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Biology 1406 Chapter Reviews for HCC This is a GENERAL review. The exam may contain, but is not exactly limited to terms/concepts described below General To know terms and definitions. Scientific method, controls, osmosis, diffusion, hydrophobic, hydrophilic, chemical bonds, properties of water. Structure and properties of proteins, carbohydrates, lipids, nucleotides. Levels of protein folding that produce a mature protein, including the types of chemical bonds that stabilize each level. Properties of good experimental design, including the purpose of controls and numbers of replicates. Chemistry To know terms and definitions. Matter, elements, compounds (incl. emergent properties of a compound). Essential and trace elements. Four main elements in human body. Atomic mass (incl. units), atomic structure. Isotopes (incl. radioactive isotopes). Energy, potential energy, electron shells (energy levels), valence shells/electrons. Element valence, chemical properties related to atomic structure. Chemical bonds (all types), electronegativity. Double-triple covalent bonds. Ionic compounds (salts). Chemical reactions, chemical equilibrium. Water To know terms and definitions. Structure of water molecule. Hydrogen bonds. Four emergent properties of water. Evaporative cooling/heat of vaporization. Energy, kinetic energy, heat, temperature. Calories, kilocalories. Specific heat. Water/ice density, hardness. The temperature of the highest water density. Solvents, solutes. Mole, molarity, molecular mass, concentration. Aquatic solutions. pH, acids and bases, pH scale, buffers, ocean acidification, acid precipitation. Organic chemistry To know terms and definitions. Origin of life and Miller-Urey experiment. Chemical properties of carbon, making it important. Different patterns of carbon skeletons. Hydrocarbons. 3 types of isomers. Functional groups and their properties. Large biological molecules To know terms and definitions. Macromolecules and polymers. Carbohydrates: the main groups of carbohydrates, their properties and role. Polysaccharides – cellulose, starch, glycogen, chitin. Lipids. Saturated and unsaturated fatty acids; phospholipids and steroids. The role of phospholipids in cellular membrane. Proteins. Biological role and functions of proteins. Amino acids. Four levels of protein structure. Denaturation and renaturation. Nucleic acids and their components. Structure of nucleotides. Structure of DNA and RNA, it’s relation to hereditary information. The cell To know terms and definitions. Microscopy (different types of microscopes and their usage). Prokaryotic cells vs. eukaryotic cells. Plant cells vs. animal cells. Structures within eukaryotic cell and their function: endomembrane system, mitochondria and chloroplasts. The evolutionary origin of mitochondria and chloroplasts. The structure of mitochondria and chloroplasts. The cytoskeleton: components and their function. Cilia vs. flagella. Extracellular components and their role in intra- and intercellular activities. Cell junctions in animal and plant cells. Membrane structure and function To know terms and definitions. Fluid mosaic model of cellular membranes. The role of cholesterol in regulation of membrane’s fluidity. Membrane proteins and their function (six main functions). Selective permeability of membranes. Diffusion, passive and active transport across the membrane. Concentration gradient. Osmosis. Tonicity. The role of membrane proteins in passive and active transport. Examples of active transport: the sodium-potassium pump and the proton pump. Understanding of electrochemical gradient. Cotransport. Bulk transport: exocytosis and endocytosis. The three types of endoytosis. Metabolism To know terms and definitions. Catabolic and anabolic pathways. Different forms of energy and their transformation. Understanding of thermodynamics and its two laws. Entropy. Exergonic and endergonic reactions. Equilibrium. Energy coupling: the use of Exergonic reaction to drive an endergonic one. ATP/ADP cycling. Enzymes as biological catalysts. The activation energy (EA) and the role of enzymes in lowering of EA. Substrate specificity of enzymes: enzyme-substrate complexes, active site. Effect of different factors (e.g., temperature, pH, salinity) on enzyme activity. Competitive and noncompetitive inhibitors of enzymes. Understanding of allosteric regulation of