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Biological Sciences

Bio 1 Final Review EXAM 1 INFORMATION Characteristics of Life • Organization • The higher the complexity, the more properties emerge • There is a correlation between structure and function at all levels • Genetic Information • Cells are the most basic units of life, and they contain DNA • Energy and Matter • Energy in a system flows in one direction • Energy is lost with each transfer as heat • Interactions • Occur at every level • Evolution • About 1.4 million species on Earth right now are about 1% of all that have ever existed • A large number of species have many features in common • Explains how commonalities are shared because of a common ancestor The Scientific Method • 1. Observation • 2. Question • 3. Hypothesize • 4. Make a prediction • 5. Test the prediction • Evaluate with statistics and re-examine experiment • Methods of Reasoning • Inductive Reasoning - observations --> theory • Deductive Reasoning - theory --> observations • Controlled experiments compare an experimental and control group • The independent variable is the manipulated factor • The dependent variable is the factor measured for change Elements of Life • Essential elements are needed by organisms to be healthy and reproduce • 20-25% of the 92 naturally occurring elements • Trace elements are needed by organisms in minute quantities • Make up 1% of our bodies • Combining elements makes compounds • Matter has the natural tendency to move toward lowest possible potential energy • Elements are made of atoms; atoms are made of subatomic particles • Atoms combine to form molecules and ionic compounds • Protons and neutrons weigh 1 Dalton (1.7 x 10^(-24) g) • Chemical behavior of an atom depends on the number of electrons in the outermost shell • Some atoms of a given element have more neutrons (isotopes) • Radioactive isotopes - spontaneously decay in their nucleus and release particles and energy in the process; stable isotopes do not Chemical Bonds • Covalent Bonds • The sharing of a pair of valence electrons by 2 atoms • H2 and O2 are pure elements, not compounds • The stronger the electronegativity, the stronger it pulls the electron(s) toward itself • Ionic Bonds • Occur when the more electronegative atom completely strips electrons from its partner • Hydrogen Bonds • When an already bonded Hydrogen atom is attracted to a nearby electronegative atom • Van der Waals Interactions • Random instantaneous accumulation of electrons in one region • Chemical reactions make and break chemical bonds W ater and its • Water is the only substance that can be gas, liquid, or solid in nature • Emergent properties Behavior • Cohesive behavior • H2O molecules form H bonds with each other • Adhesion allows it to pass between organisms (ex: up plants’ roots) • Bonding of H2O molecule with a different molecule • Surface tension - how difficult it is to break or stretch the surface of a liquid • Temperature moderation • Moderates air temp by absorbing heat from warm air and releasing stored heat to cool air • Heat bank because it has little change to own temperature • When objects of different temperature come together, thermal energy (kinetic energy associated with random molecule movement) passes from warmer objects to cooler objects • Water has a high specific heat due to H bonding • Heat must be absorbed to break H bonds, and released to form H bonds • Expansion upon freezing • H2O becomes less dense as a solid • Versatility as a solvent • Hydrophilic and hydrophobic substances Carbon • Biological molecules are primarily based on C • Compounds containing C are organic compounds • Frequent bonding partners for C are H, O, and N • Multiple C atoms link to form chains; some form rings • Organic molecules with only C and H are hydrocarbons • Can release a relatively large amount of energy (potential E) • Chemical groups attached to C skeletons are important to molecular function • Hydroxyl (-OH), Carbonyl ( C=O), Carboxyl (OH-C=O), Amino (H-N-H), Sulfhydryl (-SH), Phosphate (O-P-O), Methyl (H-C-H) • All are hydrophilic, and can form H bonds, except sulfhydryl (hydrophobic) • FIGURE 4.9 • Phosphate groups are an important source of potential energy for cell function Large Molecules • Macromolecules are polymers built from monomers linked by covalent bonds • Polymers are synthesized through dehydration reactions and broken down by hydrolysis • 4 major classes: • Carbohydrates • Lipids • Proteins • Nucleic Acids Carbohydrates • Monosaccharides = monomers • Have 1 carbonyl group and multiple hydroxyl groups • Categorized based on location of carbonyl group (at end = aldose, in middle = ketose) or size of skeleton (3-7 carbons) • Glycosidic linkage = covalent bond produced by dehydration reaction; links polysaccharides • Storage polysaccharides (sugars for cells after hydrolysis) • Starch in plants, glycogen in animals • Structural polysaccharides (structure and function determined by monomer type, and position of glycosidic linkage • Cellulose in plant cell walls, chitin in animals