellular respiration occurs  Generate most of the ATP in the cell  Requires oxygen  Outer mitochondrial membrane: smooth and covers outside of the organelle  Inner mitochondrial membrane: surface are is expanded by folds called cristae  Mitochondrial matrix: innermost compartment  Contains DNA and ribosomes that resemble the equivalent structures in bacteria  This suggests that mitochondria originated from ancient bacteria that became permanent residents of the cytoplasm during the evolution of eukaryotic cells o Cytoskeleton  Interconnected system of protein fibres and tubes that extends throughout the cytoplasm  3 major types: microtubules, intermediate filaments and microfilaments  Microtubules:  Smallest  Dimers are organized head-to-tail in each filament, giving the microtubule a polarity o Contains a 1 (plus) end and 2 (minus) end  Dynamic-changing lengths as required by their function  Change length by addition or removal of tubulin dimers o Adding or detaching occurs more rapidly at the 1 (plus) end  Many of the cytoskeleton microtubules in animal cells are formed and radiate outward from a site called the CELL CENTRE or CENTROSOME  At its midpoint=centrioles  Microtubules that radiate from the centrosome anchor the ER, Golgi complex, lysosomes, secretory vesicles and mitochondria in position o Also provides tracks along which vesicles move from the cell interior to the plasma membrane   Animal cell movements are generated by “motor” proteins that push or pull against microtubules o One end is firmly fixed o Other end has reactive groups that “walk” along another microtubule by making an attachment, forcefully swivelling a short distance, and then releasing o Motor proteins that walk along microfilaments are called MYOSINS and the ones that walk on microtubules are called DYNEINS and KINESINS  Intermediate filaments o Only found in multicellular organisms o Tissue specific in their protein composition o Providing structural support in man cells and tissues  Microfilaments o Largest o Consists of 2 polymers of actin subunits wound around each other in a long helical spiral o Asymmetrical in shape o Have polarity o Have 1(plus) end and 2 (minus) end o Best known as one of the 2 components of the contractile elements in muscle fibres of vertebrates o Involved in the actively flowing motion of cytoplasm called cytoplasmic streaming  When animal cells divide, microfilaments are responsible for dividing the cytoplasm o Flagella: propel a cell through a watery medium o Cilia: move fluids over the cell surface - Specialized structures of plant cells o Chloroplasts:  Sites of photosynthesis  Members of a family of plant organelles called PLASTIDS  Amyoplasts: colour-less plastids that store starch, a product of photosynthesis  Chromoplasts: contain red and yellow pigments and are responsible for the colours of ripening fruits or autumn leaves  All plastids contain DNA genomes and molecular machinery for gene expression and the synthesis of proteins on ribosomes  Contain outer and inner boundary membrane  These two boundary membranes completely enclose an inner compartment called the STROMA   Within the stroma is a third membrane system that consists of flattened sacs called THYLAKOIDS. o In higher plants, the thylakoids are stacked one on top of the other forming GRANA o Thylakoid membranes contain molecules that absorb light energy and convert it to chemical energy is photosynthesis  Primary molecule absorbing light is chlorophyll- green pigment present in chloroplast o Central vacuole  Large vesicles  Membrane that surrounds the central vacuole called the TONOPLAST, contains transport proteins that move substances into and out of the central vacuole  As plant cells mature, they grow primarily by increases in the pressure and volume of the central vacuole o Cell wall  Extracellular structure because it is located outside the plasma membrane  Provide support to individual cells, contain the pressure produced in the central vacuole and protect cells against invading bacteria and fungi - Specialized cells in animals o Cell adhesion molecules: bind cells together o Cell junctions: seal the spaces between cells and provide direct communication between cells o Extracellular matrix (ECM): supports and protects cells and provides mechanical linkages o Cell adhesion:  Glycoproteins embedded in the plasma membrane  Bind to specific molecules on other cells  As an embryo develops into an adult, the connections made by cell adhesion become permanent and reinforced by cell junctions o Cell junctions:  Anchoring junction: adjoin cells adhere at a mass of proteins anchored beneath their plasma membrane by many intermediate filaments  Tight junction: form between adjacent cells by fusion of plasma membrane proteins on their outer surfaces  Seal tight enough to prevent leaks and of ions or molecules between cells  Gap junction: cylindrical arrays of proteins form direct channels that allow small molecules and ions to flow between the cytoplasm of adjacent cells  o ECM  Primary function is protection and support  Glycoproteins are the main component  Collagen: forms fibres with great tensile strength and elasticity Chapter 3 – Defining life and its origins (3.4b,3.4e,3.5) - Heterotrophs: organisms that obtain carbon from organic molecules o Earliest forms of life - Autotrophs: obtain carbon from the environment in an inorganic form, most often carbon dioxide. o Eg. Plants and other photosynthetic organisms - All present day organisms can be categorized into one of 3 domains: Archae, Bacteria and Eukarya o Archaea are more closely related to eukaryotes than to bacteria - All life forms currently on Earth share a remarkable set of common attributes: o 1) cells made of lipid molecules brought together forming a bilayer o 2) a genetic system based on DNA o 3) a system of information transfer-DNA to RNA to protein o 4) a system of protein assembly from a pool of amino acids to translation using messenger RNA (mrna) and transfer RNA (trna) using ribosomes o 5) reliance on proteins as the major structural and catalytic molecule o 6) use of ATP as the molecule of chemical energy o 7) the breakdown of glucose by the metabolic pathway of glycolysis to generate ATP o *the fact that these 7 attributes are shared by all life on Earth suggests that all present-day organisms descended from a common ancestor o LUCA: the original life form from which all archaea, bacteria and eukaryotes are descended  Last Universal Common Ancestor - Present-day eukaryotic cells have 2 major characteristics that distinguish them from archaea and bacteria o 1) separation of DNA and cytoplasm by a nuclear envelope o 2) presence in the cytoplasm of membrane-bound compartments with specialized metabolic and synthetic functions - A large amount of evidence indicates that mitochondria and chloroplasts are actually descended from a prokaryote: mitochondria came from aerobic bacteria and chloroplast came from cyanobacteria o Endosymbiosis: state that the prokaryotic ancestors of modern mitochondria and chloroplast were engulfed by larger prokaryotic cells, forming a mutually advantageous relationship called a SYMBIOSIS   Slowly over time the host cell and the endosymbionts became inseparable parts of the same organism - 6 lines of evidence suggest that mitochondria and chloroplast have distinct prokaryotic characteristics o 1) Morphology: same shape to that of archaea and bacteria o 2) Reproduction: mitochondria and chloroplast are derived from pre-existing mitochondria and chloroplast. They divide by binary fission, which is how bacteria and archaea divide o 3) Genetic information: Both mitochondria and chloroplast contain their own DNA, which contains protein-coding genes that are essential for organelle function o 4) Transcription and translation: Both chloroplast and mitochondria contain a complete transcription and translation machinery o 5) Electron transport: Both have ETCs and it is contained in the inner membrane o 6) Sequence analysis: sequencing of the RNA that makes up the ribosomes of chloroplasts and mitochondria firmly establishes that they belong on the bacterial branch - Genome: defined as the complete complement of an organism’s genetic material - Horizontal Gene Transfer (HGT) (development of the nucleus): o Change in location of the gene-the nucleus as opposed to the mitochondria o Chain of events:  1) some of the genes that were within the protomitochondrion