Principles of Biology II Professor MV (TTh 12:30-1:45)
Principles of Biology II Professor MV (TTh 12:30-1:45) Bio 102
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January 26th Biological diversity definition o Diversity of all life 3 main types of diversity o Genetic X o Physical morphology X o Metabolic Textbook Notes 28.1 (pages 506510) Phylogenetic Trees Phylogeny: evolutionary history of a group of organisms Phylogenetic Tree: graphical summary of history, showing the ancestordescendant relationships among populations, species, or higher taxa, and clarifying who is related to whom FOR PRACTICE: Look at BioSkill10 o Branch:Represents a population through time o Node: Represents hypothetical common ancestors, where a branch splits into two or more branches o Outgroup: A taxon that diverged prior to the taxa that are the focus of the study; helps to root the tree o Root: Most ancestral branch o Polytomy: A node that depicts an ancestral branch dividing into three or more descendant branches; usually indicating insufficient data were available to resolve which taxa are more closely related o Tip: Where the taxa themselves are located, end of a branch o Sister Taxa: Tips connected by a single node on a tree Tree of Life: Most universal of all phylogenetic trees, depicting the evolutionary relationships among all living organisms Phylogenetic trees must be estimated from the best available data Usually morphological or genetic or both characteristics are used to create a data matrix o To reconstruct relationships among contemporary human populations, sequences of bases are usually compared Character: any genetic, morphological, physiological, or behavioral characteristic being studied Outgroup: A Species that is closely related to the group being studied, but not part of it o Used to establish the polarity of each trait (whether it’s ancestral or derived) Ancestral Trait: Characteristic that existed in an ancestor Derived Trait: Characteristic that is a modified form of the ancestral trait, found in an descendant o Originate via mutation, selection, and genetic drift Synapomorphies: Closely related species are likely to share derived traits Synapomorphy: Trait found in two or more taxa that is present in their most recent common ancestor but is missing in more distant ancestors (SHARED/DERIVED TRAIT) Cladistic Approach is based on the principle that relationships among species can be reconstructed by identifying derived characters synapomorphies Cladistics was introduced by German biologist Willi Hennig in 1960’s Synapomorphies allow biologists to recognize monophyletic groups (called clades or lineages) Monophyletic Group: an evolutionary unit that includes an ancestral population and all of its descendants, but not others Homology: Similarity of organisms due to common ancestry Homoplasy: Similarity in organisms due to reasons other than common ancestry Polyphyletic Group: An unnatural group that does not include the most recent common ancestor Paraphyletic Group: A group that includes an ancestral populations and some of its descendants, but not all Traits can be similar in two species, not because those traits were present in a common ancestor, but because similar traits evolved independently in two different lineages Reversal in a change occurs, where A → C transition in a nucleotide in one branch followed by C → A change in the same nucleotide in a subsequent branch, creating an appearance that no change occurred Sometimes the species forms a monophyletic group noe way according to one trait in the matrix and a different way according to a different way in the matrix Researchers identify the tree using parsimony: the most likely explanation or pattern is the one that implies the least amount of change Biologists use computer programs to count the number of changes in DNA sequences Tree that implies the fewest overall evolutionary changes is hypothesized to be the one most accurately reflecting what really happened during evolution Trees created using cladistic analysis (cladograms) focus on branching patterns Convergent Evolution: occurs when natural selection favors similar solutions to the problems proposed by a similar way of making a living in different species All Hox genes share a 180 base pair sequence called the homebox, it binds to DNA and regulated the expression of other genes o Products of Hox genes have similar functions 29.3 Pages 538544 Metabolic Diversity Bacteria and Archaea are diverse in the types of compounds they can use as food o They both have two fundamental nutritional needs: Acquiring chemical energy in the form of ATP Obtaining molecules with carboncarbon bonds that can be used as building blocks for the synthesis of fatty acids, proteins, DNA, RNA, and other large, complex compounds required by the cell Bacteria and Archaea produce ATP in 3 ways o Phototrophs: (Light feeders) use light energy to excite electrons. ATP produced by photophosphorylation o Chemoorganotrophs: Oxidize organic molecules with high potential energy, such as sugars. ATP produced by cellular respiration