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[VERSION 2] GENERAL BIOLOGY I Study Guide for Test 2

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Biological Sciences
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Biology Exam 2 Study Guide - Nesbitt 125 at 8am LIGAND IS A SIGNALING MOLECULE Photosynthesis Photosynthesis (CO2 is reduced, H2O is oxidized): • Light-dependent reaction: use light energy; in THYLAKOID MEMBRANE; produce ATP, NADPH, and O2 o Pigments (chlorophyll a and b; carotenoids) form photosystems (PSI and PSII) in the thylakoids o Absorption spectrum: wavelengths that are absorbed by different pigments o Action spectrum: rate of photosynthesis by whole plant at specific wavelengths • Carbon fixation: fixing carbon into organic molecules • Light-independent reaction: Calvin-Benson cycle: occurs in STROMA; uses CO2, ATP, and NADPH to incorporate CO2 into carbohydrate G3P (to make carbohydrates) • Mostly occurs in mesophyll Chloroplast Parts • Outer + Inner membrane (intermembrane space is between) • Thylakoid membrane: contains pigment molecules o Forms thylakoids and encloses thylakoid lumen • Granum: stack of thylakoids • Stroma: fluid filled region between thylakoid membrane and inner membrane • ATP synthesis in chloroplasts: o Achieved by chemiosmotic mechanism called photophosphorylation o Driven by flow of H from thylakoid lumen into stroma via ATP synthase  H+ gradient generated three ways: + • ↑H in thylakoid lumen by splitting of water • ↑H by ETC pumping H into lumen • ↓H in stroma from formation of NADPH Photophosphorylation • Light causes chlorophyll to give up electrons • E released from transfer of electrons (oxidation) of chlorophyll through a system of carrier molecules is used to generate ATP Noncyclic and cyclic electron flow: • Noncyclic o Electrons begin at PSII and eventually transfer to NADPH o Produces both ATP and NADPH in equal amounts o Steps:  PSII (thylakoid membrane)- excited electrons travel to PSI (makes ATP) + • Water is oxidized- generates O a2d H • Releases energy in ETC • H gradient 1. Light E absorbed by pigment molecule to boost an e-‘s E lvl 2. E transferred among pigment molecules until it reaches P680, converting it to P680* 3. The high-E electron on P680* is transferred to the primary electron acceptor. P680* becomes P680+ 4. A low-E electron from water is transferred to P680+ to convert it to P680. Oxygen is produced.  PSI – primary role to make NADPH (boosts e- to even higher E lvl) • Addition of H to NADP contributes to H electrochemical gradient o Products:  Oxygen, O 2 • Produced in thylakoid lumen by oxidation of H O2by PSII • Two electrons transferred to P680 molecules  NADPH • Produced in the stroma from high-energy electrons that start in PSII and are boosted in PSI • NADP + 2 electrons + H → NADPH  ATP • Produced in stroma by ATP synthase using the H electrochemical gradient 1. Light excites electrons within components of PSII. Excited electrons move down an electron transport chain to more electronegative atoms to produce a H+ electrochemical gradient. Electrons are removed from water and transferred to a pigment called P680. This process creates O2 and places additional H+ in the lumen. 2. Electrons from PSII reach PSI… A second input of light boosts them to a very high energy level. They follow the path shown by the red arrow. 3. Two high-energy electrons and one H+ are transferred to NADP+ to make NADPH. This removes some H+ from the stroma. 4. H+ electrochemical gradient is generated by: production of O2, pumping of H+ across thylakoid membrane, and synthesis of NADPH. This gradient is used to make ATP via an ATP synthase in the thylakoid membrane. • Cyclic photophosphorylation o Electron cycling releases energy to transport H into lumen driving ATP synthesis o Produces only ATP o PSI electrons excited, release energy and eventually return to PSI Calvin Cycle • CO2 incorporated into glyceraldehyde 3 phosphate o Precursor to glucose and other organic molecules o Used for energy storage o Requires massive input of E (for every 6 CO2 incorporated, 18 ATP + 12 NADPH needed) o Product: 2 G3P (glucose is later made from G3P) 1. Carbon fixation a. CO i2corporated into 5C Ribulose Biphosphate (RuBP) b. taking gas form – “fixing” it… c. making a 6 C molecule and splitting into 3 pieces 2. Reduction and carbohydrate production a. ATP is used to convert 3PG into 1,3-bisphosphoglycerate (1,3-BPG) b. NADPH electrons reduce it to glyceraldehyde-3-phosphate (G3P or GAP) c. 6 CO →212 G3P i. 2 G3P used for carbohydrates ii. 10 G3P used for RuBP 3. Regeneration of RuBP a. 10 G3P converted into 6 RuBP using 6 ATP Variations in Photosynthesis: light intensity, T, water availability • C3 and C4 (and CAM: Crassulacean Acid Metabolism) plants o C3: wheat plants, oak leaves (90% of plants)  Better in cooler climates (uses less energy to fix CO2) o C4: corn  CAM: type of C4 plant that separate processes using time (like cactus) • Open stomata at night o CO2 enters and oxaloacetate formed; converted to malate • Stomata close during the day to conserve water • Malate used as source of CO t2 drive Calvin cycle during the day  