Chapter 1 Cell and Molecular Biology PDF

1 - CELL AND MOLECULAR BIOLOGY 1.1 Building Blocks of Living Organisms Matter Matter – Anything that has mass and occupies space Element - a substance that can’t be broken down into a simpler substance (Na, Si, H2) Compound - a substance composed of more than one element (CO2...

1 - CELL AND MOLECULAR BIOLOGY 1.1 Building Blocks of Living Organisms Matter Matter – Anything that has mass and occupies space Element - a substance that can’t be broken down into a simpler substance (Na, Si, H2) Compound - a substance composed of more than one element (CO2, NaCl, NaHCO3) Atom – the smallest unit of an element (composed of protons, neutrons, electrons) Molecule – a substance composed of more than one atom BONDING Ionic Bond Bond between cations (+ ion) and anions (- ion) Covalent Bond Sharing of electrons between nonmetals Nonpolar Equal sharing of electrons Covalent Bond Small Electronegativity Difference between atoms Usually between 2 of the same atom or C-H Polar Large Electronegativity Difference between atoms Covalent Bond Significant partial positive/negative charges Coordinate ‘Special’ bond between nonmetal and metal ions Covalent Bond (Such as with the heme group in hemoglobin) INTERMOLECULAR / INTRAMOLECULAR FORCES Hydrogen Bonding Interaction between F-H, O-H, or N-H with F, O, or N Usually stronger than Dipole-Dipole and London forces Dipole-Dipole Forces Interaction between polar molecules The larger the electronegativity difference, the larger the force London Dispersion Forces Weak, transient (temporary) dipole (van der Waals Forces) All molecules have London forces Only force present for nonpolar molecules Greater with higher M.W. and larger surface area PROPERTIES OF WATER – SOLVENT OF LIFE A wide variety of ionic and polar solutes are soluble in water. This makes it a great solvent for chemical reactions and a great intracellular and extracellular medium. Water also exists as a liquid over a wide temperature range (0oC to 100oC) and has a high heat capacity. Cohesion - attraction of water molecules for other water molecules -leads to high surface tension Adhesion - attraction of water molecules to other substances -capillary action is important for water transport up xylem tissue in plants Hydrophilic (“Water-loving”) – relatively polar and forms strong intermolecular forces with water Hydrophobic (“Water-fearing”) – relatively nonpolar and repels water or fails to mix with water ChadsPrep.com 1 Proteins Proteins are polymers of amino acid monomers. 20 naturally occurring amino acids Classified as nonpolar (aliphatic), polar, acidic, or basic. Amino acids vary in the side chain (‘R’ group) attached. Small chains of amino acids are often referred to as polypeptides. Many proteins have hundreds or thousands of amino acids. The amide bond between amino acids is called a peptide bond. The free amino end of a protein is called the N-terminus. The free carboxy end of a protein is called the C-terminus. PROTEIN FUNCTIONS 1. Structural (e.g. hair and cytoskeleton) 2. Binding (e.g. receptors and hemoglobin) 3. Motor Proteins (e.g. actin and myosin) 4. Enzymes (Catalysis) ChadsPrep.com 2 Protein Structure Primary Structure The primary structure is simply the amino acid sequence. All that is necessary for proper protein folding is contained in the primary structure. Secondary Structure Comprised of local structural elements held together by H-bonding in the backbone. Alpha Helix - H-bonding is parallel to principal axis Beta Sheet - H-bonding is perpendicular to principal axis Alpha Helix Tertiary Structure The 3-dimensional shape of a protein (a single polypeptide). Myoglobin A variety of interactions are involved in the tertiary structure: Hydrophobic Effect - Nonpolar amino acids are sequestered to the interior of globular proteins to minimize interactions with water (entropic effect). Disulfide Bridge - Covalent bond between two cysteine residues. Salt Bridge - Electrostatic interaction between amino acids with opposite charges. Intermolecular Forces - H-bonding, dipole-dipole forces, and London forces are all involved too. Quaternary Structure Hemoglobin Present in proteins comprised of more than one polypeptide chain. Each polypeptide chain is referred to as a subunit. Quaternary structure describes the interactions between the individual subunits. Disulfide bridges, salt bridges, and IM Forces can all be involved here too. Protein Folding Protein folding is often unaided and spontaneous. Protein folding can be aided by other proteins (chaperones). Protein denaturation (unfolding/misfolding) can result from a change in pH, high salt concentrations, organic solvents, and/or high temperatures. ChadsPrep.com 3 Carbohydrates Carbohydrate monomers are called monosaccharides. Monosaccharides have the general formula Cn(H2O)n. Monosaccharides are either aldoses or ketoses. Monosaccharides can cyclize to form hemi-acetals/hemi-ketals. Disaccharides are comprised of two monosaccharides connected via a glycosidic bond. Sucrose = glu-fru lactose = gal-glu maltose = glu-glu Polysaccharides are long chains of monosaccharides connected via glycosidic bonds. Starch is comprised of two similar glucose polymers and is used as the chief energy storage molecule in plants. Amylose is linear with α-(1-4) glycosidic bonds, and amylopectin is branched with α-(1-4) and a few α-(1-6) glycosidic bonds. Glycogen is a branched glucose polymer with α-(1-4) and α-(1-6) glycosidic bonds. It is used for energy storage in the muscle and liver cells in mammals. Cellulose is a linear glucose polymer with β-(1-4) glycosidic bonds. It is a structural element in plant cell walls. Chitin is a linear polymer of N-acetylglucosamine (glucose derivative) with β-(1-4) glycosidic bonds. It is a structural element in fungal cell walls and the exoskeletons of insects and arthropods. amylose ChadsPrep.com 4 Nucleic Acids DNA – Deoxyribonucleic Acid Nucleoside - Sugar (deoxyribose) + base (A C G T) Nucleotide - Sugar + base + phosphate RNA – Ribonucleic Acid Nucleoside - Sugar (ribose) + base (A C G U) DNA / RNA Bases Nucleotide - Sugar + base + phosphate DNA Structure Right-handed double helix (B-form) Alternative Forms: A-form (right-handed) & Z-form (left-handed) Strands are antiparallel and complimentary Strands are held together by H-bonding and base-stacking Nucleotides connected via phosphodiester bond Watson-Crick Base Pairing A-T & G-C Base Pairs (Watson-Crick) G-C: 3 Hydrogen bonds A-T: 2 Hydrogen bonds ChadsPrep.com 5 Lipids Lipids are hydrophobic molecules that are relatively low in polarity and insoluble in water. LIPID FUNCTIONS Triglycerides Energy Storage; Insulation Phospholipids Cell Membranes Cholesterol Cell Membranes (Add Fluidity); Steroid Precursor Steroids Hormones Sphingolipids Variety of Roles in the Central Nervous System Prostaglandins Chemical Messengers (Autocrine/Paracrine) Terpenes Variety of Roles in Plants; Used in Cholesterol Synthesis Fatty Acids Fatty acids are carboxylic acids with long hydrocarbon tails. Saturated fatty acids have no double bonds. Unsaturated fatty acids have double bonds (can be cis or trans) Polyunsaturated fatty acids have more than one double bond. Triglycerides Triacylglycerols (triglycerides) are polymers of 3 fatty acids bonded to glycerol via ester bonds. Triglycerides are stored by adipocytes for energy and insulation. Phospholipids Phospholipids are the major component of cell membranes. Phospholipids are amphipathic having some regions hydrophobic and some hydrophilic. The polar ‘head’ group faces outward with the hydrophobic ‘tails’ facing inward. Unsaturated phospholipids don’t pack as tightly resulting in greater fluidity. ChadsPrep.com 6 