enzymes. Feedback inhibition. Cellular respiration and fermentation To know terms and definitions. Energy flow and chemical recycling in ecosystems. The relationship between photosynthesis and cellular respiration. Catabolic pathways and production of ATP using organic fuel. Aerobic respiration vs. fermentation. Redox reactions. Reduction and oxidizing in Chemistry. The chemical equation of cellular respiration. The stages of cellular respiration: 1) glycolysis, 2) pyruvate oxidation and citric acid cycle, and 3) oxidative phosphorylation (electron transport and chemiosmosis). The location and yield at each stage. Electron transport chain. ATP production in each stage of cellular (aerobic) respiration. ATP production at fermentation and anaerobic respiration. The comparison of fermentation, anaerobic, and aerobic respiration. The versatility of catabolism. Photosynthesis To know terms and definitions. Autotrophs and heterotrophs. Photoautotrophs. The importance of photosynthesis as conversion of light energy to the chemical energy. The sunlight as ultimate source of energy on the Earth. Chloroplasts as the sites of photosynthesis in plants. Where chloroplast are located in the leaf. The structure of chloroplasts. The chemical equation of photosynthesis. Two main stages of photosynthesis: light reactions and Calvin cycle. The role and location of light reactions. The nature of sunlight: wavelength, electromagnetic spectrum, photons. Photosynthetic pigments as light receptors. Photosystem II and I. Understanding of linear and cyclic electron flow. Chemiosmosis in chloroplasts vs. chemiosmosis in mitochondria. The Calvin cycle as consumer of chemical energy from light reactions. Carbon fixation. Output of each Calvin cycle’s turnover. Photorespiration. Photosynthetic adaptations. Understanding of photosynthesis’s peculiarities in C4 plants and CAM plants. Cell communication To know terms and definitions. Conversion of external signals into responses within the cell. Signal transduction pathway. Local and long-distance signaling. The three stages of cell signaling: reception, transduction, and response. Ligands. The role of proteins in signal transduction pathways. First messengers and second messengers. Fine-tuning of the response: signal specificity and amplification. The role of scaffolding proteins in signal transduction. Apoptosis. The cell cycle To know terms and definitions. The cell division as an integral part of the cell cycle. Genome, chromosomes, somatic cells and gametes. Eukaryotic cell division. Phases of cell cycle: interphase and mitotic phase. Phases of interphase and mitotic phase. The older division of mitosis into 4 stages and newer division of it into 5 stages. Events in each stage of mitosis (the first phase in mitotic phase). Cytokinesis as the second phase of mitotic phase: cytokinesis in plant and animal cells. Binary fission in Bacteria. The evolution of mitosis. The cell cycle control system. G1, G2, and M checkpoints. Growth factor, anchorage dependence, and density-dependent inhibition. Loss of cell cycle controls in cancer cells. Transformation, tumors, metastasis. Meiosis and sexual life cycles To know terms and definitions. Sexual reproduction vs. asexual reproduction. Genes inheritance. Life cycle vs. cell cycle. Karyotype. Diploid cell vs. haploid cell. Chromosome sets in human life cycle. Alternation of generations in sexual life cycles – three main types. The stages of meiosis. Meiosis vs. mitosis: similarities and differences. The sources of genetic variation and its evolutionary significance. Mendelian Genetics To know terms and definitions. Character, trait, true-breeding, hybridization. Mendel’s experimental approach and his two main laws of inheritance: the law of segregation and the law of independent assortment. Alleles, loci, homo-, heterozygous organisms, geno-, phenotype, testcross, Punnett square. Mono- and dihybrid cross. The laws of probability. The multiplication and addition rules. Solving genetic problems. Extending Mendelian Genetics (incomplete dominance, codominance, multiple alleles, pleiotropy, epistasis, polygenic inheritance). The environmental impact on phenotype. Pedigree analysis. Recessively and dominantly inherited disorders. Genetic testing and counseling. Contemporary Genetics To know terms and definitions. Chromosome theory of inheritance. Morgan’s experiments with Drosophila melanogaster. Sex-linked