Biology Lecture Notes Ii

Lecture Notes II I. Cell Theory A. Cell – functional unit of all living things – the smallest unit with the properties of life 1. All have a region of DNA, all have cytoplasm, all have plasma membrane B. Types 1. Prokaryotic – primitive cells – no membranous fixed inner structure or nucleus 2. Eukaryotic – has a true nucleus and is a more complex cell. Plant & animal cells are eukaryotes C. Cell Structure – General Cellular Parts 1. Plasma membrane – selective barrier allowing passage of oxygen, nutrients and waste to cell i. Consists of a lipid bilayer that selectively prevents water soluble substances from crossing 2. Nucleus – contains the DNA of eukaryotes – directly communicates with the (rough) ER i. Nucleolis – mass of proteins & copies of genes coding for ribosomal RNA 3. Nucleoid – region of cytoplasm in prokaryotes containing DNA 4. Endoplasmic Reticulum (ER) i. Smooth ER – assists in the packaging and transport of materials in the cell ii. Rough ER – contains protein clumps (ribosomes) on membrane wall, synthesizes lipids, 5. Ribosomes – contained on wall of rough ER and in cytoplasm – assist in TRANSLATION of proteins 6. Mitochondria – primary ATP manufacturer of the cell (thus “powerhouse”) – have their own DNA and divide on their own 7. Golgi Body – manufacture & packaging of inner & extra cellular materials (proteins & lipids) 8. Vesicles – membrane bound grouping of cellular material act as cellular material transporters i. Lysosomes – type/subset of vesicle that can open up and release digestive enzymes breaking down cells ii. Peroxisomes – hold enzymes for digesting fatty acids, amino acids and H2O2 9. Chloroplasts (plant cell) – photosynthetic cell, transfers sunlight & water into ATP 10. Central Vacuole (plant cell) – stores amino acids, sugars, ions and waste, takes up 50 to 90% of the plant cell interior 11. Cytoskeleton – structurally supports, gives shape to and moves eukaryotic cell (not present in prokaryotes) i. Microtubules – largest skeletal elements, regulates cell organelle placement and movement ii. Microfilaments – smallest skeletal elements, reinforce cell shape, reconfigure surface, etc iii. Intermediate filaments – mid sized elements, help reinforce the nucleus II. Biological Membranes A. Composed of Phospholipid Bilayer 1. One polar head, two non-polar tails (heads hydrophilic, tails hydrophobic) 2. Highly polar objects cannot pass through bilayer because of hydrophobic tails 3. Large molecules cannot pass through 4. Gasses CAN pass through via Diffusion – O2, Limited amount of H2O, small non-polar organics B. Trans-membrane proteins – can extend though the membranes

1. Transporter membranes are thus trans-membrane proteins i. Surface Proteins – Adhesion, Acceptor, Recognition, Communication, Transport C. Dynamic Fluid Mosaic – The lipid bi-layer in which complex structures move (in constant motion – thus dynamic) D. Transport Proteins: 1. Passive Transport – only driving force is natural molecular movement (from high to low concentration). i. Facilitated Diffusion – protein whose job is to allow molecules through membrane, from high to low concentration ii. Aquaporins – specific transport proteins that allow H2O to pass iii. Ion-selective channels – may be gated (controlled by chemical or voltage changes) iv. Gas & H2O only diffuse – no active pumping v. Osmosis – Diffusion of H2O across a semi-permeable membrane a. Osmotic Pressure = Turger Pressure b. Tonicity – concentration of solute 2. Active Transport – can move molecules from low to high concentration but requires energy to do so i. Primary active transporters – get energy from cleavage of ATP; pump molecules against a concentration gradient via ATP-ase activity | always have 2 binding sites, one for ATP, other for transport of substrate ii. Secondary active transporters – “co-transporters” use energy from the gradient (ex. Mitochondria) – as energy is released from one gradient it is used to pump against another iii. ∆C/ ∆X – gradient – difference in concentration/distance = the shorter the distance needed to travel, the faster the rate of diffusion 3. Bulk Transporters – All membrane mediated i. Exocytosis – cell excretory function ii. Endocytosis – intake of cellular material (how amoebae feed) iii. Phagocytosis – Solids – ingestion of material by a cell for nutrition or distribution iv. Pinocytosis – Liquids – droplets of liquid ingested by cell III. Bio-Energetics – transformation of energy in living things A. Energy – the capacity for doing work B. Work – exertion of a force through a distance C. 1st law of Thermodynamics – Energy can neither be created or destroyed, only transferred/changed state D. 2nd law of Thermodynamics – All energy put into a system cannot be extracted. No system is 100% efficient (entropy). Amount of wasted energy = efficiency of a system E. Potential/Kinetic Energy 1. Potential: Chemical, Mechanical, Gradient, Electrical – every gradient has PE (battery) 2. Kinetic Energy – KE = 1/2MV2 i. Molecular KE – thermal energy, a.k.a. Heat – heat = # of molecules x average KE of the molecules; temperature is the measure of the average KE of a system 3. Energy diagrams – C6H12O6 + 6O2  6CO2 + H2O + Energy (ATP) F. Enzymes – proteins that are used to lower the activation energy required to start a reaction 1. Change ONLY rate at which reaction occurs – nothing else G. Reaction Participants: 1. Reactant – Starting Agent (A & B) 2. Product – Result of reaction (C & D) 3. Substrate – material binding to enzyme before reaction (A & B) 4. Intermediate – Partial steps in Reaction

