Bio exam 2 study guide - instructor: Tyler Hodges PDF

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BIO EXAM 2 STUDY GUIDE Cytoskeleton- network of protein fibers throughout the cytoplasm Is highly dynamic (can be quickly disassembled and reassembled) Protein fibers that make up cytoskeleton: Microtubules--control beating of cilia and flagella (made of microtubules)  Microfilaments (actin filaments)—polymers of protein called actin o Function in cell motility (motor protein myosin and actin)  Intermediate filaments—polymers of intermediate filament proteins, including keratin Microtubules grow out from the centrosome (near nucleus) Centrosome is the microtubule organizing center (MTOC) Centrosome—cloud of amorphous material surrounding a pair of centrioles (made of microtubules) Collagen—extracellular matrix glycoprotein that forms strong fibers outside the cells Cell junctions—communication through direct physical contact/ four types:  Plasmodesmata—channels between adjacent plant cells  Tight junctions— press neighboring cells together to prevent leakage of extracellular fluid  Desmosomes—fasten cells together into sheets  Gap junctions—cytoplasmic channels between cells that help cell communication Peroxisome- break down long-chain fatty acids to be used as fuel Enzymes transfer hydrogen to O2 producing hydrogen peroxide (H2O2) This is toxic to cells but is confined to peroxisome and easily converted to H2O and H __________________________________________________________________________________________________________________ ____________________________________________________________________________________________ CHAPTER 7: MEMBRANE STRUCTURE & FUNCTION  Lipids and proteins in membrane drift laterally  Membranes rich in unsaturated fatty acids are more fluid than saturated fatty acids Cholesterol- (animal cells) used in membranes, in warm environments—restrains membrane movement, in cold environments—keeps membrane fluid Peripheral proteins- attached to one side of membrane Integral proteins- span entire membrane (transmembrane) Cells recognize each other by binding to surface molecules (carbs) on the membrane There is an asymmetrical distribution of proteins, carbs, and lipids, determined in the ER and Golgi were membranes are constructed Hydrophobic, nonpolar molecules can easily pass through Hydrophilic, polar molecules cannot Water diffuses slowly: it is small and polar (osmosis) Transport proteins allow passage of hydrophilic substances (facilitated diffusion)  Channel proteins—hydrophilic channel specific molecules or ions can use Aquaporins—passage of water  Carrier proteins—bind to molecules and change shape to shuttle them across (Na/K pump) PASSIVE TRANSPORT HIGH TO LOW Diffusion—the tendency of molecules to spread out evenly into the available space Dynamic equilibrium—as many molecules cross one way as cross in the other direction Osmosis- diffusion of a solvent from the side of low concentration to the side of high concentration

WATER FOLLOWS SOLUTE Tonicity- the ability of a solution to gain or lose water  Isotonic solution- solute is the same outside and inside  Hypertonic solution- more solute outside than inside, water leaves, cell shrinks (shriveled)  Hypotonic solution- more solute inside than outside, water enters, cell swells (lysed) Osmoregulation—necessary for life, the control of solute concentrations and water balance  Cell walls help regulate this in plants (hypo- turgid, iso- flaccid, hyper- plasmolysis (membrane separates from cell wall) ACTIVE TRANSPORT Maintains concentrations that are different from their surroundings LOW TO HIGH  Sodium-potassium pump—both Na and K are pushed from low to high  Electrogenic pumps—sodium potassium pump in animals, proton pumps in plants, fungi, and bacteria  Cotransport—solute indirectly drives transport of another solute o Plants use H+ proton pumps to drive the active transport of nutrients into the cell (sugars)  Bulk transport—large molecules (polysaccharides, proteins) cross membrane in bulk via vesicles Endocytosis—cell takes in macromolecules (or entire cells) by forming vesicles from the membrane; 3 types:i  Phagocytosis—cell engulfs a particle with a vacuole, vacuole fuses with lysosome, it digests the particle  Pinocytosis—molecules in extracellular fluid are taken up when fluid is engulfed into vesicles  Receptor-mediated—binding of ligands to receptors triggers vesicle formation Exocytosis—transport/secretory vesicles fuse with the plasma membrane and push contents out of cell __________________________________________________________________________________________________________________ _______________________________________________________________________________________________________