Steroids/Cholesterol Cholesterol is a component of cell membranes providing increased fluidity. Cholesterol is the precursor for steroid hormones, vitamin D, and bile. Cholesterol and its derivatives should be recognized by their characteristic tetracycle structure. Sphingolipids Sphingolipids are found in nervous system tissue membranes and serve a variety of functions. Prostaglandins Prostaglandins are derived from arachidonic acid and serve a variety of autocrine/paracrine functions including mediating the inflammatory response. Terpenes Terpenes are made from multiple isoprene subunits, and there are thousands of biological terpenes. Notably, terpenes are a precursor for cholesterol and steroid synthesis, and B- carotene, the orange pigment in carrots that is converted to vitamin A, is a terpene. ChadsPrep.com 7 1.2 Thermodynamics and Kinetics in Living Systems (Including Enzyme Kinetics) Thermodynamics Gibbs Free Energy – the energy available to do work MEANING OF G VALUES G < 0 Spontaneous (Exergonic) G > 0 Nonspontaneous (Endergonic) G = 0 At Equilibrium G = H - TS H o S o -TS o CONDITIONS FOR SPONTANEITY - + - Spontaneous at all temperatures + - + Nonspontaneous at all temperatures - - + Spontaneous at low temperatures + + - Spontaneous at high temperatures G and Keq EQUILIBRIUM CONSTANTS G = -RTlnKeq Keq >> 1 Favors Products G < 0 Keq > 1 Keq 0 Keq < 1 10-3 < Keq < 103 both present at equilibrium G = 0 Keq = 1 Kinetics Reaction Coordinate Diagrams Characteristics of Catalysts 1. Speeds up a reaction (in both directions) 2. Lowers the activation energy (in both directions) 3. Provides an alternate mechanism (pathway) for the reaction to occur 4. Is NOT consumed in the reaction 5. Does NOT shift the equilibrium in either direction ChadsPrep.com 8 Enzyme Kinetics Lock and Key Model - active site and substrate are complimentary--specificity Induced Fit Model - Substrate binding induces a conformational change in the enzyme that causes the active site to be complimentary to the substrate Michaelis-Menten Kinetics 𝑉𝑚𝑎𝑥 [𝑆] 𝑉= 𝐾𝑚 + [𝑆] The Michaelis constant (Km) is inversely related to substrate affinity. [S] = Km at ½Vmax Competitive Inhibition Binds to the active site and inhibits substrate binding Km increases & Vmax is unchanged Noncompetitive Inhibition Inhibitor binds free enzyme or ES complex somewhere other than the active site Inhibits catalysis rather than substrate binding Vmax decreases & Km is unchanged ChadsPrep.com 9 1.3 Cell Structure and Cellular Processes PROKARYOTES EUKARYOTES 1. No nucleus 1. Membrane-bound nucleus 2. No membrane-bound organelles 2. Membrane-bound organelles 3. Single circular chromosome 3. Multiple linear chromosomes 4. Plasmid DNA 4. No plasmid DNA 5. Reproduce via fission (no 5. Reproduce via mitosis (centrosomes) centrosomes) 6. Plant/fungal cells have a cell wall 6. Cell wall (and often a capsule) ChadsPrep.com 10  ORGANELLES Organelle Function Stores DNA and site of transcription Surrounded by a nuclear envelope (2 lipid bilayers) Nucleus Nuclear pores regulate traffic of large molecules Contains the nucleolus (dark spot -- site of rRNA synthesis) Protein Synthesis (present in both pro- and eukaryotes) Ribosomes Ribosomes of rough ER synthesize membrane and secreted proteins Free ribosomes make cytosolic proteins ER associated with ribosomes Rough ER Glycoprotein synthesis (membrane-bound and secreted proteins) Synthesis of phospholipids and steroid hormones Smooth ER Breakdown of toxins in liver cells Modification (glycosylation) and ‘packaging’ of proteins into vesicles for Golgi secretion or transport to cellular destinations (like lysosomes) Apparatus Incoming vesicles on cis face; outgoing on trans face Site of oxidative phosphorylation (ATP synthesis) Site of PDC, Citric Acid Cycle and the Electron Transport Chain Mitochondria Site of fatty acid catabolism (-oxidation) Contain