Exam One

BIOLOGY
Nature of Science
SCIENCE: The use of evidence to construct testable explanations and predictions of natural phenomena as well as knowledge generated through this process Science originates in questions about the natural world Uses observations and evidence to construct explanations about phenomena and testable hypotheses o The more observations or evidence that support the hypothesis, the stronger that hypothesis is

Scientists
Employ a variety of technology to investigate natural world Make explanations public Critique explanations o In discussion section of publication o Reviewing manuscripts and grant proposals

Our Typical Experience

Body temperature: 37*C 1 atm

Range of Conditions for Life

The upper temperature for life is 132*C Cell/body temperature from -2*C to 132*C Range of pressures: 1 atm to 1100 atm The most common habitat for life on the planet is the deep ocean o Conditions at average depth of ocean 2*C to 4*C 380 atm pressure No sunlight

Organisms confront problems due to environment

Endotherms o Organism warmed by heat generated by their own metabolism o Great white shark, swordfish Ectotherms o Organism warmed by external sources

o Most fish are ectotherms Piezophiles o Pressure loving o Barophiles o Thrives at high pressures Thermophiles o High temperature loving o Temperatures up to 132*C (can grow at 122*C) o Hydrothermal vents Halophiles o Salt loving o Live in osmotic (e.g. with 3M salt) o Owens Lake, CA Examples o Antarctic fish Live and have body temperature of -2*C (they are ectothermic) Pagothenia bernathii o Penguins Keep warm at similar temperatures (endothermic) o Diving seals Can hold breath for 90 minutes Dive 1500m Weddell seal o Deep sea fish 7000m High pressure, cold temperatures, low food availability Rattails o Sharks Live with half molar urea in their tissues Their urea is a potent denaturant of proteins o Tuna Raise temperature of muscles above ambient temperature As much as 15*C above water temperature Endothermic o Gutless tubeworms Thrive at deep sea hydrothermal vents

Midwater fish and invertebrates

Organisms living in water column achieve neutral buoyancy despite density of biological material

CHEMISTRY BACKGROUND
Elements o Pure substances that cant be broken down into simpler substances 92 naturally occurring 112th copernicium (Cn) 6 others Atom o Smallest unit into which an element can be divided o Components Nucleus Proton - +1 charge, 1 Dalton mass Neutron 0 charge, 1 Dalton mass Electron - -1 charge, essentially without mass Atomic number o Number of protons in nucleus Atomic mass o Sum of number of protons and neutrons Electrical charge o Number of electrons equals the number of protons o In an ion, the number of electrons does not equal the number of protons Compound o Substance that can be broken down to 2 or more elements (e.g. water) o Composition is definite and exact o Energy is involved in synthesizing or decomposing (burning gasoline) o Elements lose individual characteristics Electron o An electrons energy is correlated with its average distance from the nucleus o Electrons found in different electron shells Have characteristic average distance and energy level S-level holds 2 electrons P-level holds 6 electrons D-level holds 10 electrons F-level holds 14 electrons o Valence Outer electrons Valence shell outermost electron shell Valence bonding capacity of an atom Valence electrons determine chemical behavior of atom Ion charged atom or molecule Mass of molecule is calculated by the sum of the masses of the atoms involved Chemical bonds

Strong bonds Covalent bond: the sharing of a pair of valence electrons by two atoms Nonpolar: when the two atoms have same electronegativity Polar: When one atom is more electronegative than the other o Weak bonds Hydrogen bond: the noncovalent attraction between a hydrogen and an electronegative atom Ionic bond: when cations and anions attract each other, exchanging electrons Van der Waals: ever-changing positive and negative charge that enable all atoms to stick to one another. o Electronegativity The attraction of a particular atom for the electrons of a covalent bond pH A review o Acids, bases, salts Acids Produce H+ ions (protons) HCl H+ + Cl Bases Produce OH- ions NaOH Na+ + OH Salts Produce neither NaCl Na+ + Clo pH = -log[H+] (proton concentration) actually activity of hydrogen ions rather than concentration o Scale Log base 10 Difference between pH of 3 and pH of 4 10 fold higher concentration of protons Difference between pH of 3 and pH of 5 100 fold higher concentration of protons pH of 7 is neutral pH below 7 is acidic pH above 7 is basic o pOH pOH = -log[OH-] pH + pOH = 14 o Neutrality [H+] = [OH-] -log[H+] = -log[OH-] pH = pOH

