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Gen Bio Study Guide

by: Ileanna lesko

Gen Bio Study Guide BIOL 101-01

Ileanna lesko
Loyola Marymount University

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General Biology I
Mary McElwain
Study Guide
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This 12 page Study Guide was uploaded by Ileanna lesko on Sunday September 4, 2016. The Study Guide belongs to BIOL 101-01 at Loyola Marymount University taught by Mary McElwain in Fall 2016. Since its upload, it has received 9 views. For similar materials see General Biology I in Biology at Loyola Marymount University.

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Date Created: 09/04/16
Ileanna Lesko Exam 1 Study Guide 2/7/16 Biochemistry 1. Define a. Element: a substance that cannot be converted to simpler substances by ordinary chemical means b. Atoms: the smallest unit of a chemical element. Consists of a nucleus and one or more electrons. c. Proton: 1) a subatomic particle with a single positive charge. The number of protons in the nucleus of an atom determine its element. 2) a hydrogen ion H+. d. Electron: a subatomic particle outside the nucleus carrying a negative charge and very little mass. e. Neutron: one of the three fundamental particles of matter, with mass slightly larger than that of a proton and no electrical charge. f. Atomic mass: the sum of the number of protons and neutrons in an atom’s nucleus. g. Atomic number: the number of protons in the nucleus of an atom; also equals the number of electrons around the neutral atom. Determines the chemical properties of the atom. h. Valence electron: an electron of an atom, located in the outermost shell (valence shell) of the atom, that can be transferred to or shared with another atom. i. Cation: an ion with one or more positive charges. j. Anion: a negatively charged ion. k. Isotopes: isotopes of a given chemical element have the same number of protons in their nuclei (and thus are the in the same position on the periodic table), but differ in the number of neutrons. l. Molecules: a chemical substance made made up of two or more atoms joined by covalent bonds or ionic attractions. m. Compound: composed of two or more elements; can be acids or bases. n. Solute: a substance dissolved in a given solution. o. Solvent: a liquid in which other molecules dissolve. p. Solution: a homogenous, molecular mixture of two or more substances. q. Acid: gives up H+ ions to a solution, increases the H+ content of a solution. r. Base: in nucleic acids, the purine or pyrimidine that is attached to each sugar in the sugar-phosphate backbone; accepts H+ and decreases the amount of H+ ions in the solution. s. pH: the symbol for the logarithm of the reciprocal of hydrogen ion concentration in gram atoms per liter, used to express the acidity or alkalinity of a solution on a scale of 0 to 14, where less than 7 represents acidity, 7 neutrality, and more than 7 alkalinity. 2. Identify the “Big 4” elements that living organisms contain. - Carbon, oxygen, hydrogen, nitrogen; “Big 6” = phosphorus, sulfur 3. Use information from the periodic table (e.g. atomic mass and atomic number) to calculate the number of protons, neutrons, and electrons of a particular element. (Including isotopes and ions) 4. Identify and give examples of atoms, molecules, compounds, elements, isotopes 5. Explain the importance of valence electrons in bond formation. Be able to determine the number of valence electrons for the Big 4 atoms + P + S. How are P and S different? - Behavior of electrons determines whether a chemical bond will form between atoms and what shape the bond will have. When atoms share electrons, they form stable associations called molecules. - Each electron shell is subdivided into subshells made up of orbitals. - First shell: holds 1 orbital (hold up to two electrons) - Second shell: 4 orbitals (8 electrons) - Octet rule: the tendency of atoms to form stable molecules so that they have eight electrons in their outermost shells. 6. Compare, contrast and differentiate bond types (ionic, covalent, hydrogen bonds, hydrophobic interactions, van der Waals forces). Explain how these bonds relate to interactions between atoms to form molecules. Explain how these bonds relate to interactions between different molecules. - Inion attraction: attraction of opposite charges. WEAK - Covalent bonds: sharing of electron pairs. STRONG - Hydrogen bond: attraction between H and a strongly electronegative atom. WEAK - Hydrophobic bonds: interaction of nonpolar substances in the presence of polar substances (especially water). - Van der Waals interaction: interaction of electrons of nonpolar substances. 