or protochloroplast were lost  2) many of the genes within them were relocated to the nucleus o Pertains to any movement of genes between organisms other than to offspring - Development of the endomembrane system: o Most widely held hypothesis is that it is derived from the infolding of the plasma membrane - Increased complexity requires increased energy - Unlike a true multicellular organism, a cell colony is a group of cells that are all of one type: there is no specialization in cell structure or function Chapter 4-Energy and Enzymes - Life (chemical+physical) are energy-driven processes. o We detect it through its ability to do work o Energy: capacity to do work o Energy can exist in many different forms, including heat, chemical, electrical and mechanical forms. - Energy can be grouped into 2 types:  1) Kinetic energy: energy possessed by an object because it is in motion. a. Falling rock, kicked football, flow of electrons b. Photons of light are also a form of kinetic energy 2) Potential energy: stored energy-the energy an object has because of its location or chemical structure. a. A boulder at the top of a cliff Thermodynamics-the study of energy and its transformations o System: object being studied a. Isolated: one that does not exchange matter or energy with its surroundings. Eg thermos bottle b. Closed: can exchange energy but not matter with its surroundings. E.g greenhouse or earth. c. Open: both energy and matter can move freely between the system and its surroundings. Eg ocean. o Surrounds: everything outside the system o Universe: total of the system and the surroundings - First Law of thermodynamics: energy can be transformed from one form into another or transferred from one place to another, but it cannot be created or destroyed. Also called the “principle of the conservation of energy”. Eg Niagara Falls. - Each time energy is transformed from one form into another, some of the energy is lost and unavailable to do work. o Eg heat: energy associated with random molecular movement. o In most cases, heat cannot be harnessed to do work; instead, it is simply lost to the environment. o The unsuable energy that is produced during energy transformations results in an increase in the disorder or randomness of the universe=ENTROPY - Second Law of thermodynamics: the total disorder of a system and its surroundings always increases. o Systems will move spontaneously toward arrangements with greater disorder- greater entropy o It takes energy to maintain low entropy - Does life obey second law of thermodynamics: yes o Living things bring in energy and matter and use them to generate order out of disorder. o Some food supplies muscles but most food energy is used to simply maintain our cells in their highly ordered state. o Living things give off heat and carbon dioxide which increases the entropy of the surroundings.   The entropy of a system is allowed to decrease as long as the entropy of the universe as a whole increases. - Spontaneous reactions: a reaction will occur. May proceed slowly or quickly. o 2 factors are needed to determine whether a reaction is spontaneous: 1) The change in energy content of a system a. Reactions tend to be spontaneous if the products have less potential energy than the reactions. i. The potential energy in a system is called ENTHALPY or H ii. Endothermic: products have more potential energy than reactants iii. Exothermic: reactants have more potential energy than products 2)Change in entropy b. Reactions tend to be spontaneous when the products are less ordered than the reactants. i. Generally, changes from solid to liquid etc increase entropy. Changes from liquid to solid etc decrease entropy ii. Eg. Glass of ice: melting ice at 25C is endothermic but spontaneous because of increase in entropy. - Free energy : portion of a system’s energy that is available to do work (G) o In living organisms, free energy accomplishes the chemical and physical work involved in activities such as the synthesis of molecules, movement, and reproduction. o G=Gfinal state-Ginitial state o G=H-TS  H=change in enthalpy  S=change in entropy  T in absolute temperatue=+273.16  Free energy change as a system goes from the initial to the final state is the sum of the changes in energy content and entropy o For a reaction to spontaneous, G has to be negative (free energy of products must be less than that of reactants=exergonic (catabolic). o Systems that have high free energy are less stable than systems that have less free energy. - Chemical equilibrium: the point at which there is no longer any overall change in the concentration of products and reactants o The point of equilibrium is related to the G for the reaction. Eg some reactions have G close to 0 and are thus readily reversible.  o Free energy of the system are lower when the products are “contaminated” or diluted by some molecules of reactant than when the system is made up of pure produce because the mixture has higher entropy. - Metabolism: defined as the sum of all of the chemical reactions that take place within an organism. Ending of one reaction is the beginning of another. o Exergonic reaction: releases free energy…G is negative o Endergonic reaction: consumes free energy…G is positive o Catabolic pathway: energy is released by the breakdown of complex molecules to simpler compounds. Eg cellular respiration o Anabolic pathway: consume energy to build complicated molecules from simpler ones; often called biosynthetic pathways. Eg photosynthesis or synthesis of macromolecules. o Both catabolic and anabolic can be made up of both exergonic and endothermic reactions. o Living organisms are defined as having a –G and reach equilibrium when they die. ATP - ATP consists of a five-carbon sugar (ribose), linked to the nitrogenous base adenine and a chain of 3 phosphate groups - Breakdown of ATP in an aqueous solution is a HYDROLYSIS reaction that liberates free energy and results in formation of ADP and inorganic phosphate. - High free energy of hydrolysis of ATP is due to 3 factors: 1) Both products of hydrolysis reaction carry a negative charge, and the repulsion between these ionic products favours hydrolysis. 2) Release of terminal phosphate allows greater opportunity for hydration and thi is an energetically favoured state. 3) Inorganic phosphate group can exist in a wide variety or resonance forms, not all of which are available when it is bonded. *The high free energy of hydrolysis is simply due to the large difference in the usable energy content of the reactants (high) as compared to the products (low). - How do cells harness the high free energy available in ATP to do cellular work? - energy coupling: the exergonic release of energy when ATP is converted to ADP and Pi is used to drive an endergonic reaction. - The reason that energy is not simply lost as heat when ATP is broken down is that ATP is not actually hydrolyzed during energy-coupling reactions. - ATP is a renewable resource that is made by recombining ADP and Pi. - ATP cycle: continued breakdown and resynthesis of ATP. Laws of thermodynamics do not tell us anything about the speed of a reaction  - A reaction is “thermodynamically unstable” if the free energy change of the reaction is negative. - In a “kinetically unstable” reaction, the reactants will rapidly be converted into products. Activation energy: initial energy investment required to start a reaction Transition state: molecules that gain the necessary activation energy, where bonds are unstable and are ready to be broken. Why using heat to speed up reaction is bad idea: - High temperatures destroy the structural components of cells - Increase in temperature would speed up all possible chemical reactions in a cell, thus the critical regulation of metabolic pathways would be lost. Catalyst: chemical agent that speeds up rate of reaction without taking part in reaction - Most common biological catalyst: enzyme. Activation energy represents a real KINETIC barrier that prevents spontaneous reactions from proceeding quickly. - Enzymes increase rate of reaction by lowering this barrier. - Enzymes make it possible for a greater proportion of reactant molecules to attain the activation energy. - Although they lower activation energy, they do not alter change in free energy, only difference is path the reaction takes. In enzymatic reactions, an enzyme combines briefly with reacting molecules and is released unchanged when the reaction is complete. - Reactant that an enzyme acts on is called enzyme’s substrate. - Enzymes are specific - Substrate interacts with only a very small region of the enzyme=active site…where catalysis takes place. - Induced –fit hypothesis: enzymes are flexible. Just before substrate binding, enzyme changes its shape so that the active site becomes even more precise in its ability to bind substrate. - Because enzymes are released unchanged they can continue doing this process. - Cofactor: nonprotein group that binds very precisely to enzyme, often metals. o Essential for catalytic activity o Organic cofactors are called coenzymes. Enzymes increase the rate of reaction by increasing the number of substrate molecules that attain the transition state conformation.  - Bringing the reacting molecules together o Reacting molecules can assume the transition state only when they collide; binding to an enzyme’s activie site brings reactants together in the right orientation for catalysis to occur. - Exposing the reactant molecule to altered charge environments that promote catalysis o In some systems, the active site of the enzyme may contain ionic groups whose positive and negative charges alter the substrate in a way that favours catalysis - Changing the shape of a substrate molecule o The active site may strain or distort substrate molecules into a conformation that mimics the transition state. Rate of catalysis is proportional to the amount of enzyme: As enzyme concentration increases, the rate of product formation increases. In this system, what is limiting the rate of reaction is the amount of enzyme in the reaction mixture. - At very low concentrations, substrate molecules collide so infrequently with enzyme molecules that the reaction proceeds slowly. - As enzyme molecules approach max rate, increasing substrate concentration has smaller and smaller effect and rate of reaction levels off=at this point the enzyme is said to be saturated with substrate. The rate at which an enzyme can catalyze a reaction can be lowered by enzyme inhibitors, which are non-substrate molecules that bind to an enzyme and decrease its activity. Some inhibitors work by binding to the active site of an enzyme, whereas other inhibitors bind to critical sites located elsewhere in the structure of the enzyme. - Competitive inhibitor: competes with normal substrate for access to the active site o If concentration of inhibitor is high enough, reaction may stop completely. - Noncompetitive inhibitor: specific molecules inhibit enzyme activity that bind somewhere else on enzyme. o Decreases enzyme activity because upon binding it changes the conformation of enzyme, reducing ability to bind to substrate. - Reversible inhibitors: binding of inhibitors to enzyme is weak and readily reversible, with enzyme activity returning to normal following inhibitor release. - Irreversible inhibitors: strong bind to enzyme through covalent bonds that enzyme is completely disabled. o Can only be overcome by cell synthesizing more of particular enzyme. o E.g antibiotics It is important for metabolism to work efficiently  - A typical cell contains thousands of enzymes, for each enzyme that synthesizes a specific molecule there is usually another enzyme that catalyzes the reverse reaction. o If both enzymes are active in same cell compartment at same time, 2 processes would run simultaneously in opposite directions and have no overall effect other than wasting energy. To limit (the above) from happening there are two major mechanisms that directly regulate enzyme activity: 1) Allosteric regulation: enzyme activity is controlled by the reversible binding of a regulatory molecule to the allosteric site, a location on the enzyme outside the active site. i. Because these molecules alter enzyme activity by binding at sites separate from the active site, their actions are non competitive. See page 87. ii. High affinity state (active form): enzyme binds strongly to its substrate iii. Low affinity state (inactive form): enzyme binds weakly to its substrate. iv. Allosteric inhibitor: converts an allosteric enzyme from high to low affinity state v. Allosteric activator: converts it from low to high affinity state. - Allosteric inhibitors are a product of the metabolic pathway they regulate o If product is in excess…effect of inhibitor slows or stops enzymatic activity o If product is scars…effect of inhibitor slows to allow product to accumulate. o This (above0 is called FEEDBACK INHIBITION 2) Covalent modification: some enzymes are often completely inactive and are activated only when their structure changes by covalent modification. OR some enzymes are always active and are made inactive by covalent modification. i. Phosphorylation vs dephosphorylation ii. Proteolytic cleavage: some enzymes are synthesized in catalytically inactive forms that are activated after the protein is shortened slightly by an enzyme called PROTEASE. The activity of most enzymes is strongly altered by changes in pH and temperature. Characteristically, enzymes reach maximal activity within a narrow range of temperature or pH; at levels outside this range, enzyme activity drops off. - Most enzymes have a pH optimum near the pH of the cellular contents, about pH 7. - Effects of temperature: o Temperature has a general effect on chemical reactions of all kinds. As temp increases, rate of chemical reactions increases. o Temp has a more specific effect on all proteins. As temp rises, kinetic motions of amino acid chains of an enzyme increase, along with strength and frequency of  collisions. At some point, these disturbances become strong enough to denature the enzyme. o In range 0C to 40C, reaction rate doubles for every 10C increase in temp. o Above 40C, enzyme starts to denature, falls to zero at 60C. o Peak enzyme activity: 40C-50C Chapter 5 (5.2-5.7) - Fluid mosaic model: model proposes that membranes are not rigid with molecules locked into place but rather consist of proteins within a mixture of lipid molecules the consistency of olive oil. o The mosaic aspect of the fluid mosaic model refers to the fact that most membranes contain an assortment of different types of proteins.  Because they are larger than lipid molecules, proteins move more slowly in the fluid environment of the membrane. - Phospolipids: forms lipid bilayer o Consists of a head group attached to two long chains of carbon and hydrogen called a FATTY ACID. o They are amphipathic: fatty acid part is hydrophobic (water fearing…nonpolar) and phosphate-containing head is hydrophilic (water loving…polar). - Fluidity of lipid bilayer is influenced by 2 factors: o 1) the type of fatty acids that make up the lipid molecules  Saturated: linear, pack tightly together, rigid  Unsaturated: double bonds (can’t pack tightly together), FLUID o 2) temperature  The more unsaturated a group of lipid molecules, the lower the temperature has to be for gelling to occur (forming semisolid…liquid to solid). o For most membrane systems, the normal fluid state is achieved by a mixed population of saturated and unsaturated fatty acids. - Keeping membranes in a fluid state is absolutely essential to cell function. o Temp too low: can inhibit functions o Temp too high: membrane leakage. - Most organisms can actively adjust the fatty acid composition of their membranes so that proper fluidity is maintained over a broad temperature range. o Unsaturated fatty acids are produced during fatty acid biosynthesis through the action of a group of enzymes called DESATURASES.  Desaturases act on saturated fatty acids by catalyzing a reaction that removes two hydrogen atoms from neighbouring carbon atoms and introducing a double bond.   The more desaturases, the more fluid the membrane…used when temperature drops.  