Buffer Substance that maintains constant pH Solubility o Solute Molecules dissolved in solvent o Solvent Substance o What determines solubility? Like dissolves like Like in terms of polarity Polar solutes dissolve in polar solvents Nonpolar solutes dissolve in nonpolar solvents Hydrophilic substances interact with each other Hydrophobic substances avoid water Heat of fusion o Amount of heat removed to freeze 1g of water

BIOLOGICAL MOLECULES
Properties of Water o High heat capacity o High heat of vaporization o High heat of fusion o Most dense at 4C Because hydrogen bonding in structure, ice is lighter than water Ice floats, frozen benzene sinks Ice: Hydrogen bonds are stable, but in water the hydrogen bonds break and reform o High dielectric (and how this affects solubility) Good solvent NaCl Proteins o Capillary action and surface tension Due to hydrogen bonding Some organisms can literally walk on water Plants move water up leaves to roots Adhesion Cohesion o Ionization Dissociation into acid (hydronium ion) And base (hydroxyl ion)

2H2O H3O+ + OHBiological molecules o Except for water, all are built on carbon skeleton (the backbone) water carbohydrates lipids proteins nucleic acids Functional groups o Hydroxyl alcohols o Carboxyl acid group o Amino amines o Sulfhydryl thiols o Phosphate organic phosphates o Methyl CH3 (nonpolar) Biological molecules o Large molecules constructed from small molecules o Polymers constructed from monomers Mer = unit Mono = single Poly = many Synthesis of polymers covalent bond formation between monomers Condensation (dehydration) synthesis o Product: release of water molecule Breakdown of polymers breaking covalent linkage between monomers Hydrolysis o Breaking the covalent bond linking units of the polymer by the addition of a water molecule Why make large biological molecules from simple monomers? Flexible system o Array of complex molecules from a few simpler molecules Fewer enzymes to make biological molecules than if starting from scratch Carbohydrates o General formula (CH2O)n E.g. n=6 C6H12O6 o Energy roles Metabolic fuel: glucose, sucrose Storage form: starch, glycogen o Structural roles Cellulose found in cell walls of plants

Chitin found in exoskeletons of animals

Lipids o Water insoluble organic biomolecules Made up of nonpolar covalent bond groups o Structural component of cell membrane o Storage and transport forms of fuel o Protective surface coating o Cell component in cell recognition o Hormone (steroids) o Saturated fats Saturated with hydrogen, no double bonds between adjacent carbons Solids at higher temperatures than unsaturated fats Raise LDL cholesterol Butter o Unsaturated fats Double bonds Lower melting point Acyl chains of unsaturated fats are kinky and therefore require lower temperatures to be solid Olive oil o Polymers Triglycerides Phospholipids o A fat molecule has approximately 9.3 kcal/g Lipids and carbohydrates o Fats have twice the energy o Stored without water o 1g of glycogen is stored with 2 to 5g of water Disadvantage: not as rapidly mobilized as carbs o Lipids metabolized in the mitochondria in the presence of O2 Camel o Up to 20% of body mass is fat when food is plentiful o Subcutaneous fat would cause thermoregulatory problems Bear o Hibernates 100 days without eating o Rely on fat they have stored for winter Human o Normal weight 40 day reserve of energy o Moderately obese up to a year Nucleic acids o Nitrogenous heterocyclic bases

Pentose sugar Phosphoric acid Examples Coenzymes: NAD, NADP, FAD Genetic material: DNA, RNA Energy: ATP o The components of nucleic acids (figure 5.26) Differ in type of sugar Different types of bases Proteins o Excellent example of a polymer o Made of amino acids 20 naturally occurring amino acids are L-isomers Proteins vary in number and sequence of different kinds of amino acids o Serve a variety of functions Enzymes Protein catalyst Every chemical reaction in a living cell is catalyzed by a specific enzyme Storage protein Seeds Eggs Transport proteins Hemoglobin Contractile proteins Muscles Actin Myosin Defensive blood proteins Anitbodies Toxins From bacteria for example Pertussis toxin (whooping cough) Botox (botulium) Hormones and receptors Chemical messengers (hormones) o E.g. insulin Specific recognition sites for chemical messengers (receptors) Structural Silk Keratin hair, nails, hooves o Amino acids

