STUDY GUIDE for BIOL 110

Transcription

1 STUDY GUIDE for BIOL CHEMISTRY a. Structure of the Atom i) Subatomic Particles: protons, electrons, neutrons (1) Charges (2) Mass ii) Atomic Number and Atomic Mass (1) Determine number of subatomic particles (2) Isotopes iii) Electron Energy Levels (1) Electron distribution (2) Relate to energy b. Acids, Bases, Salts i) What are they (1) Recognize acids and bases ii) ph (1) Relate to acids and bases (2) What the differences between the numbers mean iii) Buffers c. Equations i) Recognize reactants and products ii) Oxidation and Reduction (1) Definitions d. Bonds i) How they are created ii) Types (1) Ionic (2) Covalent (a) Single, double, triple (b) Polar and non-polar (i) Hydrophilic and hydrophobic (3) Hydrogen e. Properties of Water f. Properties of Carbon i) Why does carbon make macromolecules ii) Recognize organic molecules iii) Recognize phosphate, methyl, hydroxyl, amine and carboxyl groups g. Biochemistry i) Dehydration synthesis and hydrolysis ii) For all the macromolecules (1) Basic molecular composition (monomer subunits) (2) Uses in cell and/or organism iii) Carbohydrates (1) Monosaccharides

2 (a) Molecular formula for glucose (b) Examples (2) Disaccharides (a) Examples (3) Polysaccharides (a) Examples iv) Lipids (1) Triglycerides (a) Composition (i) Saturated and unsaturated fatty acids (2) Phospholipids (a) Composition (b) How they form a bi-layer (3) Steroids (a) Cholesterol v) Proteins (1) 1, 2, 3, 4 structure (2) Importance of 3-D shape to function (3) Denature vi) Nucleotides (1) ATP (2) DNA (3) RNA h. Objectives for Chemistry i) Define the terms: matter, atom, element, molecule, compound, mixture, chemical and physical change. ii) Identify the subatomic particles, their location, charges and masses. iii) Given the Periodic Table or the element written in proper form, for the first 20 elements: (1) identify their symbols. (2) identify their atomic numbers. (3) identify their atomic masses. (4) determine their number of protons, neutrons and electrons for any isotope. (5) determine their number of energy shells (orbitals) and number of electrons in each shell. (6) determine their valence number. iv) Define the term ion and discuss how it is formed. v) Differentiate between oxidation and reduction. vi) For balanced equations, determine the reactants and products vii) Discuss the differences between acids, bases and salts and their relationship to ph. Discuss the role of buffers. viii) Explain the formation of covalent bonds and relate to organic molecules. ix) Explain how the electronegativity of atoms within a molecules influences the polarity of the molecule and show how the molecule is hydrophobic or hydrophilic. x) Describe hydrogen bonds and explain how they are formed. xi) Contrast the relative strengths of ionic, covalent and hydrogen bonds. xii) Describe the properties of water and explain these properties in terms of the chemistry of the water molecule.

3 xiii) Recognize the phosphate, methyl, hydroxyl, amine and carboxyl organic functional groups. xiv) Define the term isomer. Name isomers of glucose. xv) Differentiate between dehydration synthesis and hydrolysis. xvi) For carbohydrates, lipids, proteins and nucleic acids, discuss the following: (1) chemical and structural characteristics. (a) For proteins (i) Describe the formation of a peptide bond (ii) Describe the primary, secondary, tertiary and quaternary structures and why they are important. (iii) Describe what happens when a protein is denatures and predict its effect on protein function. (2) types of subunits, bonding and classification scheme. (3) examples of these macromolecules. (4) importance to cells and organisms. 2. CELLS a. Characteristics of Life i) What does it mean to have life? ii) Organization Levels iii) Taxonomy (1) Domains (2) Kingdoms b. What is Cell Theory? i) What is a cell? ii) Why are cells small? c. Prokaryotic Cells i) Basic characteristics ii) Structures: molecular composition and function (1) Cell wall (2) Cell membrane (3) Nucleoid Region (4) Ribosomes

