General Biology Lecture Notes copy
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General Biology Lecture Notes copy

Course Number: BIOLOGICAL 101, Spring 2011

College/University: Rutgers

Word Count: 23418


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General Biology Lecture 1: Chapter 4 Organization of the Cell I. Cell A. smallest unit to carry out all activities associated with life (maintenance, growth, & division) B. Viruses are acellular because they cannot independently perform metabolic activities C. Cell Theory provides consistent explanation for all verifiable data relating to living things 1. Cells are basic units of organization & function...

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Biology General Lecture 1: Chapter 4 Organization of the Cell I. Cell A. smallest unit to carry out all activities associated with life (maintenance, growth, & division) B. Viruses are acellular because they cannot independently perform metabolic activities C. Cell Theory provides consistent explanation for all verifiable data relating to living things 1. Cells are basic units of organization & function in all living organisms 2. All cells come from other cells. All living cells have evolved from a common ancestor II. Cell Organization & Size A. Relationship between cell organization & homeostasis - Cells have many organelles, internal conditions, & have to work constantly to restore & maintain these to enable their biochemical mechanisms to function. 1. homeostasis appropriate internal environment 2. Plasma membrane - surrounds the cell - separates cell from external environment - allows exchange of materials with environment - allows chemical composition of cell to be different from that outside the cell B. Relationship between cell size & homeostasis 1. Measurement -(mm) millimeter = 1/1,000 of meter = 10-3 meter -(m) micrometer = 1/1,000,000 of meter = 10-6 meter -(nm) nanometer = 1/1,000,000,000 of meter = 10-9 meter -(mm) millimeter = 1/1,000 of meter -(m) micrometer = 1/1,000 of millimeter -(nm) nanometer = 1/1,000 of micrometer 2. Surface to Volume Ratio -ratio of plasma membrane (surface area) to cell's volume -regulates passage of material into & out of cell -critical factor in determining cell size -as cell becomes larger, its volume increases at a greater rate than its surface area, decreasing surface-to-volume ratio -a long, thin cell increases ratio & allows it to be more efficient to carry out activities - microvilli, projections of plasma membrane, increase surface area for absorbing nutrients Ex. - Nerve cells need to communicate with each other; have long extensions Ex 2. Epithelial cells stacked on one another become "barrier cell" e.g. skin Ex. 3. Flagella allows sperm to "swim" III. Methods For Studying Cells A. Microscopes 1. Light microscopes minimal resolution (max is 1,000X) a. Phase contrast light microscope can be used to view stained or living cells, but at relatively low resolution 2. Electron microscope superior resolution power & magnification, since electron beams have very short wavelengths a. Transmission electron microscope (TEM) produces a high-resolution image that can be greatly magnified -looks for a specific reaction -electron beam passes through the specimen -resulting image is a thin cross section of the cell b. Scanning electron microscope (SEM) provides a clear, 3-D view of surface features -Magnification ratio of the size of the image seen to the actual size -Resolution distinguishing of fine detail; minimum distance between 2 points that can be seen separately & clearly -If wavelength decreases, resolution increases B. Cell fractionation -purifies organelles to study function of cell structures -can be studied in isolated environment a. Centrifugation Due to centrifugal force, large or very dense particles move toward the bottom of a tube & form a pellet b. Differential centrifugation Cell structures can be separated into various fractions by spinning the suspension at increasing revolutions per minute. Membranes & organelles from the resuspended pellets can then be further purified by density gradient centrifugation IV. Prokaryote vs. Eukaryote A. Prokaryote -ex. bacteria & archea -no nucleus have a nuclear area -most have cell walls -all have ribosomes -have no internal organization -have storage granum hold glycogen, lipid, or phosphate compounds -have flagella B. Eukaryote (animal) -membrane-enclosed nucleus (DNA) -cytoplasm contains organelles -cytosol (fluid component) -cytoskeleton maintains shape & integrity of cell -highly organized: control center (nucleus), transportation system (E.R.), factories (mitochondria), defense system (lysosomes) -Different organelles needed by different cells -volume of eukaryotic cell is approximately 1,000X the volume of prokaryotic cell C. Eukaryote (plant) -rigid cell walls -large vacuoles -no centrioles -chloroplasts (important in photosynthesis) V. Cell Membranes -Divide cell into compartments -Vesicles transport materials between compartments -Important in energy storage & conversion A. Endomembrane systems -Nucleus, ER, Golgi, lysosomes, vesicles, vacuoles (PM participates) -not mitochondria, chloroplasts separate functions, own DNA VI. Cell Nucleus - Control center of cell - genetic information coded in DNA - Produces messenger RNA (mRNA) A. Nuclear envelope - Double membrane B. Nucleoplasm -contents of cell nucleus C. Nuclear lamina -fibrous network of protein filaments D. Nuclear pores -communicate with cytoplasm, consist of protein complexes E. Chromatin -DNA condensed for cell division visible in dividing cells F. Nucleolus -ribosomal RNA synthesis -consists of mRNA & protein -ribosome subunit assembly VII. Organelles in the Cytoplasm A. Ribosomes 1. either free in the cytoplasm or attached to membranes 2. composed of 2 subunits that assemble polypeptides B. Endoplasmic Reticulum - Network of folded membranes in cytosol 1. Smooth E.R. - lipid synthesis - calcium ion storage - detoxifying enzymes 2. Rough E.R. - ribosomes on outer surface - protein assembly C. Protein Synthesis 1. Polypeptides synthesized on ribosomes are inserted into E.R. lumen 2. Sugars are added, forming glycoproteins 3. Transport vesicles deliver glycoproteins to cis face of Golgi complex 4. Processing, modification, & sorting by the Golgi complex 5. Glycoproteins move to trans face, where they are packaged into transport vesicles 6. Transportation to specific destinations (when protein is folded properly) - when not folded properly taken to proteasomes & broken down D. Golgi complex - processes proteins synthesis by ER - manufactures lysosomes - consists of cisternae stacks of flattened membranous sacs 1. Transport Vesicles - formed by membrane budding - move glycoproteins from ER to cis face of Golgi complex - carry modified proteins from trans face to systemic processes E. Lysosomes - acidic, contain a pH of 5 - enzymes break down structures; involved with apoptosis - used to defend cell F. Vacuoles - contains, water, food, waste - store materials in plant cell - maintains turgor pressure; homeostasis - involved in apoptosis G. Peroxisomes - produce & degrade hydrogen peroxide (catalase) produced from metabolic reactions H. Mitochondria - site of aerobic respiration (most eukaryotic cells) - Important in apoptosis programmed cell death - Chloroplasts & mitochondria both have own DNA & ribosomes, grow and replicate themselves, convert energy from one form to another 1. Outer mitochondrial membrane a. allows small molecules to pass through it 2. Inner mitochondrial membrane a. regulates the types of molecules that can move across it b. has folds (cristae) that increase the inner membrane's surface area 3. Matrix a. enclosed by inner membrane b. contains enzymes that break down food molecules and convert their energy to chemical energy 4. Aerobic Respiration - Breaks down nutrients using oxygen - Converts chemical energy present in certain foods to ATP - Carbon & oxygen atoms are removed & converted to carbon dioxide & water I. Chloroplast - Plastid - organelles that produce their own food - in cells of plants & algae 1. Stroma - fluid-filled space that contains enzymes that produce carbohydrates from CO2 & H2O 2. Thylakoids - interconnected set of flat, disc-like sacs 3. Grana - stacks of thylakoids 4. Photosynthesis a. Chlorophyll - green pigment in thylakoid membranes - traps light energy for photosynthesis - contain variety of light-absorbing yellow & orange pigments VIII. Cytoskeleton - dense network of protein fibers that gives cells mechanical strength, shape, & an ability to move A. Microtubules - hollow cylindrical fibers formed from tubulin protein subunits - found in mitotic spindles, cilia, flagella, & basal bodies - involved in the movement of chromosomes during cell division - consist of -tubulin & -tubulin, which combine to form a dimmer - Microtubules have polarity - Dimers added from plus end of microtubule; removed from minus end 1. Microtubule-Associated Proteins (MAPs) a. Structural MAP - helps regulate microtubule assembly b. Motor MAP - uses ATP to produce movement a. kinesin moves organelles towards the plus end b. dyenin transports organelles towards the minus end 2. Microtubule-Organizing Centers (MTOCs) - regions where minus ends of microtubules are anchored a. Centrosome main MTOC of animal cells - Usually contains 2 centrioles - Each centriole has 9 3 arrangement of microtubules 3. Cilia & Flagella - Thin, movable structures that project from cell surface & function in movement - Cilia are short, flagella are long - Basal body, which has 9 3 arrangement, anchors cilia & flagella - Basal body & centrioles replicate themselves - 9 + 2 arrangement in cilia and flagella proteins attached to microtubules use ATP to power them - 9 + 2 required for cilia & flagella, whose microtubules move by sliding in pairs past each other B. Microfilaments/Actin Filaments - flexible, solid fibers composed of 2 intertwined polymer chains of actin molecules - generate cell movement by rapidly assembling and disassembling - form bundles of fibers that provide mechanical support for various cell structures C. Intermediate filaments - tough, flexible fibers that provide mechanical strength for cytoskeleton & stabilize cell shape - Each consists of protofilaments, composed of coiled protein subunits IX. Cell Coverings A. Glycocalyx (Cell Coat) - formed by polysaccharide side chains of proteins & lipids that are a part of the plasma membrane - protects the cell, enables cells to communicate with one another - contributes to mechanical strength of tissues - found in most eukaryotic cells B. Extracellular Matrix (ECM) - consists of a gel of carbohydrates & fibrous proteins - found in many animal cells - main structural protein is collagen 1. Fibronectins - glycoproteins of ECM that organize the matrix and bind to integrins C. Integrins - receptor proteins in plasma membrane - may be important in cell movement & in organizing the cytoskeleton so that the cell assumes a definite shape - respond to information received from inside & outside cell D. Cell Wall - contains fibers composed of cellulose & other polysaccharides - found in bacteria, fungi & plant cells - prevents excess accumulation of water, provides structural support, & protects against disease causing organisms, to an extent Lecture 2: Chapter 10 Chromosomes, Mitosis, & Meiosis I. Eukaryotic Chromosomes A. Genes - cell's informational units, made of DNA B. Chromatin - consists of DNA & protein - makes up chromosomes (eukaryotes) C. Chromosomes - carriers of genetic information in eukaryotes D. Histone - small, positively charged (basic) proteins that bind to the negatively charged DNA E. Nucleosome - histone (protein) bead wrapped in DNA - organized into coiled loops - held together by nonhistone scaffolding proteins - each nucleosome bead contains a set of 8 histone molecules - this forms a protein core around which the double-stranded DNA winds - The DNA surrounding the histone consists of 146 nucleotide pairs - another segment of DNA, about 60 nucleotide pairs long, links nucleosome beads II. The Cell Cycle & Mitosis A. Interphase 1. First Gap Phase (G1 phase) - growth and normal metabolism occurs - enzymes required for DNA synthesis become more active - lasts 5 hours - nondividing cells are arrested at this stage, known as G0 phase 2. Synthesis (S phase) - DNA replicates & histones are synthesized in order for chromosomes to be duplicated - lasts 4.5 hours - Centromere -constricted region that joins sister chromatids - Kinetochore - Protein to which microtubules bind - Attached to centromere 3. Second Gap Phase (G2 phase) - Protein synthesis increases - Preparation for cell division - lasts 2 hours B. M Phase - lasts 30 minutes 1. Mitosis - preserves chromosome number in eukaryotic cell division - produces 2 nuclei identical to parent nucleus - identical chromosomes are distributed to each pair of the cell - nuclear envelope forms around each set a. Prophase - Chromatin condenses into duplicated chromosomes - Nuclear envelope begins to disappear - Mitotic spindle begins to form - Cytoskeleton begins to disassemble b. Prometaphase - Spindle microtubules attach to kinetochores of chromosomes - Chromosomes begin to move toward cell's midplane - Nuclear envelope breaks down completely - Nucleolus shrinks c. Metaphase - Chromosomes align on cell's midplate (metaphase plate) - Mitotic spindle is complete - Microtubules attach kinetochores of sister chromatids to opposite poles of cell d. Anaphase - Sister chromatids separate by spindle & microtubules - move to opposite poles - Kinetochore microtubules get shorter - Each former chromatid is now a chromosome e. Telophase - Nuclear envelope reforms - Nucleoli appear - Chromosomes uncoil - Spindle disappears - Cytokinesis begins 2. Cytokinesis - process that results in 2 daughter cells - chromosomes & centrioles are accurately distributed - in animal cells, caused as an actomyosin contractile ring attaches to plasma membrane & contracts to produce a cleavage furrow, separating the cytoplasm - in plant cell, a cell plate is formed, which has vesicles that help construct a primary cell wall for each daughter cell III. Regulation of the Cell Cycle A. Cyclin-dependent kniases (Cdks) - protein kinases that control cell cycle - active only when bound to cyclins B. Cyclins - regulatory proteins for the Cdks - levels fluctuate during cell cycle C. Molecular Control of Cell Cycle 1. Cyclin is synthesized & accumulated during G1 & S phase 2. During G2 phase, Cdk associates with cyclin, forming cyclin-CDk complex, M-Cdk 3. M-Cdk acts to phosphorylate & dephosphorylate proteins & enzymes, pushing the cycle into each specific phase by activating those that facilitate mitosis & inactivating those that inhibit mitosis 4. An activated enzyme complex recognizes a specific amino acid sequence in cyclin & targets it for destruction. When cyclin is degraded, M-Cdk activity is terminated, & the cell formed by mitosis enter G1 5. Cdk is not activated, but recycled & reused Lecture 3: Chapter 2 Atoms & Molecules: The Chemical Basis of Life I. Elements & Atoms A. Important Elements -Carbon, Hydrogen, Oxygen, & Nitrogen are the most abundant elements in living things (about 96% of mass) 1. Carbon - backbone of organic molecules 2. Hydrogen - component of water 3. Nitrogen - component of proteins, nucleic acids, & chlorophyll 4. Oxygen - required for cellular respiration - component of water B. Atom 1. Nucleus - contains protons (+) & neutrons (uncharged) 2. Electrons (-) -surround nucleus - Each atom is a particular element - identified by the number of protons (atomic number) C. Atomic Mass - sum of protons & neutrons D. Atomic Mass Unit - Mass of a single proton or neutron -Mass of an electron about 1/1800 of an A.M.U. -Atomic mass typically written as a superscript & atomic number written as subscript; ex. 168O E. Isotope alternate form of an element with the same number of protons & electrons, but a different number of neutrons and therefore a different mass - Unstable isotope goes through process of decay to stable isotope, by emitting radiation (-particles) F. Orbitals - Electrons move rapidly in electron orbitals outside the nucleus 1. Electron shell electrons in orbitals with similar energies, said to be at the same principal energy level 2. Valence electrons - most energetic electrons, which occupy the valence shell - represented as the outermost concentric ring in a Bohr model - An atom tends to lose, gain, or share electrons to fill its valence shell, when not full II. Chemical Reactions A. Molecules - A molecule consists of atoms joined by covalent bonds -The molecular mass of a compound is the sum of atomic masses of its component atoms for each single molecule -The amount of an element or compound whose mass in grams is equivalent to its atomic or molecular mass = 1 mole (mol); e.g. 1 mol of H2O = 18 g B. Avogadro's Number - Avogadro's Number: 6.02 1023 - 1 mole of any substance contains 6.02 1023 atoms, molecules, or ions; e.g. 1 mol of H2O = 6.02 1023 molecules - Enables scientists to "count" particles by weighing a sample III. Chemical Bonds A. Covalent Bonds - Strong, stable bonds formed when atoms share valence electrons, forming molecules - May rearrange the orbitals of valence electrons (orbital hybridization) - Single covalent bond 1 pair of electrons is shared between 2 atoms; ex. H2 - Double covalent bond 2 pairs of electrons are shared between 2 atoms; ex. O2 - Triple covalent bond 3 pairs of electrons are shared between 2 atoms; ex. N3 - Quadruple covalent bond 4 pairs of electrons are shared; ex. Carbon B. Nonpolar Covalent Bonds - Covalent bonds are nonpolar when bonds have similar electronegatives, electrons are shared equally between the 2 atoms; ex. H2 C. Polar Covalent Bonds - Covalent bonds are polar when 1 atom is more electronegative (greater electron affinity) than the other; ex. H2O D. Ionic Bonds - Formed when a positively charged cation (Na+) & a negatively charged anion (Cl-) are attracted (NaCl) - Cations lose electrons to other atoms - Anions gain electrons from other atoms - Are strong in the absence of water but relatively weak in aqueous solutions -In water (solvent): NaCl dissociates to Na+ & Cl- which is now a weak dissolved substance (solute) -Negatively charged anion (Cl-) has gained an electron from the positively charged cation (Na+) which has now lost an electron E. Hydrogen Bonds - Relatively weak bonds - Form when a hydrogen atom with a partial positive charge is attracted to an electronegative atom (usually oxygen or carbon) with a partial negative charge - Collectively strong when present in large numbers F. Van der Walls Interactions - Based on fluctuating electric charges - Electrons in constant motion can set up either: - A region with temporary excess of electrons (-) - A region with temporary deficit of electrons (+) - In these regions, adjacent molecules may be attracted to each other over long distances - Although single interaction is weak, the binding force of a large number of these interactions can be significant IV. Water A. Polar Molecules - One end has a partial positive charge and the other has a partial negative charge - Because of this, each water molecule can therefore form hydrogen bonds with a maximum of 4 neighboring water molecules B. Cohesion & Adhesion - Water molecules exhibit cohesion because they form hydrogen bonds with one another - Water molecules exhibit adhesion through hydrogen bonding to stick to many other types of substances C. Specific Heat - Hydrogen bonding is responsible for water's high specific heat - Amount of energy required