o o o

Monomers 20 kinds Structure Central carbon Amino group (NH2) Carboxyl group (COOH) Hydrogen R group (20 different R groups) side chain o Can be polar, nonpolar, or charged o Nonpolar No partial charges Hydrophobic o Polar and charged Interact with partial positive and negative charges of water Hydrophilic o Characteristic of individual amino acids determine protein Peptide bond o Does not involve R groups o Amino and carboxyl groups are involved o Covalent Structure Every protein has four levels of structure (figure 5.20) Primary Sequence of amino acids in protein of peptide Determines properties Secondary Alpha helix: fibrous proteins (e.g. a-keratin hair) Beta pleated sheet: silk, core of many globular proteins Results from hydrogen bonding involving peptide backbone R groups not involved Tertiary Folding into 3D structure (e.g. a globule) Folding is due to the properties and interactions of the R groups (amino acid side chains) R groups o Hydrophobic Buried in interior of protein o Hydrophilic Interact with one another or on surface to interact with water

Stabilizing o Weak o Strong

Hydrogen bonds Ionic interactions Hydrophobic and van der Waals interactions Covalent bond (disulfide bridge) SH groups of two cysteines form covalent bond o Stabilizes tertiary structure

Quaternary Multiple polypeptide chains (subunits) fit together to form larger protein Can be identical subunits or different polypeptide chains o Native and denatured proteins Native Properly folded and functional Denatured Unfolded and does not function Roles of weak bonds in biological systems o Easily made and broken at physiological temperature o If weak bonds were strong, it would crystallize the cell o Attract and attach substances to enzymes o Determine molecular shape compromise between backbone and side groups Supercooling o The freezing problems concerning fish Ectotherms cant come into contact with ice or they freeze when in supercooled water Avoid freezing using an antifreeze peptide Small proteins (peptides) depress freezing point of solutions Antifreeze peptides o Non-colligative (colligative=depends on number of particles, or molecules, and not on the nature of said molecules) freezing point depression o hysteresis proteins Affect freezing point, but not melting point Decrease freezing point Melting point stays at 0o Freeze at -2oC, melt at 0oC o Requires more energy to add water molecule to curved surface of ice crystal o Temperature must be lowered to add molecule o Decreased freezing point (obviously this is very fucking important!!!!) o Helical secondary structure

Proteins gone bad o Not caused by germs Not a virus, bacteria, or fungus o Not caused by organism with genetic material o Still controversial o Slow onset of disease o Disease causing agent almost indestructible o Caused by prions Proteinaceous Infectious Particles proteins Discovered in 1982 by Pruisner, resulted in Nobel Prize Normal cellular form: Alpha helix o Present in all mammals o Many protect neurons from toxic copper ions Disease form Beta pleated sheet form o Convinces alpha helix form to convert Difference between normal and diseased form Different secondary structure o Important in determining role/function of protein Disease form converts normal cellular form to beta pleated sheet protein o Mad Cow disease o Transmissiable Spongiform Encephalopathies Scrapie sheep Called scrapie because sheep would scrape wool off skin Chronic Wasting Disease muledeer and elk Bovine Spongiform Encephalopathy (mad cow disease) cattle Human diseases Genetic basis Spread through medical procedures CJD (Creutzfeld-Jacob disease) typical onset at age 60 or later Kuru laughing disease from Papua New Guinea vCJD early onset variant of CJD o first described in March 1996 o from eating meat from infected cows

CELLS: STRUCTURE AND FUNCTION

Geometric relationships explain why most cells are microscopic o Gases and nutrients have to be exchanged across cell

o More surface area the better o Geometry sets size limit Problems o Increased size Less surface area per unit of volume o Problem moving materials into and out of cell o Problem controlling and coordinating metabolic processes Overview Cell Structure o Keeping cell distinct from environment o Organize and coordinate metabolic processes o Three domains Bacteria Archaea Eukarya o Two categories Prokaryotes Archaea, eubacteria Eukaryotes Eukarya Prokaryotes o before the nucleus o No internal membrane-bound organelles o Cell walls of carbs and peptides o Ribosomes differ from eukaryotes in size and antibiotic sensitivity o No nucleus or linear (histone-complexed) chromosomes o No internal membrane o Bacteria and blue-green algae Eukaryotes o True nucleus o Have membrane-bound organelles o Larger cell size Need increased internal membranes Problem of intake nutrients Problem of coordination and control of metabolism More opportunities as a heterotroph (feed on smaller cells) Cell components o Plasma membranes Present in prokaryotes and eukaryotes Semi-fluid mosaic Phospholipids Proteins