7. Explain how electronegativity helps to determine whether a bond is ionic or covalent? - Electronegativity of an atom refers to attractive force an atomic nucleus exerts on electrons. - Electronegativity of a nucleus depends on the number of protons (more protons, more electronegativity) and distance that separates it from electrons (the closer the e-, the greater the electronegative pull) - Covalent bonds (can also be single, double, or triple)  Non-polar: atoms of similar EN (or with a change in EN < 0.5)  Polar: atoms with a change in EN between 0.5 and 1.7 for a dipole  For a change in EN between 1.7 and 2.0, the nature of the bonds depends on the nature of the atom; if non-metal atoms are involved, the bond will be polar covalent, if metal atoms are involved, the bond will be ionic (NaBr vs. HF). - Ionic bond  Atoms with a change in EN greater that 2.0 8. Explain the difference between polar and non-polar covalent bonds. Given a chemical formula and an electronegativity table, determine whether a covalent bond is polar or non-polar. - Covalent bonds: forms when two atoms share pairs of electrons; sharing of either 1, 2, 3, or 4 pairs of valence electrons by 2 atoms; each pair of shared electrons forms a covalent bond - Nonpolar bonds: equal sharing of electrons. Ex. H2, Cl2, O2, CH4 - Polar bonds: one atom more EN than the other. 9. Explain the driving force behind the formation of hydrogen bonds. Illustrate the importance of H-bonds in water and how a water molecule might interact with another molecule based on partial charges and polarity. - Hydrogen bonds: sharing of a hydrogen atom between 2 molecules. - A hydrogen bond covalently attached to a very EN atom (N, O, P) shares its partial positive charge with a second EN atom (N, O, P)  weak bonds very important for DNA stability. - A hydrogen bond forms between two molecules because of the attraction between an atom with a atrial negative charge on one molecule and a hydrogen with a partial positive charge on a second molecule. - Hydrogen bonds can form between different parts of the same large molecule. 10. Explain how a given compound makes a solution more acidic or basic and how this relates to H+ concentration ([H+]). - Under normal physiological pH, carboxyl and amino groups ionize, releasing of accepting H+ ions. - Changes in pH can alter the ionization state of these functional groups and change the charge. 11. Illustrate how a buffer works using the bicarbonate buffer system as an example. Why is this buffer system important in physiology? - Strong acid or bases fully dissociate water. - Buffers  Weak acid (and conjugate base) that do not fully dissociate in water  Resist change in pH when hydrogen or hydroxide ions are added or removed.  Any cell that is metabolically active, then producing CO2 + H2O = H2CO3 (acid)  If acid builds up in our bodies, they wont work  The bicarbonate system buffer system changes the pH levels  7.4: optimal pH body fluids  bicarbonate concentration of 24 mEq/L  partial pressure of CO2 in blood is 40 mm Hg Macromolecules 1. Define a. Polymer: a large molecule made up of similar or identical subunits called monomers. b. Monomer: a small molecule, two or more of which can be combined to form oligomers (consisting of a few monomers) or polymers (consisting of many monomers). c. Macromolecule: a giant polymeric molecule. The macromolecules are the proteins, polysaccharides, and the nucleic acids. d. Hydrocarbon: compound containing hydrogen and carbon. e. Functional group: a characteristic combination of atoms that contribute specific properties when attached to larger molecules. f. Amphipathic: of a molecule, having both hydrophobic and hydrophilic regions. g. Condensation reaction: a chemical reaction in which two molecules become connected by a covalent bond and a molecule of water is released (AH + BOH  AB + H20). h. Hydrolysis reaction: a chemical reaction that breaks a bond by inserting the components of water. i. Mono- one j. Poly- many k. Di- two l. Tri- three m. Oligo- few, little n. Pent- five o. Hex- six 2. Explain the importance of water, hydrogen bonding and hydrophobic interactions in macromolecular structure and function. - 3. Identify reactions as hydrolysis or condensation reactions 4. Describe the role of water in the formation and breakdown of macromolecule. - 5. For each of the following, identify the monomer and polymer, the bond that joins monomers, describe the main function and give an example. a. Proteins  Polymer: polypeptides  Monomer: amino acids (20 total)  Covalent bond: Peptide  Function: b. Nucleic acids  Polymer: DNA/ RNA  Monomer: Deoxynucleotides/ nucleotides  Covalent bond: phosphodiester  Function: c. Sugars  Polymer: polysaccharides  Monomer: monosaccharide  Covalent bond: glycosidic  Function: source of stored energy, transport stored energy within organisms, structural molecules give many organisms their shapes, recognition or signaling molecules can trigger specific biological responses d. Lipids  6. Draw the monomers for proteins and nucleic acids (disregarding side chain or base). 7. Draw a condensation reaction between two amino acids and two nucleotides (regardless of side chain or base). 