Bio9A Quiz 1 Study Guide

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1 Chapter 1 The Science of Biology Bio9A Quiz 1 Study Guide A. Evolutionary Principles a. Evolution is change over time. Evolutionary relationships can be described using phylogenies or trees. (Fig 1.10) b. Evolution of Cells i. All organisms made from cells (Fig 1.11) 1. Prokaryotic simple, no membrane-bound organelles 2. Eukaryotic complex, has membrane-bound organelles ii. DNA exists in all cells. They may be packaged differently. iii. Membranes are all the same c. Unity and Diversity i. Homologous structures different function/structure but common ancestor (Fig 1.9) ii. Changes in DNA explain diversity. Genetic code of DNA is the same in all organisms iii. Energy usage is virtually the same in all organisms. Breaking ATP releases energy B. Biological Information a. Genetic information is stored in nucleic acids i. DNA bases are A, T, G, C. Their sequence provides information b. Information flow in a cell i. The Central Dogma states information is expressed by being passed from DNA RNA Protein. Protein is the functional part of this information c. Heredity i. Genetic information is passed down to the next generation of cells. DNA replication allows this. DNA has evolved to be a great molecule for this. C. Scientific Inquiry: Practicing Science a. Scientific Method: Question (Observation) Hypothesis Experiment Conclusion (Fig 1.3) i. Hypothesis is an answer or prediction to the question. It must be falsifiable. ii. Experiment includes: design, data collection, and evaluation. 1. Controls (control variables) factors held constant for verification of results. 2. Independent variable factor manipulated by researcher. 3. Dependent variable what is measured by researcher. iii. Conclusion accepts or rejects hypothesis. b. Reductionism vs. systems approach. i. Reductionism break down mechanism to simplest components ii. Systems looks at relationship of components with the whole organism. Bioinformatics with computers allows this approach today. c. Social Context: the use of powerful technologies, ethics, social responsibility Chapter 4 The Cell A. Overview of the Cell a. Cell Theory i. All living things are made up of cells.

2 ii. The smallest living thing is a cell and cells may make up multicellular organisms. iii. Cells arise from preexisting cells. b. General features i. Plasma membrane allows isolation of cell contents, regulation of materials into and out of cells, interaction with other cells. ii. DNA as genetic material. iii. Cytoplasm fluid portion in the cell. iv. Organization and size permit homeostasis. 1. Cells are generally small to allow greater surface area to volume ratio (Fig 4.1) 2. Different shapes and sizes depending on function (Fig 4.2) c. Prokaryotes vs. Eukaryotes i. Prokaryotes are small, lack organelles. They have cell walls, nucleoids, ribosomes. Some have fimbriae, flagella, capsules. (Fig 4.3) ii. Eukaryotes are bigger, contain organelles, and are more complex (Fig. 4.6, 4.7). B. Eukaryotic Organelles a. Differences between plants and animals plants have a cell wall, plastids, central vacuole. Animals have centrioles. b. Nucleus control center (Fig 4.8) i. Holds DNA in form of chromatin (DNA + protein). Chromosomes are the DNA part. ii. Nucleolus is center for ribosome assembly. iii. Nuclear envelope is a double membrane. Nuclear lamina is meshwork. Nuclear pores allow RNA to exit. c. Ribosomes protein making machine (Fig 4.9) i. Made from RNA and proteins. ii. Found in cytosol, nuclear envelope, and rough ER. d. Endomembrane System (Fig 4.12) i. Endoplasmic Reticulum manufacturing center (Fig 4.10) 1. Membranes form flattened tubes. Lumen is on inside. 2. Rough ER has ribosomes. Proteins made and translocated into the lumen. 3. Smooth ER has no ribosomes. Used for lipid and carbohydrate metabolism and detoxification. 4. Buds vesicles to Golgi. ii. Golgi Complex post office (Fig 4.11) 1. Sorts incoming proteins and lipids 2. Receives at cis and ships at trans end. 3. Tags or modifies some for destination 4. Packages them for final destination in vesicles. iii. Lysosomes digestive system (Fig 4.13) 1. Contains hydrolytic enzymes at low ph. 2. Digests all classes of macromolecules. White blood cells phagocytose other cells. 3. Tay-Sach s disease is genetic and is caused by missing digestive enzyme. The enzyme digests lipids. Lipids build up and kill cell. Death occurs in children iv. Peroxisomes detox center. Metabolize small organic compounds. E.g. Hydrogen peroxide and ethanol. (Fig 4.14) v. Vacuole storage and recycling plant (Fig 4.15) 1. Store water, food, salts, pigments, and wastes. 2. Like a large vesicle.