4 d. Eukaryotic Cells i) Basic characteristics ii) Structures: molecular composition and function (1) Cell wall (2) Cytoplasma (a) Cytosol (3) Cell membrane (a) Endoplasmic Reticulum (i) Rough and smooth (4) Golgi apparatus (5) Nucleus and nucleolus (a) Chromosome (b) Chromatin (material) (6) Centrioles (7) Vacoules and vesicles (a) Lysosomes (b) Central Vacoule (c) Peroxisomes (8) Ribosomes (9) Mitochondria (a) Matrix and cristae (10) Chloroplasts (a) Thylakoids and stroma (11) Cytoskeleton (a) Flagella and cilia iii) Differences between plant and animal cells e. Endosymbiotic Theory i) How mitochondria and chloroplasts originated ii) Supporting evidence f. Objectives for Cells i) List, describe and give examples for the characteristics of living things. ii) State the hierarchy of organization and relate to increasing complexity and energy requirements. iii) Explain what is meant by the unity and the diversity of life. Give examples. iv) Identify The Cell Theory and its meaning. v) Identify the structure and functions of the major components of prokaryotic cells. (See above.) vi) Using the terms total surface area and volume, explain why cells remain small. vii) Identify the structure and functions of the major components of eukaryotic cells. (See above.) viii) Identify the major similarities and differences between: (1) prokaryotic and eukaryotic cells. (2) eukaryotic animal and eukaryotic plant cells. (3) similarities between all cells. ix) Explain (and support) how chloroplasts and mitochondria arose in eukaryotic cells.

5 3. MEMBRANES a. Fluid Mosaic Model i) Purpose of (1) Phospholipids (2) Proteins (a) Channels (b) Receptors (3) Cholesterol (4) Glycoproteins and glycolipids b. Animal and Plant Cell Junctions c. Passive Transport i) Definition (1) Requirements (a) Gradient (b) Source of energy ii) Types (1) Simple diffusion (a) Molecules moved (2) Osmosis (a) Definition (b) Hypertonic, hypotonic, isotonic (c) Problems (3) Facilitated Transport/Diffusion (a) Role of proteins (b) Molecules moved (4) Transporter Systems (a) Types (i) Uniport (ii) Symport (b) How they work (c) Examples

6 d. Active Transport i) Definition (1) Requirements (a) Gradient (b) Source of energy (c) Role of proteins ii) Types (1) Antiporter: Na-K Pump (2) Endocytosis (a) Phagocytosis (b) Pinocytosis (3) Exocytosis e. Objectives for Membranes i) Describe the structure of the plasma membrane according to the Fluid-Mosaic Model. ii) Explain why the membrane is semi-permeable. iii) State three ways that animal cell and one way that plant cells are joined together. Explain how each mechanism functions. iv) Describe and explain the general phenomenon of diffusion. Indicate what molecules are able to diffuse across the plasma membrane. v) Define osmosis and be able to apply to problem solving situations utilizing the terms isotonic, hypertonic and hypotonic. vi) Define facilitated transport/diffusion. Explain the roles of various transporter proteins in moving molecules across the membrane. vii) Define active transport. viii) Briefly describe how pump systems operate. Explain why the Na + /K + Pump is an antiporter system. ix) Compare and contrast facilitated transport/diffusion and the pump systems of active transport. x) Describe the processes of endocytosis and exocytosis and indicate the differences between phagocytosis and pinocytosis. xi) Compare and contrast the following: (1) Passive and active transport (2) Facilitated and active transport

7 4. ENZYMES a. Structure i) Active Site ii) Allosteric Site b. Role as a catalyst i) Energy of Activation c. Changing reaction rates i) Temperature ii) ph iii) Inhibitors (1) Competitive (2) Non-competitive d. Co-enzymes i) Purpose ii) NAD, NADP, FAD e. Objectives for Enzymes i) Describe the structure and function of enzymes and how enzymes lower the Energy of Activation. ii) Indicate the role of temperature, ph, concentrations and inhibitors play in altering enzyme activity. iii) Explain the function of coenzymes in metabolic pathways. Give examples of each. 5. METABOLISM a. Definition i) Anabolism ii) Catabolism b. Energy i) Definition ii) Potential and kinetic energy iii) Laws of Thermodynamics (1) Entropy (2) Endergonic and exergonic c. Objectives for Metabolism i) Define energy and how it is different from matter. ii) Explain the differences between potential and kinetic energy. Give examples of each. iii) State the first two laws of thermodynamics. Explain why life on this planet requires an outside source of energy and how energy is used to negate entropy. iv) Describe the major characteristics of the various types of metabolic reactions anabolism and catabolism; endergonic and exergonic.