with sugars acting as electron donors or via fermentation pathways o Chemolithotrophs: (Rock feeders) oxidize inorganic molecules with high potential energy, such a ammonia, or methane. ATP is produced by cellular respiration, and inorganic compounds serve as the electron donor Bacteria and Archaea obtain carboncarbon buildingblock compounds in 2 ways o By synthesizing their own compounds from simple starting materials such as carbon dioxide. Organisms that manufacture their own buildingblock compounds are termed autotrophs o By absorbing readytouse organic compounds from their environment (heterotrophs) Total of 6 methods for producing ATP and obtaining carbon o Photoautotrophs o Chemoorganoautotrophs o Chemolithoautotrophs o Photoheterotrophs o Chemoorganoheterotrophs o Chemolithotrophicheterotrophs Only two of these ways are done by eukaryotes Certain species can switch among modes of living o Depending on environmental; conditions Eukaryotes have a simple metabolism compared to bacteria and archaea Bacteria and Archaea have evolved dozens of variations on the basic processes of respiration and photosynthesis The basic chemistry required for photosynthesis, cell respiration, and fermentation originated in these lineages. o Use compounds with high potential energy to produce ATP by cell respiration (ETC) or fermentation Use light to produce high energy electrons Reduce carbon from carbon dioxide or other sources) to produce sugars (or other buildingblock molecules with CC bonds) Then the evolution of variations on each of these processes allowed prokaryotes to diversify into millions of species that occupy diverse habitats Producing ATP Through Cell Resp.: Variation in Electron Donors and Acceptors: Cellular enzymes can strip electrons from organic molecules that have high potential energy and then transfer the high potential energy electrons to the electron carriers NADH and FADH2 o feed electrons to the ETC where electrons are stepped down from high energy level to a lower energy level In eukaryotes: ETC is located in the inner mitochondrial membrane In bacteria and archaea the membrane is the plasma membrane Energy released allows different components of the ETC to accumulate a proton gradient across the plasma membrane o Resulting flow of protons back through ATP synthase (an enzyme) results in ATP Via chemiosmosis Summary of Cell Resp,: molecule with high potential energy serves as an electron donor & is oxidized while molecule with low potential energy serves as final electron acceptor and becomes reduced o (OIL RIG oxidation is loss of electron, reduction is gain of electron) Potential energy difference between the electron donor and electron acceptor is transformed into chemical energy (ATP) or is used in other processes Most eukaryotes carry out aerobic respiration o Organic compounds with high potential energy (ex. glucose) serve as electron donor o When cell resp. is done glucose is completely oxidized to carbon dioxide (given off as a byproduct) o Oxygen is the final electron acceptor o Water produced as byproduct Many bacteria and archaea rely on same molecules o common for them to “employ” an electron donor other than sugars and electron acceptor other than oxygen during cell resp. o These particular species form different byproducts than carbon dioxide and water Molecules with high potential energy serve as electron donors Substances used range from hydrogen molecules (pure hydrogen gas, hydrogen sulfide, ammonia, and methane) Compounds with somewhat low potential energy act as electron acceptors Ex: Sulfate, Nitrate, Carbon Dioxide, Ferric ions [iron ions]) o Both electrons donors and acceptors are diverse for bacteria and archaea Scientists ask if they undergo cell resp. and if so, how? Method: Enrichment Culture Technique Researchers supply specific electron donors and acceptors and try to isolate cells that can use those compounds to support growth their metabolic diversity explains why they are key in cleaning up types of pollution Species using organic solvents or petroleumbased fuels as electron donors and acceptors may excrete waste that are less toxic than the original compounds Producing ATP via Fermentation: Variation in Substrates Fermentations: a strategy for producing ATP without an ETC No outside electron acceptor is used Much less efficient way to produce ATP compared to cell resp. In many species: occurs as an alternative metabolic strategy when no electrons acceptors are available In some species fermentation doesn’t occur at all In many bacteria and archaea it is the only way cells make ATP Some eukaryotes can ferments glucose to ethanol or lactic acid Some bacteria and archaea are capable of using other organic compounds as a starting point for the process Bacteria and archaea that use fermentation as their way to produce ATP are still classified as organotrophs o but much more in substrates used Different types of bacteria can ferment: o Ethanol o Acetate o Fatty Acids o Glucose o Complex carbohydrates (cellulose, starch) o Proteins o Purines o Amino Acids o Lactose