Lipids • Hydrophobic molecules • Because of non-polar C-H bonds • Most important biologically are fats, phospholipids, and steroids • Fats are made from glycerol and fatty acids • Ester linkages form between carboxyl group in fatty acid and hydroxyl group in glycerol • Can be saturated or unsaturated • saturated fatsegetable oils are unsaturated fats, synthetically converted to • Phospholipids • Essential for cell membranes • Steroids • Characterized by C skeletons of 4 fused rings • Different steroids have particular chemical groups attached to the rings • Account for 50% of dry mass of most cells • Figures 5.13 & 4.14 • All constructed from the same set of 20 monomers (amino acids) • Amino acids are bonded by peptide bonds to form polypeptides • Figure 5.15 • Occurs via dehydration reaction • Structure of polypeptide determines function • Primary structure - a linear chain of amino acids • Slight changes can affect protein shape and function (ex: sickle-cell disease) • pH, temperature, and salinity can also lead to protein denaturation • Secondary structure - coils and folds are held together by H bonds • Can be alpha helixes or beta pleated sheets • Chaperonins assist in proper folding of other proteins • Tertiary structure - shape resulting from interaction between R-group side chains • Held together by Van der Waals interactions • H-bonds between polar side chains and ionic bonds between +/- charged side chains • Disulfide bridges form between cytosine monomers with -SH Origin and History of Life • Abiotic synthesis of small organic molecules • Bombardment by rocks and ice prevented seas from forming between 4.2-3.9 BYA • 1920s hypothesized the early atmosphere was a reducing environment where electrons were easily added to atoms to form organic compounds • In 1953, Miller and Urey shower abiotic synthesis of organic molecules in a reducing atmosphere IS possible • Suggestion that first organic compounds may have been synthesized by volcanos or deep-sea vents • Joining of these small molecules into macromolecules • Nucleotides = monomers for nucleic acids • RNA monomers can be spontaneously synthesized in the lab from simple abiotic molecules • Packaging of molecules into protocells • Replication and metabolism are key properties of life • Protocells may have been fluid-filled vesicles with membrane-like structure • Origin of self-replicating molecules • Self-replicating RNA - probably the first genetic material • RNA molecules called ribozymes can catalyze many different reactions 4 Eons Divided the Geologic Record, ad Phanerozoic • Phanerozoic lasted 1/2 billion years and encompasses multicellular eukaryotic life • Clock analogy • Oldest known fossils - 3.5 BYA • Only things on earth - 3.5-2.1 BYA • By about 2.7 BYA, O2 began to accumulate in the atmosphere • “O2 Revolution” - 2.7-2.3 BYA • Endosymbiotic theory proposes that mitochondria and plastids were formerly prokaryotes living in larger host cells • own DNA, and ribosomes are similarion is similar, they transcribe and translate their • Earliest organism (red algae) - 1.2 BYA • Other fossils - 1.8 BYA may have been multicellular eukaryotes • Larger, more diverse multicellulars in fossil record - 600 MYA • Edicarian biota - 600-535 MYA (soft bodied and grazed on ocean floor) • Cambrian Explosion - 535-525 MYA • DNA evidence suggests animal phyla diverged as early as 200 MYA - Continuation of Origin of Life • Table 25.1 and 25.8 • Fungi, plants, and animals began to colonize 500 MYA • Vascular tissue appeared in plants 420 MYA • Arthropods were among the first animals to colonize - 450 MYA • Tetrapods (4-limbed) - 365 MYA • Human lineage split from other primates 6-7 MYA • Homo sapiens originated - 195,000 YA Beginning of Cells and Microscopes • Robert Hooke (1665) coined the term “cell” • Anton van Leeuwenhoek (1674) first observed “animalcules” (protozoa) • Light microscopes pass visible light through specimens, then through glass lens • Electron microscopes focus beams of electrons through or on the surface of a specimen • 3 Key parameters in microscopy • Magnification - ratio of object’s real size to image size • Resolution - clarity of the image • Contrast - difference in brightness between dark and light areas of the image Prokaryotic vs. Eukaryotic Cells • Prokaryotic cells (bacteria and archaea) • DNA in nucleoid • No membrane-bound organelles • Smaller in size • Eukaryotic cells (protozoa, fungi, animals, and plants • DNA in nucleus • Membrane-bound organelles • Larger in size • Bigger (more volume) cells demand more nutrients Structure of Eukaryotic Cells • Animal Cells • Figure 6.8 • Plasma membrane composed of phospholipid bilayer • Membrane-bound nucleus containing DNA • Endoplasmic Reticulum packages materials (can be smooth or rough) • Ribosomes (on ER and in cytosol) are where protein synthesis occurs • Golgi apparatus packages proteins from the ER • Mitochondria is membrane bound; powerhouse of the cell • Lysosomes are vacuoles with enzymes that digest macromolecules • Peroxisomes help with the metabolism of incoming materials • Microvilli are projections that increase the surface area and increase the amount of material that can enter the cell • Cytoskeleton consists of microfilaments, intermediate filaments, and microtubules • Centrosomes are important in cell division • Some have flagellum to help them move • Plant Cells • Have cell walls that encase the plasma membrane; it has plasmodesmata that connect the innards of adjoining cells • Have chloroplasts that convert radiant energy to chemical energy and allow photosynthesis to occur • Have a central vacuole that stores water absorbed through the roots and other substances; gives plants rigidity Cell Parts • Nucleus • Contains most of the genes in the cell, and chromatin • Surrounded by nuclear envelope • Specled with nuclear pores • Nucleolus is in the very center - where rRNA is synthesized • Shape maintained by nuclear lamina • Ribosomes • Made of protein and rRNA • Consist of large and small subunit made of polypeptide folds • Carry out protein synthesis • Can be bound or free • Endomembrane System • Nuclear Envelope • Endoplasmic Reticulum • Golgi Apparatus • Lysosomes • Vacuoles Endomembrane • Nuclear Envelope System • Continuous to the ER • Endoplasmic Reticulum • Composed of tubules and sacs called cisterna • Inside of sacs = ER lumen • Smooth ER • and poisons, and stores calcium ionslism, adds hydroxyl groups to detoxify drugs • Rough ER • transport vesicles to Golgi Apparatus. produces membranes, and distributes • Golgi Apparatus • Shipping and receiving center of the cell; modifies the products of the ER • Manufactures certain macromolecules • Trans face = “shipping side” • Cis face = “receiving side” Endomembrane System Continued • Lysosomes • Sacs of digestive enzymes • Hydrolytic enzymes used to digest (hydrolyze) macromolecules (fats, polysaccharides, and nucleic acids) • Phagocytosis - • Autophagy • Vacuoles • Produced by ER and Golgi Apparatus • Food vacuoles formed by phagocytosis • Contractile vacuoles pump excess water out of cells • Central vacuoles hold organic compounds and water • Plasma Membrane • Amphipathic molecules have hydrophilic and hydrophobic parts • Fluid mosaics of lipids and proteins • Supported by freeze-fracture techniques • Can be affected by temperature • Warm temperatures restrain phospholipid movement; cool temperatures prevent tight Membrane Proteins & Carbohydrates • Membrane Carbohydrates • Glycolipids - membrane carbohydrates covalently bonded to lipids • Glycoproteins - membrane carbohydrates covalently bonded to proteins • Membrane Proteins • Peripheral proteins stick to the outside of the membrane • Integral proteins can go through the membrane • Functions • Transport • Enzymatic activity • Signal transduction • Cell-cell recognition • Intercellular joining • Attachment to the cytoskeleton and extracellular matrix Membrane Synthesis and T ransport • Rough ER --> ribosomes --> Golgi apparatus --> plasma membrane • Plasma membrane is selectively permeable • Polar molecules do not cross easily • Transport proteins regulate the passage of hydrophilic substances • Passive transport and osmosis • Diffusion • Tonicity - the ability of a surrounding solution to cause a cell to gain or lose water • Hypertonic (shriveled or plasmolyzed), Isotonic (normal or flaccid), Hypotonic (lysed or turgid) • Osmoregulation- control of solute concentration and water balance • Transport proteins are called electrogenic pumps • Voltage results in an electrochemical gradient • Electrical force - effect of membrane potential on ion’s movement T ransport Continued • solutesport occurs when active transport of a solute indirectly drives the transport of other • Bulk transport occurs by exocytosis (transport vesicles fuse with plasma membrane and plasma membrane)) and endocytosis (cell takes in macromolecules by forming vesicles from • Types of endocytosis • Phagocytosis - “cellular eating” • Pinocytosis - “cellular drinking” • Receptor-mediated endocytosis Energy and Work • Energy is the capacity to cause change • Metabolism is the totality of an organism’s chemical reactions • Catabolic pathways release energy by breaking down complex molecules into simpler compounds • Anabolic pathways consume energy to build complex molecules from simpler ones • Bioenergetics is the study of how organisms manage their energy resources • Kinetic energy is associated with motion • Thermal energy is kinetic energy associated with random movement of molecules • Potential energy is energy that matter has because of its location or structure • Chemical energy is potential energy available for release in a chemical reaction • Thermodynamics is the study of energy transformations occurring in a collection (system) of matter • Some systems are isolated from their surroundings (isolated/closed) • Open systems transfer energy and matter with their surroundings Laws of Energy • 1st Law of Thermodynamics • Energy cannot be created or destroyed, only transferred or transformed • 2nd Law of Thermodynamics • During every energy transfer or transformation, some energy is unusable and often