to raise temperature of water is quite substantial - Hydrogen bonds must break to raise water temperature - Specific heat of water is 1 cal/g of water/C, which is far higher than ethyl alcohol, which is 0.59 cal/g/C - High heat input to raise the water temperature means that oceans & large bodies of water are quite constant in temperature - Organisms can maintain relatively constant internal temperature because of this D. Heat of Vaporization - Amount of heat required to change 1 g of a substance from liquid to vapor - Measured as calories - 1 cal = heat energy required to raise temp of 1 g of water 1C - Hydrogen bonds must break for molecules to enter vapor phase - When water is heated, some molecules escape as vapor & carry heat with them, lowering the temperature of the liquid, causing evaporative cooling E. Ice - Liquid water expands as it freezes because the H-bonds joining the water molecules in the lattice keep the molecules apart & reduces density by about 10% - Because ice floats, aquatic environment is less extreme F. Three Phases Of Water a. When water boils, H-bonds are broken & steam is produced. If a greater number of H-bonds break vapor (gas) is produced b. As a liquid, H-bonds in water continually form, break, & reform c. In ice, water molecules participate in 4 hydrogen bonds in adjacent molecules; provides a regular crystalline lattice V. Acids, Bases, & Salts A. Acids - proton (H+) donor - dissociate in solution to yield H+ & an anion - e.g. HCl H+ + ClB. Bases - proton acceptors - dissociate in solutions to yield hydroxide ions (OH-) - e.g. NaOH Na+ + OHC. pH -Negative logarithm of the hydrogen ion concentration of a solution (measured in moles per liter) - Therefore, pH = -log10[H+] - In water, [H+] = 0.0000001 or 10-7 mol/L, which makes the negative logarithm = 7 1. pH of Solutions a. Neutral solution - equal concentration of H+ & OH- (10-7 mol/L), pH = 7 b. Acidic Solution - [H+] is higher than its [OH-] - pH < 7 c. Basic Solution - [OH-] greater than its [H+] - pH > 7 D. Buffers - Buffering system based on a weak acid or a weak base - Buffer resists changes in the pH of a solution when acids or bases are added E. Salts a compound in which the hydrogen ion of an acid is replaced by some other cation - HCl + NaOH H2O + NaCl - Electrolyte substance that dissociates into ions when dissolved in water; resulting solution can conduct an electric current - Nonelectrolyte substance that does not form ions when dissolved in water; does not conduct electric current Lecture 4: Chapter 3 The Chemistry of Life: Organic Compounds I. Carbon Atoms & Molecules - Carbon is central component of organic compounds - Carbon atoms join with one another or other atoms to form large molecules with a wide variety of shapes (chains, double bonds, branched chains, rings, joined rings & chains) - Most are rings A. Isomers - compounds with the same molecular formulas but different structures & properties 1. Structural Isomers - different covalent arrangement of their atoms - ex., Ethanol (C2H6O) & Dimethyl Ether (C2H6O) 2. Genetic Isomers (cis-trans isomers) - different spatial arrangements - identical covalent bonds - ex., trans-2-butene & cis-2-butene 3. Enantiomers - mirror images - central carbon is asymmetrical because it is bonded to 4 bonded groups - because of their 3-D structure, the 2 figures cannot be superimposed no matter how they are rotated B. Hydrocarbons - Organic compounds consisting of Carbon & Hydrogen only - nonpolar & hydrophobic insoluble in water; tend to cluster together - ex. Methyl group - R-CH3 - Nonpolar hydrocarbon - Non-reactive C. Polar & Ionic Functional Groups - groups of atoms that determine the types of chemical reactions & associations in which a compound participates - hydrophilic associates strongly with polar water molecules 1. Hydroxyl - ROH; polar because electronegative oxygen attracts covalent electrons - Eg. Ethanol (ethane gas; ethanol-liquid) - Polar groups make it soluble in water 2. Carbonyl - Carbon atom attracted to an O atom by a double covalent bond - Polar because electronegative oxygen attracts covalent electrons a. Aldehyde - (RCHO) carbonyl group at end of carbon skeleton - C is bonded to at least 1 H atom - eg formaldehyde b. Ketone - (RCOR) an internal carbonyl group - carbon is bonded to 2 other carbons - eg acetone 3. Carboxyl - weakly acidic; essential constituents of amino acids a. Non-ionized - (RCOOH) consists of a carbon atom joined by double covalent bond to an O atom, & by a single bond to an O atom, which is attached to an H atom b. Ionized - (RCOO- + H+) 2 electronegative O atoms in close proximity can cause H to be stripped of its electron & release an H+ D. Acidic & Basic Groups 1. Basic - accepts a H+ - becomes (+) charged - amino group 2. Acidic - release H+ - becomes (-) charged - carboxyl & phosphate groups 3. Amino - (RNH2) Polar; weakly basic since it can accept an H+ - components of amino acids & nucleic acids a. Non-ionized - includes Nitrogen atom covalently linked to 2 Hydrogen atoms b. Ionized - (RNH3+) formed as an ionized group with 1 unit positively charged 4. Phosphate - RPO4H2 - Weakly acidic; 1 or 2 H+ can be released - Ionized when 1 or 2 H+ are released - Ionized forms have 1 or 2 units of negative charge - eg nucleic acids & some lipids 5. Sulfhydrl - RSH - Atom of S covalently bonded to an H - In molecules called thiols eg. Cysteine - Disulfide bridges between amino acids important in protein folding & protein structure E. Polymers & Macromolecules 1. Polymers - long chains of linked monomers - linked through condensation reactions - water molecule released therefore also called dehydration synthesis 2. Macromolecules - large polymers - polysaccharides, proteins, & DNA - generally form when monomers are joined together by condensation - broken down by hydrolysis reaction - H from H2O attached to 1 monomer, & a hydroxyl from H2O attaches to adjacent monomer II. Carbohydrates - 1 C: 2 H: 1 O - exist naturally in ring formation - hydrophilic because it contains a lot of oxygen A. Monosaccharide - simple sugar (3-7 Cs) - glucose, fructose (isomer hexoses), riboses (pentose) B. Disaccharide - 2 monosaccharides - Formed via condensation reaction - Joined by glycosidic linkage - maltose, sucrose (structural isomers) - rings in solution C. Modified & Complex Carbohydrate 1. Monosaccharide with amino group - E.g. n-acetyl glucosamine subunits - Cell walls of fungi, insect exoskeleton, crab shell... - Strong because of H bonding 2. Protein with a glucose unit - Glycoproteins - Cell protection, adhesion, protectant present in mucus membranes of respiratory & digestive system 3. Carbohydrate with a lipid grouping: - glycolipids: - On cell surface for cell regulation D. Polysaccharides - Repeated units of simple sugars in long chains or branched 1. Storage polysaccharides a. starch (-glucose) in plant amyloplasts b. Amylose (unbranched), amylopectin (branched) c. Glycogen (-glucose) in animals - Highly branched, more soluble in starch - Storage in liver & muscle 2. Structural polysaccharide a. Cellulose - Plant cell walls, wood, cotton - 1-4 glycosidic linkages - Broken down by different enzymes than those (present in animal cells) used to break the alpha linkages in starch - Therefore, humans lack enzymes necessary to break down cellulose - Bulk in diet; good for human digestion, as remains fibrous - Cows break down cellulose with bacterial digestion III. Lipids - Consist of mainly hydrocarbon containing regions - Very few O-containing (polar or ionic) groups - Hydrophobic - Greasy or oily consistency - Relatively insoluble in water - Soluble in nonpolar solvents - Varying functions - Eg Structural components of cell membranes, important hormones, energy storage A. Triacylglycerol - main storage fat in animals - glycerol + 3 fatty acids - Produced via 3 condensation-reactions yielding: - Monoacylglycerols (1 fatty acid), then Diacylglycerols (2 fatty acids), then Triacylglycerols (3 fatty acids) - Each reaction occurs as a FA is added to the glycerol molecule (at each hydroxyl group) with 1 molecule of water released during each ester linkage formed B. Fatty acids 1. Saturated - max # of H atoms - eg Palmitic acid - Straight chain - Animal fats; solid at room temp. due to an abundance of weak Van der Waals forces between non-polar molecules, limiting free motion 2. Unsaturated - 1 or more adjacent pairs of double bonds - Chains are bent - Liquid at room temp. due to limited Van der Waals forces, allowing more free movement of molecules a. Monounsaturated - have only 1 double bond -eg Oleic acid b. Polyunsaturated - have more than 1 double bond - e.g. linoleic acid C. Trans Fatty Acids - During hydrogenation of cooking oils, unsaturated FA are converted to saturated FA - The H atoms that normally flank the same side of double bonds (cis) become rearranged (trans) preventing the bending at the site of the double bond - Contributes to the product being more solid at room temp. - Greater cardiovascular risk D. Phospholipids 1. Structure - Amphipathic one end is hydrophilic and the other is hydrophobic - Head: Glycerol, phosphate & organic base (ionized, water soluble & hydrophilic) - Tail: 2 fatty acids (water insoluble & hydrophobic) - Cell membrane component - eg phosphatidylcholine E. Carotenoids - orange and yellow plant pigments that consist of 5-carbon hydrocarbon monomers (isoprene units) - Most animals convert carotenoids to vitamin A, which can then be converted to the visual pigment retinal F. Steroids 1. C atoms arranged in 4 rings (3 contain 6 Cs, 4th contains 5 Cs) a. Cholesterol, bile salts, some hormones i. essential structural component of animal cell membranes 2. Functional groups at the 5th C ring distinguish each steroid functionally a. Cholesterol (excess = plaque & CV risk) b. Plant membranes contain similar; can be used to block intestines' absorption of cholesterol c. Bile salts then emulsify the fats, which are then hydrolyzed by enzymes 3. Steroid hormones regulate: a. Aspects of metabolism b. Reproduction c. The flight & fright responses (adrenal cortex & stress) IV. Proteins A. Polypeptides 1. long, linear compounds 2. 20 common amino acids 3. joined by peptide bonds B. Many functions 1. enzymes 2. structural components 3. cell regulators C. Amino acids 1. Amino group & carboxyl group a. Side chains i. determine chemical properties ii. nonpolar (hydrophobic), polar, acidic, or basic (polar & therefore hydrophilic) b. Form dipolar ions at cell pH (pH 7) i. Important biological buffers D. Primary Structure - Linear sequence of amino acids in polypeptide chain E. Secondary Structure a. Regular conformation i. -helix (eg fibrous proteins of hair, skin, nails) ii. H-bonds between amino acids responsible for structure; bonds can be broken & reform for stretch & elasticity iii. -pleated sheet formed when a polypeptide chain folds back on itself; globular proteins, provide strength. Eg fibroin protein in silk; half the R-groups project above the sheet, & the other half project below F. Tertiary Structure 1. Overall shape: a. Determined by individual polypeptide chains b. Dictated by R groups (side chains) belonging to same polypeptide chain c. Includes weak bonds (H, ionic, & hydrophobic) & strong covalent (S-S) bonds i. eg cysteine cysteine, H removed G. Quaternary Structure 1. 2 or more polypeptide chains 2. Same interactions as for secondary & tertiary structure - Hemoglobin in blood; 574 amino acids in 4 polypeptide chains 2 or 2 - Collagen; fibrous protein 3 polypeptide chains bonded by cross-links H. Amino acid sequence of a protein determines conformation 1. Proteins do not always fold properly 2. Facilitated by molecule chaperone proteins 3. Misfolded proteins destroyed I. Protein conformation determines function 1. Structural domains determine biological activity 2. Genetic determinants eg Sickle cell anemia; valine substitutes for glutonic acid at position 6 in chain of hemoglobin J. Protein conformation is studied through a variety of methods 1. X-ray diffraction studies 2. Mass spectrometry amino acid sequence data helps predict a protein's higher levels of structure 3. Computers once amino acid sequence of polypeptide is determined, used to search databases to find polypeptides with similar sequences V. Nucleic Acids A. polymers of nucleotides, molecular units that consist of 1. a 5-C sugar, either deoxyribose (in DNA) or ribose (in RNA) 2. 1 or more phosphate groups which make the molecule acidic 3. a nitrogenous base, a ring compound that contains hydrogen a. may be either a double-ring purine or a single ring pyrimidine B. 2 classes 1. Deoxyribonucleic Acid (DNA) a. composes the genes & contains instructions for making all the proteins 2. Ribonucleic Acid (RNA) a. participates in the process in which amino acids are linked to linked to form polypeptides Lecture 5: Chapter 5 Biological Membranes A. Plasma membrane 1. Physically separates -interior of cell from external environment -triacylglycerol & glycerol are unable to form bilayers in presence of water 2. Receives info. -about changes in environment 3. Regulates -passages of materials in & out of cell (ex. glucose) 4. Communicates -with other cells 5. Forms compartments -to allow separate functions 6. Participates in biochemical reactions Fluid mosaic model -cell membranes consist of a fluid bilayer composed of phospholipids in which a variety are embedded or peripheral to it Lipid bilayer -fluid or liquid-crystalline state -Proteins move within the membrane -Flexible & self-sealing -Capable of fusing with other membranes -allows transport of materials within cell -Forms vesicles -bud from 1 cell membrane -fuse with another membrane to facilitate movement of materials from 1 part of the cell to another -Characteristics of lipid bilayer ensure proper membrane fuction in fluctuating temp. -Transport ceases if too rigid -Low temp., motion of FA chains slowed -Membrane becomes semi-solid -Component lipids important -Double bonds cause kinks in FA chains & prevent hydrocarbon chains from interacting through Van der Waals forces -such forces prevent cellular membrane from falling apart -More fluid -Unsaturated fats lower the temperature at which membranes solidify Plasma Membrane -Integral membrane proteins -embedded in bilayer (not easily removed) -Amphipathic; hydrophilic heads extend into cytoplasm; hydrophobic regions interact with FA tails of membrane phospholipids -Transmembrane proteins -extend completely through membrane (as both helices and sheets or barrel configuration) -Peripheral Membrane Proteins --at inner or outer surface of bilayer -bound to exposed integral proteins by noncovalent bonding (easily removed) Membrane Protein Synthesis -Transport vesicle delivers glycoprotein to plasma membrane -Transport vesicle fuses with plasma membrane. Carbohydrate chain extends outward. -Replenishes plasma membrane -When a transport vesicle buds from the Golgi complex, the modified region of the protein remains inside the membrane compartment Membrane Proteins -Transport materials -Act as enzymes or receptors -Recognize cells -Structurally link cells together (a) Anchoring. Some plasma membrane proteins, such as integrins, anchor the cell to extracellular matrix; they also connect to microfilaments within cell (b) Passive transport. Certain proteins form channels for selective passage of ions or molecules, down a concentration gradient (c) Active transport. Some transport proteins pump solutes across the membrane, against the concentration gradient, which requires a direct input of energy (d) Enzymatic activity. Many membrane-bound enzymes catalyze reactions that take place within or along the membrane surface (e) Signal transduction. Some receptors (membrane protein) bind with signal molecules such as hormones & transmit information into the cell (f) Cell recognition. Some glycoproteins function as identification tags (g) Intercellular junction. Cell adhesion proteins attach membranes of adjacent cells Selectively Permeable Membranes -Allows passage of some substances but not others -Most permeable to nonpolar molecules (that can pass through lipid bilayer) -Relatively impermeable to ions & large polar molecules(water passes through slowly) -Controls volume & internal composition of cell's ions & molecules; different than external Membrane Transport Proteins -facilitate the passage of certain ions & molecules through biological membranes a. Carrier proteins: transport proteins that change shape as they bind a specific solute -eg Glucose transporter -concentration of glucose is higher in blood plasma than RBCs -glucose diffuses down its concentration gradient into RBCs b. Channel proteins: form pores or gated channels that open & close in response to electrical charges, chemical & mechanical stimuli -eg Porins -channel proteins with large pores -Barrel shaped proteins -eg Aquaporins -transmembrane proteins that provide for rapid diffusion of water Diffusion -in a lipid; atoms, ions, molecules aren't evenly distributed -2 regions exist: 1 with a higher & 1 with a lower concentration of particles -Net movement of substance, based on random movement, down a concentration gradient -From region of higher concentration to region of lower concentration (dynamic equilibrium) -Does not use metabolic energy Simple Diffusion -Molecules or ions move directly through a membrane -down their concentration gradient -function of size, shape, electric charge & temperature -eg osmosis -involves net movement of water through a selectively permeable membrane -from a region of higher concentration to a region of lower concentration Osmotic pressure -exerted on one side of a selectively permeable membrane, to prevent osmosis from the side containing the lower solute concentration An isotonic solution -When a cell is placed in a fluid that has exactly the same osmotic pressure as the cell, no net movement of water molecules occurs -fluid & cell cytoplasm are of equal solute concentration -fluid is isotonic to cell cytoplasm -net movement of water molecules is 0 A hypertonic solution -surrounding fluid of dissolved substances (solute) is greater in concentration than that of cell cytoplasm -Fluid has a higher osmotic pressure -Fluid is hypertonic to the cell -Water will come out of cell, causing it to shrink A hypotonic solution -If the surrounding fluid contains a lower concentration of dissolved materials than the cell does -Fluid has a lower osmotic pressure -Fluid is hypotonic to the cell -Water goes into cell; cell swells Turgor Pressure -In plants: solutes dissolved in the cell cytoplasm make the cell hypertonic to its outside env.: -Water moves into cell by osmosis -Fills the vacuoles, distends the cells & builds up larger pressure, until rigidity of the cell wall halts water movement -If cell wall is placed in hypertonic medium, water leaves cell & cell shrinks -Plasmolysis plasma membrane pulls away from cell wall & cytoplasm shrinks Facilitated diffusion -Specific transport proteins (carrier & channel proteins) facilitate the movement of solutes across a membrane -Membrane becomes permeable to that particular solute -Net movement is always from a region of higher solute concentration to a region of lower concentration Direct active transport -Cell uses metabolic energy -to move ions or molecules across membrane -against concentration gradient Ex. Sodium-Potassium ATP Pump -Uses ATP to pump sodium ions out of cell & potassium ions into cell -Concentration of K+ is 10-20X higher inside cell than outside -Reverse true for Na+ ions -Pump operates as an anti-porter, actively pumping Na+ out of cell against its concentration gradient while pumping K+ into cell -The exchange is unequal -2 K+ imported for every 3 Na+ exported -fewer K+ ions inside cell -more Na+ ions inside cell -Outside of cell is more positively charged, relative to inside -Unequal distribution of ions establishes an electrical gradient -Drives ions across the plasma membrane -There is an electric charge difference & a concentration difference on the 2 sides of the membrane -known as electrochemical gradient + 1. 