8 6. ATP a. Structure i) AMP to ADP to ATP b. Role as the energy carrier for the cell c. Phosphorylation Processes i) Substrate level ii) Chemeiosmotic d. Objectives for ATP i) Describe the structure and function of ATP. ii) Contrast the amounts of energy stored in glucose, NADH and ATP. Explain why having energy in ATP versus glucose is beneficial to the cell. iii) Explain the processes of substrate-level phosphorylation and chemiosmosis. 7. PHOTOSYNTHESIS a. General reaction i) Importance to life ii) Which reactants are oxidized? Reduced? b. Role of sun as the energy source i) Electromagnetic Spectrum c. Role and location of pigments i) Chloroplast structure (1) Photosystems (a) PSI/P700 and PSII/P680 (b) Purpose d. Light Dependent Reactions i) Non-cyclic pathway (1) Reactants: H 2 O, NADP, ADP, P i (2) Products: NADPH, ATP, O 2 (3) Be able to follow the path of the electron that came from H 2 O e. Light Independent Reactions/Calvin Cycle i) Reactants: NADPH, ATP, CO 2 ii) Products: NADP, ADP, P i, glucose f. Interconnectiveness between the 2 reactions g. Objectives for Photosynthesis i) State the generalized reaction for photosynthesis and indicate the accomplishments of photosynthesis which are essential to life on this planet. Be able to identify which reactants are oxidized and reduced. ii) Describe the entire electromagnetic spectrum and indicate their relative energy levels. iii) Describe the structures and functions of the components of a chloroplast. Define the role of the pigments and how they work in a Photosystem. iv) Indicate the locations, reactants and products of the light (dependent) and light independent (carbon fixation) reactions of photosynthesis. Describe how the light (dependent) reactions drive the light independent (carbon fixation) reactions. v) Describe the route taken by an electron in the cyclic and non-cyclic pathways of the light dependent reactions of photosynthesis. Indicate reactants and products in the pathways.

9 vi) For the Calvin Cycle state its purpose, reactants and products, describe the three phases and note which molecules supply energy. 8. ENERGY RELEASING REACTIONS a. Terms i) Aerobic and anaerobic ii) Slow and rapid oxidation b. Mitochondria structure c. Glycolysis i) Location ii) Major events (1) Activation Steps (2) Oxidation Steps iii) Major Reactants: glucose, 2 ADP, NAD iv) Major Products: 2 pyruvates, 4 ATP, NADH d. Aerobic Respiration i) Krebs Cycle (1) Location (2) Purpose (3) Major Products: NADH, FADH 2, ATP ii) Electron Transport System (1) Location (2) Purpose (3) Role of oxygen (4) Major Products: NAD, FAD, H 2 O iii) Total amount of ATP made iv) Efficiency of reaction relate to heat e. Fermentation i) Purpose ii) Types (1) Alcoholic (a) Types of cells (b) Products (2) Lactic Acid (a) Types of cells (b) Products iii) Total amount of ATP made iv) Efficiency of reactions f. Objectives for Energy Releasing Pathways i) State the generalized reaction for aerobic respiration and its function. Identify which reactants are oxidized and reduced. ii) Compare and contrast rapid and slow oxidation iii) Distinguish between aerobic and anaerobic processes. iv) Indicate the major reactants, products, location and purpose of glycolysis. v) Describe the transition reaction. Indicate its location. vi) Indicate the reactants, products, location and purpose of the Krebs Cycle.