CHAPTER 8: METABOLISM Metabolic pathway- begins with a specific starting molecule and ends with a product, each steps catalyzed by an enzyme Catalyst—speeds up a chem reaction without being consumed (most are proteins) Metabolic pathways can be… CATABOLIC ANABOLIC --build complex molecules from simpler ones --Breaks down complex molecules to simpler ones --endergonic/ consume energy/ decreases --exergonic/release energy/ increases entropy entropy --example: breakdown of glucose --example: synthesis of proteins from amino acids, Glucose+ fructosesucrose Energy—the capacity to perform work, which rearranges molecules via chem reactions  Kinetic--motion; energy of substrates is increased as the amount of heat increases  Heat (thermal)—kinetic; random movement of atoms  Potential—energy that matter possesses bc of location/structure  Chemical—potential energy available for release in chem reactions Thermodynamics- study of energy transformations First Law of Thermodynamics—energy cannot be created or destroyed Second Law of Thermodynamics—every energy transfer ultimately increases the entropy (disorder) of the universe Open system- energy can be transferred between the system and its surroundings (biological systems) Closed system- isolated from environment ENTROPY Takes the form of heat May decrease within an organism, but the processes of life increase the universes total entropy Free energy (G)- energy available to perform work when temp and pressure are uniform EXERGONIC ENDERGONIC +G -G Absorb free energy (anabolic) Release of free energy (catabolic) Example: ADP+P= ATP spontaneous Energy coupling—using exergonic processes to drive endergonic ones, most mediated by ATP Cell does 3 types of work:  Chemical (synthesis of macromolecules)  Mechanical (contraction of muscle cells and movement of chromosomes)  Transport (vesicles along cytoskeletal tracks by motor proteins) ENZYMES Activation energy (EA)—the initial energy needed to start a chem reaction Enzymes catalyze chem reactions by lowering thenitrogenous activation energy (they are not consumed  Consists of adenine base, ribose 5-carbon sugar, 3 and do not affect the change in G) phosphate groups Substrate- the reactant the acts on phosphates are broken by hydrolysis (water is added to  enzyme Bonds between Enzyme-substrate complex--enzyme break themand apart) substrate bond o Energy is released bc ADP is more stable than ATP  Can drive endergonic reactions by phosphorylation—adding a phosphate group to another molecule (makes a molecule phosphorylated)  ATP is renewable by adding a phosphate group to ADP

Induced fit—shape change after binding of substrate that enhances the reaction (orients substrates correctly, provides a favorable microenvironment) Enzyme activity can be affected by temp, pH, and chemicals Cofactors-non-protein compound bound to an enzyme and required to catalyze a biochemical reaction An organic cofactor is called a coenzyme Competitive inhibitors- compete with substrate for binding at the active site (may be permanent or reversible) Noncompetitive inhibitors- bind to the allosteric site, changing the shape of the enzyme and affecting its ability to function correctly Allosteric regulation- a regulatory molecule binds to a protein at one site and affects the function at another site  May inhibit or stimulate enzyme activity  Has active and inactive forms  Cooperativity- amplify enzyme activity (binding to an active site stabilizes favorable conformational change Feedback Inhibition- the end product of a metabolic pathway binds to an earlier enzyme and shuts down the pathway  Prevents a cell from producing more product than needed  Enzymes can be in specific organelles (enzymes for cellular respiration are in the mitochondria) __________________________________________________________________________________________________________________ ________________________________________________________________________________________________________ CHAPTER 9: CELLULAR RESPIRATION & FERMENTATION Autotrophs- convert sunlight into glucose (anabolic process of photosynthesis) Heterotrophs- obtain energy catabolically (catabolic process of cellular respiration) Aerobic respiration- with O2 (glycolysis, Krebs, ETC) Anaerobic respiration- consume compounds other than O2 (fermentation) CELLULAR RESPIRATION Oxidation Reduction many times this is in H+ Is Is Loss of eGain of eGlucose is oxidized (loses H+), oxygen is reduced (gains H+) NAD+/ NADH Nucleotide and electron shuttle NAD+ accepts 2e- and H from glucose in glycolysis and to become NADH and H+ which is taken to ETC  e- are given to O2 (reducing it, oxidizing glucose)