3 Na bind to transport protein 2. Phosphate group is transferred from ATP to transport protein 3. Phosphorylation causes carrier protein to change shape, releasing 3 Na+ outside cell 4. 2 K+ bind to transport protein 5. Phosphate is released 6. Phosphate release causes carrier protein to return to its original shape -resulting in release of 2 K+ into cell Indirect Active Transport -Carrier protein co-transports 2 solutes -1 solute moves down its concentration, & provides the energy for, -transport of some other solute up its concentration gradient Co-transport -Carrier protein transports Na+ down its concentration gradient, while using that energy to co-transport glucose molecules against their concentration gradients -The carrier proteins involved -Anti-porter moves 2 substances in different direction (eg Na+ K+ ATP pump) -Symporter moves 2 substances in same direction (co-transport of Na+ & glucose) Exocytosis -Removal of substances -Cell ejects waste products, secretes hormones -Fusion of vesicle with plasma membrane -Vesicle approaches plasma membrane, fuses with it, & releases its contents outside cell -PM replenished Endocytosis -Materials enter cell -Membrane surface area decreases -Phagocytosis -cell ingests large, solid particles -ex. WBC ingesting bacteria; protists ingesting food -Pinocytosis -ingestion of dissolved materials, pinch off as tiny vesicles -Receptor-mediated endocytosis -Eukaryotes take in macromolecules; specific molecules combine with receptor proteins in the plasma membrane Phagocytosis 1. Folds of plasma membrane surround large particle to be ingested, forming small vacuole around it 2. Vacuole then pinches off inside cell 3. Lysosomes fuse with vacuole & pour potent hydrolytic enzymes onto ingested material Pinocytosis 1. Tiny droplets of fluid are trapped by folds of plasma membrane 2. These pinch off into cytosol as small fluid-filled vesicles 3. Contents of these vesicles are then slowly transferred into cytosol Receptor-mediated endocytosis 1. LDL attaches to specific receptors in coated pits on plasma membrane 2. Endocytosis results in formation of a coated vesicle in cytosol. Seconds later coat is removed 3. Uncoated vesicle fuses with endosome 4. Receptors are returned to plasma membrane & recycled 5. Vesicle containing LDL particles fuses with lysosome, forming a secondary lysosome. Hydrolytic enzymes then digest cholesterol from LDL particles for use by cell (a) Uptake of low density lipoprotein (LDL) particles, which transport cholesterol in the blood Lecture 6 Chapter 7: Energy & Metabolism A. Energy -capacity to do work (measured in kilojoules or kilocalories) -Potential Energy stored energy -Kinetic Energy energy of motion -Chemical Energy potential energy of chemical bonds; powers many life processes B. Thermodynamics study of energy -Closed System does not exchange energy with its surroundings -Open System does exchange energy with its surroundings -Organism can't produce energy, but as open systems they can capture it -Maintain organization only with input of energy from surroundings -1st Law of Thermodynamics -energy in the universe is constant; it can't be created or destroyed but it can be transferred and changed in form -2nd Law of Thermodynamics -during energy conversions, some useful energy is lost as heat, random motion that contributes to entropy, or disorder C. Free Energy -As entropy increases, the amount of free energy decreases -G = H - TS -G = free energy; H = enthalpy (total potential energy of system) -T = absolute temperature (measured in Kelvin); S = entropy -Free energy of reactants & products impossible to measure -We can measure, however, the change in free energy D. Exergonic & Endergonic Reactions -Exergonic Reactions -free energy decreases; negative value of G -spontaneous reaction (requires activation energy) -releases free energy that can perform work -Endergonic Reactions -free energy increases -nonspontaneous -requires input of energy -Coupled reaction -the input of free energy required to drive an endergonic reaction is supplied by an exergonic reaction E. Dynamic Equilibrium -the rate of change in 1 direction is exactly the same as the rate of change in the opposite direction -system can do no work because the free-energy difference between the reactants & products is 0 F. ATP -Adenosine Triphosphate -immediate energy currency of the cell -participates in coupled reactions -donates energy by means of its terminal phosphate group -formed by the phosphorylation of ADP [adenosine diphosphate] (endergonic reaction) -ADP + Pi + energy ATP -ATP + H2O ADP +Pi -common link between exergonic & endergonic reactions -common link between catabolism & anabolism -catabolism degradation of large complex molecules into simple molecules -anabolism synthesis of complex molecules from simpler molecules -Components of metabolism all the chemical reactions of a living organism G. Transfer of Energy Through Oxidation-Reduction (Redox) Reactions -Oxidation compound loses electrons & energy -Reduction compound gains electrons & energy -A substance becomes oxidized giving up electrons to another substance, which is reduced -Electrons are commonly transferred as part of hydrogen atoms -NAD+ & NADP+ accept electrons as part of hydrogen atoms & become reduced to form NADH & NADPH, respectively. -NAD+ NADH ; NADP+ NADPH ; FAD FADH2 -These electrons (along with some of their energy) can be transferred to other acceptors -Cytochromes protein molecules that contain iron - participates in redox reactions since iron has 2 forms H. Enzymes -biological catalysts (mostly proteins, sometimes RNA) -greatly increases the speed of a chemical reaction -lowers activation energy required to start a reaction -enables reactants with less kinetic energy to react -Active site 3-D region of an enzyme where substrates come into close contact & bind more readily -When a substrate binds to an active site, an enzyme-substrate complex forms in which the shapes of the enzyme & substrate change slightly -This induced fit facilitates the breaking of bonds and formation of new ones. -A coenzyme is an organic, nonpolypeptide molecule that transfers a small functional group or electrons -ex. ATP, NADH, coenzyme A I. Regulation of Enzymes -Enzymes work best at specific temperature & pH conditions -As temperature or pH increases, enzyme increases until an optimal condition is reached -A cell can regulate enzymatic activity by controlling the amount of enzyme produced & by regulating metabolic conditions that influence the shape of the enzyme -allosteric sites noncatalytic sites to which an allosteric regulator binds, changing the enzyme's activity -Some allosteric sites are subject to feedback inhibition, in which the formation of an end product inhibits an earlier reaction in the metabolic pathway. Enzyme 1 Enzyme 2 Enzyme 3 Enzyme 4 -ABCDE -ex. increasing concentration of E is signal for enzyme 1 to stop -Reversible inhibition an inhibitor forms weak chemical bonds with the enzyme -Competitive inhibitor competes with the substrate for the active site -Noncompetitive inhibitor binds with the enzyme at the allosteric site -Irreversible inhibition an inhibitor combines with an enzyme & permanently inactivates it Lecture 7 Chapter 8: How Cells Make ATP A. Cellular Respiration -plants convert CO2 into organic compounds, & animals, plants and fungi convert organic compounds back into CO2 -the catabolic processes that convert the energy stored in ATP then occur inside cells -2 types: aerobic & anaerobic respiration B. Aerobic Respiration -Glucose + O2 CO2 + H2O + Energy -C6H12O6 + 6 O2 + 6 H2O 6 CO2 + 12 H2O + energy (36-38 ATP) -Involved redox reactions since glucose is oxidized & oxygen is reduced -the cell can obtain the most energy from NADH -Glycolysis -occurs in the cytosol -1 molecule of glucose is degraded to 2 molecules of pyruvate -Net yield of 2 ATP & 2 NADH - C6H12O6 + 2 ATP + 2 ADP + 2Pi + 2 NAD+ 2 pyruvate + 4 ATP + 2 NADH + H2O -Energy Investment Phase -phosphorylation reaction - a phosphate group is transferred from ATP to the sugar -Glucose + 2 ATP 2 G3P + 2 ADP -Energy Capture Phase -substrate-level phosphorylation ATP forms when a phosphate group is transferred to ADP from a phosphorylated intermediate - 2 G3P + 2 NAD+ + 4 ADP 2 pyruvate + 2 NADH + 4 ATP -Acetyl CoA Formation -takes place in the mitochondria -The 2 pyruvate molecules each lose 1 molecule of carbon dioxide, & the remaining acetyl groups each combine with coenzyme A, producing 2 molecules of acetyl CoA; 1 NADH is produced per pyruvate -2 pyruvate + 2 NAD+ + 2 CoA 2 Acetyl CoA + 2 NADH + 2 CO2 -Citric Acid Cycle -Each acetyl CoA combines with a 4-C compound, oxaloacetate, to from citrate, a 6-C compound -2 acetyl CoA molecules enter the cycle for every glucose molecule -For every 2 carbons that enter the cycle as a part of an acetyl CoA molecule, 2 leave as carbon dioxide -For every acetyl CoA, hydrogen atoms are transferred to 3 NAD+ & 1 FAD -1 ATP is produced by substrate level phosphorylation, when a phosphate group is transferred to ADP from a phosphorylated intermediate -2 Acetyl CoA + 6 NAD+ + 2 FAD + 2 ADP + 2 Pi + 2 H2O 4 CO2 + 6 NADH + 2 FADH2 + 2 ATP + 2 CoA -Electron Transport/Chemiosmosis -Hydrogen atoms (or their electrons) removed from fuel molecules are transferred from 1 electron acceptor to another down an electron transport chain located on the mitochondrial inner membrane -These electrons reduce molecular oxygen, forming water. -In oxidative phosphorylation, the redox reactions in the electron transport chain are coupled to synthesis of ATP through the mechanism of chemiosmosis -Complex I (NADH-ubiquinone oxidoreductase) accepts electrons from NADH molecules that were formed during the first 3 stages of aerobic respiration -Complex II (succinate-ubiquinone reductase) accepts electrons from FADH2 molecules that were produced during the citric acid cycle -Complex III (ubiquinone-cytochrome c oxidoreductase) accepts electrons from reduced ubiquinone (produced from Complex I & II) & passes them on to cytochrome c -Complex IV (cytochrome c oxidase) accepts electrons from cytochrome c & uses these electrons to reduce molecular oxygen, forming water in the process -When the 10 NADH & 2 FADH2 pass through the electron transport chain, 32-34 ATPs are produced by chemiosmosis -Chemiosmosis some of the energy of the electron in the electron transport chain is used to pump protons across the inner mitochondrial membrane into the intermembrane space. - this establishes a proton gradient across the inner mitochondrial membrane - Protons (H+) accumulate within the intermembrane space, lowering the pH - The diffusion of protons through channels formed by the enzyme ATP synthase, which extends through the intermembrane space to the mitochondrial matrix, provides the energy to synthesize ATP -NADH + 3 ADP + 3 Pi + O2 NAD+ + 3 ATP + H2O -FADH2 + 2 ADP + 2 Pi + O2 FAD+ + 2 ATP + H2O C. Protein Catabolism -Amino acids undergo deamination, & their carbon skeletons are converted to metabolic intermediates of aerobic respiration. D. Lipid Catabolism -Both the glycerol & fatty acid components of lipids are oxidized as fuel -Fatty acids are converted to acetyl CoA molecules by the process of -oxidation E. Anaerobic Respiration -Electrons are transferred from fuel molecules to an electron transport chain that is coupled to ATP synthesis by chemiosmosis -The final electron acceptor is an inorganic substance such as nitrate or sulfate, not oxygen F. Fermentation -anaerobic process that does not use an electron transport chain -net gain of only 2 ATP per glucose -these are produced by substrate-level phosphorylation during glycolysis -To maintain the supply of NAD+ essential for glycolysis, hydrogen atoms are transferred from NADH to an organic compound derived from the initial nutrient -Alcohol Fermentation -carried out by yeast cells, in which ethyl alcohol & carbon dioxide are the final waste products - C6H12O6 2 CO2 + 2 ethyl alcohol + energy (2 ATP) -Lactate (Lactic Acid) Fermentation -carried out by certain fungi, prokaryotes, and animal cells, in which hydrogen atoms are added to pyruvate to form lactate, a waste product - C6H12O6 2 lactate + energy (2 ATP) - conversion of pyruvate to lactate in muscles is associated with the oxidation of NADH Lecture 8 Chapter 9: Photosynthesis Capturing Energy A. Physical Properties of Light -Light consists of particles called protons that move as waves -Electromagnetic spectrum: vast, continuous range of radiation -Visible light: 380 nm (Violet, short wavelength) 760 nm (Red, longer wavelength) -Photons with shorter wavelengths have more energy than those with longer wavelengths -Pigments are substances that absorb visible light, photons of a certain wavelength -White light is composed of wavelengths long & short -When molecule absorbs a photon of light energy, one of its electrons becomes energized -atom may return to its ground state all electrons are in their normal, lowest-energy levels; its energy dissipates as heat (fluoresence) -energized electron may also leave atom & be accepted by an electron acceptor molecule B. Chloroplast -Photosynthesis occurs in chloroplasts, which are located mainly within mesophyll cells inside the leaf -Chloroplasts are organelles enclosed by a double membrane -The inner membrane encloses the stroma in which membranous, saclike thylakoids are suspended -Each thylakoid encloses a thylakoid lumen -Thylakoids arranged in stacks called grana -ATP is formed when hydrogen ions leave the thylakoid lumen C. Chlorophyll -Pigment involved in photosynthesis -does not absorb green light -ring structure with long carbon tail -at center of ring is magnesium -chlorophyll a, chlorophyll b, carotenoids, & other photosynthetic pigments are components of the thylakoid membranes of chloroplasts -chlorophyll a main or primary -chlorophyll b accessory pigment -carotenoid accessory pigment; attached to binding proteins in the membranes of chloroplast -The combined absorption spectra (plot of a pigment's absorption of light of different wavelengths) of chlorophylls a & b are similar to the action spectrum (relative effectiveness of different wavelengths of light) for photosynthesis D. Photosynthesis -redox process in which light energy is captured & converted to the chemical energy of carbohydrates -hydrogens from water are used to reduce carbon, & oxygen derived from water becomes oxidized, forming molecular oxygen -carbon dioxide is reduced and water is oxidized -most atoms in a glucose molecule originate from the atmosphere Light energy 6 CO2 + 12 H2O C6H12O6 + 6 O2 + 6 H2O Chlorophyll -two types of reactions: light dependent reactions & carbon fixation reactions E. Light-Dependent Reactions Light 12 H2O + 12 NADP+ + 18 ADP + 18 Pi 6 O2 + 12 NADPH + 18 ATP Chlorophyll -Photosystems I & II are the 2 types of photosynthetic units involved in photosynthesis -Each photosystem includes chlorophyll molecules & accessory pigments organized with pigment-binding proteins into antenna complexes. -Only a special pair of chlorophyll a molecules in the reaction center of an antenna complex give up energized electrons to a nearby electron acceptor. -P700 is the reaction center for photosystem I; P680 is the reaction center for photosystem II -Noncyclic electron transport -Electrons are supplied to system from the light splitting (photolysis) of H2O by photosystem II, with release of O2 as by-product. -When photosystem II is activated by absorbing photons, electrons are passed along electron transport chain & are eventually donated to photosystem I -Only chlorophyll can transfer electrons directly to the electron transport chain -From primary electron acceptor to plastoquinone to cytochrome complex to plastocyanin -Production of ATP by chemiosmosis -High energy electron from P680 replaces electron lost from Photosystem I -Electrons in photosystem I are "re-energized" by absorption of additional light energy & are passed to NADP+, forming NADPH -From primary electron acceptor to electron transport chain to ferredoxin -Cyclic electron transport -Electrons from photosystem I are eventually returned to photosystem I -ATP is produced by chemiosmosis, but no NADPH or oxygen is generated -ATP synthesis by Chemiosmosis -Photophosphorylation is the synthesis of ATP coupled to the transport of electrons energized by photons of light -The electron donor & acceptor in cyclic photophosphorylation is chlorophyll -Some of the energy of the electrons is used to pump protons across the thylakoid membrane, providing the energy to generate ATP by chemiosmosis -As protons diffuse through ATP synthase, an enzyme complex in the thylakoid membrane, ADP is phosphorylated to form ATP F. Carbon Fixation Reactions 12 NADPH + 18 ATP + 6 CO2C6H12O6 + 12 NADP+ + 18 ADP + 18 Pi + 6 H2O -proceed by way of the Calvin cycle, known as the C3 pathway -CO2 uptake phase -CO2 is combined with ribulose biphosphate (RuBP), a 5-C sugar, by the enzyme rubisco (ribulose bisphosphate carboxylase/oxygenase), forming the 3-C molecule phosphoglycerate (PGA) -rubisco reduces photosynthetic efficiency, occurs in light, requires oxygen, & produces CO2 & H2O -Carbon Reduction Phase -the energy & reducing power of ATP & NADPH are used to convert PGA molecules to glyceraldehyde-3-phosphate (G3P) -For every 6 CO2 molecules fixed, 12 molecules of G3P are produced, & 2 molecules of G3P leave the cycle to produce the equivalent of 1 molecule of glucose -RuBP Regeneration Phase -the remaining G3P molecules are modified to regenerate RuBP G. Photorespiration -C3 plants consume oxygen & generate CO2 by degrading Calvin cycle intermediates but do not produce ATP -significant on hot, dry days when plants close their stomata, conserving water but preventing the passage of CO2 into the leaf, reducing photosynthetic efficiency H. C4 Pathway -the enzyme PEP carboxylase binds CO2 effectively, even when CO2 is at a low concentration -take place within mesophyll cells -The CO2 is fixed in oxaloacetate, which is then converted to malate -The malate moves into a bundle sheath cell, & CO2 is removed from it -The released CO2 then enters the Calvin cycle -reduces amount of photorespiration occurring Lecture 9 Chapter 23 (Systematics), 21 (Origin & Evolutionary History of Life) A. Classifying Organisms -Biodiversity -the variety of living organisms and the variety of ecosystems they form -1.7 million species named -4-100 million more unidentified -Systematics -scientific study of the diversity of organisms and their evolutionary relationships -Taxonomy -science of naming, describing, & classifying organisms -Taxonomic Categories -domain, kingdom, phylum, class, order, family, genus, species -system proposed in 1700s by Carolus Linnaeus -Taxon -a formal grouping of organisms -Three Domains -Bacteria & Archae (Prokaryotic cells), Eukarya (Eukaryotic cells) -Six Kingdoms -Bacteria, Archae, Fungi, Protists, Plants, Animals -Species -only part of scheme where organisms actually exist -share a common gene pool; can interbreed -Binomial System of Nomenclature -genus + specific epithet/term -ex. white oak Quercus alba -Phylogenic tree -scientists use evolutionary relationships to place organisms into proper genus & species -graphically represents the evolutionary history of a group of species -To determine whether various species share a common ancestor, scientists examine.. -Physical characteristics -Fossil record -Molecular similarities -amino acid sequence, nucleotide sequence in RNA, etc. B. Evolutionary History of Life Evolution -genetic changes in a population over time -leads to transformations in life forms from few to many Genetic Variability -basis on which evolution builds -push comes from environmental pressure or opportunity Origin of Life -Earth was formed 4.6 bya -Evidence of life 3.5 bya Chemical Evolution -hypothesis that life developed from nonliving matter -Oparin & Haldane proposed concept that simple organic molecules such as sugars, nucleotide bases, and amino acids could form spontaneously from simpler raw materials -4 requirements for chemical evolution 1. absence of oxygen, which would have reacted with and oxidized abiotically produced organic molecules 2. energy to form organic molecules 3. chemical building blocks, including water, minerals, and gases present in the atmosphere, to form organic molecules 4. sufficient time for molecules to accumulate and react -Carbon Dioxide (CO2), Water Vapor (H2O), Carbon Monoxide (CO), Hydrogen (H2), Nitrogen (N2), Ammonia (NH3), Hydrogen Sulfide (H2S), and Methane (CH4) were the molecules that most likely existed in the early earth's atmosphere. -Abiotic synthesis of monomers was able to take place on the early earth in part because of a reducing atmosphere -Inorganic Molecules Simple Organic Molecules Complex Organic Molecules Precells (protobionts) 1st living cell Prebiotic Soup Hypothesis -proposes that organic molecules were formed near the Earth's surface, accumulating in shallow seas Iron-Sulfur Hypothesis -proposes that organic precursors formed at cracks in the ocean's floor where hot water, carbon monoxide, and minerals such as sulfides of iron and nickel spew forth, in hydrothermal vents Test of 1st Process of Chemical Evolution -Miller & Urey designed a close apparatus that presumably existed on early Earth -Spark chamber filled with inorganic compounds (H2, CH4, H2O, NH3) -exposed this chamber to electric discharge that simulated lightning -amino acids & other organic molecules had formed after 1 week -Nowadays scientists don't think there initially was much CH4 & NH3 -May have been more CO2, CO Evidence of 2nd Process -organic polymers may have formed & accumulated on rock or clay surfaces -clay binds organic monomers & contains zinc and iron ions that may have served as catalysts -experiments have shown that organic polymers form spontaneously from monomers on hot rock or clay surfaces Evidence of 3rd Process -Protobionts -assemblages of abiotically produced organic polymers, synthesized by scientists -maintain an internal environment separate from the external -respond to osmotic changes -exhibit selective absorption -when protobionts form from abiotically produced polypeptides, they are known as microspheres Molecular Reproduction -according to RNA world model, RNA was first informational molecule to evolve in the progression toward a self-sustaining, self-reproducing cell -RNA can encode information -RNA is often catalytic (ribozymes) -RNA molecules can bind certain amino acids -Natural selection at the molecular level eventually resulted in the information sequence DNA RNA protein -DNA is a double helix & is more stable than RNA st 1 Living Organism -prokaryotic anaerobic heterotroph -obtained organic molecules from the environment -had a plasma membrane & genetic code -used ATP to store energy -stromatolites fossil evidence of cyanobacteria, oldest known prokaryotes -depleted the environment of spontaneously generated organic molecules -mutations occurred that allowed these cells to produce ATP from light st 1 Autotroph -prokaryotes that carry out photosynthesis -split H2S rather than water; produced sulfur -later organisms (cyanobacteria) evolved to split H2O & produce oxygen -changed environment from reducing environment to oxidizing environment Lecture 10 Chapter 24 Prokaryotes & Viruses A. Prokaryotic Cell -archea & bacteria -have a plasma membrane -generally live in a hypotonic environment -Cell wall made of peptidoglycan amino sugars linked by polypeptides -No organelles (no chloroplasts, mitochondria, Golgi, E.R.) -Circular/Naked DNA -no protein coat no histones -located in nucleoid region -bacterial chromosome -Plasmid -DNA that encodes for catabolic enzymes -resistant to antibiotics -Ribosomes -protein synthesis; free in cytoplasm -Storage vacuoles -store lipids, phosphate compounds, carbohydrates, glycogen -Shape -spherical: coccus (1), diplococcus (2), streptococcus (long chain), staphylococcus (irregular) -rod: bacillus -spiral: spirillum (rigid), spirochete (flexible) -comma shaped: vibrio -Cell Wall Structure -Gram positive bacteria that absorb & retain crystal violet Gram stain - have a thick layer of peptidoglycan molecules held together by amino acids -Gram negative bacteria that do not retain the stain when rinsed with alcohol - have a thin layer of peptidoglycan covered by an outer membrane - cell wall is made up of thin peptidoglycan layer and outer membrane, which has lipoproteins & polysaccharides -Antibiotics such as penicillin interfere with peptidoglycan synthesis -Gram (+) cells inhibited more; Gram () cells more resistant -Capsule - slime layer that surrounds the cell wall - may provide the cell with added protection against phagocytosis -tend to be resistant to white blood cells -Pili -protein structure that helps bacteria adhere to one another or attach to certain surfaces -Flagella -helps prokaryotes move -Motor/basal body -anchors flagellum into the cell wall by disc-shaped plates -bacterium uses energy from ATP to pump protons out of cell -diffusion of these protons back into the cell powers the motor -Hook -connects basal body to filament -Filament -extends into the outside environment -Reproduction -Prokaryotes are asexual & most reproduce by binary fission -occurs in about 20 minutes -the circular DNA replicates -an ingrowth of the plasma membrane & the cell wall forms a transverse wall -Comparable to a eukaryotic (somatic) cell undergoing mitosis -Single parent produces offspring that have identical hereditary traits -Budding -a cell develops a bud that enlarges, matures, & separates from the mother cell -Fragmentation -walls develop within the cell, which then separates into several new cells -Transfer of Genetic Information -Transformation -bacterium dies & releases DNA -fragments of foreign DNA bind to proteins on surface of living bacterium -DNA enters cell, & some DNA is incorporated into host cell by reciprocal recombination -Transduction -DNA is carried from 1 prokaryote to another by a virus -Conjugation -donor bacterium transfer plasmid DNA via pili to a recipient bacterium -Mutation -main source of genetic variability -Survivability -when environment is unfavorable, prokaryotes produce endospores to survive -becomes a resting cell highly resistant to heat, radiation, & disinfectants -when conditions are right, endospores regerminate & bring back prokaryotic cell -Metabolic Diversity -Chemotroph - obtains its energy from chemical compounds -Phototroph - captures energy from light -Heterotrophs obtain carbon atoms from organic compounds of other organisms -Chemoheterotroph (saprobes or saprotrophs) -obtains energy & carbon from dead or decaying organic matter -Photoheterotroph - uses photosynthetic pigments such as chlorophyll to obtain chemical energy from light & make ATP -obtains carbon from organic source -Autotroph uses CO2 as a source of carbon for making organic compounds -Photoautotroph -cyanobacteria -uses light energy to synthesize organic compounds from CO2 & other inorganic compounds -Chemoautotroph -uses CO2 to produce organic material -gets energy from oxidation of inorganic material (ex. NH3 ammonia) -Most prokaryotes are aerobic require oxygen for cellular respiration -Some are anaerobic -Facultative Anaerobes -use oxygen for cellular respiration if available -can carry metabolism anaerobically if necessary -Obligate Anaerobes -respire with terminal electron acceptors other than oxygen -some are killed by oxygen -Two Prokaryotic Domains -Archea -No peptidoglycan in cell wall -Plasma membrane -no fatty acids -glycerol bound to long chain carbohydrates by ether linkages -Can survive in extreme conditions -Extreme Halophiles -heterotrophs that live in saturated brine (salt) solutions -use aerobic respiration to make ATP -Extreme Thermophiles -require a very high temperature for growth (45-110C) -Methanogens -obligate anaerobes that produce methane gas from simple carbon compounds -important in recycling components of organic products of organisms that inhabit swamps -inhabit oxygen-free environments in sewage & swamps; common in digestive tracts of humans & other animals -Bacteria -have plasma membranes that have straight-chain fatty acids linked to glycerol molecules by ester linkages -Proteobacteria (Gram-Negative) -Cyanobacteria -ex. Blue Green Algae -Gram-negative, Photosynthetic -use chlorophyll a -have thylakoids -contain accessory pigments Phycocyanic & Phycoenythrin -contain chlorophyll a and use a photosynthetic process similar to that of plants & algae -Fix N2 NH3 specialized cells heterocysts -anaerobic process -Gram-Positive Bacteria -Actinomycetes -superficially, resemble fungi -however, they have peptidoglycan in their cells, lack nuclear envelopes -most are saprotrophs that decompose organic materials in soil -have branching filaments -contain streptomyocin compound that kills other bacteria -important in stopping tuberculosis -discovered by Selman Waksman -Ecological Roles of Prokaryotes -essential decomposers recycle nutrients -some carry out photosynthesis (cyanobacteria) -nitrogen fixation (cyanobacteria) -antibiotic bacteria (actinomycetes) -many are symbiotic with other organisms -Symbiosis -mutualism both partners benefit -Commensalism -one partner benefits other not helped or harmed -Parasitism -parasite benefits; host is harmed causes disease B. Virus -infectious particle -acellular not composed of cells -reproduces by taking over translational & transcriptional machinery of another cell -obligate intercellular parasites viruses survive only by using the resources of a host cell -Structure -protein coat (capsid) -nucleic acid core DNA or RNA -mimivirus contains DNA & RNA -RNA viruses -In most, RNA synthesis takes place with the help of RNA polymerase -Retrovirus RNA virus that has reverse transcriptase, a DNA polymerase that transcribes the RNA genome into a DNA intermediate - This becomes integrated into the host DNA by an enzyme also carried by the virus - Copies of viral RNA are synthesized as the incorporated DNA is transcribed by host RNA polymerases - HIV is a retrovirus that causes AIDS -Evolution of Viruses -one hypothesis states that virus evolved from existing cells as escaped pieces of nucleic acid -explains specificity of viruses -another hypothesis states that viruses evolved very early before the domains -lost ability to reproduce & became obligate parasites -Reproduction -bacteriophages are viruses that attack bacteria -Lytic reproductive cycle -virus attaches to receptors on host cell -virus penetrates the host plasma membrane and moves into the cytoplasm -virus degrades the host cell nucleic acid & replicates its own nucleic acid -capsid proteins & other needed molecules are synthesized -newly synthesized viral components are assembled into new viruses -lytic enzymes destroy the plasma membrane & viruses are released from cell -Lysogenic reproductive cycle -temperate viruses do not always destroy their hosts -phage attaches to cell surface of bacterium -phage DNA enters bacterial cell -phage DNA integrates into bacterial DNA -integrated prophage replicates when bacterial DNA replicates -lysogenic conversion occurs when bacterial cells containing temperate viruses exhibit new properties -UV light & X-rays may cause a lysogenic cell to revert to a lytic cell Lecture 11 Chapter 25: Protists I. Eukaryotic Cells -formed 2.2 bya -evolved from prokaryotic cells (endosymbiotic process) A.Chloroplast -photoautotroph living inside heterotroph -Red Algae have accessory pigments (Phycocyanin & Phycoerythrin) -Chloroplasts of red algae, green algae, & plants arose in a single primary endosymbiotic event -Multiple secondary endosymbioses led to chloroplasts in euglena and brown algae B.Mitochondria -aerobic heterotroph living inside anaerobic heterotroph -cannot grown on their own; dependent on material in nucleus C.Chloroplasts & Mitochondria -probably originated from endosymbiosis -size similar to bacteria -reproduce by splitting reminiscent of binary fission -contain circular DNA -ribosomes similar to the size of ribosomes in prokaryotes -base sequence of RNA -produce protein -double membrane -expected when one cell engulfs another cell D.Other organelles -evolved from infolding of plasma membrane E.Primary Endosymbiosis -ancient eukaryotic cell engulfed a cyanobacteria, which survived and evolved into a chloroplast -mitochondria surely evolved before chloroplasts F.Secondary Endosymbiosis -a heterotrophic eukaryotic cell engulfed a eukaryotic cell with chloroplasts -cell survived and evolved into a chloroplast surrounded by three membranes II. Protists -most are unicellular -some form colonies, loosely connected groups of cells -some are coenocytic, consisting of a multinucleate mass of cytoplasm -some are multicellular A.Ancestral Protists -Plants photoautotrophs algae -Animals Ingestive Autotrophs -Fungi Absorptive Heterotroph B. Life Cycle (Animal) -Multicellular Diploid (2n) stage predominant -Only haploid cells are the gametes -Meiosis forms haploid (n) gametes, which fuse during fertilization to form a zygote (2n) -Mature adult is formed by a large number of mitotic divisions C. Life Cycle (Simple Eukaryote) -Unicellular Haploid (n) stage predominant -Only diploid cell is the zygote -Zygote immediately undergoes meiosis upon germination -All other cells are formed by mitosis D. Life Cycle (Plants & Some Algae) -Spends part of its life as a multicellular haploid organism and part as a multicellular haploid organism (alternation of generations) E. Algae -Phytoplankton -basis of the marine food chain -photosynthetic a. Discicristaes -Disc-shaped cristae in their mitochondria i. Euglenoids (Phylum Euglenophyta) -1/3 of the species Euglena can photosynthesize -versatile -most live in fresh water -indicator organisms of organic pollution, such as sewage in a lake or stream -have eyespot helps Euglena move to light of an appropriate intensity -have pellicle flexible protein coat -have paramylon body polysaccharide that stores energy reserves b. Alveolates -unicellular protists with alveoli, flattened vesicles located inside plasma membrane -have similar ribosomal DNA sequences -dinoflagellates & diatoms are responsible for the most photosynthesis in oceans i. Dinoflagellates (Phylum Dinoflagellata) -some are photosynthetic -vesicles beneath the plasma membrane -impregnated with cellulose and silica -contain chlorophyll a & c & carotenoid fucoxanthin (yellow/brown pigment) -reproduction is primarily asexual, by mitosis, although some species reproduce sexually -nucleus is distinctive because the chromosomes lack histones, are permanently condensed, and always evident -store oil & polysaccharides -some are heterotrophic -others are autotrophic -some live as Endosymbionts that live in the bodies of marine invertebrates such as mollusks, jellyfish, and corals, lacking cellulose plates & flagella (zooxanthellae) -lack cellulose & no flagella -live in mollusks, jellyfish, & coral animals -cause red tides -algal bloom population -kills fish & birds -produce a nerve toxin -paralytic shellfish poisoning in humans c. Heterokonts -diverse group, but all have motile cells with two flagella, one with tiny, hairlike projections off the shaft i. Diatoms (Phylum Bocilaryhyta) -mostly unicellular photosynthetic protists (some colonial) -most are nonmotile, but some move by gliding -contain chlorophyll a, c, & carotenoids (fucoxanthin) -produce carbohydrate chrysolaminarin -major producers (1-2 million/gal) -cell wall made of silica (glass-like); does not grow -Reproduction -often reproduce asexually by mitosis, becoming progressively smaller with each succeeding generation -when a diatom reaches a fraction of its original size, sexual reproduction occurs, restoring the diatom to its original size -Diatomaceous Earth -deposits of diatoms that are used as filtering, insulating, & soundproofing materials ii. Brown Algae (Phylum Phaeophyta) -multicellular, often quite large, photosynthetic protists (kelp) -biflagellate reproductive cells -most have a life cycle that exhibits alternation of generations -chlorophyll a, c, & fucoxanthin -store carbohydrate laminarin -sea weeds -found in cool, temperate waters -multicellular -have a cell wall composed of cellulose & polysaccharide algin -algin extracted and used as a thickening agent -ice cream, toothpaste, & moisturizing cream -provide vitamins (Iodine) -Kelp -blade -photosynthesis occurs here -stipe -stalk that forms part of the body -holdfast -basal structure for attachment to solid surfaces -form "Forests of the Sea" d. "Plants" -photosynthetic organisms with chloroplasts bounded by outer & inner membranes i. Red Algae (Phylum Rhodophyta) -mostly multicellular, mainly marine protists (some unicellular) -contain chlorophyll a & chlorophyll d, & carotenoids -also have accessory pigments phycocyanin & phycoerythrin -contain carbohydrate floridean starch (Glycogen-like) -do not produce motile cells -seaweed -found in warm, deep tropical water -Helps build tropical reefs -some Red Algae incorporate Calcium into cell wall -No flagella -produce agar -used as a growing media for bacteria -produce carageenan -gives creamy texture to ice cream -Food source -produce Vitamin A & C -reproduction alternates between sexual and asexual stages -cyanobacteria are believed to be ancestral to plastids of red algae ii. Green Algae (Phylum Chlorophyta) -believed to share a common ancestor with land plants -photosynthetic, containing chlorophyll a, chlorophyll b, & carotenoids -cell wall made of cellulose -store main energy reserves as starch -form cell plate during mitosis -has unicellular, colonial, siphonous, and multicellular forms -some are motile and flagellate -reproduction can be sexual or asexual -isogamous 2 flagellate gametes identical in size -anisogamous 2 flagellate gametes of different sizes -found in both aquatic and terrestrial environments -ex. Chlamydomonas is a green alga that has motile cells with haploid nuclei Lecture 12 Chapter 26 Fungi A. Fungi - eukaryotic, mainly multicellular - cells contain membrane-enclosed nuclei, mitochondria, and other membrane organelles - can thrive in harsh environments - lack swimming reproductive cells 1. Absorb Food from the Environment - cannot produce their own organic materials from a simple carbon source - heterotrophs - infiltrate a food source and secrete digestive enzymes onto it 2. Cell Wall Structure - cell walls contain complex carbohydrates, including chitin - Fungal cells are enclosed by cell walls during at least some stage in their life cycle 3. Filamentous Body Plan - Simplest fungi are yeast, which are unicellular, non-filamentous, with a round or oval shape - Most fungi are molds - fast growing mycelium of any asexually reproducing fungus - consist of long, branched, threadlike filaments called hyphae - Hyphae are a fungal mode of nutrition - absorbs nutrients through its large surface area - develops from a unicellular spore; they form a tangled mass of tissue like aggregation as known mycelium - separated by cross walls called septa - are perforated by a pore that may be large enough to permit organelles to float from cell to cell - coenocytic fungi lack septa 4. Reproduction by Spores - Fungi produce nonmotile spores asexually or sexually - produced on aerial hyphae or in fruting structures - Structures in which the spores are produces are called sporangia - The aerial hyphae of some fungi produce spores in large, complex reproductive structures referred to as fruiting bodies. 