Like many proteins, desaturase abundance is regulated at the level of gene transcription, which results in changes to desaturase transcript (MRNA) abundance. o Sterols also influence membrane fluidity  Found in animal cells but not in plants  Act as buffers  At high temps: they help restrain the movement of lipid molecules  At low temps: they disrupt fatty acids from associating by occupying space between lipid molecules thus slowing the transition to the nonfluid gel state. - Two major types of proteins are associated with membranes: integral and peripheral membrane proteins. - Membrane proteins can be separated into 4 major functional categories: o Transport: a protein may provide a hydrophilic channel that allows movement of a specific compound. o Enzymatic activity: a number of enzymes are membrane proteins. o Signal transduction: Membranes often contain receptor proteins on their outer surface that bind to specific chemicals such as hormones. On binding, these receptors trigger changes on the inside surface of the membrane that lead to transduction of the signal through the cell. o Attachment/recognition: on inside + outside surface of membrane…act as attachment points for a range of cytoskeleton elements, as well as components involved in cell to cell recognition. - Proteins that are embedded in the phospholipid bilayer are called Integral Membrane Proteins o A subset of integral membrane proteins that traverse the entire lipid bilayer are referred to as “transmembrane proteins”.  Because the transmembrane proteins interact with both the aqueous sides of the membrane and the hydrophobic core, it has domains with different polarity.  Domain that interacts with lipid bilayer (hydrophobic core) is mostly non polar…this forms a secondary structure called an “alpha helix”  Domain that interacts with aqueous sides on either side of membrane is mostly polar. o Primary structure: amino acid sequence of a protein o Tertiary structure: folding due to R group interactions o Fourth structure: more than one polypeptide.  o How to tell if it is a transmembrane protein: stretches of non polar amino acids.  Most transmembrane proteins span the membrane more than once. - Peripheral membrane proteins: are positioned on the surface of a membrane and do not interact with the hydrophobic core of the membrane o Are held to membrane by noncovalent bonds o Are found on cytoplasmic side of the plasma membrane and form part of the cytoskeleton o They are made up of polar and non polar amino acids. Passive membrane transport - The hydrophobic nature of membranes severely restricts the free movement of many molecules into and out of cells and from one compartment to another. - Passive transport: movement of a substance across a membrane without the need to expend chemical energy such as ATP o Diffusion drives passive transport o Above absolute zero (-273C) molecules are in constant motion o Driving force behind diffusion is an increase in entropy  When in initial state (one region with more molecules than other) molecules are more ordered and in a state of lower entropy. As diffusion occurs, when molecules are disturbed, entropy increases.  As it reaches maximum disorder, molecules release free energy, which can accomplish work o Rate of diffusion depends on the concentration difference (concentration gradient).  The larger the gradient, the faster the rate of diffusion. - Simple diffusion (passive): movement of molecules directly across a membrane without the involvement of a transporter. o Depends on : molecular size and lipid solubility o Molecules that use this are : O2, CO2, steroid hormones, water or glycerol.  Membrane is practically impermeable to charged molecules. o Slow but never plateaus - Facilitated diffusion (passive): diffusion of molecules across a membrane through the aid of a transporter. o Carried out by two transport proteins: channel and carrier o Channel proteins: form hydrophilic pathways in the membrane through which molecules can pass.  Diffusion of water is facilitated by water-specific transport proteins called AQUAPORINS.  Very narrow  Specific for water   Show presence of positive charges in centre of channel that are thought to repel the transport of protons.  Gated channel: these transporters can switch between open, closed and intermediate states and are critical to the movement of most ions.  Gates are open or closed by changes in voltage across membrane. o Carrier proteins: each carrier protein binds a single specific solute and transports it across the lipid bilayer….UNIPORT.  Carrier protein undergoes conformational changes that progressively move the solute binding site from one side of the membrane to the other, thereby transporting the solute. o Is quick and can plateau. - Osmosis: diffusion of water molecules across a selectively permeable membrane. o Hypotonic: more concentration in cell than out…water comes in…cell swells o Hypertonic: more concentration out of cell…water comes out…cell shrinks Active Membrane Transport - Active transport: transport of molecules across a membrane against a concentration gradient (movement from LOW to HIGH concentration) requires expenditure of energy. - 3 main functions of active transport: 1) Uptake of essential nutrients from the fluid surrounding cells even when their concentrations are lower than in cells 2) Removal of secretory or waste materials from cells or organelles even when the concentration of those materials is higher outside the cells or organelles 3) Maintenance of H, Na, K and Ca - Membrane potential: voltage across a membrane. - Primary active transport: the same protein that transports a substance also hydrolyses ATP to power the transport directly - Sodium-potassium pump: o Pushes 3 Na+ ions out of the cell and two K+ ions into the cell in the same pumping cycle o Inside of cell becomes negatively charged o Voltage: electrical potential difference across the plasma membrane results from this difference in charge as well as from unequal distribution of ions across the membrane created by passive transport. - Electro-chemical gradient: both a concentration difference of ions and an electrical charge difference on the two sides of the membrane o Store energy that is used for other transport mechanisms…aka secondary active transport. - Secondary active transport: the transport is indirectly driven by ATP….extension of primary active transport.  o Occurs by 2 mechanisms: 1) Symport: the cotransported solute moves through the membrane channel in the same direction as the driving ion known as COTRANSPORT….both ion and molecule move in same direction. 2) Antiport: the driving ion moves through the membrane channel in one direction, providing the energy for the active transport of another molecule in the opposite direction known as EXCHANGE DIFFUSION….ion and molecule move in opposite directions. Exocytosis vs Endocytosis - Eukaryotic cells import and export larger molecules by endocytosis and exocytosis. o Both require energy - Exotysosis: secretory vesicles move through the cytoplasm and contact the plasma membrane. o Vesicle fuses with plasma membrane, releasing the vesicle’s contents to the cell exterior. - Endocytosis: trap in depressions that bulge inward from the plasma membrane. o Depression then pinches off as an endocytic vesicle o Bulk phase endocytosis: extracellular water is taken in along with any molecules that happen to be in solution in the water  No binding by surface receptors takes place o Receptor mediated endocytosis: molecules to be taken in are bound to the outer cell surface by receptor proteins. Receptors recognize and bind only certain molecules from the solution surrounding the cell. After binding, receptors collect into depression in plasma membrane called COATED PIT because of network of proteins that coat and reinforce the cytoplasmic side. o Phagocytosis is eg Signal Transduction 1) Reception: binding of a signal molecule with a specific receptor of target cells is termed reception. Target cells have receptors that are specific for the signal molecules. a. Found on plasma membrane 2) Transduction: process whereby the signal reception triggers other changes within the cell necessary to cause the cellular response in transduction. a. Signalling cascade 3) Response: transduced signal causes a specific cellular response. - Membrane receptors recognize and bind signal molecules are integral membrane proteins that extend through the entire membrane. o Specifc  o Molecular structure of that receptor changes so that it transmits the signal through the plasma membrane, activating the cytoplasmic end of the receptor protein. - A common characteristic of signalling mechanisms is that the signal is relayed inside the cell by PROTEIN KINASES, enzymes that transfer a phosphate group from ATP to one or more sites on particular proteins. o Active only when called upon o Act in a chain, catalyzing a series of phosphorylation reactions called a PHOSPHORYLATION CASCADE, to pass along a signal. o Last protein in cascade is Target Protein. - Effects of protein kinases in the signal