8. Explain the difference between glucose polymers and give reasons why they have different structural and solubility characteristics. - Monosaccharide: one simple sugar (glucose, ribose, fructose); have up to 7 C atoms, position of the carbonyl group determines if aldose (C = O on C1) vs. ketose (C = O on C2); forms rings by allowing the aldehyde group to react with the hydroxyl group on carbon 5 - Disaccharide: two simple sugars linked by covalent bonds - Oligosaccharide: several simple sugars (3 to 20) - Polysaccharide: many simple sugars such as in starch and glycogen and cellulose (>20) 9. Explain why phospholipids are amphipathic and how they form a bilayer. - Phospholipid: two fatty acids and a phosphate group bound to glycerol - Fatty acids are amphipathic; they have a hydrophilic end and a hydrophobic tail - The phosphate group has a negative charge, making that part of the molecule hydrophilic - In an aqueous solution, they form a bilayer - The nonpolar, hydrophobic “tails” pack together and the phosphate- containing “heads” face outward, where they interact with water 10. Explain why certain substances do not dissolve in water - Lipids are hydrophobic: insoluble in water due to nonpolar covalent bonds (C – H) - Fats and oils are hydrophobic: triglycerides, have very little polarity - Triglycerides consist of: three fatty acid chains, nonpolar hydrocarbon chain attached to a polar carboxyl group; synthesis of a triglyceride involves three condensation reactions to form three ester linkages 11. Explain the difference between a saturated and an unsaturated fatty acid - Saturated fatty acids: all bonds between carbon atoms are single; they are saturated with hydrogens, closely packed, solid art room temp. - Unsaturated fatty acids: hydrocarbon chains have one or more double bonds, provides space, low melting temp. 12. Describe the physical change that occurs when you hydrogenate oils. What is the purpose of hydrogenating oils? - Converts unsaturated fats to saturated, but also creates trans- fats 13. Identify and differentiate the following a. Cis unsaturated fatty acid: b. Trans unsaturated fatty acid c. Saturated fatty acid 14. Differentiate between RNA and DNA - RNA: single-stranded, bases are AUCG and the sugar is ribose - DNA: double-stranded, bases are ATCG and the sugar is deoxyribose 15. Explain the basis for the “directionality” of proteins and nucleic acids. - 16. Describe the 4 levels of protein structure and explain what type of chemical bonds and interactions are important at each level. - Primary structure: linear sequence of aa linked together through peptide bonds (defined by genetic code = central dogma) - Secondary structure: regular and repeated patterns determined by hydrogen bonds between amino acids and carboxyl groups. - Tertiary structure: folding of a given polypeptide chain into specific shapes through various bonds involving R groups - Quaternary structure: assemblage of 2 or more polypeptide chains through various bonds involving R groups to form a larger protein. 17. Classify amino acids as hydrophobic or hydrophilic and explain why an amino acid would be found on the surface of a protein, inside of a folded protein, or in a membrane Cell and Protein Trafficking/ Cellular Membranes 1. Define a. Organelle: any of the membrane-enclosed structures within a eukaryotic cell. b. Exocytosis: a process by which a vesicle within a cell fuses with the plasma membrane and releases its contents to the outside. c. Endocytosis: a process by which liquids or solid particles are taken up by a cell through invagination of the plasma membrane. d. Cis: e. Trans: f. Transmembrane protein: an integral membrane protein that spans the phospholipid bilayer. g. Lipid anchored protein: h. Peripheral membrane protein: proteins associated with but not embedded within the plasma membrane. i. Diffusion: random movement of molecules or other particles, resulting in even distribution of the particles when no barriers are present. j. Osmosis: movement of water across a differentially permeable membrane, from one region to another region where the water potential is more negative. k. Passive transport: diffusion across a membrane; may or may not require a channel or carrier protein. l. Active transport: the energy-dependent transport of a substance across a biological membrane against a concentration gradient— that is, from a region of low concentration to one of high concentration. m. Facilitated diffusion: passive movement through a membrane involving a specific carrier protein; does not proceed against a concentration gradient. n. Hypertonic: having a greater solute concentration. o. Hypotonic: having a lesser solute concentration. p. Signal transduction: the series of biochemical steps whereby a stimulus to a cell is translated into a response of the cell. q. Kinase: an enzyme that catalyzes the addition of a phosphate group from ATP to target a protein. 2. Structures in a cell a. Cell membrane: lipid bilayer also containing proteins and other molecules that encloses the cytoplasm of the cell and separates it from the surrounding environment. b. Nucleus: the centrally located compartment of eukaryotic cells cells that is bounded by a double membrane and contains chromosomes. c. Mitochondria: an organelle in eukaryotic cells that contains the enzymes of the citric acid cycle. d. Chloroplasts: an organelle bounded by a double membrane containing the enzymes and pigments that perform photosynthesis. Chloroplasts occur only in eukaryotes. e. Cell wall: a relatively rigid structure that encloses cells of plants, fungi, many protists, and most prokaryotes, and which give these cells their shape and limits their expansion in hypotonic media. f. Ribosome: a small particle in the cell that is the site of protein synthesis. g. Cytoplasm: the contents of the cell, excluding the nucleus. h. Golgi apparatus: a system of concentrically folded membranes found in the cytoplasm of eukaryotic cells; functions in secretion from the cell by exocytosis. i. Lysosomes: a membrane-enclosed organelle originating from the Golgi and containing hydrolytic enzymes. j. Peroxisome: an organelle that houses reactions in which toxic peroxides are formed and then converted to water. k. Rough ER: the portion of the ER whose outer surface has attached ribosomes. l. Smooth ER: portion of the ER that lacks ribosomes and has a tubular appearance. m. Vacuole: membrane-enclosed organelle in plant cells that can function for storage, water concentration, or hydrolysis of stored macromolecules. n. Vesicle: within the cytoplasm, a membrane-enclosed compartment that is associated with other organelles; the Golgi complex is one example. 