lost as heat • Every energy transfer increases the entropy of the universe • Living things can cause order/disorder consistent with the laws of thermodynamics • There is an unstoppable trend towards entropy Free Energy • Spontaneous processes proceed without requiring the input of energy • Free energy (G) is a living system’s energy that can do work when temperature and pressure are uniform • delta G = deltaH - deltaS x T • Processes with a positive G require energy (non-spontaneous) • Free energy is the measure of a system’s instability, and its tendency to change to a more stable state • During spontaneous change, free energy decreases and stability in the system increases • Figures 8.5, 8.6 & 8.7 • Cells are not in equilibrium (they do 3 main kinds of work) • Chemical (ex: synthesis of polymers) • Transport (ex: transport substances across membranes) • Mechanical (ex: muscle contraction and cilia movement) • Cells manage energy resources by energy coupling (the use of an exergonic process to drive an endergonic process) mediated by ATP A TP • ATP is a renewable resource regenerated by the addition of a phosphate group to ADP • Catalysts speed up reactions by lowering activation energy barriers • Activation energy is the initial energy required to start a chemical reaction • Many enzymes require non-protein helpers (cofactors) for catalytic activity • Inorganic cofactors include metals in the ionic form • Organic cofactors include vitamins • An enzyme’s activity can be affected by temperature and pH • Certain chemicals selectively inhibit the action of specific enzymes (competitive and noncompetitive inhibitors) • Catalysis often occurs in the enzyme’s active site • The active site can lower the activation energy barrier by • Orienting substrates correctly • Straining substrate bonds • Providing a favorable microenvironment • Briefly covalently bonding to the substrate • Figure 8.16 Life requires the transfer of energy from outside sources to perform work • Figure 9.2 • Catabolic pathways yield energy by oxidizing organic fuels • The breakdown of organic molecules is exergonic • Several catabolic processes break down organic compounds to simpler molecules and the energy released is used for work • Fermentation - partial degradation of sugars that occurs without O2 • Aerobic respiration consumes organic molecules and O2 yields ATP • Anaerobic respiration is similar to aerobic respiration, but consumes other compounds (not O2) • Cellular respiration includes both aerobic and anaerobic respiration • The transfer of electrons during chemical reactions releases energy stored in organic molecules, which us ultimately used to synthesize ATP • Chemical reactions that transfer electrons between reactions = redox reactions • OILRIG • Electron donor = reducing agent, electron receptor = oxidizing agent Cellular Respiration • Electrons from organic compounds are usually first transferred to NAD+, a coenzyme, which functions as an oxidizing agent since it is an electron acceptor • Each NADH (reduced form) represents stored energy that is tapped to synthesize ATP • NADH passes the electrons to the ETC • Glycolysis breaks down glucose into 2 molecules of pyruvate • The Citric Acid Cycle completes the breakdown of glucose • Oxidative Phosphorylation accounts for most of the ATP synthesis because it’s powered by redox reactions (almost 90% of the ATP generated by cellular respiration) • Figure 9.6 • A smaller amount of ATP is generated by glycolysis and the citric acid cycle by substrate-level phosphorylation Figure 9.7 • For each molecule of glucose the cell makes up to 32 molecules of ATP (net gain) Glycolysis • “Splitting of sugar” breaks down glucose into 2 molecules of pyruvate • Occurs in cytoplasm with energy investment phase, and energy payoff phase • Occurs whether or not O2 is present !!! • Figures 8.8 & 8.9 • In the presence of O2, the pyruvate (product of energy payoff phase) enters the mitochondrion • Oxidation of pyruvate to Acetyl coA • Before citric acid cycle begins, pyruvate must be converted to acetyl coA • Acetyl coA links glycolysis to the Citric Acid Cycle The Citric Acid Cycle • “Krebs Cycle” • Completes breakdown of pyruvate to CO2 • Generates 1 ATP, 3NADPH, and 1FADH2 per turn • Has 8 steps, each catalyzed by a specific enzyme • The acetyl group of acetyl coA joins the cycle combining with oxaloacetate, forming citrate • The next 7 steps decompose citrate back to oxaloacetate, making the process a cycle • The NADH and FADH2 produced by the cycle relay electrons extracted from food to the ETC (part of oxidative phosphorylation process) • Figure 9.12 Oxidative Phosphorylation • Chemiosmosis couples electron transport to ATP synthesis • Produces most of the ATP • Following glycolysis and the citric acid cycle, NADH and FADH2 account for most of the energy extracted from food • Donate electrons to the ETC which powers ATP synthesis vis oxidative phosphorylation • The ETC is in the inner membrane (cristae) of the mitochindrion • Electrons drop in free energy as they go down the chain, and are finally