mitochondrial DNA (circular) and ribosomes for self-replication Degradation of old organelles or phagocytosed materials Lysosomes Contains digestive enzymes (and pH~5) Produced from the Golgi Apparatus Involved in reduction of reactive oxygen species including hydrogen peroxide Peroxisomes Breakdown of fatty acids, amino acids, and various toxins Carries out the glyoxalate cycle in germinating plant seeds A centrosome is composed of two centrioles Centrosomes Centrioles are MTOCs that create the spindle apparatus used for cell division & Centrioles Not present in plant cells Membrane-bound vesicles used for storage of nutrients (plants & animals) Vacuoles Plant cells have a large central vacuole that maintains turgor pressure in addition to storing water & nutrients Chloroplasts Site of photosynthesis in plant cells (not present in animal cells) In plants—made of cellulose (glucose polymer) In fungi—made of chitin (N-acetylglucosamine polymer) In bacteria—made of peptidoglycans Cell Wall In archaebacteria—made of polysaccharides Not present in animal cells In plant cells, provide tensile strength, mediating mechanical/osmotic stress ChadsPrep.com 11 Plasma Membrane Separates a cell from its surroundings Principally composed of a phospholipid bilayer Fluid Mosaic Model – Components free to move laterally throughout the membrane PLASMA MEMBRANE COMPOSITION 1. Phospholipids and Glycolipids Ex. phosphatidylcholine, phosphatidylserine, etc. Unsaturated fatty acids increase membrane fluidity. Membrane is asymmetrical. 2. Cholesterol Modulates membrane fluidity Increases membrane fluidity at low temperatures Decreases membrane fluidity at high temperatures 3. Membrane Proteins Peripheral Membrane Proteins – adhere to membrane surface via electrostatic interactions Integral Membrane Proteins – anchored to and embedded in the membrane (but on one side) Transmembrane Proteins – span the membrane and include channel proteins, carrier proteins, porins Membrane Receptors - recognition glycoproteins on the cell surface that interact with hormones or other molecules and relay signals into the cell Intercellular Junctions Gap Junctions – Exchange of nutrients & cell-to-cell communication Ex. cardiac muscle cells Tight Junctions – Seals the space between cells preventing leakage Ex. intestinal epithelial cells Desmosomes – ‘Spot welds’ between cells giving adhesion / mechanical strength Anchored to the cytoskeletons Ex. skin cells Cytoskeleton Microfilaments – Made from actin Involved in cellular motility, muscle contraction, and cytokinesis ATP dependent myosin motors can move along actin Intermediate Filaments – support and maintain the shape of the cell Microtubules – Made from tubulin Function as a ‘railroad’ for intracellular transport Found in the spindle apparatus of mitosis (MTOCs/centrioles), flagella, and cilia Flagella/cilia constructed of a “9+2” arrangement of microtubules (eukaryotes) (Prokaryotic flagella are composed of flagellin.) ChadsPrep.com 12 Membrane Transport Diffusion – Movement of a solute from high to low concentration Osmosis – Diffusion of water Hypertonic –Higher relative solute concentration Hypotonic –Lower relative solute concentration Isotonic–Equal relative solute concentration Crenation – The shriveling of a cell (ex. RBC) when placed in a hypertonic solution due to osmosis Plasmolysis – The shrinking of plant cells when placed in a hypertonic solution due to osmosis Cytolysis – The swelling and rupture of a cell when placed in a hypotonic solution PASSIVE TRANSPORT ACTIVE TRANSPORT Transport with the concentration gradient Transport against the concentration gradient No energy required Requires energy (ATP hydrolysis) 1. Simple Diffusion 1. Primary Active Hydrophobic molecules and small polar Ex. Na/K pump molecules (uncharged) can diffuse 3Na+ pumped out / 2K+ pumped in across the