Diversity of enzymatic pathways observed by bacterial and archaeal fermentations extends their metabolic capabilities/”repertoire” Diversity of substrates fermented also supports claim that as a group, bacteria and archaea can use almost any molecule with relatively high potential energy as a source of highenergy electrons to produce ATP Producing ATP via Photosynthesis: Variation in Electron Sources and Pigments Phototrophs use photosynthesis to produce their energy instead of using molecules Photosynthesis can happen in 3 different ways among bacteria and archaea o Lights activates a pigment (bacteriorhodopsin) that absorbs the light and uses it to transport protons across the plasma membrane and out of the cell Resulting flow of protons back into cell drives the synthesis of ATP by chemiosmosis o Bacterium that lives near hydrothermal vents on ocean floor performs photosynthesis by absorbing geothermal radiation o Pigments that absorb light raise electrons to a higher energy state Electrons are stepped down to lower energy states by ETCs Energy released is used to generate ATP Requires source of electrons In cyanobacteria and plants, required electrons come from water o When organism “split” the water molecules to obtain electrons, they generate oxygen o Species that use water as a source of electrons for photosynthesis are said to complete oxygenic “oxygenproducing” photosynthesis o Many phototrophic bacteria use other molecules other than water as a source of electrons Hydrogen sulfide Ferrous ion o Produce elemental sulfur, and ferric ion as byproducts o Type of photosynthesis is called “anoxygenic” Photosynthetic pigments found in plants are chlorophylls a and b o Cyanobacteria have both Several other chlorophylls from different lineages of bacterial phototrophs Each type of chlorophyll absorbs light best at different wavelengths Obtaining BuildingBlock Compounds: Variation in Pathways for Fixing Carbon Organisms use 2 mechanisms to obtain usable carbon o Making their own o Getting it from other organisms In many autotrophs (including cyanobacteria and plants) enzymes of the Calvin cycle transform carbon dioxide into organic molecules that can be used to synthesize cell material o Carbon atom in carbon dioxide is reduced during the process o Said to be “fixed” Not all bacteria and archaea autotrophs use the Calvin cycle to making buildingblock molecules o Not all start out with carbon dioxide as a source of carbon atoms Animals and fungi obtain carbon from o Living plants of animals o absorbing the organic compounds released by dead tissue’s decay Methanotrophs: methane eaters (use methane as their carbon source) o Some bacteria use carbon monoxide or methanol as their starting material Compared with eukaryotes, the metabolic capabilities of bacteria and archaea are more complex and diverse Ecological Diversity and Global Impacts Metabolic diversity of bacteria and archaea explain why they can thrive in a wide range of habitats o Array of electron donors and acceptors, and fermentations substrates allows them to live anywhere o the evolution of 3 types of photosynthesis (based on bacteriorhodopsin, geothermal energy, or pigments) extends the types of habitats supportive of phototrophs Complex chemistry the cells carry out, along with their numerical abundance has made them forced of global change throughout history Bacteria and archaea have altered the chemical composition of the ocean, atmosphere, and terrestrial environments The Oxygen Revolution Oxygen = about 21% of the atmosphere No free molecular oxygen existed for the first 2.3 billion years of Earth’s existence based on 2 observations o No plausible source at the time Earth formed o Chemical analysis of the oldest rocks suggests that they formed in the absence of atmospheric oxygen Early in history the atmosphere was dominated by nitrogen and carbon dioxide Oxygen we breathe came/comes from cyanobacteria o First became numerous in oceans around 2.72.5 bya o 1st organisms to perform oxygenic photosynthesis (“oxygen producing” One oxygen was common in the oceans, cells could use it as the final electron acceptor during cell resp. o Aerobic respiration was now possible Aerobic respiration was a crucial event o Oxygen is extremely electronegative efficient electron acceptor o more energy is released as electrons move through ETCs with oxygen as the ultimate acceptor than is released with other substances Data indicate cyanobacteria were responsible for a fundamental change in the Earth's atmosphere Nitrogen Fixation and the Nitrogen Cycle Researchers suggest plant growth is often limited by the availability of nitrogen Organisms must have nitrogen to synthesize proteins and nucleic acids Molecular oxygen is extremely abundant in the atmosphere o Most organisms can’t use it because of the string triple bond linking the atoms To incorporate nitrogen into amino acids and nucleotides o all eukaryotes and many bacteria and archaea have to obtain nitrogen in the form of ammonia and nitrate o Certain bacteria and archaea are the only species that are capable