transduction pathways are balanced and reversed by another group of enzymes called PROTEIN PHOSPHATASES, which remove phosphate groups from target proteins. o Most of the protein phosphatases are continuously active in cell Why not have receptor activation lead directly to response? - Signal transduction pathways amplify the original signal. - Amplification: an increase in the magnitude of each step as a signal transduction pathway proceeds. o Generally, the more enzyme-catalyzed steps in a response pathway, the greater the amplification. - Cyclic AMP Signal Transduction Pathway 1) Signaling molecule binds to a receptor 2) Receptor conformational change activates G protein 3) Activated G protein travels and activates adenylyl cyclase 4) Activated adenylyl cyclase catalyzes the conversion of ATP to cyclic AMP 5) Cyclic AMP binds to and activates protein kinase A 6) Activated protein kinase A phosphorylates other proteins in the cell Chapter 6-Cellular Respiration Cellular Respiration: collection of metabolic reactions within cells that breaks down food molecules to produce ATP. o Transform the potential energy found in food molecules into a form that can be used for metabolic processes. - Life and its systems are driven by a cycle of electron flow that is powered by light in photosynthesis and oxidation in cellular respiration  - An electron that is farther away from the nucleus contains more energy than an electron that is more closely held by the nucleus o Electrons that from the covalent C-H bond are equidistant from both atomic nuclei-not being strongly held by either.  Can be easily removed  Fat is almost entirely C-H bonds, while proteins and carbohydrates contain varying amounts of other atoms including oxygen - The more electronegative an atom, the greater the force that holds the electrons to the atom, and, therefore, the greater the energy required to remove the electrons. - Oxidized: when molecules lose electrons - Reduced: when molecules gain electrons - Concept of redox reactions: 1) Although many oxidation reactions involve oxygen, others, including a number involved in cellular respiration, do not. 2) The gain or loss of an electron in a redox reaction is not always complete - Cellular respiration is controlled combustion o Combustion of glucose releases energy as electrons are transferred to oxygen, reducing it to water, and the carbon in glucose is converted to carbon dioxide. o Energy of C-H bonds is not liberated suddenly, producing heat, but is slowly released in a stepwise fashion, with the energy being transferred to other molecules. o Dehydrogenases: group of enzymes that facilitate the transfer of electrons from food to a molecule that acts as an energy carrier or shuttle  Most common energy carrier: NAD+ Cellular Respiration can be divided into 3 parts: 1) Glycolysis: Enzymes break down a molecule of glucose into 2 molecules of pyruvate. Some ATP and NADH is synthesized. 2) Pyruvate oxidation and the citric acid cycle: Acetyl Co-A which is formed from the oxidation of pyruvate, enters a metabolic cycle, where it si completely oxidized to carbon dioxide. Some ATP and NADH synthesized. Complete oxidation of glucose. 3) Oxidative phosphorylation: the NADH synthesized by both glycolysis and the citric acid cycle is oxidized, with the liberated electrons being passed along an electron transport chain until they are transferred to oxygen, producing water. The free energy released during electron transport is used to generate a proton gradient across a membrane, which, in turn, is used to synthesize ATP. Bulk generation of ATP Mitochondrion  - Where citric cycle and oxidative phosphorylation occurs - Outer membrane + inner membrane form intermembrane space. Glycolysis - Breakdown - Consists of 10 sequential enzyme-catalyzed reactions - 6 carbon sugar glucose - Produces 2 molecules of the 3 carbon compound pyruvate - Glycolysis is the most fundamental and ancient of all metabolic pathways: 1) Glycolysis is universal, found in all 3 domains of life 2) Glycolysis does not depend upon the presence of O2 3) Glycolysis occurs in the cytosol of all cells - 3 major concepts to follow in glycolysis 1) Energy investment followed by payoff a. Initial 5 step energy investment followed by 5 step energy payoff 2) No carbon is lost a. Since glucose has been oxidized, potential energy in 2 molecules of pyruvate is less than that of one molecule of glucose 3) ATP is generated by substrate-level phosphorylation a. Involves transfer of phosphate group from a high-energy substrate molecule to ADP, producing ATP. Pyruvate oxidation and the citric acid cycle - The pyruvate synthesized during glycolysis must pass through both the outer and inner mitochondrial membranes. - Pyruvate is converted to acetyl Co-A - Citric acid cycle: consists of 8 enzyme catalyzed reactions: seven are soluble enzymes in mitochondrial matrix and 1 is bound to matrix side of inner mitochondrial membrane o Oxidation of ATP, NADH and FAD - The citric acid cycle is the stage of respiration where the remaining carbon atoms that were originally in glucose at the start of glycolysis are converted into carbon dioxide. Oxydative phosphorylation - Inner mitochondrial membrane - Complex 1: NADH dehydrogenase o Many proteins - Complex 2: Succinate dehydrogenase o Single peripheral membrane protein - Complex 3: cytochrome complex o Many proteins - Complex 4: cytochrome oxidase  o Many proteins - Ubiquinone: shuttles electrons from complexes 1 and 2 to complex 3. o Hydrophobic molecule found in core of membrane - Cytochrome C: second shuttle transfers electrons from complex 3 to complex 4 o Located on intermembrane space side of membrane - In an electron transport chain, it is not the proteins themselves that transfer the electrons, but rather electron transfer is facilitated by nonprotein molecules called PROSTHETIC groups. o Are redox-active cofactors that alternate between reduced and oxidized states as they accept electrons from upstream molecules and subsequently donate electrons to downstream molecules. - Any single component has a higher affinity for electrons than the preceding carrier in the chain. o Molecules such as NADH contain an abundance of free energy and can be readily oxidzided o O2, terminal electron acceptor, is strongly electronegative and can be easily reduced. - The energy that is released during electron transport is used to do work, work of transporting protons across the intermembrane space. o H+ concentration becomes much higher in intermembrane space compared to matrix  Situation in which one side of the inner mitochondrial membrane has a higher concentration of protons than other side represents potential energy that can be harnessed to do work.  Potential energy by proton gradient has 2 factors 7) Concentration of H+ is not equal 8) There’s an electrical difference - Proton-motive force: combination of a concentration gradient and a voltage difference across a membrane producing stored energy. Proton-motive force powers H+ movement which in turn spins ATP synthase headpiece and catalyses ADP+Pi-ATP - Chemiosmosis: harnessed proton-motive force to do work o In mitochondria: energy comes from oxidation of energy rich molecules such as NADH by electron transport chain - Oxidative phosphorylation: mode of ATP synthesis that is linked to the oxidation of energy-rich molecules by an electron transport chain. - ATP synthase: oxidative phosphorylation relies on the action of a large multiprotein complex that spans the inner mitochondrial membrane. o Active transport pump is an ATP synthase that is operating in reverse.  Doesn’t synthesize ATP but uses the free energy from hydrolysis of ATP to provide energy necessary to pump ions across a membrane.  