passed to O2, forming H2O • The carriers alternate reduced and oxidized states as they accept and donate electrons • Figure 9.13 • The ETC does not generate ATP directly; it breaks the large free energy drop from food to O2 into smaller steps that release energy in manageable amounts Chemiosmosis • The energy coupling mechanism • The use of energy in a H+ gradient to drive cellular work • Electron transfer in the ETC cause proteins to pump H+ from the mitochondrial matrix to the inter-membrane space against their concentration gradient • H+ moves back across the membrane passing through ATP synthase • ATP synthase uses the exergonic flow of H+ to drive phosphorylation of ATP • Figures 9.14 & 9.15 • The energy stored in a H+ gradient across a membrane couples the redox reactions of the ETC to ATP synthesis • The H+ gradient = a proton motive force A TP • motive force --> ATP sequence: glucose --> NADH --> ETC --> proton- • making about 32 ATPergy in a glucose mol,cule is transferred to ATP • The rest of the energy is lost as heat • Figure 9.16 EXAM 2 INFORMATION Photosynthesis • The process that converts solar energy into chemical energy • Autotrophs - organisms that sustain themselves without eating anything from other organisms • “Producers” • Almost all plants are photo-autotrophs (use sunlight energy to make organic molecules) • Heterotrophs - obtain their organic material from other organisms • “Consumers” • Chloroplasts are the sight of photosynthesis in plants • Leaves are the primary location wither it occurs • Chloroplasts are found mainly in the mesophyll (interior tissue) of a leaf • Figure 10.4 - anatomy of a leaf and chloroplast • 6CO2 + 12H2O +light energy -----> C6H12O6 + 6H2O • molecules and releasing O2 as a byproduct - Figure 10.5electrons of H into sugar • Redox and endergonic process Stages of Photosynthesis • Light reactions - the “photo” part • Occur in the thylakoids • Split H2O • Release O2 • Reduce NADP+ to NADPH • Generate ATP from ADP by photophosphorylation • Convert solar energy to the chemical energy of ATP and NADPH • Dark reactions (the Calvin cycle) - the “synthesis” part • Occurs in the stroma • Forms sugar from CO2 using ATP and NADPH • Begins with carbon fixation, incorporating CO2 into organic molecules • Figure 10.6 Pigments and Wavelengths in • Figure 10.7s to Photosynthesis • The shorter the wavelength, the higher the energy • Photosynthetic pigments are light receptors; different pigments absorb different wavelengths • Wavelengths that are not absorbed are reflected or transmitted • Figure 10.8 • Chlorophyll a - main photosynthetic pigment • Acessory pigments (ex: chlorophyll b) - broaden the spectrum used for photosynthesis • Figure 10.11 • Carotenoids absorb excessive light that would damage chlorophyll • A spectrophotometer measures a pigment’s ability to absorb various wavelengths • Figure 10.9 • Absorbtion spectra plot a pigment’s light absorption vs. wavelength • Figure 10.10 • Theodor Engelmann (1883) demonstrated the action spectrum (profiles the relative effectiveness of different wavelengths of radiation in driving a process) Photosystems • Organize chlorophyll molecules in the thylakoid membrane • Consist of light-harvesting complexes (pigment molecules bound to proteins) which transfer the energy of photons to the reaction center • Figure 10.13 • Photosystem II • Functions first • Best at absorbing a wavelength of 680nm; reaction center is PS680 • Photosystem 1 • Best at absorbing wavelengths of 700nm; reaction center is PS700 2 Routes for Electrons • Linear Flow • Primary pathway involving both PSII and PSI, and produces ATP and NADPH using light energy • Figures 10.14 & 10.15 • Cyclic Flow • No O2 is released • Generates surplus ATP • Figure 10.16 Chemiosmosis in Chloroplasts vs. Mitochondria • Mitochondria transfer chemical energy from food toTP • Chloroplasts transform light energy into chemical energy oTPA • Figure 10.17 Ps Summary • ATP and NADPH are produced on the side facing the stroma, where the Calvin Cycle takes place • Figure 10.18 • Light reactions generate ATP and increase the potential energy of electrons by moving them from H2O to NADPH • The Calvin Cycle uses chemical energy of ATP and NADPH to reduce CO2 to sugar • The Calvin Cycle regenerates its materials after molecules enter and leave the cycle (like the Citric Acid Cycle does) • The cycle builds sugar from smaller molecules by using ATP • Figure 10.19 Cell Division • Cell division is an integral part of the cell cycle • Most cell division results in genetically identical daughter cells • Exception is meiosis • Figures 5.23 and 5.24a • Nucleoside = sugar + nitrogenous base • Nucleotide = nucleoside + phosphate group • Nucleotides come together to form chains with neighboring phosphate groups (forms 5’ -> 3’ end, where the 3’ end is ready to bond) • Bases: pyrimidines (single C ring - C, T, U) & purines (double C ring - A, G) • Bases attach to pentose sugar (deoxyribose or ribose) • 2 structures of DNA double helix run antiparallel • Nitrogenous bases in DNA pair up and for H-bonds • Complementary base-pairing DNA in Cells • All DNA in a cell constitutes the cell’s genome • DNA molecules are packaged into chromosomes • Figure 12.3 • Eukaryotic chromosomes consist of chromatin • Somatic cells have 2 sets of chromosomes • Gametes have half the number of chromosomes in somatic cells • In preparation for cell division, DNA is replicated and the chromatin condense • Each duplicated chromosome has 2 sister chromatids • The centromere = the narrow “waist” of the duplicated chromosome • Figures 12.4 & 12.5 • Meiosis results in nonidentical daughter cells that have only one set of chromosomes The Cell Cycle • Consists of 2 major phases • Mitotic (M) phase - mitosis & cytokinesis • Interphase - cell growth and copying of chromosomes in preparation for cell division • 90% of the cell cycle • g1, s, and g2 phases • The cell grows during all 3 phases, but chromosomes are duplicated only during the s phase • g1 (“first gap”) --> s (DNA synthesis) --> g2 (“second gap”) --> mitosis --> cytokinesis • Walter Flemming (1882) developed dyes to see chromosomes go through mitosis • Figure 12.6 • 5 phases Mitosis • Figure 12.17 • Prophase - chromatin condense • Prometaphase - sister chromatids form • Metaphase - chromatids line up and are connected to mitotic spindles • Anaphase - chromatids are pulled apart • Sister chromatids separate and move along the kinetochore microtubules towards opposite ends of the cell • Telophase - cell splits and forms 2 daughter cells • Genetically identical daughter nuclei form at opposite ends of the cell The Mitotic Spindle • Structure made of microtubules and controls chromosome movement • Assembly of spindle microtubules in animal cells begins in centrosome • prometaphaseeplicates during interphase and forms 2 that migrate to opposite ends during prophase and • An aster (radial array of short microtubules) extends from each centrosome • Includes centrosomes, spindle microtubules, and asters • Figure 12.8 • Kinetochores are protein complexes associated with centromeres • Figure 12.9 • Microtubules can begin to get shorter around centrosome • Cytokinesis begins during anaphase or telophase and the spindle eventually disassembles Binary Fission • Prokaryote cell division • Chromosome replication begins, replication continues, replication finishes, and two daughter cells result • Figure 12.12 • Mitosis probably evolved from binary fission • Figure 12.13 Mendel and Pea Plants • Character - a specific property of an organism that is inherited • Trait - each variant of a particular character • Table 14.1 • Applied quantitative methods, not just descriptions • Used an experimental approach • He developed true-breeding lines; all individuals of the true-breeding line express the same phenotype • Phenotype can be physical or chemical expression of genes • He ensured true-breeding for 2 years before beginning experiment • Tested the “blending inheritance hypothesis” and proved it false • Crossed true-breeding plants with contrasting traits • passed from generation to generation the characters are determined by heritable factors Findings from Mendel’s • Alleles - alternative versions of genes; each gene is at the same locus on homologous chromosomes, but vary slightly in nucleotide sequence • Figure 14.4 • each characterherits 2 copies (alleles) of a gene from each parent for • The dominant allele determines an organism’s appearance (masks appearancele); the recessive allele has no noticeable affect on • Law of Segregation - the 2 alleles for a heritable character separate gametesch other during gamete formation and end up in different • If different alleles are present, half of the gametes get one allele, the other half get the other Mendel’s Laws • Law of Segregation • Figure 13.8 • Segregation of alleles is a chance event • Law of Independent Assortment • 2 or more genes sort independently during gamete formation • Each pair of alleles segregates independently of other alleles • Only works if alleles are on different pairs of homologous chromosomes • Basis is meiosis • Depends on how homologous pairs line up • Results in genetic recombination • Reflect the probability that apply to rolling dice; probability is expected frequency Crosses • Monohybrid Cross • Multiplication rule: 1 event does not affect the probability that the other event will occur (Pthis & Pthat = P1xP2) • Addition rule: Mutually exclusive events cannot occur simultaneously - if one event happens, the other cannot (Pthis or Pthat = P1xP2 + P3xP4) • Test Cross • Individual with dominant phenotype mated with homozygous recessive • Dihybrid Test Cross • Mates a homozygous recessive at both loci • Punnett Squares Chromosomes and Inheritance • Chromosomes are the basis of inheritance • Chromosomal Theory of Inheritance (1902) • Genes have specific loci on chromosomes • Chromosomes undergo segregation and independent assortment • Figure 15.2 • location of “factors” with fruit fly studyt chromosomes are • Findings provided support for chromosome theory of inheritance • Genes on sex chromosomes exhibit unique inheritance