NAD+ accepts 2e- from Calvin Cycle (Krebs) to take to ETC MAKING ATP substrate-level phosphorylation- direct transfer of phosphate from a substrate to ADP (glycolysis and Krebs) oxidative phosphorylation- binding ADP to an inorganic phosphate LOCATIONS OF CYCLES Glycolysis—cytoplasm outside the mitochondria Pyruvate conversion—matrix CAC (Krebs)—matrix ETC—inner membrane GLYCOLYSIS =2 ATPs Occurs in cytoplasm Anaerobic (no oxygen present) Pyruvate—when a 6-Carbon is broken down to 3-carbon molecule 2 ATP are produced per pyruvate, but 2 ATP are used during glycolysis, so only 2 ATP remain Substrate-level phosphorylation 1 NADH per pyruvate = 2 NADH produced OXIDATION OF PYRUVATE Pyruvate enters mitochondrion and goes into matrix Redox reaction—carbons are oxidized, NAD+ is reduced to NADH + H Pyruvate + CoA + NAD+ acetyl-CoA + CO2 +NADH + H  1 carbon removed, 1 NADH produced, no ATP  Decomposes acetyl-CoA to 2-carbon molecule, other carbon bonds to oxygen and leaves as CO2

CITRIC ACID CYCLE (KREBS) = 2 ATPs Occurs in matrix Aerobic (oxygen present) 3 NADH, 1 FAD per pyruvate = 6 NADH, 2 FAD produced Takes 2 cycles to fully oxidize acetyl-CoA  Leftovers are converted to CO2 and are released from cell Substrate-level phosphorylation ELECTRON TRANSPORT CHAIN (ETC) =34 ATPs Occurs in inner membrane Oxidative phosphorylation e- are passed down proteins until they reach the final e- acceptor—O2  Oxygen bonds with H+ to form water All NADH and FADH2 made are used to power proton pumps  Proton pumps—pump H+ against the gradient  Converts NADH and FADH2 back into NAD+ and FAD (which are taken back to glycolysis and Krebs) Chemiosmosis--ATP synthase (in inner membrane) uses the gradient of H+ to combine ADP and Pi (oxidative phosphorylation) to make ATP FERMENTATION =2 ATP per glucose Two types: lactic acid and alcohol  Lactic acid fermentation produces lactate (makes muscles sore)  Alcohol fermentation forms ethanol Final e- acceptor is an organic molecule, either lactate or ethanol  Body does this to oxidize NADH back into NAD+ for glycolysis to continue

ANAEROBES Obligate anaerobes—cannot survive in the presence of oxygen Facultative anaerobes—can survive using aerobic or anaerobic methods __________________________________________________________________________________________________________________ _______________ CH 10: PHOTOSYNTHESIS Photoautotrophs—energy from light (plants, algae, euglena) Chemoautotrophs—energy from inorganic chemicals (bacteria surrounding deep-sea vents) Mesophyll—tissue inside a leaf where photosynthesis happens Stomata—pores where CO2 enters and O2 exits Chlorophyll—green pigment in chloroplast Thylakoids—sacks of chlorophyll Granum—stack of thylakoids Wavelength—distance between crests of waves (shorter wavelengths produce better intensities of light) LIGHT REACTIONS (ELECTRON TRANSPORT CHAIN) occurs in the thylakoid membrane 1. PS II—a photon hits chlorophyll, and chlorophyll molecule will split an H2O molecule, taking its e-, and releasing water as a byproduct 2. Cytochrome C—primary e- acceptor; pumps protons into thylakoid, picked up by PS I or pushed through ATP synthase 3. ATP synthase—proton gradient makes ATP (oxidative) 4. PS I—pump protons to NADP+ reductase 5. NADP+ reductase—change NADP+ to NADPH Use ATP and NADPH produced here to fund Calvin cycle CALVIN CYCLE (DARK REACTIONS) Occurs in stroma 1. Carbon fixation—CO2 is incorporated into a sugar (catalyzed by Rubisco) a. Incorporates CO2 by attaching it to a 5-carbon sugar, making it unstable and breaking into 2, 3-carbon molecules 2. Reduction— CO2 is reduced; creates G3P 3. Regeneration—of the CO2 acceptor RuBP 9 ATP and 6 NADPHs are spent for each G3P (light reactions regenerate it)