3 3. Some protists have contractile vacuole 4. Huge in plants=central vacuole e. Mitochondria powerhouse i. Produce ATP from glucose ii. Structure: double membrane, intermembrane space, cristae (folds), matrix that has enzymes. (Fig 4.16) f. Chloroplasts solar power plant (Fig 4.17) i. Family of plastids that produce and store food. ii. Makes glucose using chlorophyll and carotenoids iii. Has three membranes. Inner most makes up thylakoid. Grana are stacks of thylakoids. Stroma is inside space. Thylakoid lumen is inside thylakoid. Enzymes in both stroma and thylakoid lumen. C. Cytoskeleton a. Involved in support, movements, and cell division b. Fibers (Fig 4.19) i. Microfilaments made from actin monomers. Small and helixed. Involved in structure and movements. E.g. muscle contraction, cytoplasmic movements ii. Intermediate filaments medium sized. Structural role. iii. Microtubules alpha and beta tubulin subunits wrapped in large helix. 1. Vesicle movement using motor proteins (Fig 4.21) 2. Centrosomes organizing center for cell division. Animal cells contain a centriole (Fig 4.20) 3. Cilia and Flagella movement and water movement. (Fig 4.23) a. Cilia are small and numerous, eyelash b. Flagella are large and few, whip c. Uses microtubules connected by dynein arms. Mechanism of movement is similar to motor protein movement D. Extracellular Components a. Extracellular matrix is outside of membrane (Fig 4.26) b. Junctions in animal cells (Fig 4.28) i. Tight junctions cement leak proof. ii. Desmosome staple attaches adjacent cells iii. Gap (communicating) junctions hole that allows messages through. c. Plant cells have a cell wall. (Fig 4.25) i. Made from tough cellulose. ii. Have plasmodesmata to allow communication (Fig 4.29 Chapter 5 Membrane Structure and Function A. Membrane Structure a. Fluid-Mosaic Model Singer and Nicolson 1972 (Fig 5.3) i. Phospholipid bilayer is fluid 1. Fluidity a. Amphipathic phospholipids polar head and nonpolar tails (Fig 5.1) b. Phospholipids move freely within its layer 2. Semipermeable to small nonpolar molecules only (water is exception) 3. Cholesterol helps stiffen membranes ii. Proteins and carbohydrates give mosaic 1. Integral are embedded into hydrophobic part (Fig 5.8) while peripheral are only attached to a surface.

4 2. Variety of functions (Fig 5.7). Transport, cell recognition, signaling, and structure b. Evidence of structure i. Frye and Edidin 1970: different cells were labeled with different color tags. Fusion of cells prove fluidity because colors blended (Fig 5.5) B. Transport Across Membranes a. Passive transport diffusion (Fig 5.9) i. Down a concentration gradient (high low) ii. Osmosis diffusion of water across a membrane (Fig 5.11) iii. Tonicity relation of solute concentrations across a membrane (Fig 5.12) 1. Isotonic: = 2. Hypotonic < (in relation to cell) 3. Hypertonic > (in relation to cell) 4. These lead to certain conditions in plant and animal cells a. Plant cells become turgid when in hypotonic solution and plasmolysed when hypertonic solution. b. Animal cells will lyse when in a hypotonic solution and crenate when in a hypertonic solution. iv. Proteins (e.g. carrier, channel protein) can allow solutes across that are too big to cross lipid bilayer (Fig 5.10). 1. Channel proteins are pores that are non-specific. 2. Carrier proteins bind specific substances. b. Active transport i. Against concentration gradient ii. Requires energy iii. Examples 1. Na-K pump a bi-directional pump (Fig 5.13) a. Binding of Na allows ATP hydrolysis conformation shift Na out. b. K binding releases phosphate shift K in. 2. Coupled transporters use one active transporter to create a gradient to drive a cotransporter. (Fig 5.14) C. Exocytosis and Endocytosis a. Transport of large particles (bulk transport) uses vesicles b. Exocytosis particles are excreted. (Fig 5.16) c. Endocytosis particles are taken in. (Fig 5.15) i. Phagocytosis large particles are taken in cell eating. Vacuole is formed which may fuse with a lysosome. ii. Pinocytosis small particles are ingested cell drinking.vesicle then allows contents to bleed into cytosol. iii. Receptor-mediated endocytosis uses a receptor for specific particle uptake. E.g. LDL uptake 1. Receptors wait on surface. LDL binds. 2. Coat proteins bind and organize receptors. This causes endocytosis. 3. Vesicle forms and coat is removed. 4. Vesicle sent to lysosome. LDL released and receptors recycled. iv. Disease, hypercholesterolemia, due to defective LDL receptors.

