BIOL 1020/1027 Fall 2021 Study Guide PDF

Study Guide for Final Exam: BIOL 1020/1027: Fall 2021 Unit 1 Chapter 1: Evolution, Themes of Biology, Scientific Inquiry 1.1 The study of life reveals common themes -Review commonalities of all living organisms: evolution, order/organization, reproduction, growth and development, energy processing,...

Study Guide for Final Exam: BIOL 1020/1027: Fall 2021 Unit 1 Chapter 1: Evolution, Themes of Biology, Scientific Inquiry 1.1 The study of life reveals common themes -Review commonalities of all living organisms: evolution, order/organization, reproduction, growth and development, energy processing, internal regulation, response to the environment. -Biosphere → molecule (and all levels in between) -Domain → species (and all taxa in between) 1.2 Evolution accounts for the unity and diversity of life -The central theory of biology is evolution by means of natural selection -It explains why cilia are the same in lungs and paramecia, for example -It explains the nested hierarchy of organismal groups (tigers are cats, carnivores, mammals, vertebrates, animals, and eukaryotes) 1.3 Scientists make observations and form and test hypotheses -Scientific method: observation, hypothesis, experiment, and analysis Chapter 2: Chemical context of life 2.1 Matter consists of chemical elements in pure form and in combinations called compounds -Notation of elements (C, N, Na), the periodic table, elements most important for life 2.2 An element’s properties depend on the structure of its atoms -Subatomic particles (p+, n0,e-): their mass and charge 2.3 Chemical bonds -interactions between electrons: covalent, polar covalent, ionic, hydrogen bonds, van der Waals interactions 2.4 Chemical reactions -making and breaking chemical bonds, dynamic equilibrium Chapter 3: Water and life 3.1 Polar covalent bonds àhydrogen bonding 3.2 Four emergent properties of water contribute to Earth’s suitability for life -ice floats, surface tension, specific heat, solvent 3.3 Acids and bases -Water dissociates into H+ and OH-, pH scale: 0-14, pH=-log10[H+], acids and bases, buffers, effects of acid precipitation Chapter 4: Introduction to Organic Chemistry 4.1 Carbon compounds -“organic” compounds because of role in living organisms, but not restricted to living organisms (mechanism vs. vitalism) 4.2 Diversity of carbon compounds because of four bonds -hydrocarbon chains (just carbon and hydrogen) can vary in length of chain, branching, placement of double bonds, etc. -types of isomers, structural, cis-trans, enantiomers 4.3 Functional groups - molecules that change chemistry of organic molecules, - frequently found in living organisms -OH, COOH, C=O, -SH, -NH2, -PO42- ,CH3 Chapter 5: Structure and function of large biological molecules 5.1 Macromolecules are polymers, built from monomers - Repeating units make life possible - Formed by dehydration synthesis, broken down by hydrolysis 5.2 Carbohydrates are fuel and building material -Monomers: simple sugars, mono- and disaccharides. (CH2O)n is basic formula, all have carbonyl group (aldoses, ketoses) and carbon backbone (triose, pentose, hexose) -Polysaccharides: cellulose (most abundant, used for structure in plants), glycogen (used for storage in animals) and starch (AKA amylose, used for storage in plants), chitin (used for structure in fungi and arthropods) -linkages between monomers may vary, alpha and beta forms 5.3 Lipids are diverse and hydrophobic -fatty acids (FA) are primarily long hydrocarbon chains with COOH group. -FA may have double bonds in cis- or trans- (unsaturated) -saturated FAs, longer chains, trans-unsaturated more likely to be solid at room temperature -Steroids are four-ring lipids, fats are triacylglycerol -Functions: insulation, long-term energy storage, membranes (phospholipids), steroids -not true polymers 5.4 Proteins are diverse and have many functions -subunits are amino acids (AAs), amine group (NH2) + alpha carbon + carboxyl group (-COOH) + R-group (substitution on alpha carbon) -AAs are grouped by chemistry of R-group (polar, nonpolar, charged) -LOTS of functions! Enzymes, structure, hormones, storage of AAs, etc. -peptide bonds between COOH and NH2 form primary structure -hydrogen bonding between peptide bonds in different parts of chain form secondary structure -interactions between R-groups form tertiary structure -interactions between polypeptide chains form quaternary structure 5.5 Nucleic acids store, transmit and express hereditary information -two types àRNA and DNA -Monomers are nucleotides= nitrogenous base + 5-C sugar + PO42- -RNA has ribose (AUCG), DNA has deoxyribose (ATCG) -purines = A,G; pyrimidines = C,T,U -Sugar phosphate backbone, 5’à3’, antiparallel in DNA UNIT 2 Chapter 6: Tour of the Cell 6.1 Microscopy and other biochemical tools to study cells -Compound light microscopes, TEM and SEM -Centrifugation 6.2 Eukaryotic cells have internal membranes to compartmentalize functions -Prokaryotes: NO membrane bound organelles, smaller (1-room house) -Eukaryotes: membrane-bound organelles including nucleus (many-room house) 6.3 Nucleus and ribosomes -Nuclear envelope = dbl membrane, contains DNA, nucleolus, pores, nuclear lamina -Ribosomes: small and large subunits, may be attached to RER. Different sized subunits in proks and euks 6.4 Endomembrane system -Rough endoplasmic reticulum and smooth endoplasmic reticulum (RER and SER) different functions (what are they?) -Golgi apparatus (=Golgi bodies), shipping and receiving, cis- and trans-faces. Stack of pancakes -Vesicles and vacuoles 6.5 Endosymbiont Theory of mitochondria and chloroplasts - Both have inner and outer membranes, own DNA and ribosomes, reproduce independently from other organelles/structures -mitochondria: the powerhouse of the cell. Cristae, matrix, intermembrane space, home of Krebs cycle and oxidative phosphorylation in euks -chloroplasts: the REAL powerhouse of the cell. Runs on solar energy (photosynthesis), stacks of thylakoids=grana, made of membranes, 6.6 Cytoskeleton -Three types of members, all made of structural proteins -Microtubules: made of alpha and beta tubulin, aid in mitosis, power flagella and cilia, move vesicles on “monorail”, resist compaction -Microfilaments: made of actin, muscle contraction (with myosin), contractile, cortical, cleavage furrow, -Intermediate filaments: in between, may be made of different proteins but keratin is typical. Make up nuclear lamina and ECM 6.7 Extracellular components -junctions: desmosomes, tight junctions, gap junctions, plasmodesmata -ECM=extra cellular matrix, helps with cell communication and cell signaling Chapter 7: Membrane structure and function 7.1 Fluid mosaic model of cell membrane structure -Phospholipid bilayer studded with proteins -Proteins function as transporters, cell-cell recognition, signal transduction, anchoring enzymes together, cell-cell joining, and anchorage to ECM 7.2 Selective permeability -Small, non-polar molecules (like gasses) can pass through phospholipid bilayer - Polar, charged, and large molecules require transport via protein channels -Tonicity: hypotonic =lower solute concentration, isotonic = equal solute concentration, hypertonic = higher solute concentration. 7.3 Passive transport -Diffusion is movement from an area of high solute concentration to an area of lower solute concentration -Osmosis is diffusion of water across a semipermeable membrane with its concentration gradient, from hypotonic to hypertonic -Channel proteins and carrier proteins can allow solute molecules to pass through without investment of energy as long as they flow with their concentration gradient (hi to lo) 7.4 Active transport -Solutes that flow against their concentration gradients require input of energy, typically through ATP hydrolysis -Active transport can generate concentration gradients than can do cellular work (like in oxidative phosphorylation) 7.5 Bulk transport -Large molecules/particles require energy to move into/out of cell even with concentration gradient -Exocytosis= moving out -Phagocytosis, pinocytosis, receptor-mediated endocytosis = moving in. Chapter 8: Intro to metabolism 8.1 Laws of thermodynamics -Energy is limited, so cells must manage energy resources =bioenergetics -Energy comes in many forms: e.g. kinetic, chemical, electromagnetic, potential -Metabolism = all cellular chemical reactions. Anabolism= building up, catabolism = breaking down -1st law of thermodynamics: conservation of energy. “Energy can be transferred or transformed, but it cannot be created or destroyed” -2nd law of thermodynamics: “Every transfer or transformation of energy is