10 vii) Explain what is accomplished by the mitochondrial electron transport system. Indicate its location. viii) Explain fermentation in terms of its general usefulness, products and energy yield. ix) List the three processes used by different cells to oxidize NADH after glycolysis is complete. State whether the processes are examples of aerobic respiration or fermentation. x) Compare the efficiency of aerobic respiration to fermentation. xi) Explain the interconnection between energy and matter when discussing photosynthesis and aerobic respiration. 9. HOW A CELL STORES & PROCESSES INFORMATION a. DNA i) Structure (1) Backbone (a) Anti-parallel (i) 3 and 5 ends (2) Purines & pyrimidines (a) Complementary base pairings (3) Bonds present ii) Organization in eukaryotic cell (1) Chromatin material (a) Histones (2) Chromosome (a) Centromere (b) Sister chromatids iii) Replication (1) Major enzymes: helicase, primase, DNA polymerase, ligase (2) Results (a) Semi-conservative replication iv) What is a gene? v) Objectives for DNA (1) Discuss the location, chemical composition, structure and function of DNA. Be able to utilize the following terms: primers, 1, 3, 5, nucleotide, adenine, guanine, cytosine, thymine, purine, pyrimidine, sugar-phosphate backbone, covalent and hydrogen bonds. (2) Describe the process and results of DNA replication. Include the roles of helicase and other proteins in producing the replication fork. Discuss the roles of primase, DNA polymerase and DNA ligase and how they function on the continuous (leading) strand and the discontinuous (lagging) strand. (3) Define semi-conservative replication and how it ensures the integrity of the genetic code. b. RNA i) Structure (1) Differences between DNA and RNA ii) Types (1) mrna (a) Codons (b) Function (2) trna

11 (a) Anti-codons (b) Function (3) rrna (a) Function c. Protein Synthesis i) Transcription (1) Location (a) RNA polymerase (2) Process (a) Promotor and terminator regions (b) Exon and intron regions (c) Caps and tails ii) Translation (1) Location (2) Process (a) Start and stop codons (3) Using a codon table or wheel and given either a DNA, mrna or trna sequence determine the amino acid sequence iii) Mutations (1) Definition (2) Types (3) Result of a mutation (4) Importance to evolution

12 iv) Objectives for RNA (1) Indicate the similarities and differences between DNA and RNA. (2) Explain how information is stored in DNA and be able to explain the relationship between the nucleic acid sequence in DNA and the amino acid sequence of a protein. (3) Explain how the message in the chromosome is transcribed and how mrna is processed before it leaves the eukaryotic nucleus. Be able to explain the role of promoter and terminator regions, exons and introns, upstream and downstream sequences and start and stop codons. (4) Explain how RNA is translated into the primary structure of a protein. (5) Given a DNA sequence and a genetic dictionary, indicate the following sequences: mrna, trna and amino acids. (6) Define mutation. Be able to discuss various types of mutations, causative agents and how DNA protects itself from mutations. (7) Explain how mutations are the fuel for evolution. 10. CELL DIVISIONS a. Asexual Processes i) Purpose ii) Prokaryotic binary fission iii) Eukaryotic Cells (1) Type of cells (a) Somatic (b) Diploid, 2N (2) Cell Cycle (a) Interphase (i) 3 Steps (ii) What occurs in each (b) M Phase (i) Mitosis 1. 4 steps a. What occurs in each (ii) Cytokinesis i. Cell Furrowing ii. Cell Plate b. Sexual Process i) Type of cells produced (1) Animal Cell Cycle (a) Gametes, haploid, N ii) Meiosis (1) Meiosis I (a) What occurs in each step (i) Homologous chromosomes (2) Meiosis II (a) What occurs in each step

13 iii) Sources of variation (1) Processes (a) Crossing over (b) Independent Assortment (c) Fertilization (2) Importance (a) Genetic diversity (i) Survival of species (b) Tool for evolution iv) Meiotic Errors (1) Diagnosis (2) Human conditions c. Objectives for Cell Divisions i) Indicate the functions of cell division in single celled and multicellular organisms and why being multicellular is an advantage. (Relate to genetic diversity) ii) Indicate how cell division occurs in prokaryotic cells and what it is called. iii) Define the following terms in relation to eukaryotic cells: chromatin, chromosomes, sister chromatids, homologous chromosomes, centromere, centrioles, polar spindle fibers, synaptonemal complex, and chiasmata. iv) Explain the terms diploid and haploid. v) Indicate the major phases and events of the cell cycle. vi) Explain the purpose of mitosis. vii) Indicate the major phases and events of mitosis in plant and animal cells. viii) Describe the life cycle in animals. ix) Explain the purpose of meiosis. x) Indicate the major phases and events of meiosis. xi) Describe the process of crossing over and independent assortment result in genetic diversity. xii) Explain why some genes are more likely inherited together. Relate crossing over and independent assortment to linkage. xiii) Compare and contrast the outcomes of mitosis and meiosis. xiv) Describe how a human karyotype is prepared and how it is used. xv) Indicate the chromosomal similarities and differences between human males and females. Indicate the symptoms and cause of the some chromosomal disorders (example: Downs Syndrome)