ATP is synthesized by chemiosmosis which consumes the proton gradient generated by electron transport. - Uncoupling of chemiosmosis and electron transport o When this occurs, the free energy released during electron transport is not converted by the establishment of a proton-motive force but instead is lost as heat o Inner mitochondrial membrane o Regulation of body temperature. Efficiency - 1 NADH=3 ATP - 1 FADH2=2 ATP - 2 ATP from glycolysis - 2 ATP from citric acid cycle - 34 from oxidative phosphorylation - Theoretical max is 36 o Energy costs of transporting NADH generated by glycolysis into mitochondrion….consumes 1 ATP o Inner mitochondrial membrane is somewhat leaky to protons - 38% of energy in glucose is converted to ATP - Phosphofructokinase: key enzyme in glycolysis o Allosteric Oxygen - Fermentation: does not utilize an electron transport chain o Pyruvate remains in cytosol, where it is reduced, consuming the NADH generated by glycolysis 1) Lactate fermentation: pyruvate is converted into lactate a. Vigorous muscle activity b. Temporarily stores electrons 2) Alcohol fermentation: occurs in microorganisms such as yeast - Anaerobic respiration: uses an electron transport chain that employs a molecule other than oxygen as the terminal electron acceptor ***as long as there is sufficient NAD+, glycolysis will continue to operate and generate ATP. Phosphofructokinase: o Major control point in pathway o Inhibited by ATP, activated by AMP (allosteric regulation)  - Advantage to aerobic respiration: the affinity of oxygen for electrons is greater than that of many of the other electron acceptors; the consequence of this was increased efficiency at converting the energy in food molecules into ATP. - Strict aerobes: they have an absolute requirement for oxygen to survive and are unable to live solely by fermentation. - Facultative anaerobes: can switch between fermentation and full oxidative pathways, depending on oxygen supply. - Strict anaerobes: they require an oxygen-free environment to survive Oxygen=bad - Partially reduced O2 are formed when O2 accepts fewer electrons, producing what are called REACTIVE OXYGEN SPECIES. o Powerful oxidizing molecules that readily remove electrons from proteins, lipids and DNA, resulting in damage. o Aerobes: antioxidant defence system=includes enzymes and nonenzymes that have the role of intercepting and inactivating reactive oxygen molecules as they are produced within cells  Catalse, superioxide dismutase o Chapter 7-Photosynthesis Photosynthesis: conversion of carbon dioxide into organic molecules using light energy - Photosynthetic organisms are autotrophs because they make all of their required organic molecules from carbon dioxide. o Some are photoautotrophs…use light energy to synthesize organic molecules  Known as primary products because they represent the source of organic molecules for CONSUMERS  Not present in Archea o Phototrophy: includes any process that converts light energy into chemical energy - The conversion of carbon dioxide into carbohydrates requires integration of 2 processes: 1) Light reactions: involves capture of light energy by pigment molecules and the utilization of that energy to synthesize both NADPH and ATP 2) Calvin cycle: electrons and protons carried by NADPH and the energy of ATP are used to convert CO2 into an organic form - Carbohydrate units : (CH2O)n…n indicating the different carbohydrates are formed from different multiples of the carbohydrate unit. - Oxygenic photosynthesis: O2 is produced as a by-product by the light-dependent splitting of water. - 3 carbon sugars are major direct product of the calvin cycle - In photosynthetic eukaryotes, both the light reactions and the Calvin cycle take place within the chloroplast. o Outer membrane: covers entire surface of organelle o Inner membrane: lies just inside the outer membrane o Intermembrane compartment: between outer and inner o Stroma: aqueous environment within inner membrane  Enzymes that catalyze the reactions of Calvin cycle o Thylakoid membranes: third membrane system….form flattened sacs  Components that carry out the light reactions of photosynthesis o Thylakoid lumen: space enclosed by a thylakoid *Cells lacking chloroplasts may still be photosynthetic - Photosynthesis is initiated by light absorption by pigment molecules that are bound precisely to specific proteins - Photosystem: pigment-protein complexes - To be used as a source of energy, photons of light must be absorbed by a molecule o A major class of molecules that are very efficient at absorbing visible light are pigments because their structure results in a number of excitable electrons - 2 important concepts about light absorption: 1) A single photon of light excites only a single electron within a pigment molecule, raising it from the ground state to an excited state. 2) A photon of light can only excite an electron when the energy of the photon matches the amount of energy required to raise the electron from the ground state to an excited state - After a pigment molecule absorbs a photon of light, 3 things can happen 1) Fluorescence …releases energy and goes back to original state…REFLECTION 2) Transferred 3) Absorbed - Light is absorbed by molecules of green pigments called chlorophylls and yellow-orange pigments called cartoenoids. - Chlorophyll: green o Does not have an excited state o Always reflected or transmitted o Chlorophyll a and b - Absorption spectrum: plot of the absoroption of light as a function of wavelength o Chlorophyll a strongly absorbs blue and red light - Action spectrum: plot of effectiveness of light of particular wavelengths in driving a process - Photosynthesis pigments are required not only to absorb photons of light but also to transfer the energy to neighbouring molecules. o Bound very precisely to specific proteins  o Organized within the thylakoid membrane into complexes called PHOTOSYSTEMS-composed of antenna complex  Trap photons of light and use the energy to oxidize a reaction centre chlorophyll, with the electron being transferred to the primary electron acceptor. - Antenna complex: pigment-protein that surrounds a central reaction center. ***check out diagrams** - Photosystem 1: chlorophyll a is P700 - Photosystem 2: chlorophyll is P680. - Key events in photosystem 2: 1) The absorption of photons by the antenna complex and funnelling of energy to the reaction centre result in an electron within P680 being excited. 2) Once in the excited state, P680* can be easily oxidized to P680+ by the primary electron acceptor. This oxidation-reduction reaction initiates electron transport. 3) P680+ is reduced back to P680 by donation of an electron from water. This is facilitated by the oxygen-evolving complex. - P1 and P2 are light-trapping components - As in all electron transport systems, the electron carriers of the photo-synthetic system consist of nonprotein cofactors that alternate between being oxidized and reduced as electrons move through the system. - 3 major protein complexes of electron transport chain: 1) Photosystem 2 2) Cytochrome complex 3) Photosystem 1 - Plastiquinone: electron flow between photosystem 2 and cytochrome complex - Plastocyanin: electron flow from cytochrome complex to photosystem 1 - Linear electron transport: pathway of electron flow from photosystem 2 through photosystem 1 to synthesize NADPH - All electron transport chains operate with electrons flowing spontaneously from molecules that are easily oxidized to molecules that are progressively more easily reduced. o By converting P680 into P680*, the absorption of light energy produces a molecule that is easily oxidized by the electron transport chain, and electron flow is a spontaneous process from P680* to photosystem 1. A second photon of light absorbed by photosystem 1 results in the formation of P700*, which is easily oxidized by the primary electron acceptor of photosystem 1, and in turn ferredoxin, before finally the electron is donated to NADP+ - In photosynthetic electron transport, the proton gradient across the thylakoid membrane is derived from 3 processes:  1) Protons are translocated into lumen by cyclic reduction and oxidation of plastoquinone as it migrates from photosystem 2 to tcytochrom complex and back again 2) Gradient is enhanced by addition of 2 protons to the lumen from the oxidation of water 3) Removal of one proton from stroma for each NADPH molecule synthesized further decreases the H+ concentration in the stroma, thereby enhancing the gradient - Photophosphorylation: process of using light to generate ATP - You need a total of 8 photos of light, 4 for each photosystem, to make a single molecule of O2. - Cyclic electron transport: photosystem 1 can function independently of photosystem 2 o Reduced ferredoxin donates electrons back to the plastoquinone pool…..get continually reduced and oxidized and keeps moving protons across membrane without involvement of electrons coming from photosystem 2. o NADPH is not formed o Reduction of carbon dioxide by calvin cycle requires more ATP than NADPH and the additional ATP molecules are provided by cyclic cycle. Calvin cycle - Only after 3 turns of the calvin cycle that one actually generates a separate molecule - Calvin cycle can be divided into 3 phases: 1) Fixation: phase involves the incorporation of a carbon atom from CO2 into one molecule of RuBP to produce 2 molecules of 3-phosphoglycerate. 