Better in warm/dry climates (conserve water and prevent photorespiration)  Adapted: • Mesophyll cells o CO e2ters via stomata and 4 carbon compound formed • Bundle-sheath cells o 4 carbon molecule transferred that releases steady supply of CO 2 minimizing photorespiration • Keeps CO2 concentration high Photorespiration • More likely in hot/dry environments • Occurs when CO2 is low and O2 is high • Evolved a mechanism to minimize respiration (aka maintain high CO2/O2 ratio) • Rubisco functions as a carboxylase o RuBP + CO2 → 2 3PG o C3 plants make 3PG o Preferred in normal conditions • BUT if CO2 is really low…Rubisco can also be an oxygenase o Adds O 2o RuBP eventually releasing CO 2 o oxaloacetate (4 carbon molecule) made in the first step of carbon fixation o C4plants • Using O 2nd liberating CO i2 wasteful Cell Communication Cell Signaling: Highly coordinated processes in multicellular organisms; necessary to respond to a changing environment (SURVIVAL) • receive signal (we’ll talk about receptors) • signal transduction (the signal has to get transmitted) • pathway activation/downstream effects Stages of Cell Signaling 1. Receptor activation: ligand (AKA SIGNALING MOLECULE) binds noncovalently to receptor with high specificity and rapid turnover a. The binding of a signaling molecule causes a conformational change in a receptor that activates its function; once ligand is released, receptor reverts and is inactive until another ligand binds b. Types of cell surface receptors (all are transmembrane/integral proteins) i. Enzyme-linked receptors 1. Found in all living species 2. Extracellular domain binds signal 3. Intracellular domain becomes functional catalyst 4. Most are kinases a. Ex: tyrosine or serine/threonine b. “Receptor tyrosine kinase” (RTK) c. “receptor serine/threonine kinases” (RSTK)* ii. G-protein coupled receptors (GPCR) a. Found in all eukaryotes, common in animals b. 7 transmembrane segments c. Activated receptor binds to G protein 2. G-proteins will bind GTP / GDP a. GTP = “on” b. GDP = “off” c. GTP binding causes G protein to dissociate from receptor d. parts of G protein – the α subunit and the β/γ dimer will interact with other proteins in a signaling pathway “downstream” 3. ligand binds GPCR a.  G protein binds 4. G protein exchanges GDP for GTP a.  G-protein dissociates from GPCR b.  G-protein separates into subunits: alpha and β/γ dimer 5. Transmits to downstream signals a.  G protein α subunit hydrolyzes GTP to _____ b.  α subunit and the β/γ dimer will reassociate iii. Ligand-gated ion channels 1. Plant and animal cells 2. Ligand binding causes ion channels to open and ions to flow through the membrane 3. In animals  synaptic signals between neurons and muscles or between two neurons 4. two ligands bind to extracellular domain of receptor (channel) 5. conformation change and ions can pass along gradient iv. Intracellular (inside cell): ligand must get into cell and then bind 1. Ex: estrogen a. Hormone diffuses through cell membrane and into the nucleus where it binds estrogen receptor b. this complex binds DNA and can mediate transcription 2. Signal transduction: activated receptor stimulates series of changes called signal transduction pathway (STP) a. The activated receptor stimulates a series of proteins that forms a signal transduction pathway b. cascade of intracellular kinases i. Receptor Tyrosine Kinases (RTK), RSTK signaling 1. Category of enzyme-linked receptors found in animals 2. Recognize various types of signaling molecules a. Growth factor – hormone that acts to stimulate cell growth or division 3. example: Epidermal Growth Factor (EGF) a. One function is to stimulate epidermal cells to divide b. Functions in many different contexts c. EGFR Signaling 1. Receptor activation: Two EGF molecules bind to 2 EGF receptor subunits, causing them to dimerize and phosphorylate each other on tyrosines 2. Relay between the receptor and protein kinase cascade: Grb binds to the phosphorylated receptor and then to Sos. Sos stimulates Ras to release GDP and bind GTP. 3. Protein kinase cascade: Ras activates Raf, which starts a protein kinase cascade in which Raf phosphorylates Mek, and then Mek phosphorylates Erk. 4. Activation of transcription factors: Erk enters the nucleus and phosphorylates transcription factors, Myc and Fos 5. Cellular response: Myc and Fos stimulate the transcription of specific genes. The mRNAs are translated into proteins that cause the cell to progress through the cell cycle and divide. c. second messengers, or generation of intracellular signals called i. G-protein coupled receptors (GPCR) signaling: ligands binding to cell surface receptors; Many signal transduction pathways lead to production of second messengers like cAMP, Ca2+, DAG and IP3 1. ligand binds GPCR a.  G protein binds 2. G protein exchanges GDP for GTP a.  G-n separates into subunits: alpha and β/γ dimer 3. Transmits to downstream signals a.  G protein α subunit hydrolyzes GTP to _____ b.  α subunit and the β/γ dimer will reassociate 4. cAMP (Cyclic adenosine monophosphate) a. generated by adenylyl cyclase b. broken down b
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