of converting molecular nitrogen to ammonia Steps in nitrogen fixation are highly endergonic redox (reductionoxidation) reactions o Key enzyme that catalysis the reaction: nitrogenase o Found in only some bacterial and archaeal lineages Many of these organisms are freeliving, but some have an important relationship with plants o Some species of cyanobacteria live in association with a water fern and helps fertilize plants o In terrestrial environments nitrogenfixing bacteria live in close association with plants, often taking residence in special root structures (nodules) When nitrogenase is exposed to oxygen it become irreversibly poisoned and is degraded o Only organisms that have the nitrogenase gene are ones that live in anaerobic habitats or are able to protect the enzyme from oxygen Nitrate is produced by some bacteria as a byproduct of respiration o doesn’t build up in the environment Instead, other species of bacteria and archaea use it as an electron donor, and it is oxidized to molecular nitrate o Nitrate is then reduced to molecular nitrogen Bacteria and archaea are responsible for driving the nitrogen atoms through ecosystems = nitrogen cycle o The same process occurs with phosphorus, sulfur, and carbon Nitrate Pollution Most crops don’t live in association with nitrogenfixing bacteria To increase yields of crops fertilizers are used that are high in nitrogen Massive additions of nitrogen (mostly in the form of ammonia) are causing serious pollutions issues Nitrate molecules are extremely soluble in water and are usually washed out of soil into groundwater and streams o Eventually reaches the ocean where it causes pollution “Dead Zone” is caused when decomposers use so much oxygen the oxygen levels become so depleted there isn't enough for the other organisms o Causes death of fish, and other organisms that require oxygen Bacteria and archaea, due to their abundance, ubiquity, and processes of chemistry they have a huge influence on the environment Lecture 2/2 Cell Rep starts with glucose as an electron donor Oxygen is electron donor end with carbon dioxide, ATP, and water LOOK AT PP TO GET PIC Requirements of living organisms o CC bonding o ATP o fjeohf Feeding Strategies o Humans Electron acceptor: O2 Electron donor: Glucose ATP is from: Cell Resp. Carbon is from: Organic molecules other organisms o Microbes Electron acceptor: LOTS, Electron Donors: LOTS ATP is from: Cell Pesp, Fermentation, Photosynthesis Carbon is from: Organic molecules, organisms 29.3 chart: KNOW THIS Cell Resp: organic or inorganic molecules with high potential energy We are chemoorganoheterotrophs Quiz Questions o A prokaryote that obtains energy from light is an: phototroph o Cyanobacteria is an example of autophototroph First to perform photosynthesis Microbes that live in hydrothermal vents are examples of: Nitrification o Electron acceptor: oxygen o Electron donor: NH3 o By product: NO2 and NO3 Denitrification o Electron acceptor: NO3 o Electron donor: Organic C o Byproduct: N2, N2O GOAL: BEING ABLE TO DISTINGUISH DONORS AND ACCEPTORS What’s so special about oxygen? o Highly electronegative o efficient electron acceptor Cyanobacteria o responsible for changing the earth's LOOK AT PP How did eukaryotes gain ability to use oxygen? o All eukaryotes are protists except for animals, fungi, and land plants How did eukaryotes gain to respire oxygen? o Endosymbiosis hypothesis (means both are benefitting) Mitochondria comes from bacteria swallowed whole and continued to live peacefully mitochondria come from nuclear DNA o High potential energy compound and oxygen ETC high ATP yield o High potential energy compound ETClow ATP yield 30.3 Pages 559565 What Themes Occur in the Diversification of Protists? Protists range from bacteriasized single cells to giant kelp Paraphyletic group o Do NOT share derived characteristics that set them apart from all other lineages on the tree of life Once an important new innovation arose in protists, it triggered the evolution of species that live in a wide array of habitats and make a living in diverse ways What Morphological Innovations Evolved in Protists? Virtually all bacteria and archaea are unicellular Logical to conclude the first eukaryote was also singlecelled All eukaryotes alive today have o either mitochondria or genes that are normally found in mitochondria o a nucleus and endomembrane system o a cytoskeleton Based on the distribution of cell walls in living eukaryotes, it is likely that the first eukaryotes lacked them Biologists hypothesized the earliest eukaryotes were probably singlecelled organisms, with mitochondria, a nucleus with endomembrane system, and a cytoskeleton, but no cell wall o Also likely they swam with flagellum Bacteria and eukaryotic flagella evolved independently Eukaryotic flagella is made up of microtubules o dynein is a major motor protein o dynein molecules walk down microtubules Flagella of bacteria and archaea are composed of flagellin o a protein called flagellin o rotate to produce movement Endosymbiosis and the Origin of the Mitochondrion organelles