3. Explain how compartmentalization of eukaryotic cells is an advantage over prokaryotes. - Eukaryotic cells have a cytoskeleton composed of protein fibers, and outside the cell membrane, an extracellular matrix. 4. Identify organelles that are part of the endomembrane system. - The interconnected system of enclosed-membrane compartments includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, and lysosomes. 5. Explain how where different proteins are made and trafficked throughout an eukaryotic cell. - 6. Explain the difference between Gram + and Gram – bacteria. 7. Give an example of a prokaryote and a eukaryote. - Bacterium - Animal and plant cells 8. Describe three similarities and three differences between prokaryotes and eukaryotes. - Similarities: the cell membrane encloses the cell, separating its interior from the external environment, and regulates the traffic of materials into and out of the cell. - Differences: eukaryotes have a nucleus, prokaryotes do not; prokaryotes have a flagella and a cytoskeleton. 9. Describe the journey of a secreted protein starting with DNA in the nucleus. - 10. Compare and contrast plant and animal cells - Plant cells have cell walls 11. Identify the important functions of the cytoskeleton. - Made of protein, function in cellular structure, movement of organelles and cellular adhesion and anchoring, dynamic instability (ability to rapidly build or breakdown cytoskeletal fibers for cellular function) - Microfilaments: help in cellular movements in association with myosin (muscle contraction), cellular support and determine cell shape - Intermediate filaments: provides resistance to the mechanical stress the cell undergoes, do not exhibit dynamic instability. - Microtubules: rigid internal skeleton, network of movement of organelles and molecules by motor proteins, responsible for movement of flagella and cilia with motor proteins. 12. List and describe the structures and function of cell-cell junctions. - Tight junctions: prevent materials or fluids from passing between cells - Desmosomes: (anchoring junction) connect cells together through keratin protein (cytoskeletal fibers) that extend in the cell - Gap junctions: (communicating junction) protein channels that pass the membranes of neighboring cells and allow particles and fluid to pass between cells 13. Explain how the function of different cells is reflected in their structure. - 14. Draw a cell membrane indicating the hydrophobic and hydrophilic ends of the phospholipids 15. Draw a membrane that contains the following proteins a. Transmembrane protein b. Lipid-anchored protein c. Peripheral membrane protein 16. Explain why the membrane is considered a semi- permeable, fluid mosaic - The plasma membrane allows some molecules in/out, but not others - If molecules are small enough they can get through - H2O can get through, but very slowly - Glucose and amino acids can’t get through because they are too large 17. Distinguish among hypertonic, hypotonic and isotonic solutions - Isotonic: cells retain their normal size and shape, water moves in and out (loss of blood) - Hypertonic: cells lose water by osmosis and shrink in a hypertonic solution (contain a higher concentration of solutes than are present inside the cell) (get stuff out of the cell, ex. Edema) - Hypotonic: cells take on water by osmosis until they become bloated and burst (contains a lower concentration of solute than present in the cell) (intracellular dehydration) 18. Predict the direction of osmosis given concentrations of solutes on both sides of a membrane 19. Give examples of membrane permeable and impermeable molecules - Permeable: gases, hydrophobic molecules, H2O (very slow) - Not permeable: ethanol, glucose, amino acids, ions 20. Describe different ways that large molecules are transported across the cell membrane - Passive transport: no input of energy required (requires driving force; high to low; down concentration gradient) simple diffusion, protein-facilitated diffusion, osmosis - Active transport: requires energy (ATP or ion gradient) to drive transport (low to high; against concentration gradient) - Exocytosis and endocytosis 21. Diagram the following and compare and contrast- a. Active transport b. Diffusion c. Facilitated diffusion 22. Distinguish which method of transport must be used by a cell when given an example of a molecule at certain concentrations inside and outside of the cell. Defend your answer. - 23. Explain how signals are transmitted across the membrane without molecules actually crossing the bilayer and how those signals might change the cell. Identify the steps and major contributors to signal transduction. -


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