genes and the chromosomal basis of sex. X-inactivation in female mammals. Calico (tortoiseshell) cats. Linked genes and their tendency to be inherited together. Genetic recombination. Crossing over. Genetic maps, map unit. Abnormalities in chromosome number. Meiotic nondisjunction. Aneuploidy vs. polyploidy. Alterations of chromosome structure: deletion, duplication, inversion, translocation. Human disorders due to chromosomal alterations (syndromes). Down syndrome, Klinefelter syndrome, Turner syndrome. The molecular basis of inheritance To know terms and definitions. The history of search for the genetic material. Griffith experiment, Hershey-Chase experiment, Chargaff rules, Wilkins-Franklin’s works, and finally Watson-Crick discovery of DNA structure. Double helix DNA model, antiparallelism of DNA strands, monomers of DNA (nucleotides), the structure of nucleiotide(s). Base pairing of nitrogenous bases in DNA molecule. Semiconservative model of DNA replication. The process of DNA replication. Terminology (leading and lagging strands, Okazaki fragments, etc.), enzymes involved, proofreading and repairing DNA, telomeres. Packing of DNA molecule (chromatin structure). From gene to protein (protein synthesis) To know terms and definitions. The flow of genetic information and gene expression. Garrod’s ideas about gene expression. Understanding of Beadle and Tatum’s experiments with Neurospora. The development of the idea “one gene – one polypeptide”. Transcription and translation. mRNA. The genetic code: triplets of nucleotides in DNA. Codons in mRNA. Coding of amino acids, start and stop codons. The codon table for mRNA. The transcription process: location, stages, enzymes involved. Transcription unit, promoter, terminator. Synthesis of mRNA: initiation, elongation, termination. mRNA processing: 5’ cap, poly-A tail. RNA splicing. Introns and exons. Ribozymes. The translation process: location, stages, enzymes involved. tRNA structure and anticodons. Ribosome structure and three binding sites (P site, A site, and E site). Stages of translation: initiation, elongation, and termination. Polyribosomes and their importance. Mutations and their effect on protein structure and function. Point mutations. Silent mutations. Missense and nonsense mutations. Frameshift mutations. Mutagens. Gene expression in Bacteria, Archaea, and Eukarya. More detailed definition of a gene. Regulation of gene expression To know terms and definitions. Regulation of transcription in Bacteria: the effect of environment. The basic concept (and definition) of operon. Operator, repressor. Repressible and inducible operons. Inducers. The lac operon as the classic example of inducible operon. The stages of eukaryotic gene expression. Post-transcriptional (RNA processing, mRNA degradation, etc.) and post-translational (degradation of a protein by a proteasome) regulation. The development of different cell types in a multicellular organism. Differentiation and morphogenesis. Induction. Determination. Homeotic genes. Genetic changes affect cell cycle control and cause cancer. Viruses To know terms and definitions. The definition of a virus as a subcellular unit, which exists in a shady area between lifeforms and chemicals. The discovery of tobacco mosaic virus. Structure of viruses. Phages, bacteriophages. Replication of viruses. Lytic cycle and lysogenic cycle. Stages of viral replicative cycle. Virulent and temperate viruses (phages). Prophage. Enveloped viruses. Retroviruses, reverse transcriptase. HIV and AIDS. Origination of viruses. Viroids and prions. Vaccine and vaccination. Emerging viruses, epidemies and pandemies. Biotechnology To know terms and definitions. Recombinant DNA, biotechnology, bioengineering. Plasmids, gene cloning. Restriction enzymes and how do they work. Restriction fragments, sticky ends, DNA ligase involvement. Cloning vectors. The process of gene cloning. DNA libraries. Genomic library. Complementary DNA (cDNA) and cDNA library. Amplifying DNA, polymerase chain reaction (PCR). Gel electrophoresis and it’s modification – Southern blotting. Understanding of DNA sequencing principle. Cloning of plants; totipotent cells. Cloning of animals: nuclear transplantation. Stem cells of animals. Embryonic (pluripotent) and adult stem cells. The practical applications of DNA technology. Gene therapy. Transgenic animals, “pharm” animals. Genetically modified organisms.