that generate ATP using pyruvate as an electron donor and oxygen as the electron acceptor Endosymbiosis Theory o mitochondria originated when a bacterial cell took up residence inside another cell About 2 billion years ago o “Inside together living” o Symbiosis is said to occur when individuals of two different species live in physical contact o Endosymbiosis occurs when an organism's of one species live inside the cells of an organism's of another species o Debated on when this actually happened o Some think a eukaryote engulfed a bacterium and failed to digest it with its lysosome o Recent evidence indicates all protists originally had mitochondria,and some lost them o New idea: first eukaryotic cell may have been formed as a result of endosymbiosis between two protists an archaeal host and a bacterium o Celled later developed nuclei and became much larger o Both of these changes seem to have been triggered by the bacterial invader Relationship between the archaeal host and the engulfed bacterial cell o mutual advantage existed between them o Host supplied the bacterium with protection and carbon compounds from its prey o Bacterium produced much more ATP than the host cell could have synthesized on its own Several observations about the structure of mitochondria are consistent with the endosymbiosis theory o The size of an average aproteobacterium o Replicate by fission as do bacterial cells duplication of mitochondria takes place independently of division by the host cell when eukaryotic cells divide, each daughter cell receives some of the mitochondria present o Have their own ribosomes and manufacture some of their own proteins Mitochondrial ribosomes closely resemble bacterial ribosomes in size and composition poisoned by antibiotics that inhibit bacterial (but not eukaryotic) ribosomes o Have double membranes consistent with the engulfing mechanisms o Have their own genomes Organized as circular molecules Much like a bacterial chromosome Mitochondrial genes code for a few of the proteins needed to conduct electron transport and RNAs needed to translate the mitochondrial genome Key was to find data that tested predictions against the theory o that mitochondria evolved within eukaryotic cells, separately from bacteria “Withineukaryotes” theory o the genes found in the mitochondria are derived from nuclear genes found in ancestral eukaryotes o Predicted tested by studies on the phylogenetic relationships of mitochondrial genes Researchers compared gene sequences isolated from eukaryotic mitochondria DNA with sequences of similar genes isolated from eukaryotic nuclear DNA and with DNA from several species of bacteria Mitochondrial gene sequences are much more closely related to the sequences from the aproteobacteria than to sequences from the nuclear DNA of eukaryotes o As the endosymbiosis theory predicted Mitochondrial genomes typically encode less that 50 genes, whereas the genomes of their bacterial cousins code for about 1500 genes o Most of the genes from the endosymbiotic bacterium moves into the nuclear genome in what was one of the most spectacular lateral gene transfer The Nuclear Envelope Hypothesis to explain the origin of the nuclear envelope is based on infoldings of the plasma membrane Elaborated by mutation and natural selection over time The infolding could eventually become detached from the plasma membrane o The infoldings would have given rise to the nuclear envelope AND the endoplasmic reticulum Evidence to support this hypothesis: o Infoldings of the plasma membrane occur in some bacteria living today o the nuclear envelope and ER of today’s eukaryotes are continuous The evolution of the nuclear envelope was advantageous o separated transcription and translation o alternative splicing and other forms of RNA processing could occur giving the early eukaryotes a novel way to control gene expression o gave the early eukaryotes a new way to manage and process genetic information******* Once nucleus evolves it went through diversification o Ciliates have diploid microtubes that are only involved in reproduction polyploid macronucleus where transcription occurs o Diplomonads have 2 nuclei that look identical o Foraminifera, red algae, and plasmodial slime molds, certain cells contain many nuclei o Dinoflagellates have chromosomes that last histones and attach to the nuclear envelope Distinctive structure of the nucleus is a synapomorphy that allows biologists to recognize these lineages as distinct monophyletic groups Structures for Support and Protection Many protists have cell walls outside their plasma membrane Others have shells Others have rigid structure inside the plasma membrane Novel structures represent synapomorphies that identify monophyletic groups among protists o the diversification of protists has been associated with the evolution of innovative structures for support and protection Multicellularity Mutations probably first caused cells to stick together Eventually cells became specialized for different functions Not all cells represent the same genes Multicellularity arose