membrane Fueled by ATP hydrolysis Includes CO2, O2, lipids including steroid Establishes resting membrane potential hormones, some drugs 2. Facilitated Diffusion 2. Secondary Active Diffusion of ions/polar solutes via a Uses one solute’s gradient (established by carrier or channel protein (ex. glucose) ATP hydrolysis) to accomplish the transport of another Ex. Na+/glucose cotransport Endocytosis – The ingestion of extracellular material into vesicles inside the cell Phagocytosis (“Cellular Eating”) – Endocytosis of solid material Pinocytosis (“Cellular Drinking”) – Endocytosis of dissolved solutes Receptor-Mediated Endocytosis – Endocytosis initiated by solute binding membrane receptors Exocytosis – Expulsion of intracellular materials via vesicle secretion ChadsPrep.com 13 1.4 Mitosis and Meiosis Mitosis and the Cell Cycle CELL CYCLE G1 Preparation for DNA synthesis Production of organelles Increase in cell volume G1 checkpoint: DNA damage / inadequate cell growth G0 Phase of cells not actively undergoing cell division Quiescence (temporary) vs senescence (permanent) S DNA Replication G2 Continued growth in preparation for mitosis Mitochondria and/or chloroplasts divide G2 checkpoint: DNA damage MITOSIS Chromosomes condense Nuclear envelope breaks down Prophase Polarization of the centrioles (MTOCs) Spindle fibers begin to form Spindle fibers attach to centromeres (via kinetochores) Prometaphase Chromosomes begin migrating toward the equator Metaphase Chromosomes are aligned on the metaphase plate Spindle fibers pull sister chromatids apart towards the centrioles Anaphase Cleavage furrow begins to form Chromosomes cluster at opposite poles and decondense Telophase Nuclear envelopes reform (karyokinesis = nuclear division) Cytokinesis begins Cleavage furrow forms dividing the cells (animals) Cytokinesis Cell plate forms dividing the cells (plants) ChadsPrep.com 14  MEIOSIS Interphase Protein and DNA synthesis to prepare for replication G1/S Production of organelles Chromosomes condense and tetrad formation (synapsis) Prophase I Recombination (Longest phase) Nuclear envelope breaks down & polarization of the centrioles (MTOCs) Spindle fibers attach at centromeres via kinetochores Metaphase I Chromosomes line up on metaphase plate Spindle fibers pull homologous chromosomes apart towards the centrioles Anaphase I Cleavage furrow begins forming Nuclear membranes reform Telophase I Completion of cytokinesis Chromosomes condense Prophase II Nuclear envelope breaks down & polarization of the centrioles (MTOCs) Spindle fibers attach at centromeres via kinetochores Metaphase II Chromosomes line up on metaphase plate Spindle fibers pull sister chromatids apart towards the centrioles Anaphase II Cleavage furrow begins forming Nuclear envelopes reform Telophase II Completion of cytokinesis Nondisjunction – failure of tetrads to separate during meiosis I or sister chromatids in meiosis II Ex. Down Syndrome (trisomy 21), Turner Syndrome (X), Kleinfelter Syndrome (XXY) ChadsPrep.com 15 1.5 Cellular Metabolism Metabolism Catabolism – breakdown of molecules to release energy Anabolism – construction of molecules (consumes energy) ATP Hydrolysis Endergonic reactions can be coupled to ATP hydrolysis to make them spontaneous. Anaerobic Metabolism GLYCOLYSIS FERMENTATION OXIDATION: glucose → 2 pyruvate OXIDATION: NADH → NAD+ REDUCTION: NAD+ → NADH REDUCTION: pyruvate → CO2 + ethanol REDUCTION: pyr → lactate Net production of 2 ATP Regenerates NAD+ for continued glycolysis (2 ATP consumed / 4 ATP produced) Also occurs in aerobes w/o adequate O2 ChadsPrep.com 16 Aerobic Metabolism Pyruvate Oxidation occurs in the mitochondrial matrix. The Citric Acid Cycle occurs in the mitochondrial matrix. The ETC Complexes are located in the inner mitochondrial membrane. -Proton’s are pumped (actively) from the matrix to the intermembrane space. ATP synthase is located in the inner membrane and synthesizes ATP on the matrix side. ChadsPrep.com 17 Glycolysis Glycolysis occurs in the cytosol. Glycolysis converts glucose (6C) to 2 pyruvate (3C). 