patterns • Figure 15.4 Sex Chromosomes • Autosomes (not sex chromosomes) are homomorphic (same shape) and homologous (pair up) • 1 pair of chromosomes • Carry sex-determining genes • Heteromorphic • Act homologous during meiosis • They synapse • Can have crossing-over between specific regions • Also contain sex-linked genes not having to do with sex determination Sex Determination in Humans • Males (heterogametic) XY • Y chromosome carries SRY gene required o make a male (discovered in 1990) • Every allele on male’s X is expressed, regardless of dominance • VERY IMPORTANT PHENOTYPICALLY • Females (homogametic) XX • Female phenotype is determined in absence of Y • 1X in each cell is inactivated during embryonic development • Inactive chromosome = Barr body (dense, and lies on inside of nuclear envelope) • Active X chromosome is indistinguishable from other autosomes • Ex: X inactivation in tortoiseshell cats • Human X chromosome contains about 1,100 genes • X chromosomes have as many genes as autosomes of the same size • X chromosomes don’t determine sex; contain many loci required in both sexes Linkage • Violates Mendel’s principle of independent assortment • Genes that are linked are close together on the same chromosome • How does it occur? • During prophase I, crossing over can occur between non-sister homologous chromatids • We can determine linkage with dihybrid test crosses • Unlinked: F1 has 50% parental, 50% recombinant gametes • Completely Linked: 100% parental, 0% recombinant gametes • Incompletely linked: >50%, <100% parental, >0%, <50% recombinant • Ways to get genetic recombination • With unlinked genes through independent assortment • With linked genes through crossing over Role of DNA in Heredity • First discovered by studying bacteria and viruses (1928 - Frederick Griffith) • Figure 16.2 • Transformation is a change is genotype and phenotype due to assimilation of external DNA by a cell • Alfred Hershey and Martha Chase (1952) showed DNA, not proteins are genetic material responsible for heritable changes • Erwin Chargaff (1950) found the base composition of DNA varies between species, of C&Gr each species the proportion of A&T are roughly equal, as are the proportion • Now known as Chargaff’s rules • Wilkins and Franklin used x-ray crystallography to produce a picture of a DNA molecule • Franklin indicated the 2 strands in DNA, and concluded the sugar-phosphate backbones were on the outside • Watson and Crick (1953) published a molecular model for DNA DNA Models of Replication • Suggested to be semi-conservative • Semi-Conservative model • Conservative Model - parental DNA separates, copies, and realigns • Dispersive Model - DNA strands separate, and bits and pieces copy in different places; daughter copies have bits of parent strands • Figure 16.10 • Mendelson and Stahl (1958) successfully test predictions from conservativeA models and find that the true model is semi- DNA Replication • Begins at the origin of replication • Can be very accurate • Replication forks are at the end of the replication bubble • Can have multiple origins and multiple bubbles in one cell • Origin of replication in a eukaryotic cell Figure 16.12 • Proteins participate in the start of DNA replication Figures 16.13 & 16.14 and form a “DNA replication machine” which may be stationary during replication • Helicase untwists the DNA molecules • Single -strand binding proteins prevent it from rebinding • Topoisomerase relieves stress from untwisting and prevents breakage • Primase constructs on RNA primer • DNA polymerase catalyzes synthesis of new DNA • Can only add nucleotides to 3’ end • New DNA strand can only elongate in the 5’ --> 3’ direction • Synthesizes a leading strand by moving toward the replication fork • Must work in the direction away from the replication fork to synthesize the lagging strand; series of “Okazaki fragments” joined together by DNA ligase Figure 16.16 • Figure 16.17 antiparallel elongation Proofreading and Repairing of DNA • DNA polymerases proofread newly made DNA and replace any incorrect nucleotides • Mismatch repair of DNA is done by repair enzymes that correct errors in base pairing • DNA can be damaged by exposure to harmful chemicals or physical agents • DNA can also undergo spontaneous changes • generationsanges can be permanent and passed on to • Mutations are ultimately a source of genetic variation that natural selection can operate on What does a Sequence of DNA in Nucleotides Actually Say? • Gene expression is the process of DNA directing the synthesis of proteins • Genes provide the instructions for making proteins, but don’t make proteins directly • Proteins = the link between genotype and phenotype • The “bridge” between DNA and proteins is RNA • Processes of gene expression • Transcription - synthesis of RNS using information in DNA • DNA is transcribed into RNA (DNA --> mRNA) • Translation - synthesis of a polypeptide using the information in mRNA • Occurs in ribosomes where amino acids are linked into a polypeptide chain • In prokaryotic cells • Transcription and translation