independently in a wide array of eukaryotic lineages An array of novel morphological traits played a key role as protists diversified o the mitochondrion o the nucleus o endomembrane system o structures for protection and support o multicellularity Evolutionary innovations allowed protists to build and manage the eukaryotic cell in new ways Subsequent diversification was often triggered by ways of o finding food o moving o reproducing How do Protists Obtain Food? Bacteria and archaea cas use a variety of molecules as electron donors and electron acceptors during cellular respiration o Some get these molecules by absorbing them directly from the environment o Some make their own food via photosynthesis Many groups of protists photosynthesize or absorb their food directly from the environment Many protists ingest their food o Eat bacteria, archaea, or other protists whole Phagocytosis Some protists ingest food along with perform photosynthesis Important to recognize that all three lifestyles (ingestive, absorptive, and photosynthesis) can occur within a single lineage Within each of the 7 major lineages of eukaryotes, different methods for feeding helped trigger diversification Ingestive Feeding Based on eating living or dead organisms or on scavenging loosid bits of organic debris Many protists are large enough to surround and ingest other protists or even microscopic animals Feeding by phagocytosis is possible in protists that lack a cell wall o “swallow” prey using pseudopodia “false feet” Phagocytosis was a prerequisite for the endosymbiosis event that led to chloroplasts Some protists attach themselves to their prey by cilia that surround their mouth o motion creates water currents that sweep food particles into the cell Absorptive Feeding When nutrients are taken up directly from the environment o Across the plasma membrane o usually through transport proteins Common among protists Decomposers: feed on dead organic matter, or detritus Parasite: when they absorb nutrients from their host that damages that organism Photosynthesis Endosymbiosis and the Origin of Chloroplasts Photosystems I and II evolved in bacteria o occur in cyanobacteria none of the basic machinery evolved in eukaryotes o “stole” it via endosymbiosis Eukaryotic chloroplast originated when a protist engulfed a cyanobacterium o Once inside, the photosynthetic bacterium provided its eukaryotic host with oxygen and glucose in exchange for protection and access to light (Evidence for this on page 564) Chloroplast genome is very small compared to genomes of living cyanobacteria o most of the original genes were lost or transferred to the nucleus Photosynthesis Primary versus Secondary Endosymbiosis Occurred in a plant’s common ancestor o That species eventually gave rise to all subgroups in the Plantae lineage o Chloroplasts occur in four other major lineages of protists Excavata Rhizaria Alveolata Stramenopila o Chloroplast is usually surrounded by more than two membranes, usually four Hypothesize the ancestor of these groups acquired their chloroplasts by ingesting photosynthetic protists that already has chloroplasts o Secondary endosymbiosis Occurs when an organism engulfs a photosynthetic eukaryotic cell and retains its chloroplasts as intracellular symbionts o Once protists obtained the chloroplast it was “swapped around” to ne lineages via secondary endosymbiosis 10.110.2 Pages 177184 Photosynthesis Harnesses Sunlight to Make Carbohydrates Plants convert electromagnetic energy of sunlight into chemical energy in CC and CH bonds of carbohydrates 6CO2 + 6H20 + LIGHT ENERGY > C6H12O6 + 6O2 Endergonic suite of redox reactions Photosynthesis: Two Linked Sets of Reactions Cornelius van Niel’s Research was important because o Showed that H2S is the equivalent to H2O is the plant reactions, and CO2 does NOT combine directly during photosynthesis o Oxygen atoms in CO2 are NOT released as O2 Biologists hypothesized that the oxygen atoms released during plant photosynthesis must come from water Two distinct sets of reactions o used light to produce O2 from H2O o Converts CO2 into sugars Melvin Calvin = Calvin Cycle o Reactions that reduce CO2 and produces sugar o Can only function id the lightcapturing reactions are occurring Two reactions are linked by electrons that are released when water is split to for O2 gas o During lightcapturing reactions, electrons are promoted to a highenergy state by light and then transferred through a series of redox reactions to a phosphorylated version of NAD+ (NADP+) Forms NADPH+ which functions as a reducing agent similar to NADH produced in cell respiration Some energy is released from these redox reactions is also used to make ATP Calvin Cycle o electrons in NADPH and potential energy of ATP and used to reduce CO2 to carbohydrate o Resulting sugars are used in cell respiration to produce ATP for the cell o Plants oxidize sugars in their mitochondria and consume O2 Photosynthesis Occurs in Chloroplasts When membranes derived from chloroplasts were found t release O2 after exposure to sunlight it was accepted