5. Asexual Reproduction - Yeasts produce asexually, primarily by forming buds that pinch off from the parental cell - Spores are produced through mitosis - Conidiophores are specialized hyphae that produce asexual spores called conidia 6. Most Fungi Reproduce Sexually - Hyphae of two genetically compatible mating types come together, and their cytoplasm fuses, a process known as plasmogamy - This cell gives rise by mitosis to other cells with two nuclei - At some point the two haploid nuclei fuse (karyogamy) - results in cell containing a diploid nucleus known as a zygote - Hyphae that contain two genetically distinct, sexually compatible nuclei within each cell are described as dikaryotic (n+n) because two separate haploid nuclei - Karyogamy produces a zygote nucleus that undergoes meiosis 7. Fungal Diversity - Like plants, all fungi have cell walls, but unlike plants, fungal cells do not contain cellulose - Like animals, some fungi have flagellate cells, which propel themselves with a single posterior flagellum - Like animals, fungal cells have platelike cristae in their mitochondria - Are assigned to the opisthokont clade, a monophyletic group 8. Phylum Chytridiomycota - ex. Chytridiomycetes/Chytrids - parasites and decomposers found mainly in fresh water - motile cells (gametes & zoospores) contain single, posterior flagellum - reproduce both sexually and asexually (alternation of generations) - spends part of its life as a multicellular haploid thallus and part as a multicellular diploid thallus - The thallus may have slender extensions, called rhizoids that anchor it to a food source and absorbs food - haploid zoospores produced in resting sporangia - most are decomposers that degrade organic matter - probably the earliest fungi to evolve from a flagellate protist, the common ancestor of all fungi 9. Phylum Zygomycota - ex. Zygomycetes (molds) - important decomposers that live in the soil on decaying plant or animal matter - some are insect parasites - produce sexual resting spores (zygospores) and nonmotile, haploid, asexual spores in sporangium - hyphae are coenocytic - many are heterothallic (2 mating types) sexual reproduction occurs only between a member of a (+) strain and one of a (-) strain - ex. Microsporidia are opportunistic pathogens that infect animals - ex. Black bread mold (Rhizopus stolonifer) breaks down bread when a spore falls on it and then germinates and grows into a mycelium 10. Phylum Glomeromycota -ex. Glomeromycetes -symbionts that form intracellular mycorrhizal associations with roots of most trees and herbaceous plants -reproduce asexually with large, multinucleate spores (blastospores) -endomycorrhizal fungi glomeromycetes extend their hyphae through the cell walls of root cells but do not penetrate the plasma membrane, as the membrane only surrounds it -arbuscular mycorrhizae the hyphae inside the root cells form branched, treeshaped structures (arbuscles), which are the site of nutrient exchange between the plant & the fungus -enhance plant nutrition by absorbing water & sugar from the roots through the fungal hyphae 11. Phylum Ascomycota -ex. Ascomyetes or sac fungi (yeasts, powdery mildews, molds, morels, truffels) -important symbionts -98% of lichen-forming fungi belong to this phylum -some form mycorrhizae -during sexual reproduction: ascospores are formed in sacs (asci) -plasmogamy takes place as hyphae of two different mating types fuse -plasmogamy occurs, & nuclei are exchanged -dikaryotic stage occurs in which hyphae form and produce asci & an ascocarp -After karyogamy & meiosis, the recombinant nuclei divide by mitosis, producing 8 haploid nuclei that develop into ascospores -When the ascospores germinate, they can form new mycelia -during asexual reproduction: spores (conidia) are produced, which pinch off from conidiophores; process of budding -hyphae usually have perforated septa -Ascomycetes cause important plant diseases such as Dutch elm disease 12. Phylum Basidiomycota -ex. Basidiomycetes or club fungi (mushrooms, bracket fungi, puffballs) -many form mycorrhizae with tree roots -during sexual reproduction: basidiospores are formed on basidium -plasmogamy occurs with the fusion of two hyphae of different mating types -a dikaryotic secondary mycelium forms -A basidiocarp develops and basidia form -Karyogamy occurs, producing a diploid zygote nucleus -Meiosis produces 4 haploid cells that become basidiospores -When basidiospores germinate, they form haploid primary mycelia -asexual reproduction uncommon -heterothallic -hyphae usually have perforated septa 13. Lichens - symbiotic relationships between a fungus and a photoautotroph (an alga or cyanobacterium) - Cructose lichens - flat and grow tightly against their substrate - Foliose lichens - flat, with leaflike lobes - Fruticose lichens grow erect and have many branches - Lichens reproduce asexually usually by fragmentation, in which the soredia break off and land to make more. - Indicator of air pollution 14. Fungi & Plant Diseases - Parasitic fungi often produce special hyphal branches called haustoria Lecture 13 Chapter 27 The Plant Kingdom: Seedless Plants I. Similarities Between Plants & Green Algae A. Chlorophyll a, b, & Carotenoids B. Produce starch as a storage product C. Cellulose Cell Wall D. Form cell plate during cytokinesis II. Adaptations of Plants to Land A. Waxy cuticle 1. covers the aerial portion of a plant 2. prevents desiccation, or drying out, of plant tissue by evaporation 3. Because it covers the external surfaces of leaves and stems, however gas exchange through the cuticle between the atmosphere and the interior of cells is negligible B. Stomata 1. pores that facilitate gas exchange C. Multicellular Gametangia 1. fertilized egg develops into a multicellular embryo within the female gametangium 2. Antheridia produce sperm and Archegonia produce egg D. Alternation of Generations 1. The haploid portion of the life cycle is called the gametophyte generation because it gives rise to haploid gametes by mitosis 2. When two gametes fuse, the diploid portion of the life cycle, called the sporophyte generation begins 3. sporophyte generation - produces haploid spores by the process of meiosis; these spores represent the first stage in the gametophyte generation 4. The haploid gametophytes produce male gametangia, known as antheridia in which sperm cells form and the female gametangia known as archegonia 5. One sperm cell fertilizes the egg to form a zygote, a fertilized egg 6. The mature sporophyte has sporogenous cells that divide by meiosis to form haploid spores a. All plants produce spores by meiosis whereas algae and fungi may produce spores by mitosis or meiosis E. Lignin 1. strengthening polymer incorporated into cell wall a. in cells whose main functions include support & transport III. Four Major Groups of Plants Evolved A. Bryophytes 1. Nonvascular plants with a dominant gametophyte generation a. Do not produce seeds, and do not have vascular tissues (xylem & phloem) 2. Small, require a moist environment 3. Mosses (Phylum Bryophyta) a. gametophytes are differentiated into "leaves" and "stems" b. has tiny hairlike absorptive structures called rhizoids and an upright, stemlike structure that bears leaflike blades c. do not have true roots, stems, or leaves; the moss structures are not homologous to roots, stems, or leaves in vascular plants d. Life Cycle 1. Green moss gametophyte often bears its gametangia at the top of the plant 2. Sperm cells, which have flagella, are transported from antheridium to archegonium by flowing water 3. Zygote formed by fertilization (syngamy) grows by mitosis into a multicellular embryo that develops into a mature moss sporophyte 4. Diploid Sporophyte grows out but is still nutritionally dependent on the gametophyte 5. Sporogenous cells undergo meiosis in the sporangium 6. When spores mature, the capsule opens and releases the spores, which are then transported by wind or rain 7. When it lands in a comfortable place it grows into a filament of cells called protonema B. Seedless Vascular Plants 1. Vascular plants with a dominant sporophyte generation 2. Reproduction depends on water as a transport medium for motile sperm cells 3. Ferns (Phylum Pteridophyta) a. Life Cycle 1. the fern sporophyte consists of a horizontal underground stem, or rhizome that bears leaves called fronds and bears fruits a. Many species bear the sporangia in clusters called sori 2. Sporogenous cells undergo meiosis to form haploid spores. The sporangia burst open and discharge spores that may germinate and grow by mitosis in the gametophytes 3. The mature fern gametophyte is a tiny heart shaped structure that grows flat against the ground 4. This structure is called the prothallus. 5. Each archegonium contains a single egg 6. Ferns use water as a transport medium, the flagellate sperm swim from a nearby prothallus, however the sporophyte becomes free living. C. Vascular Seed Plants with Naked Seeds (Gymnosperms) D. Vascular Seed Plants with Seeds Enclosed in Fruit (Angiosperms) Lecture 14 Chapter 28 The Plant Kingdom: Seed Plants; Chapter 36: Reproduction in Flowering Plants A. Plants developed certain characteristics 1. Elimination of free living Gametophyte Gametophyte stage dependent on sporophyte stage 2. Elimination of swimming sperm sperm now travels by wind, animal, insect, etc. 3. Greater protection for young sporophyte (seed) seed replaces spore as primary means of dispersal success rate is greater with the seed because it carries a multicelled sporophyte seed also contains food supply seed has a hard, multicelled seed coat & can survive for long periods of time at a reduced metabolic rate Gymnosperms seed producing plant that has naked/unprotected seed (no ovary wall) -Phylum Coniferophyta (pine tree) -produces heterospores rather than homospores -Homospores spores are all similar; produces gametophyte with both antheridia & archegonia -characteristic of bryophytes and most ferns -Heterospores -1. microspore produces microgametophyte (male) -2. megaspore produces megagametophyte (female) -sperm travels from microgametophyte to megagametophyte to produce sporophyte, & seed develops around it -megasporangium undergoes meiosis & produces megaspore, which leads to development of megagametophyte, which produces egg in archegonia -egg is fertilized which produces zygote, which divides to form embryonic sporophyte -outer covering (integument) of megasporangium will harden & form the seed coat -characteristic of gymnosperms and angiosperms Pine Life Cycle -sporophyte generation (2n) dominant stage -reproductive structure is the cone -2 types of cones: small (male) & large (female) -Male Cone -believed to be a modified leaf that produces spores (sporophyll) -microsporocyte (2n) undergoes meiosis to become microspore (n) -microspores undergo meiosis & cytokinesis to become extremely reduced gametophytes (pollen grains) -each consists of 4 cells: 2 prothallial cells, 1 generative cell, & 1 tube cell -air current carries microgametophytes with it -Female Cone -believed to have evolved from modified stem -megasporocyte (2n) undergoes meiosis to become 4 megaspores (3 of which die) -megaspore undergoes mitosis & cytokinesis to become a megagametophyte, which produces egg in archegonia -microgametophytes carried by air current attach to sticky substance near megasporangium and goes inside -tube cell grows toward the archegonia and forms a pollen tube -the generative cell follows the tube cell towards the archegonia, divides by mitosis, which produces a stalk cell and a body cell -the body cell produces 2 sperm; 1 dies and 1 fertilizes the egg - -each seed has a papery wing attached to enable dispersal by air currents -process takes 2 years to complete -pollination movement of microgametophyte (pollen) to female part of plant -fertilization egg and sperm combine to produce zygote I. Angiosperms -flowering plant; most successful plants A. Phylum Anthophyta -Monocotyledones & Eudicotyledones Monocot Eudicot Herbaceous (green); don't develop wood Can be either herbaceous or woody Long narrow leaves with parallel veins Leaves are broad & veins are netted Fibrous root system (xylem & phloem) Taproot system Flower parts are in groups of 3 Flower parts are in groups of 4 or 5 1 embryonic seed leaf (cotyledon) 2 embryonic seed leaves (cotyledons) Mature seed still has some endosperm Mature seed has no endosperm; as 2 cotyledons serve as the food storage organ Pollen grains have 1 furrow or pore Pollen grains have three furrows or pores Vascular bundles in stem cross section are Vascular bundles in stem cross section are usually scattered or have a more complex arranged in a ring arrangement B. Flower believed to be a group of modified leaves C. Flower Structure 1. Peduncle - flower stalk that holds all 4 flower parts; may terminate in a single flower or a cluster of flowers (inflorescence) 2. Sepal lowermost & uppermost whorl on a flower shoot that covers & protects the other flower parts when the flower is a bud a. calyx all sepals of a flower 3. Receptacle tip of the stalk that bears the flower parts 4. Petals whorl just above the sepals that are broad, flat, & thin; play important role in attracting animal pollinators a. corolla all petals of a flower 5. Stamen male part of a flower a. filament thin stalk b. anther produces microspores and, ultimately, pollen grains 6. Pistil female part of a flower; consists of 1 or more closed carpels a. stigma section on which pollen grain lands b. style necklike structure through which pollen tube grows c. ovary enlarged structure that contains 1 or more ovules -A flower is said to be complete if it has all 4 parts (petal, stamen, pistil, & sepal) -A flower is perfect if it has both stamens & carpels -If a flower has a bright color & it has an odor or nectar (sugar solution), it was pollinated by an animal -If it has a blue or yellow color it was pollinated by an insect (pollinate flowers most) -If it has a red or orange color it was pollinated by another animal (bird, etc.) D. Flower Reproduction/Double Fertilization 1. The ovule in an ovary contains a megasporocyte that undergoes meiosis to produce 4 haploid megaspores (3 of which disintegrate) 2. 1 megaspore divides by mitosis & develops into an embryo sac (mature female gametophyte) a. An embryo sac contains 7 cells with 8 haploid nuclei b. 3 antipodal haploid cells, 2 haploid synergids (closely associated with egg), 1 haploid egg, & 1 dikaryotic central cell with polar nuclei 3. Each microsporangium (pollen sac) of the anther contains numerous microsporocytes, each of which undergoes meiosis to form 4 haploid microspores 4. Every microspore develops into an immature male gametophyte, which consists of the tube cell & the generative cell 5. The anthers open and spread pollen, being transferred to the stigma by wind, water, insects, or other animal pollinators 6. The pollen grain germinates, as the tube cell forms a pollen tube that grows down the style & into the ovary 7. Generative cell enters pollen tube and divides by mitosis to produce 2 sperm a. 1 sperm fertilizes egg and forms 2n zygote b. 1 sperm combines with polar nuclei to produce endosperm (3n), a nutrient tissue rich in carbohydrates, lipids, & proteins that nourishes the growing embryo 8. apical cell, which develops into the plant embryo, divides to form a small cluster of cells (proembryo) 9. basal cell develops into a suspensor, an embryonic tissue that anchors the developing embryo & aids in nutrient uptake from the endosperm 10. Globular embryo develops as cell division continues, forming a sphere of cells 11. Heart shaped embryo develops as eudicot embryo starts to develop its 2 cotyledons 12. Torpedo shaped embryo develops as cotyledons elongate and embryo crushes suspensor 13. Ovary wall surrounding seed (developed from ovule) enlarges and develops into a fruit. E. Adaptations of Flowers 1. Seed production gives flower a great success rate because the seed contains the food supply, a multicelled sporophyte, and its durable seed coat allows it to survive for long periods of time. 2. Closed carpels give rise to fruits that surround the seeds 3. The process of double fertilization increases chances of reproductive success 4. Has interdependent relationships with animal pollinators, which disperse pollen from one flower to another. 5. This transfer of pollen results in cross-fertilization, which promotes genetic variation 6. Most flowers have carbohydrate-conducting sieve tube elements in their phloem 7. Broad, expanded leaves are very efficient at absorbing light for photosynthesis. 8. The sporophyte generation readily adapts to changing environments. F. Evolution of Flowering Plants 1. Seed plants arose from seedless vascular plants 2. Progymnosperms descended from these plants, and had... a. leaves with branching veins (megaphylls) b. woody tissue (secondary xylem) 3. Progymnosperms probably gave rise to conifers as well as to seed ferns, which in turn likely gave rise to cycads and possibly ginkgo. 