2 ATP are consumed and 4 ATP produced (2 net). 2 NADH are produced. These are either recycled via fermentation or shuttled to the Electron Transport Chain in the mitochondria. Upon entering the cell, glucose is phosphorylated by Hexokinase to produce glucose-6- phosphate which prevents it from diffusing back out of the cell. It is eventually converted into fructose-1-6-bisphosphate by phosphofructokinase-1 (PFK-1) in the major regulatory step. PFK-1 REGULATION IN GLYCOLYSIS Activated By Inhibited By AMP ATP Fructose-6-Phosphate Fructose-1,6-Bisphosphate Insulin Glucagon Fructose-1,6-bisphosphate is cleaved into two 3 carbon fragments which both ultimately become glyceraldehyde-3-phophate. Glyderaldehyde-3-phosphate is oxidized to 1,3- bisphosophoglycerate with NAD+ being reduced to NADH. The final four steps convert two 1,3-bisphosophoglycerate to two pyruvate accompanied by the production of 4 ATP. ChadsPrep.com 18 Pyruvate Oxidation (PDC Complex) The Pyruvate Dehydrogenase Complex (PDC) is located in the mitochondrial matrix. Pyruvate is oxidized to acetyl-CoA with the loss of CO2 (decarboxylation). NAD+ is reduced to NADH. Citric Acid Cycle (a.k.a. Kreb’s Cycle or Tricarboxylic Acid Cycle or TCA Cycle) The enzymes of the Citric Acid Cycle are located in the mitochondrial matrix. Acetyl-CoA (2C) combines with oxaloacetate (4C) to form citrate (6C). Citrate is converted in a series of reactions, including two decarboxylations and several oxidations, back into oxaloacetate to begin the cycle anew. 3 NADH and 1 FADH2 are produced per acetyl-CoA (x2 per glucose). 1 GTP is produced per acetyl-CoA which can be readily converted to ATP (x2 per glucose). Substrate-Level Phosphorylation - production of ATP in Glycolysis and the Citric Acid Cycle Oxidative Phosphorylation – production of ATP via chemiosmosis (Electron Transport Chain) Oxidation of NADH/FADH2 creates a proton gradient that powers ATP Synthase (chemiosmosis). 1NADH ~ 2.5ATP 1FADH2 ~ 1.5ATP Electron Transport Chain (ETC) complexes are in the inner mitochondrial membrane. Protons are translocated by Complexes I, III, and IV. ATP YIELD FROM AEROBIC GLUCOSE CATABOLISM PROCESS ENERGY-RELATED ATP PRODUCTS Yield 2 ATP (net) 2 GLYCOLYSIS 2 NADH 5 PDC 2 NADH 5 2 ATP 2 CITRIC ACID 6 NADH 15 CYCLE 2 FADH2 3 TOTAL 30-32 ChadsPrep.com 19 Gluconeogenesis The production of glucose from pyruvate. Effectively, this is the reverse of glycolysis and even uses many of the same enzymes. Takes place primarily in the liver (but also in the kidneys to a smaller extent). The liver can produce glucose for release into the blood stream when needed. REGULATION OF GLUCONEOGENESIS Activated By Inhibited By High [ATP] Low [ATP] High [Glucose] Insulin Glycogen Synthesis and Glycogenolysis Glycogen is a glucose polymer used to store glucose in the liver and muscle tissues. When glucose is abundant in the diet, glycogen is produced (stimulated by insulin). Muscles use glycogen as a ready store of glucose during vigorous exercise. The liver uses glycogen to produce glucose for release into the blood stream when needed (stimulated by glucagon and epinephrine). REGULATION OF GLYCOGEN METABOLISM GLYCOGEN SYNTHESIS GLYCOGENOLYSIS Activated By Inhibited By Activated By Inhibited By Insulin Low [ATP] High [ATP] Glucagon Epinephrine Metabolism of Fats Triacylglycerides are stored in adipocytes. When needed, lipases lead to the release of fatty acids into the blood stream for catabolism (β-oxidation). Each round of β-oxidation cleaves two carbons from a fatty acid to produce 1 NADH, 1 FADH2, and 1 acetyl-CoA. The acetyl-CoA is then fed into the citric acid cycle. Unsaturated fatty acids have a lower