2) Reduction: each 3-phosph…get an additional phosphate added from the breakdown of ATP. Each of these molecules is subsequently reduced by electrons from NADPH, producing G3P. 3) Regeneration: for each turn of the calvin cycle, 2 molecules of G3P are produced-a total of 6 carbon atoms. a. 5 of these carbons are rearranged to regenerate the single molecule of RuBp required for the next round of carbon fixation. b. For synthesis of extra G3P, 9 ATP and 6 NADPH are required. - Sucrose is the main form in which the products of photosynthesis circulate from cell to cell in plants. - Rubisco o Enzyme responsible for catalyzation of CO2 o High abundance of rubisco in photosynthetic cells is explained by the fact that this very important enzyme is catalytically very slow. o Inefficient at fixing carbon dioxide  Activity site of rubisco is not specific to CO2, a molecule of O2 can bind to it as well.   Photorespiration: when O2 reacts with RuBP…very wasteful - Carbon-concentrating mechanism: concentration of CO2 in water is low but within cell its high. - Leaf: o Major photosynthetic part of plant o Cuticle prevents water loss - C4 plants perform better when its hotter o Much higher concentrations of CO2 at RuBP - CAM plants: when the can change between C3 and C4 cycles depending on temperature **cellular respiration can occur in plants. Chapter 8…notes from moodle 1) Direct channels a. Gap junctions (animals) b. Plamodesmata (plants) 2) Specific cell contacts a. Surface molecules binding to other cells/ECM 3) Intercellular chemical messengers a. Controlling/Signalling cell: makes and secretes signal molecule (ligand). b. Signalling molecule: Binds to targetcell c. Target cell: Binds signalling molecules via receptors and responds d. Forms a Ligand-Receptor complex and triggers a conformational change in the receptor - Signal molecules can act via short distances (neurotransmitters) or long distances (hormones). o Eg for short distances: Acetylcholine released from a nerve cell (neuron) binds to acetycholine rececptor on the cell which leads to muscle contraction - Hormone: o Released into the blood o Carried throughout the body o Billions of cells exposed to the hormone o Initiates responses in cells with receptor - Long distance signalling in plants: o Hormones travel in vessels, through cells, through the air o Eg. Ethylene initiates growth and fruit ripening - Cell communication and signalling molecule-receptor interaction o Chemical released by signaling cell= signaling molecule o Signaling molecule must bind with an associated RECEPTOR in order to initiate a response.  o Pg 163 diagram - Cell communication signaling and target cells o Cells can receive chemicals and release chemicals. Therefore a cell can be a signaling cell and a target cell. o The terms are used to clarify which cell is releasing a chemical (signaling) and which is receiving the chemical (target) in a particular situation - Cell surface and intracellular receptors…getting the message in …LOOK AT DIAGRAMS - Receptor within a chell: steroid hormone: o Small and non-polar, so passively diffuse through membrane o Bind to receptors in cytoplasm/nucleus o Complex moves to nucleus and regulates transcription (response) BOOK - New progeny cells are needed for expanding population size (single-celled organisms), multicellular tissue growth (new leaves), asexual reproduction, and replacement of coordinating their growth, DNA replication, and cell division in the face of a changing environment Cell cycle in prokaryotic organisms - Binary fission: mechanism of prokaryotic cell division-splitting or dividing into 2 parts o 1) Following birth, cells may grow for some time before initiating DNA synthesis o 2) Once the chromosomes are replicated and separated to opposite ends of the cell o 3) the membrane pinches together between them and 2 daughter cells are formed - Nucleoid: central region where chromosomes are compacted - When nutrients are abundant, prokaryotic cells have no need for a 2 nd period o Under such optimal conditions, populations of E. coli cells can double every 20 minutes - Current research indicates that bacterial chromosomes rapidly separate in an active way that is linked to DNA replication events and is independent of cell elongation - Origin of replication: specific region where replication of the bacterial chromosome commences o Ori: in the middle of the cell, where the enzymes for DNA replication are located - Cytoplasmic division is associated with an inward constriction of CYTOKINETIC RING of cytoskeletal proteins. o New plasma membrane and cell wall material is assembled to divide the cell into 2 equal parts. - Prokaryotes: have only single chromosome, thus if a daughter cell receives at least one copy of the chromosome, its genetic info is complete. - Eukaryotes: if a daughter cell fails to receive a copy of even one chromosome, the effects are usually lethal. o Eukaryotic chromosomes are contained within the nuclear membrane - Mitosis enables cells to keep track of such long replicated chromosomes and to orient them relative to the cytoskeleton at the proper time to ensure precise distribution to daughter cells. - In organisms such as yeast: a SPINDLE of microtubules made of polymerized tubulin protein forms and chromosomes segregate to daughter nuclei without the disassembly and reassembly of the nuclear envelope - Eukaryotes: o hereditary info of the nucleus is distributed among several linear, double- stranded DNA molecules combined with proteins that stabilize the DNA o most eukaryotes have two copies of each type of chromosome in the nuclei called DIPLOID.  Haploid: one copy of each type of chromosome eg. Baker’s yeast  The number of chromosome sets is called the PLOIDY o Replication of the DNA of each individual chromosome creates 2 new, identical, molecules called SISTER CHROMATIDS.  These sister chromatids are held together at the centromere until mitosis separates them, placing one in each of the 2 daughter nuclei.  Each daughter nucleus receives exactly the same number and types of chromosomes, and contain the same genetic info as the parent cell entering the division  The equal distribution of daughter chromosomes to each of the 2 cells that result from cell division is called CHROMOSOME SEGREGATION o Before replication, one chromosome is composed of one DNA molecule; after replication, one chromosome is composed of 2 DNA molecules. DNA replication increases the amount of DNA in the nucleus but does not increase the number of chromosomes. o The precision of chromosome replication and segregation in the mitotic cell cycle creates a group of cells called a CLONE.  All cells of a clone are genetically identical. - Interphase: o The cell grows and replicates its DNA in preparation for mitosis and cytokinesis o Begins as a daughter cell from a previous division cycle enters an initial period stage of cytoplasmic growth….this initial growth stage is called G1 (G stands for GAP meaning lack of DNA synthesis) o G1 phase: the cells makes various RNAs, proteins, and other types of cellular molecules but not nuclear DNA.   Only phase which varies in length for a given species thus whether cells divide rapidly or slowly depends primarily on the length  Also the phase which many cell types stop dividing…division arrest is called G0 phase. o If cell is going to divide, DNA replication begins, initiating the S PHASE of the cell cycle. (S stands for Synthesis, meaning DNA synthesis) o S PHASE: cell duplicates the chromosomal proteins as well as the DNA and continues the synthesis of other cellular molecules o G2 PHASE: cell continues to synthesize RNAs and proteins, including those required for mitosis, and the cell continues to grow. At the end of this phase, which marks the end of interphase, mitosis begins o *During all the steps of interphase, the chromosomes are relatively loose, but organized. o *Hallmark of cancer is the loss of normal control of the G1-S transition. - Prophase: o Greatly extended chromosomes that were replicated during interphase begin to condense into compact, rodlike structures. o Condensation during prophase packs these long DNA molecules into units small enough to be divided successfully during mitosis. o While condensation occurs, the nucleolus becomes smaller and eventually disappears in most species.  