4. Flowering plants most likely descended from ancient gymnosperms with broad, expanded leaves and closed carpels. Lecture 15: Chapter 32 Plant Structure, Growth, & Differentiation A. Fruit -develops during development of embryo; protects seed -Simple Fruit forms from 1 ovary Fleshy (ex. Tomato) or Dry (ex. Acorn) -Aggregate Fruit produced from 1 flower, but many ovaries (ex. blackberry, raspberry) -Multiple Fruit develops from many flowers on a short piece of stem (ex. pineapple) -Accessory Fruit develops from receptacle, which enlarges (ex. apple, pear) B. Plant Anatomy -Plant Cells -has plasma membrane around outside -80% of it is vacuole -Primary Cell Wall -has while cell is still growing -composed of polymer cellulose, as well as hemicelluloses and pectin -can expand because microfibrils slide past one another -Secondary Cell Wall -in addition to hemicelluloses and pectin, has lignin and cellulose to hold microfibrils together - lignin makes secondary cell walls rigid -Middle Lamella -composed of pectin -holds cells together -cells organize themselves into tissues 1. Simple tissue composed of only 1 cell type 2. Complex tissue composed of more than 1 cell type -Tissues are organized into tissue systems 1. Ground makes up most of plant; functions in storage and photosynthesis, as well as support in young plants 2. Vascular conducts and transports materials; becomes primary means of support as plant gets older 3. Dermal outer covering of plant; functions in protection C. Ground Tissue System -composed of 3 simple tissues 1. Parenchyma Tissue - composed of parenchyma cells - only has primary cell wall (mostly cellulose, also hemicelluloses and pectin) - usually fairly large; function primarily in storage (starch, oil, water, salts) and photosynthesis - function in process of secretion (resins, tannins, hormones, enzymes, nectar) - can differentiate into other cells (when plant is injured) 2. Collenchyma Tissue - composed of collenchyma cells - only has primary cell wall (mostly pectin, also cellulose and hemicelluloses) - provides support in nonwoody tissue - found in leaf veins (found in celery strings) - contain thickenings in the corners, which are composed of extra pectin 3. Sclerenchyma Tissue - only has secondary cell wall (mostly lignin, also pectin, cellulose, and hemicellulose) - provides protection and support - said to be dead at functional maturity - cell dies because nutrients can't get in and wastes can't get out - composed of two types of sclerenchyma cells: fibers and sclerids - Fibers - long, tapered cells that occur in patches or clumps - particularly abundant in the wood, inner bark, and leaf ribs (veins) of flowering plants - Sclereids - cells of variable shape - common in the shells of nuts and in the stones of cherries and peaches D. Vascular Tissue System - composed of 2 complex tissues 1. Xylem Tissue - moves water and dissolves materials from root up to top of plant - provides support - composed of parenchyma cells, fibers, tracheids, vessel elements a. Xylem Parenchyma Cells - function in storage b. Fibers (Sclerenchyma Cells) - function in support and strength c. Tracheids - evolutionarily older than vessel elements - dead at functional maturity; sit one on top of the other - function in conduction of water and nutrient materials; support - have pits, thin areas in the cell walls where a secondary wall did not form - areas through which water can diffuse more easily d. Vessel Elements - shorter and broader than vessel elements - dead at functional maturity; sit one on top of the other - end walls have perforations (holes) - function in conduction of water and nutrient materials; support - have pits in their cell walls that permit the lateral transport of water from one vessel to another 2. Phloem Tissue - conducts food materials (carbohydrates formed during photosynthesis), throughout the plant and provides structural support - composed of parenchyma cells, fibers, sieve tube elements, and companion cells a. Phloem Parenchyma Cells - function in storage b. Fibers (Sclerenchyma Cells) - provide additional structural support for the plant body c. Sieve Tube Elements - alive at functional maturity; one on top of other to form sieve tubes - lacks nucleus and other organelles at maturity - end walls are sieve plates - function in conduction of sugar in solution - has plasmodesmata, which are cytoplasmic connections through which cytoplasm extends from one cell to another d. Companion Cells - directs metabolism of sieve tube element - has nucleus and organelles - connected by plasmodesmata - living at functional maturity - assists in moving sugars into and out of sieve tube elements E. Dermal Tissue System - composed of 2 complex tissues: epidermis and periderm 1. Epidermis - composed of epidermal cells a. Epidermal cells - have no chloroplasts - transparent in order for light to penetrate the inner tissues of stems and leaves - forms protective surface of plant body - prevent water loss with waxy cuticle, which is made of cutin b. Guard cells - chloroplast-containing cell that occurs in pairs - pair changes shape to open and close stomatal pore c. Trichome - hair or other epidermal outgrowth - in root, function in uptake of water (root hairs) - some function in protection - can also function in salt removal - in hotter areas, function as a reflector (of sun, resulting in cooling) 2. Periderm - outer bark of plant; composed of cork cells, cork cambium cells, and cork parenchyma cells a. Cork cells - dead at maturity - cell walls contain suberin a water-proofing material - reduces water loss and prevents disease-causing organisms from penetrating b. Cork Cambium Cells - meristematic (form new cells) c. Cork Parenchyma Cells - function in storage F. Plant Growth - involves 3 processes: cell division, cell elongation, & cell differentiation 1. Cell Division a. results in an increase in the number of cells b. occurs in apical meristem 2. Cell Elongation a. the cytoplasm grows and the vacuole fills with water, which exerts pressure on the cell wall and causes it to expand 3. Cell Differentiation a. specialization into various cell types 4. Primary Growth - occurs as a result of the activity of apical meristems, areas located at the tips of roots and shoots - growth in length 5. Secondary Growth - growth in width and diameter - cell division occurs in lateral meristems, areas extending along the entire length of the stems and roots except at the tips - vascular cambium and cork cambium are responsible Lecture 16: Chapter 35 Roots & Mineral Nutrition I. Root Systems - two types of root systems: fibrous and tap A. Fibrous Root System - has several roots of similar size developing from the end of the stem, with lateral roots branching off these roots - form in plants that have a short-lived embryonic root - exist in monocots - adventitious roots develop from parts of a plant other than another root B. Taproot System - consists of 1 main root that formed from the seedling's enlarging radicle, or embryonic root - many lateral roots of various sizes branch out of a taproot - exist in eudicots II. Root Structure A. Root Cap - protective, slime layer many cells thick - protects apical meristem - allows easier movement of root into stem - detects detection of gravity - may orient root so that it grows downward B. Apical Meristem - area of cell division - cells divide up and down root C. Root Hairs - extension of cytoplasm of epidermal cell - increases surface area for absorption - fairly short lived - area of maturation - no waxy cuticle D. Area of Elongation - vessels pick up water and form large vacuoles - some differentiation occurs here, above the apical meristem III. Herbaceous Eudicot Root - central core of vascular tissue lacks pith, a ground tissue found in the center of many stems and roots A. epidermis covers the root B. cortex composed of loosely packed parenchyma cells - composed the bulk of a herbaceous eudicot root - primary function is storage of starch, an insoluble carbohydrate composed of glucose subunits - these reserves provide energy for growth and cell replacement following an injury - have intercellular spaces that provide a pathway for water uptake and allow for aeration of root - usually lack supporting collenchyma cells, probably because the soil supports the root C. Endodermis innermost layer of cortex that regulates the movement of water and minerals that enter the xylem 1. Casparian strip barrier to water movement through the endodermis because it is impregnated with suberin, a waterproof fatty material D. Stele/Vascular Cylinder a central cylinder of vascular tissues 1. Pericycle the outermost layer of the stele - consists of 1 layer of parenchyma cells that give rise to multicellular lateral roots - lateral roots originate when cells in a portion of the pericycle start dividing - as these roots grow, they push through several layers of root tissue before entering the soil -contains all the structures and features of the larger root from which it emerges 2. Xylem centermost tissue of the stele 3. Phloem located in patches between the xylem arms 4. Vascular Cambium gives rise to secondary tissues in woody plants; in between xylem & phloem E. Movement of Water & Dissolved Materials 1. Symplast continuum of living cytoplasm, which is connected from 1 cell to the next by plasmodesmata - some dissolved mineral ions move from the epidermis through the cortex via the symplast 2. Apoplast consists of the interconnected porous cell walls, along which water and mineral ions move freely - water and mineral ions move freely across the cortex without ever crossing a plasma membrane to enter a living cell - water and mineral ions cross a cell membrane only 4 times from soil to xylem - Water always moves via osmosis into xylem, from hypertonic to hypotonic environment, either through plasma membrane or via proteins (aquaporins) - Minerals move from lower to higher concentration (carrier-mediated active transport) IV. Monocot Root - vary considerably in internal structure - layers found in some are epidermis, cortex, endodermis, and pericycle - unlike the xylem in herbaceous eudicot roots, the phloem and xylem are in separate, alternating bundles arranged around the central pith, which consists of parenchyma cells - since secondary growth never occurs, there are no vascular cambium V. Secondary Growth in Woody Plants 1. Vascular cambium is in between the primary xylem & primary phloem 2. When secondary growth starts, vascular cambium extends out to pericycle, forming a continuous, noncircular loop 3. Vascular cambium produces secondary xylem (wood) to its inside and secondary phloem (bark) to its outside 4. The ring of vascular cambium gradually becomes circular. 5. As vascular cambium continues to divide, epidermis, cortex, and primary phloem are torn apart 6. Root epidermis is replaced by periderm, composed of cork cells & cork parenchyma VI. Soil - 45% inorganic, 5% organic, 25% air, 25% water A. Inorganic Materials - come from weathering of rock (freezing and thawing, breaking up into pieces) - plants and other living organisms break up rock because they produce CO2, which when combined with water, produces H2CO3 (carbonic acid), which acts on the rock 1. Texture of Soil - Sand - .02 2 mm - Silt - .002 - .02 mm - Clay - <.002 mm; since it is small, it has a large surface area (1 lb of clay covers 2.5 acres) 2. Cation Exchange - cations, positively charged mineral ions, are attracted and reversibly bound to negatively charged clay particles - roots secrete protons (H+), which are exchanged for other positively charged mineral ions, freeing them into the soil water to be absorbed by roots - anions are repelled by the negative surface charges of clay particles and tend to remain in solution, being washed out of the root zone by soil water B. Organic Materials - living and nonliving - holds water that can be released to the plant - Humus partially decayed organic material C. Soil pH - typically ranges from 4.0-8.0, with an optimum between 6-7 - if pH is too low, cations are washed out - Calcium and Phosphorous precipitate at high pH levels D. Plant Nutrition - 19 of 90 naturally occurring elements are essential for plant growth - 2 groups: Macronutrients and Micronutrients 1. Macronutrients - C, H, O - part of structure of all biologically important molecules -N - part of proteins, nucleic acids, and chlorophyll -K - helps maintain turgidity of cells -S - in certain amino acids and vitamins - Mg - part of chlorophyll molecule - Ca - component of middle lamella -P - component of nucleic acids and phospholipids - Si - reinforces cell walls - needed in levels greater than 0.05% of dry weight of plant 2. Micronutrients - Fe - involved in photosynthesis, respiration, and nitrogen fixation -needed in levels less than 0.05% of dry weight of plant -needed in small amounts because most function as cofactors of enzymes E. Old Leaf & New Leaf - many nutrients have different mobilities - if deficiencies are seen in... - old leaf nutrient is mobile because plant is taking nutrient from old leaf and sending it to new leaf - new leaf nutrient is immobile VII. Root Associations with Bacteria - Cyanobacteria fix N2, through their specialized cells, heterocysts - Legumes and bacteria Rhizobium have symbiotic relationship to fix nitrogen - Produce leghemoglobin located in root nodules and binds O2 -Hemo part coded by DNA of bacterium -Globin part coded by DNA of plant Lecture 17 Chapter 33-34: Leaves, Stems & Plant Transport I. Leaf Structure A. Cuticle 1. waxy layer made of cutin that reduces water loss from exterior walls of epidermal cells B. Epidermis 1. covers the upper and lower surfaces 2. relatively transparent & allows light to penetrate to the interior of the leaf where the photosynthetic ground tissue, mesophyll, is located C. Palisade Mesophyll 1. vertically stacked, columnar mesophyll cells near the upper epidermis 2. part of photosynthetic ground tissue of leaf 3. main site of photosynthesis D. Vascular Bundle/Vein - Extends through the mesophyll - supplies mesophyll with water, minerals, & dissolved sugar 1. Xylem a. located in upper part of vein 2. Phloem a. confined to lower part of vein 3. Bundle Sheath a. tightly packed parenchyma or sclerenchyma cells around vein b. provides additional support to prevent leaf from collapsing under its own weight 4. Bundle Sheath Extensions a. support columns that extend through the mesophyll from the upper to lower epidermis E. Spongy Mesophyll 1. loosely, irregularly arranged mesophyll cells near lower epidermis 2. part of photosynthetic ground tissue of leaf 3. allows diffusion of gases, particularly CO2, within leaf F. Stoma 1. minute opening for gas exchange between leaf cells and the environment 2. CO2 diffuses into leaf through stomata 3. O2 diffuses rapidly out of leaf through stomata G. Guard Cells 1. responsible for opening and closing stoma 2. only epidermal cells with chloroplasts H. Subsidiary Cells 1. provide a reservoir of water & ions that move into and out of the guard cells as they change shape during stomatal opening & closing II. Stomatal Opening & Closing A. Stomatal Opening 1. Blue light, which is a component of sunlight and has wavelengths of 400 nm 500 nm, is absorbed by yellow pigments in the guard cells, activating proton pumps located in the guard cell plasma membrane. a. Blue light triggers synthesis of malic acid & the hydrolysis of starch 2. Proton pumps use ATP to pump H+ out of guard cells, forming an electrochemical gradient a. H+ are formed when malic acid ionizes to form H+ & malate anions 3. Potassium ions enter guard cells through voltage-activated ion channels, which open when a difference in charge between the 2 sides of the guard cell plasma membrane 4. Chloride ions also enter guard cells through ion channels a. Chloride & malate ions help to electrically balance potassium ions 5. Ions accumulate in the vacuoles of guard cells, increasing their solute concentration so that eater enters guard cells from epidermal cells by osmosis B. Stomatal Closing 1. Stomata close in the late afternoon or early evening 2. Concentration of potassium ions slowly decreases throughout day 3. Concentration of sucrose increases throughout day and decreases by evening 4. Concentrations of CO2 in the leaf induce stomata to open 5. During a prolonged drought, stomata remain closed III. Transpiration & Guttation A. Transpiration 1. loss of water vapor by evaporation from aerial plant parts 2. 99% of water a plant absorbs from soil is lost by evaporation from leaves 3. Factors that increase transpiration include, temperature, light, wind, & dry air B. Guttation 1. appearance of water droplets on leaves, forced out through leaf pores by root pressure 2. occurs when transpiration is negligible and available soil moisture is high 3. typically occurs by night because stomata are closed, but water continues to move into the roots by osmosis IV. External Stem Structure A. Terminal Bud 1. embryonic shoot located at the tip of a stem 2. Bud Scale a. modified leaves that cover dormant apical meristem of terminal bud B. Axillary/Lateral Bud 1. located in the axis of a plant's leaves C. Node 1. area on a stem where each lead is attached D. Internode 1. region between 2 successive nodes E. Terminal Bud Scale Scars 1. scar on a twig left when a bud scale abscises from terminal bud F. Leaf Scar 1. shows where each leaf was attached on the stem 2. Bundle Scar a. vascular tissue that extend from the stem out into the leaf b. within a leaf scar G. Lenticel 1. site of loosely arranged cells that allow oxygen to diffuse into the interior of the woody stem V. Stem Growth & Structure A. Internal Structure of Herbaceous Eudicot Stem 1. Features epidermis, cuticle, stomata, & cortex 2. Vascular tissues are located in bundles that, when viewed in cross section, are arranged in a circle 3. Phloem Fiber Cap a. cluster of fibers towards outside of vascular bundle that helps strengthen stem 4. Pith a. ground tissue at center of stem that consists of large, thin-walled parenchyma cells that function in storage 5. Pith Rays a. areas of parenchyma between vascular bundles B. Internal Structure of Monocot Stem 1. Vascular bundles are scattered throughout stem 2. Do not have distinct areas of cortex and pith 3. Do not possess lateral meristems (vascular cambium & cork cambium) that give rise to secondary growth C. Secondary Growth 1. Annual Rings a. concentric circles composed of secondary xylem found in cross sections of wood b. exhibited by woody plants that grow in temperate climates where there is a growing period and a dormant period 2. Springwood/Early Wood a. wood formed by vascular cambium that has large-diameter conducting cells (tracheids & vessel elements), but few fibers b. formed during spring, when water is plentiful 3. Summerwood/Late Wood a. has narrower conducting cells and many fibers b. formed during summer, when water is less plentiful VI. Transport in the Plant Body A. Transport of Water & Minerals in Xylem 1. Water Potential a. free energy of water b. measure of cell's ability to absorb water by osmosis c. provides a measure of water's tendency to evaporate from cells d. Hydration i. induced by solutes; water molecules surround ions & polar molecules, keeping them in solution by preventing them from coming together e. dissolved solutes lower water potential to a negative number f. water moves from a region of higher water potential to a region of lower water potential 2. Tension-Cohesion/Transpiration-Cohesion Model - proposed by Irish botanist Henry Dixon a. water vapor transpires from surfaces of leaf mesophyll cells to drier atmosphere through stomata b. produces tension that pulls water out of leaf xylem toward mesophyll cells c. cohesion of water molecules by hydrogen bonding allows unbroken columns of water to be pulled up narrow vessels & tracheids of stem xylem d. pulls water up root xylem, causing soil water to diffuse into root, forming continuous column of water from root xylem to stem xylem to leaf xylem e. there is a water potential gradient from the least negative (soil) up through the plant to the most negative (atmosphere) B. Translocation of Sugar Solution in Phloem 1. Pressure-Flow Hypothesis - proposed by German scientist Ernst Munch - sucrose is translocated in individual sieve tubes from a source, an area of excess sugar supply (usually a leaf) to a sink, an area of storage (as insoluble starch) or of sugar use, such as roots, apical meristems, fruits, & seeds a. ATP supplies energy to pump protons out of sieve tube element b. produces a proton gradient that drives uptake of sugar through specific channels by cotransport of protons back into sieve tube elements c. due to increase in dissolved sugars, water moves by osmosis from xylem into sieve tubes, increasing turgor pressure inside them d. at sink, sugar is unloaded by active & passive mechanisms from the sieve tube elements e. water diffuses from phloem to xylem as a result of increased water potential in sieve tube Lecture 18 Chapter 37 Plant Growth & Development I. Tropisms - directional growth response elicited by environmental stimulus A. Phototropism 1. directional growth of plant caused by light 2. triggered by blue light with wavelengths less than 500 nm 3. Photoreceptor a. light-sensitive substance that absorbs light b. Phototropins i. family of blue pigments that absorb blue light & triggers phototropic response ii. light-activated kinase, enzyme that transfers phosphate groups iii. becomes phosphorylated in response to blue light B. Gravitropism 1. growth in response to direction of gravity 2. root cap is site of gravity