energy yield than saturated fatty acids. Metabolism of Proteins If other caloric sources are unavailable, proteins can be broken down into amino acids, many of which can be deaminated and converted into glycolysis or citric acid cycle intermediates for further catabolism. alanine → pyruvate serine, glycine, cysteine → 3-phosphoglycerate glutamate, proline, arginine → α-ketoglutarate aspartate, asparagine → oxaloacetate ChadsPrep.com 20 1.6 Photosynthesis Photosynthesis uses light energy to achieve carbon fixation--producing sugars (including glucose) from CO2. The net reaction that occurs during photosynthesis is the reverse of that occurring during cellular respiration. It is highly endergonic, with the energy required coming from photons of light. Ultimately, H2O is oxidized to O2 while CO2 is reduced to form sugars (typically glucose). Photosynthesis occurs in plants, algae, and photosynthetic bacteria. In plants and algae, photosynthesis takes place in membrane-bound organelles called chloroplasts. In photosynthetic bacteria, it occurs via enzymes embedded in the plasma membrane. Light is absorbed by organized systems of pigments called photosystems in the thylakoid membrane. Photosystems are generally composed of an antenna complex consisting of many chlorophyl and carotenoid pigments which surround a reaction center comprised of two specialized chlorophyl molecules. The pigments of the antenna complex absorb the energy of photons and pass it from molecule to molecule toward the reaction center. When it reaches the reaction center an electron is excited and then donated to an electron carrier. Photosynthesis is broken down into light-dependent reactions (a.k.a. light reactions) and light-independent reactions (a.k.a. Calvin Cycle or dark reactions). ChadsPrep.com 21 Light-Dependent Reactions The light-dependent reactions take place in the thylakoid membrane and include both Cyclic and Noncyclic Photophosphorylation. Noncyclic Photophosphorylation Noncyclic Photophosphorylation involves both Photosystems I and II and produces both ATP and NADPH are necessary for the Calvin Cycle. An electron is excited in Photosystem II and then transferred through a series of electron carriers before being transferred to Photosystem I. One of these carriers is the cytochrome b6-f complex which translocates protons from the stroma to the lumen. This creates a proton gradient that powers ATP Synthase (chemiosmosis). This electron passed to Photosystem I is excited once again by absorption of another photon before being passed on to more electron carriers. In the end the electrons are passed on to NADP Reductase which reduces NADP to NADPH. And the electron originally transferred from Photosystem II is replaced by the splitting of water as water is oxidized to O2. Cyclic Photophosphorylation Cyclic Photophosphorylation only involves Photosystem I and only produces ATP (no NADPH). An electron is excited in Photosystem I and then transferred through a series of electron carriers before being returned to Photosystem I by plastocyanin. One of the electron carriers is again the cytochrome b6-f complex which translocates protons across the thylakoid membrane, creating a proton gradient that powers ATP Synthase (chemiosmosis). ChadsPrep.com 22 Calvin Cycle The Calvin Cycle (a.k.a. light-independent or dark reactions) takes place in the stroma. The NADPH and ATP produced in the light-dependent reactions provide the energy used to carry out carbon fixation, converting CO2 into sugars. The Calvin Cycle leads to the production of glyceraldehyde-3-phosphate. You might recall that this is an intermediate in glycolysis (and gluconeogenesis). As such in can be transferred to the cytosol where it can serve as fuel for glycolysis ultimately for ATP synthesis. But it can also undergo gluconeogenesis to produce a variety of carbohydrates included glucose, fructose, sucrose, and starch. The Calvin Cycle occurs in 3 major steps: 1. Carbon Fixation – CO2 combines with a 5-carbon sugar (ribulose-1-5-bisphosphate) to produce two 3-carbon intermediates (3-phosphoglycerate). This reaction is catalyzed by the enzyme Rubisco 2. Reduction – 3-phosphoglycerate is reduced to glyceraldehyde-3-phosphate requiring 1 ATP and 1 NADPH per molecule. 