This represents a shutdown of all types of RNA synthesis, including the ribosomal RNA made in the nucleolus. o In the cytoplasm, the mitotic spindle (the complex of microtubules that orchestrate the separation of chromosomes during mitosis) begins to form between the two centromeres as they start migrating toward opposite ends of the cell to form the spindle poles (one of the pair of centromeres in a cell undergoing mitosis from which bundles of microtubules radiate to form the part of the spindle from that pole). The spindle develops as bundles of microtubules that radiate from the spindle poles. - Prometaphase: o Nuclear envelope breaks down…beginning of prometaphase o Complex of several proteins, KINETOCHORE, has formed on each chromatid at the centromere. o Connections between kinetochore and kinetochore microtubules determine the outcome of mitosis because they attach the sister chromatids of each chromosome to microtubules leading to the opposite spindle poles.  Microtubules that do not attach to kinetochores overlap those from the opposite spindle pole. - Metaphase:  o Spindle reaches its final form and the spindle microtubules move the chromosomes into alignment at the spindle midpoint…called the metaphase plate. o The chromosomes complete their condensation in this stage and assume their characteristic shape as determined by the location of the centromere and the length and thickness of the chromatid arms. o Only chromosomes with their centromere near the middle could ever appear as an X. o The complete collection of metaphase chromosomes, arranged according to size and shape, forms the KARYOTYPE of a given species. - Anaphase: o Sister chromatids separate and move to opposite spindle poles. o The movement continues until the separated chromatid, now called daughter chromosomes, have reached the 2 poles. - Telophase: o The spindle disassembles and the chromosomes at each spindle pole decondense and return to the extended state typical of interphase. o As decondensation proceeds, the nucleolus reappears, RNA transcription resumes, and a new nuclear envelope forms the chromosomes at each pole, producing the 2 daughter nuclei. - Cytokinesis: o Division of the cytoplasm o Usually follows the nuclear division stage of mitosis and produces 2 daughter nuclei o Cytokinesis begins during telophase or late anaphase o By the time cytokinesis is completed, the daughter nuclei have progressed to the interphase stage and entered the G1 phase of the next cell cycle. o Furrowing:  Animals  The layer of microtubules that remains at the former spindle midpoint expands laterally until it stretches entirely across the dividing cell  As the layer develops, a band of microfilaments forms just inside the plasma membrane, forming a belt that follows the inside boundary of the cell in the plane of the microtubule layer  Powered by motor proteins, the microfilaments slide together, tightening the band and constricting the cell.  This constriction forms a groove-the furrow- in the plasma membrane.  Furrow gradually deepens until the daughter cells are completely separated o Cell Plate formation:   Plants  The layer of microtubules that persists at the former spindle midpoint serves as an organization reticulum ER and Golgi complex  As the vesicles collect, the layer expands until it spreads entirely across the dividing cell.  During this expansion the vesicles fuse together and their contents assemble into a new cell wall-the cell plate- stretching completely across the former spindle midpoint.  The plasma membrane that line the two surfaces of the cell plate are derived from the vesicle membrane. - The mitotic spindle is central to both mitosis and cytokinesis. The spindle is made up for microtubules and their proteins, and its activities depend on their changing patterns of organization during the cell cycle. - Centrosome: site near the nucleus from which microtubules radiate outward in all directions. o The main microtubule organizing centre of the cell, anchoring the microtubule cytoskeleton during interphase and positioning many of the cytoplasmic organelles o Contains pair of centrioles - Centrioles: o Can be removed with no ill effect o Primary function: to generate the microtubules needed for flagella or cilia o When dna replicates in S phase so do centrioles, in M phase they separate into 2 parts. The duplicated centrosomes, with the centrials inside them, continue to separate until they reach opposite ends of the nucleus  As centrosomes move apart, the microtubules between them lengthen and increase in number. - Microtubules can be divided into 2 groups: 1) kinetochore and 2) nonkinetochore. o Nonkinetochore: extend between spindle poles without connecting to chromosomes;at the spindle midpoint, the microtubules from one pole overlap with the microtubules from the opposite pole o In nonkinetochore microtubule-based movement, the entire spindle is lengthened, pushing the poles farther apart. o In many species, the nonkinetochore microtubules also push the poles apart by growing in length as they slide. Cell Cycle Regulation - As part of the internal controls, the cell cycle has built-in checkpoints to prevent critical phases from beginning until the previous phases are completed o Hormones, growth factors and other external controls coordinate the cell cycle with the needs of an organism by stimulating or inhibiting division.  - Cyclin-dependent kinases (CDKs) are major players in the regulation of cell division, directly affecting progression through the cell cycle. o CDKs are protein kinases (add phosphate groups to target proteins) o CDKs are cyclin dependent…are “switched on” only when combined with another protein called a CYCLIN.  Since the concentration of the cyclins rises and falls during the cell cycle, so does the enzyme activity of the CDKs - At each key checkpoint, regulatory events block the cyclin:CDK complex from triggering the associated cell cycle transition until the actions of a previous phase are successfully completed. - The internal controls that regulate the cell cycle are modified by signal molecules that originate from outside the diving cells o Peptide hormones or growth and death factors - Many of these external factors bind to receptors at the cell surface which respond by triggering reactions inside the cell. These reactions often include steps that add phosphate groups to the cyclin:CDK complexes, thereby affecting their function o Speed, slow, or stop progress of cell division - Contact inhibition: when cell surface receptors come in contact with other cells it inhibits division by arresting the cell cycle - Cellular senescence: when cells stop dividing o Once telomeres diminish to a certain minimum length, cells stop dividing (senesce) and may die o Cellular senescence is an important antitumor mechanism Cancer - Cancer occurs when cells lose the normal controls that determine when and how often they will divide - Cancer cells typically lose their adhesions to other cells and often become actively mobile o Metastasis: tend to break loose from an original tumour, spread throughout the body and grow into new tumours in other body regions.  Promoted by changes that defeat contact inhibition and alter the cell surface molecules that link cells together or to the extracellular matrix - Tumours may also break through barriers o The breakthroughs cause bleeding, open the body to infection by microorganisms, and destroy the separation of body compartments necessary for normal function - When mutated genes, called ONCOGENES, encode altered version of processes. - Programmed cell death, called APOPTOSIS, is common o The main executioner is caspases  o Causes of death are nuclear DNA degradation and disrupted mitochondrial function o Corpses of dead cells are engulfed and eaten by neighbouring cells. Chapter 9- Genetic Recombination - Genetic recombination requires the following: o Two DNA molecules that differ from one another o A mechanism for bringing the DNA molecules into close proximity o A collection of enzymes to “cut”, “exchange” and “paste” the DNA back together - Process: o The sugar-phosphate backbone is held together by strong covalent bonds, whereas the bases pair with their partners through relatively weak