this is where photosynthesis takes place Enclosed by outer membrane and inner membrane Interior dominated by flattened, saclike structures: thylakoids o often occur in interconnected stacks: grana Space inside thylakoid is called the lumen Fluidfilled space between the thylakoids and inner membrane: stroma most abundant pigment in the thylakoid membrane is chlorophyll How Do Pigments Capture Light Energy? Light = type of electromagnetic radiation, a form of energy Photosynthesis converts electromagnetic energy in the form of sunlight into chemical energy in CC and CH bonds of sugar Electromagnetic radiation is characterized by its wavelength o wavelength determines the type of electromagnetic radiation Each photon of light has a characteristic wavelength and energy level Photosynthetic Pigments Absorb Light when a photon strikes an object it can either be absorbed, transmitted, or reflected A pigment molecule absorbs photons of particular wavelengths o White light: all wavelengths in the visible portion of the electromagnetic spectrum at once o Black light: pigment absorbs all the visible wavelengths/ no visible wavelength of light is reflected To determine what wavelengths are absorbed by leaves o scientists did a chromatography experiment by mashing leaves up and testing their pigments o to find out which wavelengths are absorbed by each molecule, cut out a single region of the porous material and extracted the pigment to use an instrument to record the wavelengths absorbed Different Pigments Absorb Different Wavelengths of Light Two major pigment classes in plant leaves: o Chlorophylls designated chlorophyll a and b absorb strongly in blue and red region reflect green light o Carotenoids absorb in the blue and green regions appear yellow, orange, or red belong to two classes cartenes xanthophylls Which wavelengths drive photosynthesis o T. W. Engelman o laid a filamentous alga across a microscope which was illuminated with a spectrum of colors o Idea was that the alga would begin performing photosynthesis is response to various wavelengths of light to produce oxygen o added bacterial cells from a species that is attracted to oxygen o most of the bacteria collected around the violettoblue and red regions of the slide Action spectrum for photosynthesis o Absorption spectrum: measures how the wavelength of photons influences the amount of light absorbed by a pigment Which Part of a Pigment Absorbs Light? Chlorophyll a and b o Similar in structure o Two fundamental parts long isoprenoid “tail” interacts with proteins embedded in the thylakoid membrane “head” consisting of a large ring structure with a magnesium atom in the middle where light is absorbed structure of betacarotene has an isoprenoid chain connecting two rings that are responsible for absorbing light o What is the Role of Carotenoids and Other Accessory Pigments? Carotenoids o called accessory pigments because they absorb light and pass the energy on to chlorophyll o both xanthophylls and carotenes are found in chloroplasts o Carotenoids absorb wavelengths of lights that are not absorbed by chlorophyll extend the range of wavelengths that can drive photosynthesis Many herbicides work by inhibiting enzymes that are involved in carotenoid synthesis Carotenoids serve as a protector of chlorophyll o Photons (especially high energy, short wavelength) contain enough energy to knock electrons out of atoms and create free radicals free radicals trigger reactions that can disrupt and degrade molecules o “quench” free radicals by accepting or stabilizing unpaired electrons protect chlorophyll molecules from harm when carotenoids are absent, chlorophyll molecules are destroyed and photosynthesis stops starvation and death follow When Light is Absorbed, Electrons Enter an Excited State When a photon strikes a chlorophyll molecule, the photon’s energy can be transferred to an electron in he chlorophyll molecule’s head region o electron is “excited” or raised to a higher energy state o excited electron states that are possible in a particular pigment are discrete incremental instead of continuous o Can be represented as lines of an energy scale Chlorophyll doesn’t absorb green light well because there is no discrete step o no difference in possible energy states for its electrons that corresponds to the amount of energy in a green photon If a pigment absorbs a photon with the right amount of energy, energy in the form of electromagnetic radiation is transferred to that electron o the electron now has high potential energy If the excited electron falls back to its group state the absorbed energy is released as heat or a combination of heat and electromagnetic radiation When the electron energy produces light: fluorescence o electromagnetic radiation that is given off during this has lower energy and a longer wavelength that the original photon did When photons are absorbed by pigments in chloroplasts, only about 2% of the excited electrons produce fluorescence 98% of energized pigments use their excited electrons to drive photosynthesis Chlorophyll molecules work