3. Regeneration – glyceraldehyde-3-phosphate is converted back into ribulose-1-5- bisphosphate which requires ATP hydrolysis. The Calvin Cycle must be run through 3 cycles to produce a single excess molecule of glyceraldehyde-3-phosphate which can be used for carbohydrate synthesis or glycolysis. Two molecules of glyceraldehyde-3-phosphate are required to make glucose, so the Calvin Cycle must be run through 6 cycles to produce a single glucose molecule. ChadsPrep.com 23 Photorespiration In addition to carbon fixation, rubisco also catalyzes the oxidation of ribulose-1-5- bisphosphate in a process termed photorespiration. This catalytic activity uses the same active site as carbon fixation thus competing with it. Higher [CO2] favors the Calvin Cycle while higher [O2] favors photorespiration. The product of oxidation ultimately loses CO2 thereby lowering the overall efficiency of the Calvin Cycle. Photorespiration becomes a larger problem at higher temperatures. Leaves have specialized openings called stomata through which CO2 is taken up and O2 is released. As temperatures rise the stomata close to prevent the loss of water, but this also prevents the uptake of CO2 and release of O2. This lowers the concentration of CO2 and raises the concentration of O2 inside the leaf thereby increasing photorespiration. C4 Photosynthesis Plants that undergo carbon fixation exclusively using the Calvin Cycle are termed C3 plants based upon the 3-carbon product of carbon fixation, 3-phosphoglycerate. But some plants also have an alternative mode of carbon fixation combining CO2 with phosphoenolpyruvate (PEP) to initially form oxaloacetate which is converted to malate, which has 4 carbons. The enzyme used is PEP carboxylase and such plants are termed C4 plants. PEP carboxylase does not have a competing oxygenase activity as does rubisco and binds CO2 with even greater affinity though requires more ATP for carbon fixation. Overall, C4 plants have a ‘spatial’ solution to minimize photorespiration. PEP carboxylation occurs in mesophyll cells, but the Calvin Cycle occurs in adjacent bundle-sheath cells. The malate produced in the mesophyll cells is shuttled to the bundle-sheath cells where subsequent decarboxylation releases CO2. This concentrates CO2 in the bundle-sheath cells thus minimizing photorespiration during C3 carbon fixation. C4 plants are found in in warm tropical grasslands and include corn, sugar cane, and pineapples. ChadsPrep.com 24 CAM Photosynthesis CAM plants have a ‘temporal’ solution rather than a spatial one to minimize photorespiration. Instead of spatially separating WHERE C4 and C3 carbon fixation occur, CAM plants temporally separate WHEN C4 and C3 carbon fixation occur. C4 only occurs at night while C3 occurs during the day, but both occur in the same cells. CAM plants only have their stomata open at night, thus minimizing water loss. But this also means that CO2 uptake only occurs at night. When CO2 is taken up, C4 carbon fixation occurs effectively ‘storing’ the CO2 in malate. Malate is decarboxylated during the day, thereby releasing CO2. This concentrates the CO2 in the leaf during the day for the Calvin Cycle which once again serves to minimize photorespiration. So overall, this ‘temporal’ solution allows CAM plants to minimize photorespiration AND water loss simultaneously. Therefore, it shouldn’t be surprising that CAM plants include succulents living in dry, arid climates such as cacti and agave. ChadsPrep.com 25