5 Chapter 6 Enzymes A. Enzymes Characteristics a. Enzymes are catalysts that lower energy of activation (Fig 6.5) b. Enzyme i. Specific for certain substrates ii. Reaction must already be exergonic iii. Reusable c. Substrate (reactant) Product B. Catalytic cycle: E + S ES EP E + P (Fig 6.10) a. Substrate binding: binds to active site of enzyme. Uses induced fit model instead of lock-and-key. (Fig 6.8) b. Reaction: active site provides correct environment to create product. c. Release: enzyme releases product and can be reused. C. Regulation a. Environmental factors i. Optimal ph, temperature, salt produce bell curves (Fig 6.12) ii. Substrate concentration produces logarithmic curves b. Activators i. Cofactors (non-organic) ii. Coenzymes (organic) c. Inhibitors (Fig 6.13) i. Competitive binds active site ii. Noncompetitive binds allosteric site d. Complex Regulation i. Feedback inhibition (Fig 6.15) ii. Enzyme complexes 1. Allosteric activation and inhibition as a complex 2. Cooperativity when substrate binding assists further substrate binding of other enzymes in complex iii. Localization enzymes are held in separate compartments D. Metabolism the sum of all reactions in a cell a. Catabolism breakdown molecules b. Anabolism build c. Reactions tend to be organized in pathways (Fig 6.14) Chapter 7 Cellular Respiration A. Overview of Aerobic Respiration a. C 6 H 12 O O ADP 6 CO H 2 O + 38 ATP i. Glucose oxidized carbon dioxide ii. Oxygen reduced to water b. Relationship with photosynthesis c. Energy harvest slow breakdown of glucose can allow ATP synthesis (Fig 7.2) d. ATP made in 2 ways i. Substrate-level phosphorylation direct transfer by an enzyme (Fig 7.4) ii. Oxidative phosphorylation uses an electron transport chain. 1. Two important coenzymes: NAD and FAD. These pick up electrons from glucose and transfer them to electron transport chain to make ATP. (Fig 7.3)

6 2. NAD makes 3 ATP, FAD makes 2 ATP. iii. Occurs in 4 sets of reactions: Glycolysis Acetyl-CoA Formation Citric Acid Cycle Oxidative Phosphorylation. Glycolysis occurs in cytosol, other three in mitochondria (Fig 7.5) B. Stages of Aerobic Respiration a. Glycolysis (Fig 7.6, 7.7) i. Glucose Pyruvate ii. Yields 2 ATP and 2 NADH iii. Energy investment steps 1. 2 ATPs used in 3 steps. 2. C 6 2C 3 (G3P) in 1½ steps. iv. Energy harvesting steps 1. 4 ATPs and 2 NADHs produced in 5 steps. Remember, these totals reflect doubling of reactions because of 2C 3 molecules. 2. These ATPs are made by substrate level phosphorylation v. Pyruvate moves to mitochondria. b. Acetyl-CoA formation (Fig 7.9) i. Yields 2 NADH (1 per pyruvate) ii. Occurs in matrix of mitochondria. iii. Pyruvate + CoA CO 2 + Acetyl-CoA c. Citric Acid Cycle (Fig 7.10, 7.11) i. Yields 2 ATP, 6 NADH, and 2 FADH 2 (2 turns for 2 acetyl-coa) ii. Occurs in matrix of mitochondria. iii. C 4 (oxaloacetate) + Acetyl-CoA citrate (C 6 ) + CoA iv. C6 C5 C4 yielding 2 CO 2 + energy. d. Oxidative Phosphorylation (Fig 7.12) i. Occurs on the inner mitochondrial membrane. ii. Converts energy from NADH and FADH 2 to ATP iii. Electron transport chain made from cytochromes. a. 3 carriers pump protons out b. NADH donates electron at 1 st pump, FADH 2 donates after 2 nd pump. c. Oxygen is needed to pick up electrons from last cytochrome. iv. Chemiosmosis production of ATP by a proton (H+) gradient. Protons have been pumped into intermembrane space. High concentration drives movement of protons back into matrix. ATP synthase: force of proton movement turns matrix portion which powers ATP synthesis. (Fig 7.14) e. Balance sheet: 38 ATP (34 from 10 NAD and 2 FAD) f. Efficiency: glucose gives 2870 kj/mol. ATP hydrolysis gives 32 kj/mol. 38 X 32 gives 1216 kj/mol. Therefore, aerobic respiration has about 42% efficiency. C. Metabolic pools nutrients other than glucose can fuel respiration. They can also be made from respiration intermediates (Fig 7.17). a. Catabolism breakdown of molecules can feed into respiration pathway b. Anabolism excess can be built into storage molecules c. Proteins require deamination (Fig 7.21), fats require beta-oxidation (Fig 7.22) d. Regulation feedback on phosphofructokinase. AMP can stimulate. ATP and citrate can inhibit. D. Fermentation a shortcut respiration process. a. Regenerates NAD + to run glycolysis. This produces ATP by substrate level phosphorylation only. Inefficient but very fast. (Fig 7.8) b. Alcohol fermentation done by yeast. Ethanol and CO 2 produced.

7 c. Lactic acid fermentation humans do. Lactic acid produced which may cause muscle fatigue.