5. Enzyme – Biological catalyst (e1) 6. Cofactor (co-enzyme) – additional compound needed to assist enzyme in lowering activation energy (Mg++ or B12) H. Oxidation/Reduction reactions 1. Oxygen – Family IV – loss of e- makes oxygen “oxidized” (any loss of e-, not necessarily oxygen) 2. Gain of e- = reduced 3. NAD  NADH = Reduced | NAD+ = Oxidized I. Metabolic pathways – can be linear, cyclical or branched J. Reversibility of reactions – A ↔ B 1. Reactions tend to flow in direction that releases lots of energy i. Concentration Equilibrium: Keq = [B]/[A] 2. LeChatiler’s principle – “stressing a system in equilibrium shifts the balance in the opposite direction until equilibrium is established” i. Ex. A + B ↔ C + D (+ energy) a. If: concentration of A↑, reaction speeds up, concentration of B↓,C↑, D↑ K. Enzyme function – only effect rate of reaction 1. Induced Fit Model: Warping of enzyme by substrate binding changes energy relationships in the substrate, thus lowering activation energy – changing of substrate into product(s) after reaction causes attraction between enzyme/reactant to cease 2. ↓ temperature  ↓ activity (slower molecules) 3. ↑ temperature  ↑ activity (until quaternary structure becomes denatured) 4. pH – free H+ effects H bonds in tertiary or quaternary structure – thus have a pH optimum L. Control of Enzyme Activity 1. Allosteric Activation/Inhibition – Binding of a second molecule to a 2nd binding site on the enzyme increasing/decreasing enzyme activity 2. Competitive Interference/Inhibition – process in which competitor binds to active site on the enzyme and prevents substrate from being acted upon by enzyme 3. Feedback Inhibition – The process by which the products of a reaction shut down the original reaction:  i. Allosteric – can turn on & off enzymatic action ii. Competitive – can only make enzymatic action more difficult IV. Energy Releasing Mechanisms A. Anaerobic – O2 not required 1. Glycolysis i. Alcoholic Fermentation – Yeast  CO2 + Ethanol (ethyl alcohol) ii. Lactate fermentation – complicated animals  lactic acid formed iii. Excretion of toxins in anaerobic pathways B. Aerobic respiration 1. Glucose as common metabolite – available from foods, converted from other monosaccharides, cleaved from disaccharides, glycogen & starch 2. C6H12O6 + 6O2  6CO2 + 6H2O + ATP (max yield of 36 ATP) via one of two pathways – glycolysis & oxidative phosphorylation i. Glycolysis a. The anaerobic phase: Each glucose produces 2 pyruvate molecules

b. For each glucose 2ATP must be used to di-phosphorylate the glucose c. 4ATP are produced – resulting in net gain of 2ATP d. Energy associated with the hydrogen carried on 2 NADH carriers 3. Preparatory steps to the Krebs Cycle (TCA, Citric Acid Cycle) i. The two (3-carbon pyruvates) are converted to two (2carbon) activated acetyl-Coenzyme-A complexes ii. This produces two CO2 molecules as by-product iii. And releases the energy of two NADH carriers iv. This “prepares” the Acetyl-CoA for entry into the Krebs cycle 4. Krebs Cycle – cyclic pathway that takes in the 2carbon Acetyl CoA and removes its carbons, hydrogens and electrons i. Products are 2CO2, 3NADH, FADH2 and an ATP by substrate level phosphorylation ii. Cycle cranks twice for each glucose that enters iii. Takes place in the mitochondrial inner compartment 5. Oxidative (Electron transfer) Phosphorylation – occurs through action of transmembrane enzymes in the cristal of the mitochondria – Uses energy from H+ and their associated electrons brought by the carriers NADH and FADH2 i. Chemiosmosis – ability of certain membranes to use chemical energy to pump hydrogen ions and then harness the energy stored in the H+ gradient to drive cellular work (ATP synthesis) – in this example: turns 2NADH & 2 pyruvates from glycolysis into 2FADH2 & 2 Acetyl-CoA ii. NADH & FADH2 give up their electrons, which power H+ pumps pushing the free hydrogen outside the mitochondrial matrix – this forms an electrical & concentration gradient of H+ ions. These H+ ions flow back through ATP synthase, powering ADP + Pi  ATP iii. Oxygen is the final e- acceptor, without which the entire process backs up to the pyruvate, forcing the system into anaerobic respiration as lactate (as pyruvate ↔ lactase, via LDH) iv. Energy from 1 NADH in Krebs  3 ATP | 1 FADH2 = 2 ATP

v. Thus in aerobic respiration: 1 molecule glucose = Glycolysis SLP. – 2 ATP, Krebs SLP. – 2 ATP, 6NADH in Krebs – 18 ATP, 2NADH from glycolysis – 4 ATP, 2FADH2 from Krebs – 4 ATP, 2NADH in pyruvate to Acetyl CoA stage – 6 ATP = 36 total ATP