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Semi-permeable barrier between contents of cell and environment Nucleus Present in eukaryotes ONLY Enclosed by nuclear membrane Contains linear chromosomes Contains nucleolus Region of nucleus where ribosomal subunits are assembled Also involved in cells response Genetic material in eukaryotes Linear strands of DNA complexed with proteins (histones) Genetic material in prokaryotes Circular strands of DNA naked not complexed with histones Ribosomes Present in both prokaryotes and eukaryotes Differ in size Prokaryotes have smaller, more sensitive to antibiotics Two subunits Made of rRNA and protein Site of protein synthesis Occur free in cytoplasm or in association with rough ER Endomembrane system Endoplasmic reticulum (ER) Eukaryotes only Internal membrane system Mechanism for sorting material belonging in cytoplasm from that which doesnt Lipids, sugars, and proteins synthesized in associated with ER Smooth ER o Lipid synthesis o Detox of water insoluble compounds o Sarcoplasmic reticulum calcium store in muscle Rough ER o Ribosome on cytosolic side o Prominent in cells synthesizing products destined for transport to other cells (e.g. pancreas) Golgi apparatus Eukaryotic Composed of numerous sets of membranes cisternae (discs) Function: o Components go from ER to Golgi

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Components modified and packaged for transport Traffic control for cell

Lysosome Eukaryotic Vesicle containing digestive enzymes (hydrolytic enzymes) In plants: called lytic organelles Digestive enzymes o Isolate enzymes from cell components Mitochondria Eukaryotic Two membranes Generate ATP, use oxygen Lipids metabolized here (aerobic conditions) Not part of endomembrane system Inherited maternally in humans Contain circular, naked DNA (no histone proteins, similar to prokaryotes) Ribosomes (small, prokaryote-like) Chloroplasts Plants only (though some exceptions) Site of photosynthesis Use energy in sunlight to fix carbon Oxygen is produced as a by-product Not part of endomembrane system Three membranes Inner and outer membrane Thylakoid membrane o Stacks of thylakoid called grana (singular granum) Stroma (aqueous stuff between membranes) Contain circular, naked DNA Ribosomes (small, prokaryote-like) Mitochondria and chloroplasts Endosymbiont origin (Lynn Margulis) Organelles evolved from cells eating other cells and not being able to digest them Larger cell and endosymbiont benefitted These organelles originated from small prokaryote living inside larger cells These organelles have characteristics indicating evolution from prokaryote endosymbionts Circular, naked DNA Small ribosomes Double membrane system

Evolution does not proceed by just small mutations Plant cell wall Cellulose Support and protection External to plasma membrane Central vacuole Plants Membrane-bound structure which keeps the cell turgid Plants have 3 unique features not found in animals Cell wall Central vacuole Chloroplasts Cytoskeleton Provides structure to cytoplasm Initially cytoplasm (ground substance) was thought to be without structure Improved techniques showed this to be wrong Structure and function of cytoskeleton (table 6.1) Actin cell movement, skeletal, muscles Tubulin Keratin Flagella and cilia Organelles involved in movement Bacteria have flagella but they are constructed differently from eukaryotic Same structural design (between flagella and cilia) 9+2 structure only in eukaryotes (absent in higher plants flowering plants) o Basic design o Refers to formation of microtubules 9 pairs positioned radially 2 in center Flagella are larger and are fewer in number than cilia Other elements involved in movement Sliding filaments Proteins involved in movement Microfilaments and motility (figure 6.27) Actin and myosin aligned with one another Cause muscle contraction Involved in single-cell organisms Molecular motors Proteins Use ATP

Centriole In animals (not higher plants) Similar to base of flagellum/cilium Involved in mitosis and meiosis Method of nutrition o Autotrophs Plants Synthesize own material o Heterotrophs Animals Rely on material produced by other organisms