perception in roots, and when removed, root continues to grow but loses any ability to perceive gravity 3. Amyloplasts a. contain starch b. collect towards bottom of root cap cells in response to gravity c. may initiate some of gravitropic response C. Thigmotropism 1. growth in response to mechanical stimulus, such as contact with a solid object II. Plant Hormones & Development - Plant Hormone organic compound that acts as a signal that functions in the regulation of growth & development; effects of which often occur close to where they are produced - Signal Transduction receptor converts an extracellular signal into an intracellular signal that causes some change in the cell - Enzyme-linked receptor hormone binds to receptor in plasma membrane & triggers an enzymatic reaction A. Auxins - Charles & Frances Darwin determined that the coleoptile, a collective sheath that encircles a stem, was responsible for sensing light - Frits Went proposed that chemicals could diffuse from cut tips into agar blocks - Placement of agar blocks could stimulate growth on one side of a seedling or the other; named substance auxin - Indoleacetic acid (IAA) is the most common natural auxin - Moves downward from shoot apical meristems, young leaves, & seeds from where it's produced - Movement is polar, or unidirectional - Promotes cell elongation in stems & growing shoots - Promotes apical dominance; inhibits axillary buds - Involved in root initiation & fruit development - causes wall loosening by breaking hemicellulose cross-links - Synthetic auxins are used commercially as herbicides & stimuli in plant growth and production B. Gibberellins (GA) - discovered by Japanese biologist, studying disease of rice - naturally produced by healthy plants since it promotes stem elongation - produced in young leaves & shoot apical meristems; embryo in seed - stimulates cell division; can increase fruit size - allows seed to germinate, ending dormancy & stimulating embryonic growth - absorbed by aleurone, outermost layer of seed coat in certain monocot seeds, which starts initiating protein synthesis of -amylase C. Cytokinin - induces cytokinesis, cell division, & differentiation of young, unspecialized cells into more mature, specialized cells in plants - delays leaf senescence, which is the natural plant aging & leaf loss process - produced primarily in roots D. Ethylene - gaseous hormone (C2H4) - inhibits cell elongation, promotes seed germination, promotes apical dominance - produced in fruits to induce ripening - induces leaf abscission, the natural leaf loss process - produced in stem nodes; damaged or senescing tissue E. Abscisic Acid (ABA) - promotes seed dormancy and aids in stress conditions - closes stoma under drought stress - keeps seed & plant parts dormant during winter - produced in almost all cells that contain plastids (leaves, stems, roots) F. Interactions Between Auxin & Cytokinin - auxins are made in the shoots while cytokinins are made in the roots - interactions are antagonistic since auxin inhibits the growth of axillary buds, while cytokinins promote their growth - a higher ratio of auxin induces root growth - a higher ratio of cytokinin induces shoot growth - if their ratios are equal, they form an undifferentiated mass (callus) G. Interactions Between Auxin & Ethylene (Leaf Abscission) - as a leaf ages, the level of auxin in the leaf decreases - cells in the abscission layer at the base of the petiole, where the leaf will break away from the stem, begin producing ethylene H. Interaction of Hormones (Seed Dormancy) - since ABA is being used up in the winter to keep seeds dormant, by the time spring comes, other hormones such as GA & cytokinins will break the seed's dormancy and cause growth to occur III. Light Signals & Plant Development A. Photoperiodism 1. any response of a plant to the relative lengths of daylight & darkness B. Short-day/Long-night Plants 1. flower when the night length is equal to or exceeds a certain critical length in a 24 hour period 2. detect the lengthening nights or late summer or fall 3. Qualitative a. flowering occurs only in short days 4. Quantitative a. flowering accelerated by short days C. Long-day/Short-night Plants 1. flower when the night length is equal to or less than a certain critical length in a 24 hour period 2. detects shortening nights of spring & early summer 3. Qualitative a. flowering occurs only on long days 4. Quantitative a. flowering accelerated by long days D. Intermediate-day Plants 1. have narrow night-length requirement; do not flower when night is too long or short E. Phytochrome 1. main photoreceptor for photoperiodism, germination, seedling establishment, & other light-initiated plant responses 2. family of about 5 blue-green pigment proteins, each coded for by different gene F. Circadian Rhythms 1. internal cycle that helps organism detect time of day Lecture 19 Chapter 10 Meiosis I. Mitosis vs. Meiosis A. Meiosis involves 2 successive nuclear and cytoplasmic divisions, producing up to 4 cells, while mitosis involves only one nuclear and cytoplasmic division, producing 2 cells B. Meiosis produces haploid cells while cells that undergo mitosis remain diploid or haploid 1. Meiosis maintains the correct number of chromosomes during sexual reproduction by reducing the chromosome number by half C. During meiosis, each homologous chromosome pair is shuffled, so the resulting haploid cells each have a virtually unique combination of genes. During mitosis, no such shuffling occurs, and the cells remain genetically identical to their parent cell D. There is no pairing of homologous chromosomes or crossing over during Prophase of Mitosis or Prophase II of Meiosis E. During Metaphase II of Meiosis and Metaphase of Mitosis, chromosomes line up on the midplanes of their cells F. During Anaphase II of Meiosis and Anaphase of Mitosis, chromatids (now chromosomes) separate and move toward opposite poles II. Important Definitions A. Sister chromatids 1. 2 units of a duplicated chromosome that are connected by their centromeres 2. Have the same alleles & contain identical DNA sequences B. Homologous Chromosomes 1. 2 chromosomes that are similar in size, shape, and the position of their centromeres C. Segregation 1. The separation of homologous chromosomes during meiosis 2. each gamete (or spore) gets 1 homologous chromosome D. Independent Assortment 1. random distribution of genes located on non-homologous chromosomes into gametes or spores E. Crossing-over 1. chromatids of homologous chromosomes exchange genetic material during Prophase I 2. enzymes break and rejoin DNA molecules, allowing paired homologous chromosomes to exchange genetic material F. Meiotic nondisjunction 1. abnormal separation of homologous chromosomes during Anaphase I 2. alternatively, abnormal separation of sister chromatids during Anaphase II G. Tetrad 1. chromosome complex formed by synapsis of pair of homologous chromosomes during Prophase I 2. number of tetrad per prophase I cell = haploid chromosome number H. Spermatogenesis 1. formation of male gametes I. Oogenesis 1. formation of female gametes III. Meiosis A. Meiosis I 1. Prophase I Leptotene a. chromosomes start to become visible as they condense 2. Prophase I Zygotene a. homologous chromosomes begin to pair (synapsis) with one another along their lengths 3. Prophase I Pachytene a. chromosomes are fully synapsed along their lengths, forming tetrads b. crossing over occurs, in which 2 homologous chromatids have broken in their corresponding locations and have become rejoined so that the chromosomes have now exchanged genetic material 4. Prophase I Diplotene a. homologous chromosomes start to move away from one another except at chiasmata 5. Prophase I Diakinesis a. chromosomes become shorter and thicker b. tetrads remain in place at the regions of the chiasmata c. nuclear envelope breaks down at end of diakinesis d. spindle fibers begin to appear 6. Metaphase I a. independent assortment occurs b. tetrad of chromatids lines up on the equatorial plane c. sister chromatids are oriented to the same pole d. homologous centromeres are oriented toward opposite poles 7. Anaphase I a. homologous centromeres move to opposite poles b. chromatids trail behind, since sister centromeres still adhere to one another i. forms a "double V configuration" 8. Telophase I a. chromosomes reach the poles and usually decondense b. nuclear envelopes are formed & cytokinesis occurs to form 2 cells B. Meiosis II - similar to mitosis 1. Prophase II a. chromatids become visible b. at end, nuclear envelope disappears and spindle fibers attach to centromeres 2. Metaphase II a. chromosomes line up perpendicular to metaphase plate b. sister centromeres are attached by spindle fibers to opposite poles 3. Anaphase II a. sister centromeres move to opposite poles b. attached chromatids are carried long, trailing out behind in a "v-shape" 4. Telophase II a. chromosomes reach the poles and decondense b. cytokinesis occurs to form 4 haploid cells Lecture 20 Chapter 11 Basic Principles of Heredity I. Mendel's Principles of Inheritance A. Phenotype 1. physical appearance of organism B. Genotype 1. genetic constitution of organism C. P Generation 1. parental generation D. F1 Generation 1. offspring of the P generation E. F2 Generation 1. offspring of the F1 generation F. Dominance 1. An allele is always expressed when it is present, regardless of whether it is homozygous or heterozygous G. Recessive 1. allele is only expressed when it is homozygous H. Homozygous 1. Having a pair of identical alleles for a particular locus I. Heterozygous 1. Having a pair of unlike alleles for a particular locus J. Monohybrid Cross 1. process of crossing 2 individuals with different alleles of a given locus K. Dihybrid Cross 1. process of crossing 2 individuals with different alleles at two loci L. Punnett Square 1. grid structure, first developed by Reginald Punnett, that allows direct calculation of the probabilities of the possible occurrence of all possible offspring of a genetic cross M. Test Cross 1. an individual of an unknown genotype is crossed with a homozygous recessive individual, a dominant phenotype 2. the genotypes of all offspring could be directly deduced from their phenotypes 3. can detect heterozygosity N. Chromosome Theory of Inheritance 1. inheritance can be explained by assuming that genes are linearly arranged in specific locations along the chromosomes II. Using Probability To Predict Mendelian Inheritance A. Product Rule 1. probability of 2 independent events occurring together is calculated by multiplying the probabilities of each event occurring separately (and) B. Sum Rule 1. probability of an outcome that can be obtained in more than one way is calculated by adding the separate probabilities (or) III. Inheritance & Chromosomes A. Linkage 1. tendency for a group of genes on the same chromosome to be inherited together in successive generations B. Recombinant Types 1. appearance of new gene combinations resulting from meiotic events, either crossing-over or shuffling of chromosomes C. Parental Types 1. identical to gametes produced by P generation D. Sex Chromosomes 1. contain major sex-determining genes E. Autosomes 1. chromosomes other than the sex chromosomes F. Hemizygous 1. males having only one copy of each X-linked gene 2. damaging recessive phenotypes are expressed because a male only needs to receive the recessive gene from his mother 3. females would have to receive 2 copies of the recessive gene to express the trait G. Barr Body 1. dense, metabolically inactive X chromosome 2. during interphase, forms a dark spot of chromatin in each female mammalian cell when stained & microscopically observed 3. cells compensate for extra X chromosome material by rendering all but 1 X chromosome inactive IV. Extensions of Mendelian Genetics A. Incomplete Dominance 1. an F1 heterozygote has a phenotype intermediate between its parents 2. ex. red rose & white rose produce pink rose B. Codominance 1. F1 heterozygote simultaneously expresses phenotypes of both types of homozygotes 2. Human Blood Types a. Type A has genotypes IAIA, IAi b. Type B has genotypes IBIB, IBi c. Type AB has genotype IAIB d. Type O has genotype ii Lecture 21 - Chapter 12 DNA: The Carrier of Genetic Information I. DNA (Deoxyribonucleic Acid) A. Nucleic acid that is the molecular basis of inheritance B. Mechanisms of DNA, repair are conserved in all organisms C. Genes that carry out the same function are evolutionarily conserved D. Contains genetic code 1. The nucleotide sequence of a DNA coding region determines the amino acid sequence of a protein a. Protein sequences can be represented as a series of 20 letters II. Evidence of DNA as the Hereditary Material A. Frederick Griffith's Transformation Experiment, 1928 1. Injected mouse with live avirulent rough (R) cells; the mouse lived 2. Injected mouse with live virulent smooth (S) cells; the mouse died 3. Injected mouse with heat-killed S cells; the mouse lived 4. Injected mouse with a mix of live R cells & heat-killed S cells; the mouse died a. Living S cells were obtained from the last mouse b. Concluded that some substance from the dead S cells had been transferred to the living R cells and transformed them into S cells c. Transformation permanent genetic change in which the properties of one strain of dead cells are conferred on a different strain of living cells B. Oswald Avery et al. Transformation Experiment, 1944 1. Treated R strain bacteria with highly purified DNA from S strain bacteria 2. These R strain bacteria were then transformed into S strain bacteria C. Alfred Hershey's & Martha Chase's Experiment's, 1952 1. Found that viral DNA enters the bacterial cells and is required for the synthesis of new viral particles III. DNA Structure A. Nucleotide 1. Deoxyribose Sugar a. pentose sugar lacking a hydroxyl (-OH) group on carbon-2' 2. Phosphate Group a. functional group that releases few H+ b. bonds with sugar & base 3. Nitrogenous Base a. Purine i. has carbon and nitrogen atoms in 2 attached rings ii. Adenine iii. Guanine b. Pyrimidine i. composed of a single ring of carbon & nitrogen atoms ii. Thymine iii. Cytosine 4. 3', 5' Phosphodiester Linkage a. 3' carbon of one sugar is bonded to the 5' phosphate of the adjacent sugar 5. 5' end a. 5' carbon attached to a phosphate 6. 3' end a. 3' carbon attached to a hydroxyl group B. Chargaff's Rules 1. the number of purines is equal to the number of pyrimidines C. Double Helix 1. 2 polynucleotide chains arranged in a coil 2. Antiparallel two strains run in opposite directions 3. Discovered by Frankin & Wilkson by x-ray diffractions from 1951-1953 4. Watson & Crick derived models from their data D. Bases 1. Adenine & Thymine form 2 hydrogen bonds 2. Guanine & Cytosine form 3 hydrogen bonds 3. Complementary base pairs the sequence of nucleotides in one chain dictates the complementary sequence of nucleotides in the other IV. DNA Replication A. Semiconservative Replication 1. Each daughter helix consists of an original strand from the parent molecule and a newly synthesized complementary strand 2. Verified by Meselson & Stahl, experimenting with E. Coli in 15N growth medium B. Enzymes for DNA Replication 1. Helicases unwind the DNA 2. Topoisomerases deal with knots and tangles 3. DNA polymerases link the nucleotides together 4. Primase synthesizes the RNA `primer' for lagging strand DNA synthesis 5. Ligases close the phosphodiester bond (between 3' OH and 5' phosphate group) in the growing strand; links 2 linear DNA fragments by covalent bonds 6. Single-strand binding protein binds to single strands of DNA & prevents the helix from reforming before it can be used as a template for replication C. Separation of DNA Strands 1. Small sections of the double helix unwind at the origins of replication 2. DNA Helicases bind to DNA here and break hydrogen bonds 3. Single-strand binding proteins bind to single DNA strands, stabilizing them 4. Topoisomerases produce breaks in the DNA molecules, preventing excessive coiling before replication, and then rejoin them D. DNA Synthesis 1. Always occurs in a 5'3' direction a. polynucleotide chain is elongated by the linkage of the 5' phosphate group of the next nucleotide subunit to the 3' hydroxyl group 2. DNA polymerase can only add nucleotides to a 3' growing end 3. Occurs in the nucleolus 4. Exergonic reaction, since phosphate groups are released in the form of ATP when nucleotides are added. E. RNA Synthesis 1. RNA primer is synthesized at the point where replication begins a. Synthesized by DNA primase, which starts a new strand of RNA opposite a short stretch of the DNA template strand 2. DNA polymerase displaces the primase & adds subunits to the 3' end of the RNA Primer F. Leading & Lagging DNA Strands 1. Leading/Template/Sense strand a. one DNA polymerase molecule adds nucleotides to the 3' end of the new strand that is always continuously growing toward the replication fork 2. Lagging strand a. another DNA polymerase molecule adds nucleotides to the 3' end of the other new strand b. synthesized discontinuously and away from the replication fork c. forms from Okazaki fragments that become linked by DNA ligase G. DNA Synthesis is Bidirectional 1. starts at the origin of replication and proceeds in both directions from that point H. Repairing Enzymes 1. DNA polymerases proofread each newly added nucleotide against its template nucleotide 2. When an error in base pairing is found, DNA polymerases immediately removes the incorrect nucleotide and inserts the correct one 3. Mismatch repair a. enzymes recognize incorrectly paired nucleotides and remove them; DNA polymerases then fill in the missing nucleotides 4. Nucleotide excision repair a. repairs DNA lesions caused by the sun's UV radiation or harmful chemicals I. Telomeres 1. eukaryotic chromosome ends that are short, noncoding, repetitive DNA sequences 2. shorten slightly with each cell cycle but can be extended by the enzyme Telomerase Lecture 22 - Chapter 13 Gene Expression I. Discovery of the Gene-Protein Relationship A. Evidence that Genes Specify Protein Structure 1. Archibald Garrod hypothesized that the genetic disease alkaptonuria was caused by a gene mutation that results in the loss of an enzyme that oxidizes homogentistic acid B. One-Gene, One Enzyme Hypothesis 1. Beadle & Tatum looked for mutations from that interfere with metabolic reactions that produce essential molecules in the Orange mold Neurospora 2. They exposed Neurospora spores to X-rays or UV radiation to induce mutant strains 3. They also identified strains that carried a chemical essential for growth, the amino acid arginine 4. They concluded that each mutant strain had a mutation in only 1 gene & that each gene only affected 1 enzyme 5. Gene DNA nucleotide sequence that contains information needed to produce specific RNA or polypeptide product II. Information Flow from DNA to Protein: An Overview A. RNA Structure 1. Ribonucleic Acid (RNA) is usually single stranded 2. The pentose sugar in RNA is ribose, which has a hydroxyl group at the 2' position 3. The pyrimidine base uracil substitutes for thymine and forms 2 hydrogen bonds with adenine 4. Formed from nucleotide subunits covalently joined by 5'-3' linkages to form an alternating sugar-phosphate backbone 5. Synthesized from DNA template strand a. Template strand of DNA & RNA strand are antiparallel b. RNA synthesized in 5'3' direction; DNA template read in 5'3' direction 6. Information flows as follows: DNARNAProtein 7. Upstream a. toward 5' end of mRNA sequence or 3' end of template DNA 8. Downstream a. towards 3' end of RNA or 5' end of template DNA B. Types of RNA 1. Messenger RNA (mRNA) Transcription Translation a. specifies the amino acid sequence of a protein b. each codon, a sequence of 3 consecutive bases, specifies 1 amino acid c. production catalyzed by enzyme RNA polymerase II d. has noncoding leader sequence at its 5' end, which has recognition sites for ribosome binding, which properly position the ribosomes to translate the message 2. Transfer RNA (tRNA) a. binds to specific amino acid & serves as adapter molecule when amino acids are incorporated into growing polypeptide chain b. has a sequence of 3 bases, the anticodon, that hydrogen bonds with the mRNA codon by complementary base pairing c. production catalyzed by RNA polymerase III 3. Ribosomal RNA (rRNA) a. has both structural & catalytic (ribozyme) roles in ribosome b. production catalyzed by RNA polymerase I (sometimes RNA polymerase III) C. Genetic Code 1. assignment of codons for amino acids and for start and stop signals 2. the start codon AUG specifies the amino acid methionine and signals the ribosome to initiate translation 3. 