14 11. CLASSICAL GENETICS a. Mendelian i) Terms (1) Allele and loci (2) P1, F1, F2 (3) Dominant and recessive (4) Phenotype and genotype (5) Homozygous and heterozygous ii) Mendle s 2 Laws of Inheritance (1) Gene linkage iii) Problems (1) Solve monohybrid crosses (2) Create dihybrid gametes iv) Examples in human genetics (1) Why the heterozygote has an environmental advantage? (2) Examples of autosomal recessive and autosomal dominant genetic disorders b. Incomplete Dominance i) Solve genetic problems c. Co-dominance i) ABO Blood System (1) Solve genetic problems d. Sex-linked i) Solve genetic problems ii) Examples (1) Eye color in fruit flies (2) Human genetics e. Classical Genetics Objectives i) Correlate the chromosomal events of meiosis as they apply to Mendel's Laws of Segregation and Independent Assortment. ii) Define the following terms: alleles, genes, loci, heterozygous, homozygous, recessive, dominant, genotype and phenotype. iii) Apply the Laws of Probability or Punnett Squares to the distribution of hereditary traits in monohybrid crosses and assign proper genotypes and phenotypes to the parents predicted offspring. iv) Determine the gametes that can be produced from a dihybrid cross. v) Be able to solve genetic problems involving incomplete dominance, ABO blood types and sex-linkage. vi) Define the role the environment has on genotype expression. (Keep general, do not go into the molecular mechanisms for turning genes on and off. vii) Describe the mode of inheritance, major characteristics and treatments for the various human genetic disorders that display autosomal recessive, autosomal dominant and sex-linked inheritance patterns. (Use the textbook for examples.) When appropriate explain the advantage of the heterozygote. viii) Explain the relationship between recessive phenotypes, incomplete dominance and nonfunctioning and/or missing proteins.

15 12. BIOTECHNOLOGY a. Definition b. Procedures i) Restriction enzymes ii) Interpret a gel produced from gel electrophoresis c. Products produced through recombinant DNA i) Stem Cells (1) Definition (2) Types (3) Genomics and proteomics d. Objectives for Biotechnology i) Describe the role of vectors in the process of recombinant DNA. ii) Explain the process in making recombinant DNA. iii) Explain the uses of PCR, RFLP and gel electrophoresis. Explain the various techniques used to visualize molecules separated in a gel. iv) Give examples of some recombinant engineered products and their uses. v) Define transgenic organisms. Give examples including applications for transgenic plants and animals. vi) What are possible applications of genetic engineering and biotechnology techniques, both present and future, to humans? 13. EVOLUTION a. Definition b. Darwian Evolution i) What is Natural Selection c. Some evidence of evolution d. Microevolution i) Antibiotic resistance in bacteria e. Objectives for Evolution i) Define evolution and explain the premises of evolution by natural selection as proposed by Charles Darwin. ii) List some of the supporting evidence in today s world for evolution. iii) Explain how bacteria demonstrate microevolution.

16 14. PROCESSES USED IN SCIENCE a. Scientific Method i) Steps (1) Support (not prove) or refute a hypothesis ii) Limitations (1) Science is based on evidence (a) Propositions which do not lead to testable predictions are not scientific iii) Define and contrast explanation, scientific hypothesis and theory (1) Contract scientists use of these words with their use in the general public b. Interpret a graph c. Metric System i) Conversitions within the system d. Microscope i) Proper use of light microscope e. Cell Structures f. Objectives for Processes Used in Science i) Describe the basic steps of the Scientific Method. ii) Apply the Scientific Method to solve a given problem. iii) Differentiate between negative and positive controls. iv) Describe and contrast science, pseudo-science, bad science, and scientific misconduct. v) Be able to make conversions from one unit to another in the Metric System by using the following prefixes: k, c, m and. vi) Correctly select and use the appropriate measurement tool. vii) Construct a best-fit straight line graph. viii) Be able to interpret and make inferences from a graph. ix) Identify the components of the compound light microscope and state the functions of those parts. x) Define the following & be able to use them correctly in reference to a microscope: resolution, magnification, contrast. xi) On a picture or a model of plant and animal cells, be able to identify the structures that are listed in Section 2 of this outline.