occur in cytosol; translation of mRNA can begin before transcription ends • In eukaryotic cells • Transcription occurs in nucleus; nuclear envelope separates transcription and translation T riplet Code • 4 nucleotides, but 20 amino acids that can be coded for • 3 nucleotides is the smallest number that can code for all amino acids • Each codon (3 nucleotides) specifies an amino acid • All 64 codons deciphered by mid-1960’s • translation code for amino acids, 3 code for “stop” signals for • More than one codon can specify a particular amino acid, but no AMBIGUOUS)ifies more than 1 amino acid (REDUNDANT BUT NOT Molecular Components of • RNA synthesis is catalyzed by RNA polymerase • RNA polymerase separates DNA strands and joins RNA nucleotides • RNA is complementary to DNA template strand • A promoter signals the transcription starting point Stages of • Initiation T ranscription • In eukaryotic cells • Promoter includes a specific sequence (TATA box) • Transcription factors bind to the promoter region, and then RNA polymerase an come to begin unwinding DNA • In prokaryotic cells • No TATA box, no need for transcription factors • Elongation • RNA polymerase untwists DNA double helix 10-20 bases at a time • Nucleotides added to the 3’ end of growing RNA molecule • A gene can be transcribed by several RNA polymerases simultaneously • Termination • Bacteria have a “terminator” sequence in DNA that signifies polymerase to detach and release transcript • Eukaryotes have a “polyadenylation signal sequence” in DNA • Eukaryotic cells modify RNA after transcription ( RNA processing) • Some interior parts of the molecule are cut out, and others spliced together • 5’ end receives a modified nucleotide (guanine) - 5’ cap; 3’ end gets a poly-A tail (50-250 adenine nucleotides) • Facilitates export of mRNA from nucleus to cytoplasm and protects mRNA from hydrolytic enzymes RNA Splicing • Removes large, non-coding parts of pre-mRNA called intervening sequences (introns) • Other regions are eventually expressed (exons) and usually translated into amino acid sequences • Figure 7.11 • RNA splicing removes introns and joins exons • RNA splicing is carried out by spliceosomes • Consist of various proteins and several small nuclear ribonuclear proteins (snRNPs) that recognize splice sites and help catalyze splicing Figure 17.12 • Ribozymes are RNA molecules that function as enzymes • 3 properties of RNA allow it to function as an enzyme • It can form a 3D structure because of its ability to base-pair with itself • Some bases in RNA contain functional groups that may participate in catalysis • RNA may H-bond with other nucleic acid molecules (DNA or RNA) Molecular Components of • tRNAs transfer amiTranslation a growing polypeptide in a ribosome • Figure 17.14 • Molecules of tRNA are not identical • Each carries a specific amino acid on one end and an anticodon on the other end • Anticodon base-pairs with the complementary codon on mRNA • Figure 17.15 • Because of H-bonds, tRNA twists and folds into an L-shaped 3D molecule • tRNA must first be matched with the right amino acid • Done by the enzyme aminoacyl tRNA synthase • Figure 17.16 • tRNA codon must also match the correct mRNA codon • Only 45 types of RNA exist, but there are 61 codons • Some tRNAs can bind to more than one codon • Flexible pairing (“wobble”) occurs most often in synonymous codons for one amino acid • Ribosomes couple tRNA anticodons with mRNA codons in protein synthesis Ribosomes • Made of 2 ribosomal subunits and rRNA • Ribosomes of bacteria and eukaryotic cells are similar but: eukaryotic ribosomes are larger, have a slightly different molecular composition, and have 4 rRNA molecules while bacterial ones only have 3 • Have 3 binding sites for tRNA • P site - holds the tRNA carrying to growing polypeptide chain • A site - holds the tRNA carrying the next amino acid to be added to the chain • E site - exit site where discharged tRNA leaves the ribosome • Figure 17.17 Stages of T ranslation • Initiation • Requires energy (GTP) • Small ribosomal subunit binds to mRNA and initiator tRNA with start codon AUG (methionine) • Figure 17.18 • Initiation factors (proteins) being all these components together • Elongation • Requires energy (GTP) • 3 steps: codon recognition, peptide bond formation, translocation • Figure 17.19 • Termination • Occurs when stop codon in the mRNA reaches the ribosome’s A site • Release factor causes addition of H2O molecules instead of amino acids • Figure 17.20 Bacterial Gene Expression • Changes in environmental conditions can alter gene expressions that facilitate their survival • A bacterial cell can regulate the production of enzymes by feedback inhibition or gene regulation • Figure 18.2 • A basic mechanism for the control of gene expression in bacteria is the operon model • Describes the coordinated expression of a group of genes by a single “on-off switch” • The regulatory “switch” is a segment of DNA called an operator • to genes clustered togetherin a promoter region and contr
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