in groups o Antenna complex: accessory pigments are organized by an array of protein called this and the reaction center o Photosystem: formed when these complexes, along with molecules that capture and process excited electrons The Antenna Complex when a red or blue photon strikes a pigment molecule in this, the energy is absorbed and an electron is excited in response o This energy is passed to the nearby chlorophyll molecule, where another electron is excited in response KNOWN AS RESONANCE ENERGY TRANSFER This transfer is only possible between pigments that are able to absorb different wavelengths of photons Organization of the complex makes it possible for this resonance energy to be efficiently moved between pigments as the potential energy drops each step Once energy is transferred, original excited electron falls back to ground state o Most of this resonance energy is directed to a particular location in a photosystem: the reaction center The Reaction Center when a chlorophyll molecules is excited in this, its excited electron is transferred to an electron acceptor when the acceptor becomes reduced, the energy transformation event that started with the absorption of light becomes permanent o Electromagnetic energy is transformed to chemical energy o redox reaction that occurs results in the production of chemical energy from sunlight Note: in the absence of light the electron acceptor doesn’t accept electrons o remains in oxidized state because the redox reaction that transfers an electron acceptor is ENDERGONIC o When light excited electrons in chlorophyll to a highenergy state, the reaction becomes EXERGONIC Energy released from these electrons can o Be emitted in the form of light vis fluorescence o be given off as heat slone o excite an electron in a nearby pigment and induce resonance o be transferred to an electron acceptor in a redox reaction Fluorescence is typical of isolated pigments Resonance energy transfer occurs in antenna complex pigments Redox occurs in reaction center pigments 10.3 Pages 185186 Converting Light Energy into Chemical Energy Photosystem II o Begins with the antenna complex transmoits resonance energy to the reaction center electron is them acceptor pheophytin o Pheophytin: identical to chlorophyll except lacks magnesium in its head region Functionally, molecules are very different Accepting highenergy electrons from the excited reaction center chlorophylls Reduction of pheophytin (& accompanying oxidation of the reaction center chlorophyll pigment) is a key step in the transformation of light to chemical energy o Electrons that reduce pheophytin are passed through additional carriers to ETC o Redox reactions that occurs in ETC of both photosystem II and mitochondria result in protons being actively transported from one side to the other o Proton electrochemical gradient forms a protonmotive force drives ATP production via ATP synthase o Triggers chemiosmosis and ATP synthesis in the chloroplast Plastoquinone (PQ) o small hydrophobic molecules that transport electrons between molecules o Lipid soluble o Not anchored to the membrane, free to move from one side of the membrane to the other o When receives electrons from PII, carries them across the membrane to the lumen side and delivers them t more electronegative molecules in the cytochrome complex o Potential energy released by these reactions allows protons to be picked up from the stroma and dropped off in the lumen side of the thylakoid membrane o Protons transported by this results in a large concentration of protons in the thylakoid lumen o Concentration of H+ is 1000 times higher in the lumen than the stroma o Stroma becomes negatively charged o Sets up a large proton electrochemical gradient resulting in a protonmotive force that drives H+ out of the lumen and into the stroma o Protonmotive force drives the production of ATP o Proton flow down the electrochemical gradient is exergonic that drives the endergonic synthesis of ATP o Stream of protons through ATP synthase causes conformational changes that drive the phosphorylation of ADP Called Photophosphorylation: energy harvested from light o Depends on chemiosmosis Photosystem II Obtains Electrons by Oxidizing Water Recall Reaction: sunlight + CO2 yields Sugar and O2 O2 must come from H2O Water must be oxidized for this to happen 2H2O → 4 H+ + 4 e + O2 o Splitting of water o Supplies electrons for photosystem II o catalyzed by enzymes that are physically integrated into photosystem II complex o High endergonic reaction o Light energy harvested in photosystem II is responsible for splitting water Excited electrons leave Photosystem II and enter ETC, photosystem becomes so electronegative that enzymes can remove electrons from water, leaving protons and oxygen Photosystem II is the only protein complex that can catalyze the splitting of water molecules Perform oxygenic photosynthesis: generate oxygen Other organisms use different electron donors, such as H2S in the purple sulfur bacteria: anoxygenic photosynthesis
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