3 stop codons UAA, UGA, & UAG terminate polypeptide synthesis 4. the genetic code is virtually universal, implying that all organisms are descended from a common ancestor 5. the genetic code is redundant because some amino acids are specified by more than 1 codon a. this is because there are 64 possible codons and 20 amino acids b. Wobble Hypothesis Crick accounted for the possible variation in base pairing between the 3rd base pair of a codon & the corresponding base in its anticodon D. Formation of Aminoacyl-tRNA 1. Aminoacyl-tRNA synthetase a. enzyme that uses ATP to covalently link amino acids to tRNA molecules b. resulting complex is aminoacyl-tRNA E. Ribosome Structure - consist of 2 subunits made up of protein & rRNA 1. Large Subunit a. P site/ Peptidyl site i. holds tRNA holding the growing polypeptide chain b. A site/ Aminoacyl site i. holds aminoacyl-tRNA delivering the next amino acid in the sequence c. E site/ Exit site i. where tRNAs that have delivered their amino acids to the growing polypeptide chain exit the ribosome 2. Small Subunit a. Initiation Factors i. proteins involved in translation III. Transcription A. Initiation 1. RNA polymerase attaches to promoter region and unwinds DNA double helix 2. Moves past the promoter region to initiate RNA synthesis B. Elongation 1. As each additional nucleotide is incorporated at the 3' end of the RNA, 2 phosphates of RNA are removed in an exergonic reaction 2. Leaves the remaining phosphate to become part of the sugar-phosphate backbone 3. DNA double helix reforms following transcription 4. Last nucleotide to be incorporated has an exposed 3'-hydroxyl group C. Termination 1. RNA polymerase recognizes termination sequence consisting of a specific sequence of bases in the DNA template 2. RNA transcript & RNA polymerase are released IV. Translation - occurs in the cytoplasm, either with the free-floating ribosomes or the ribosomes of the Rough E.R. A. Initiation 1. Small ribosomal unit bind to mRNA at AUG start codon 2. Leader sequence of upstream of AUG sequence helps the ribosome identify the AUG sequence 3. Initiator tRNA, which is bound to amino acid methionine, binds to start codon, releasing one initiation factor 4. Large ribosomal subunit binds to small subunit, releasing remaining initiation factors 5. Initiator tRNA attaches to P site of large ribosomal subunit B. Elongation 1. Appropriate tRNA recognizes the codon in the A site & binds to it, using energy from GTP (Guanosine Triphosphate) 2. Growing polypeptide chain detaches from tRNA molecule and becomes attached by a peptide bond to the amino acid linked to the tRNA at the A site 3. Translocation a. ribosome moves 1 codon toward the 3' end of mRNA, using energy from GTP b. growing polypeptide chain is transferred to the P site c. uncharged tRNA in E site leaves the ribosome C. Termination 1. When the ribosome reaches a stop codon, A site binds to a protein release factor 2. Release factor hydrolyzes bond between polypeptide chain and tRNA, causing the release of the polypeptide chain from the tRNA molecule in the P site 3. The remaining parts of the translation complex dissociate V. Variations in Gene Expression in Different Organisms A. Transcription & Translation in Prokaryotes 1. Transcription and translation are coupled 2. Ribosomes bind to 5' end of growing mRNA and initiate translation long before the message is fully synthesized 3. both occur in the cytoplasm B. Transcription & Translation in Eukaryotes 1. Precursor mRNA/ pre-mRNA a. original transcript later modified after transcription b. When RNA transcript is 20-30 nucleotides long, enzymes add a 5' cap to the 5' end of the mRNA chain i. needed to bind to eukaryotic ribosomes c. Polyadenylation i. enzymes cut the mRNA molecule at the poly-A tail, a sequence of bases near the 3' end that serves as a signal for adding many adenine-containing nucleotides ii. helps export the mRNA from the nucleus 2. Introns a. intervening, noncoding sequences later removed from pre-mRNA b. spliceosomes catalyze the reactions that remove introns 3. Exons a. expressed sequences that code for the protein b. spliced together to produce a continuous polypeptide-coding sequence C. Retroviruses 1. Reverse transcriptase enzyme, an RNA-directed DNA polymerase, synthesize DNA using an RNA template VI. Mutations A. Base Substitution 1. change in only 1 pair of nucleotides 2. Missense Mutation a. results in replacement of 1 amino acid by another b. if this occurs by or at the active site of an enzyme, the activity of the altered protein may decrease or be destroyed c. if this occurs far from the active site, the mutation may be undetectable 3. Nonsense Mutation a. converts an amino acid-specifying codon to a stop codon b. usually destroys the function of the gene product B. Frameshift Mutation 1. 1 or 2 nucleotide pairs are inserted into or deleted from the molecule 2. alters the reading frame and specifies a new sequence of amino acids 3. if this occurs in a gene specifying an enzyme, it usually results in a complete loss of enzyme activity Lecture 23 Chapter 14: Gene Regulation I. Gene Regulation in Bacteria A. Transcriptional-level Control 1. most common method for prokaryotes to regulate gene expression 2. organizes related genes into groups that are rapidly turned on & off as units a. allows synthesis of only gene products needed at particular time 3. requires rapid turnover of mRNA molecules to prevent messages from accumulating and continuing to be translated when not needed B. Constitutive Genes 1. encode proteins that are always needed & are always transcribed C. Operon 1. gene complex consisting of a group of structural genes with related functions, plus the closely linked DNA sequences responsible for controlling them 2. Structural Gene a. enzyme-coding sequence of DNA 3. Promoter a. nucleotide sequence in DNA to which RNA polymerase attaches to begin transcription b. located upstream from coding sequences 4. Operator a. sequence of bases upstream from 1st structural gene in operon b. controls mRNA synthesis 5. Repressor Protein a. binds tightly to operator to prevent transcription 6. Repressor Gene a. encodes repressor protein b. adjacent structural gene located upstream from promoter site 7. Inducer a. binds to repressor protein, converting it to its inactive form, which is unable to prevent transcription 8. Corepressor a. binds to a repressor protein, converting it to its active form, which is capable of preventing transcription D. Inducible Operon 1. normally inactive because a repressor molecule is attached to its operator 2. transcription is activated when an inducer binds to the repressor, making it incapable of binding to the operator E. Repressible Operon 1. normally active, but can be controlled by a repressor protein, which becomes active when it binds to a corepressor 2. active repressor binds to operator, making operon transcriptionally inactive F. Negative Control 1. regulatory mechanism in which the DNA binding regulatory protein is a repressor that turns off transcription of the gene G. Positive Control 1. regulation by activator proteins, which stimulate transcription when bound to DNA H. Lac Operon 1. Structural genes lacZ, lacY, & lacA code for -galactosidase, lactose permease, and transacetlyase, respectively, enzymes for lactose metabolism 2. Lactose repressor is repressor protein that binds to operator in absence of lactose 3. When lactose is present, it is converted to allolactose, an inducer that binds to the repressor at an allosteric site, altering the structure of the protein so that it no longer binds to the operator a. RNA polymerase is able to transcribe structural genes 4. Lac operon is inducible operon in E. coli & features both positive and negative control 5. When glucose & lactose levels are high, cAMP (cyclic adenosine monophosphate) is low a. CAP (catabolite activator protein), a regulatory protein, is in its inactive form and cannot stimulate transcription b. Transcription occurs at a low level or not at all, since lac operon has low affinity for RNA polymerase 6. When lactose levels are high & glucose levels are low, each CAP polypeptide has cAMP bound to its allosteric site a. active form of CAP binds to the DNA sequence, & transcription becomes activated I. Trp Operon 1. Amino acid tryptophan binds to allosteric site on repressor protein, changing its conformation 2. Active form of repressor binds to operator region, blocking transcription of operon until tryptophan is required by cell 3. Trp operon is repressible operon & features negative control J. Translational Controls - posttranscriptional controls that regulate rate at which mRNA is translated K. Posttranslational Controls - activates or inactivates enzymes, thereby letting the cell respond to changes in the intracellular concentrations of essential molecules, such as amino acids 1. Feedback Inhibition a. regulates activity of existing enzymes in a metabolic pathway II. Gene Regulation in Eukaryotic Cells A. Heterochromatin 1. regions of a chromosome that contain inactive genes B. Euchromatin 1. regions of a chromosome that contain active genes C. Enhancer Sequence 1. Recognition site for protein that makes DNA more accessible to RNA polymerase, thereby boosting activity of nearby genes several hundredfold D. TATA Box 1. promoter to which RNA polymerase binds to allow transcription to occur Lecture 25 Chapter 15: Genetic Engineering I. DNA Cloning A. Restriction Enzymes 1. enzymes from bacteria that cut DNA molecules only in specific places 2. many cut palindromic sequences, in which the base sequence of one strand reads the same as its complement when both are read in the 5'3' direction 3. Sticky ends a. portion of DNA segment that can pair with single-stranded ends of other DNA molecules that were digested by the same enzyme b. DNA molecules with complementary sticky ends associate by hydrogen bonds 4. DNA ligase covalently joins resulting fragments of DNA & plasmid to form recombinant DNA B. Vectors 1. carrier such as a bacteriophage or plasmid capable of transporting the DNA fragment into a cell 2. researchers introduce plasmids into bacterial cell by transformation, the uptake of foreign DNA by cells 3. in host cell, recombinant DNA is copied and turned on to produce gene product C. Producing Genomic Library - Genome total DNA in a cell - Genomic DNA Library collection of DNA fragments that represent all DNA in genome - Chromosome Library contains all DNA fragments in specific chromosome 1. Restriction enzyme cuts DNA, generating population of DNA fragments with identical sticky ends 2. Plasmid DNA cut with same restriction enzyme, converting circular plasmids into linear molecules with sticky ends complementary to those of previous DNA fragments 3. DNA ligase covalently bonds paired ends of plasmid DNA & previous DNA, forming recombinant DNA 4. Plasmids inserted into antibiotic-sensitive bacterial cells by transformation 5. Antibiotic-sensitive cells incubated on nutrient medium that includes antibiotics a. only those cells grow that have incorporated plasmid, which contains gene for antibiotic resistance 6. Colony - clone of genetically identical cells originating from single cell - all cells contain same recombinant plasmid D. Complementary DNA (cDNA) 1. DNA complementary to mRNA 2. lacks introns 3. copies constructed from copies of mRNA from which introns have been removed 4. enzyme reverse transcriptase synthesizes single-stranded cDNA, separated from mRNA, which is degraded by specific enzymes 5. cDNA made double stranded by DNA polymerase 6. cDNA library a. formed using mRNA from a single cell type as starting material b. double-stranded cDNA inserted into plasmid or virus vectors, which multiply in bacterial cells 7. cDNA helps determine certain characteristics of protein encoded by gene, including amino acid sequence 8. can also be used to produce eukaryotic protein in bacteria & study structure of mature mRNA E. Polymerase Chain Reaction (PCR) - developed by U.S. biochemist Kary Mullis - can amplify & analyze DNA from variety of sources 1. Heat-resistant DNA polymerase uses nucleotides & primers to replicate a DNA sequence in virto 2. DNA is denatured (separated into single strands) by heat 3. Primers attach to primer-binding site on each DNA strand 4. Each DNA strand acts as template for DNA synthesis a. Number of DNA molecules doubles each time cycle is repeated II. DNA Analysis A. Gel Electrophoresis - exploits fact that macromolecules - proteins, polypeptides, DNA fragments, & RNA carry charged groups that cause them to migrate in an electrical field 1. Nucleic acids of DNA migrate through gel toward positive pole of electric field since they have negatively-charged phosphate groups 2. Because gel slows down large molecules more than small molecules, DNA is separated by size B. DNA, RNA, & Protein Blots 1. Southern Blot a. separates DNA by gel electrophoresis & transfers fragments to a nitrocellulose or nylon membrane 2. Northern Blot a. RNA molecules are separated by electrophoresis and transferred to a membrane 3. Western Blot a. consists of proteins or polypeptides separated by gel electrophoresis C. Dideoxynucleotide a. synthetic nucleotide incorporated by replicating DNA strand b. strand cannot elongate beyond this point c. lacks hydroxyl groups on 2' carbon & 3' carbon III. Genomics - studies entire DNA sequence of organism's genome to identify all genes, determine all their RNA or protein products, & ascertain how genes are regulated A. Human Genome Project 1. sequencing of human genome IV. Applications of DNA Technologies A. Genetic Tests 1. determines whether individual has a particular genetic mutation associated with a disease or disorder B. Gene Therapy 1. use of specific DNA to treat genetic disease by correcting genetic problem C. DNA Fingerprinting/DNA Typing 1. analysis of DNA extracted from individual, which is unique to that individual D. Transgenic Organisms 1. plants & animals in which foreign genes have been incorporated 2. transgenic animals can produce genetically engineered proteins 3. transgenic plants are important in agriculture by preventing plant tumors Lecture 26 Chapter 16: Human Genetics I. Studying Human Genetics A. Cytogenetics 1. study of chromosomes and their role in inheritance B. Karyotype 1. individual's genetic composition C. Pedigree 1. "family tree" that shows inheritance patterns, the transmission of genetic traits within a family over several generations 2. enables geneticists to predict how phenotypic traits that are governed by genotype at a single locus are inherited 3. identifies 3 modes of single locus inheritance: autosomal dominant, autosomal recessive, & X-linked recessive II. Abnormalities in Chromosome Number & Structure A. Polyploidy 1. presence of multiple sets of chromosomes B. Aneuploidy 1. abnormalities caused by presence of single extra or absence of a chromosome C. Down Syndrome 1. most common chromosome abnormality in humans; caused by trisomy 21 2. meiotic nondisjunction is responsible for the presence of an extra chromosome D. Klinefelter Syndrome 1. males with two X's and 1 Y E. Turner Syndrome 1. female with only 1 X chromosome F. XYY Karyotype 1. males with 1 X & 2 Y chromosome G. Duplication 1. segment of chromosome is repeated several times H. Inversion 1. orientation of a chromosome segment is reversed I. Deletion 1. breakage causes loss of part of a chromosome, along with genes on that segment 2. can cause cri du chat syndrome, a monosomy in which part of the short arm of chromosome 5 is deleted J. Translocation 1. chromosome fragment breaks off & attaches to nonhomologous chromosome 2. can cause translocation Down syndrome K. Reciprocal Translocation 1. 2 nonhomologous segments exchange segments L. Fragile Site 1. place where part of a chromatid appears to be attached to the rest of the chromosome by a thin thread of DNA 2. Fragile-X Syndrome most common cause of mental retardation III. Genetic Diseases Caused By Single-Gene Mutations A. Autosomal Recessive Disorders - gene for disease located in non-sex chromosomes of both parents 1. Tay-Sachs Disease a. affects central nervous system & results in blindness and severe mental retardation b. selective advantage is resistance to tuberculosis 2. Phenylketonuria a. accumulation of high levels of phenylalanine 3. Sickle Cell Anemia a. red blood cells shaped like sickles b. heterozygote advantage immune to malaria without expressing sickled cells 4. Cystic Fibrosis a. abnormal secretions produced primarily in organs of respiratory & digestive systems b. selective advantage is the prevention of excess water loss associated with certain types of diarrhea B. Autosomal Dominant Disorders - gene for disease located in non-sex chromosomes of either parent 1. Huntington's Disease a. causes severe mental & physical deterioration, uncontrollable muscle spasms, personality changes, & ultimately, death C. X-Linked Recessive Disorders - gene located in X chromosomes 1. Hemophilia A a. severe internal bleeding in the head, joints, & other areas from even a slight wound 2. Color Blindness 3. Duchenne's Muscular Dystrophy IV. Gene Therapy - aims to replace a mutant allele in certain body cells with a normal allele 1. gene is cloned & DNA introduced into appropriate cells 2. packages normal allele in a viral vector, a virus that moves normal allele into target cells that currently have mutant allele V. Genetic Diseases and Counseling A. Amniocentesis - diagnoses genetic diseases prenatally during 16th week of pregnancy 1. 20 mL of amniotic fluid containing cells sloughed off from fetus is removed through mother's abdomen 2. Fluid is centrifuges & amniotic fluid is analyzed 3. Fetal cells are checked to determine sex, & purified DNA is analyzed 4. Some cells are grown for 2 weeks in culture medium 5. Karyotype is analyzed for sex chromosomes or any chromosome abnormality 6. Cells are analyzed biochemically for presence of about 40 metabolic disorders B. Chorionic Villus Sampling - during 8th or 9th week of pregnancy, chorionic cells genetically identical to the embryo are sampled to detect genetic disorder - removes & studies cells that will form fetal contribution to placenta - may possibly harm fetus since process occurs so early in pregnacy C. Genetic Screening 1. systematic search through a population for individuals with a genotype or karyotype that might cause a serious disease in themselves or their offspring D. Genetic Counseling 1. provides medical & genetic information pertaining to reproductive decisions 2. helps individuals understand their situation & avoid feeling stigmatized