G3P can be used to make anything the plant needs C3 plants—(normal) use CO2 directly from the air C4 plants— (hot environment) close stomata to conserve water; can still carry out photosynthesis through a 4-carbon intermediate CAM plants—open stomata at night to conserve water (pineapple, cacti) __________________________________________________________________________________________________________________ ____________________________________________________________________________________________________ CH 11: CELL COMMUNICATION Signal transduction pathways are carried out by enzymes, which are activated by second messengers or other enzymes 3 stages 1. Reception—signal molecule (ligand) binds to a specific receptor a. Conformational change—receptor changes shape in order to better fit the ligand; INITIAL STEP IN TRANSDUCTION 2. Transduction—signal from activated receptor is relayed to downstream proteins 3. Response—downstream components (transcription factors) activate or inhibit cellular responses CELL JUNCTIONS Directly connect the cytoplasm of adjacent cells 2 types…  Gap junctions—between animal cells (allow small solutes to pass through)  Plasmodesmata—between plant cells (allow small solutes to pass through)  Tight junctions—membranes are fused, making sure no extracellular fluid escapes LOCAL CELL SIGNALING Cell-cell recognition—cells have receptors that recognize signal molecules on inducing cells Local regulators—signal molecules that travel short distances  Paracrine signaling—target cell is near the inducing cell  Synaptic signaling—nerve cells and neurotransmitters Endocrine signaling—long distance (hormones like insulin, steroids) RECEPTOR TYPES 1. G-protein-coupled receptor— (not an enzyme) plasma membrane receptor that works with the help of G-protein

a. When bound to GDP: inactive (off) b. When bound to GTP: active (on) 2. receptor tyrosine kinase—enzymes that attach phosphate groups to proteins (protein kinase) to form a dimer 3. Ligand-gated ion channel receptor—a ligand binds to the receptor and allows specific ions (Na+ or Ca+) through a channel (gated) 4. Intracellular receptors—in cytosol or nucleus; can act as transcription factor—regulate transcription of DNA into mRNA a. Steroid and thyroid hormones System is able to turn protein activities on and off:  Protein phosphorylation—phosphorylation of other proteins or themselves; carried out by protein kinase)  Dephosphorylation—protein phosphatase removes phosphate groups via hydrolysis SECOND MESSENGERS (first messenger is ligand) Second messenger—small, nonprotein, water-soluble molecules that spread in a cell by diffusion (WILL NOT BE A KINASE) Participate in G-protein-coupled receptors and tyrosine kinases 1. Cyclic AMP (cAMP) a. Adenylyl cyclase—converts ATP to cAMP in response to extracellular receptor b. cAMP activates protein kinase A (PKA) which in turn creates a cellular response c. phosphodiesterase—inactivates cAMP d. cAMP is regulated by G protein systems that inhibit adenylyl cyclase 2. Calcium ions and IP3 a. Can be a second messenger bc of regulation through ion pumps b. Pathway involving IP3 and diacylglycerol (DAG) must be used to release calcium ions i. IP3 opens calcium channels NUCLEAR AND CYTOPLASMIC RESPONSE Transcription factor- will amplify or specify response Scaffolding proteins- large relay proteins that other transduction proteins are attached to Increases efficiency by grouping together proteins in the same pathway APOPTOSIS Programmed cell death Cell is chopped and packaged into vesicles then digested by scavenger cells (macrophages) CH 12: THE CELL CYCLE...