All Lectures 115 - General Biology I (Rutgers University) PDF

lOMoARcPSD|46266463 All Lectures 115 General Biology I (Rutgers University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 Table of Contents I. LECTURE 1 biology and learning.................................................................................................................. 5 A. Memory and learning.......................................................................................................................................5 II. LECTURE 2 scientific method and chemistry................................................................................................ 6 A. Themes in biology.............................................................................................................................................6 B. Methods of investigating biology.....................................................................................................................6 C. Basic Chemistry................................................................................................................................................6 D. Emergence properties of water........................................................................................................................7 III. LECTURE 3 biological molecules.................................................................................................................. 8 A. Importance of Carbon......................................................................................................................................8 B. Biological macromolecules...............................................................................................................................9 IV. LECTURE 4 origin of life............................................................................................................................. 12 A. 4 steps of abiogenesis....................................................................................................................................12 B. History of life..................................................................................................................................................13 V. LECTURE 5 cell structure........................................................................................................................... 14 A. Cellular diversity and characteristics..............................................................................................................14 B. Components of Eukaryotic cells......................................................................................................................15 VI. LECTURE 6 membrane and transport........................................................................................................ 17 A. Membrane structure......................................................................................................................................17 B. Bulk transport.................................................................................................................................................19 VII. LECTURE 7 metabolism........................................................................................................................ 20 A. Metabolism and energy change.....................................................................................................................20 B. Enzymes..........................................................................................................................................................22 C. Redox reactions..............................................................................................................................................22 VIII. LECTURE 8 photosynthesis................................................................................................................... 23 A. Introduction to photosynthesis......................................................................................................................23 B. Structures in photosynthesis..........................................................................................................................23 IX. LECTURE 9 respiration.............................................................................................................................. 26 A. Introduction to cell respiration.......................................................................................................................26 B. The stages of cellular respiration...................................................................................................................27 C. Electron transport chain.................................................................................................................................30 Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 X. LECTURE 10 cell cycle............................................................................................................................... 31 A. Organization of genetic material...................................................................................................................31 B. Phase of cell cycle...........................................................................................................................................31 XI. LECTURE 11 meiosis................................................................................................................................. 33 A. Introduction to heredity.................................................................................................................................33 B. Life cycles of different organisms...................................................................................................................34 C. 4 stages of meiosis.........................................................................................................................................34 XII. LECTURE 12 mendel............................................................................................................................. 36 A. Mendel’s Experimental Approach..................................................................................................................36 B. Genetic crosses...............................................................................................................................................37 C. Probability in genetics....................................................................................................................................38 XIII. LECTURE 13 chromosomes................................................................................................................... 39 A. Chromosomal theory of inheritance..............................................................................................................39 B. inheritance patterns of sex chromosomes.....................................................................................................40 C. Violations of independent assortment...........................................................................................................41 XIV. LECTURE 14 dna................................................................................................................................... 42 A. DNA is the genetic material...........................................................................................................................42 B. Structure of DNA............................................................................................................................................42 C. DNA replication..............................................................................................................................................44 XV. LECTURE 15 gene expression................................................................................................................ 46 A. Relationship between genes and proteins.....................................................................................................46 B. Transcription – DNA to RNA...........................................................................................................................47 C. Translation......................................................................................................................................................49 XVI. LECTURE 16 gene regulation................................................................................................................. 50 A. Prokaryotic gene regulation...........................................................................................................................50 B. Eukaryotic gene regulation............................................................................................................................52 XVII. LECTURE 17 dna tech........................................................................................................................... 54 A. PCR: Polymerase chain reaction.....................................................................................................................54 B. DNA sequencing.............................................................................................................................................55 C. Application of DNA tools................................................................................................................................56 XVIII. LECTURE 18 human genetics................................................................................................................ 56 A. Study of human genetic variance...................................................................................................................56 B. Mendelian Inheritance Patterns.....................................................................................................................57 Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 C. Non-Mendelian inheritance patterns.............................................................................................................57 D. Genetic testing and counseling......................................................................................................................59 XIX. LECTURE 19 darwinian evolution.......................................................................................................... 60 A. Pre-Darwinian ideas.......................................................................................................................................60 B. Darwin’s work and ideas................................................................................................................................61 C. Evidence for evolution....................................................................................................................................63 XX. LECTURE 20 population genetics.......................................................................................................... 65 A. Variation in individuals...................................................................................................................................65 B. Detecting evolution in populations................................................................................................................65 C. Mechanisms of Evolution...............................................................................................................................66 XXI. LECTURE 21 Speciation......................................................................................................................... 68 A. Species concepts.............................................................................................................................................68 B. Reproductive Isolation....................................................................................................................................69 C. Process of speciation......................................................................................................................................71 XXII. LECTURE 22 phylogenies...................................................................................................................... 73 A. Systematics.....................................................................................................................................................73 B. Basics of phylogenetics..................................................................................................................................74 C. Making phylogenies.......................................................................................................................................76 XXIII. LECTURE 23 animal behavior................................................................................................................ 77 A. Understanding Behavior................................................................................................................................77 B. Stimuli and behavior......................................................................................................................................77 C. Growth & development and behavior............................................................................................................78 D. Evolution and behavior..................................................................................................................................79 XXIV. LECTURE 24 ecology............................................................................................................................. 80 A. Introduction to population ecology................................................................................................................80 B. Model of population growth..........................................................................................................................82 C. Life history......................................................................................................................................................83 D. Factors influencing population size................................................................................................................84 XXV. LECTURE 25 community ecology........................................................................................................... 84 A. Community interactions.................................................................................................................................84 B. Species diversity in a community...................................................................................................................86 C. Trophic structure............................................................................................................................................86 D. Community development...............................................................................................................................87 Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 XXVI. LECTURE 26 ecosystem ecology............................................................................................................ 88 A. Community interactions.................................................................................................................................88 B. Energy transfer between trophic levels..........................................................................................................88 C. Biochemical cycles..........................................................................................................................................90 XXVII. LECTURE 27 biomes and aquatic ecology.......................................................................................... 91 A. Earth’s climate................................................................................................................................................91 B. Terrestrial biomes...........................................................................................................................................93 C. Aquatic biomes...............................................................................................................................................93 XXVIII. LECTURE 28 conservation biology.................................................................................................... 95 A. Biodiversity.....................................................................................................................................................95 B. Population conservation................................................................................................................................96 C. Human actions are changing the Earth.........................................................................................................97 D. Landscape and regional conservation............................................................................................................97 Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 I. LECTURE 1 biology and learning A. Memory and learning a. Neuronal development i. Nervous system = neurons and supporting cells ii. Before birth – brain development and growth iii. Genetics – basic structure Neuronal developments iv. Gene expression – how your DNA is used v. Signal transduction – when expression occurs b. Neuronal plasticity i. Neuronal plasticity = modifications after birth 1. Connections in the brain remodeled by experiences ii. Activity at synapse (junction between neurons) tells the brain what is important iii. Neuron = nerve cell iv. Plasticity = remodeling v. Neuronal plasticity = long lasting changes in the brain that occur throughout your life 1. Neurons increase their connections to each other as you learn vi. Use it or lose it c. Types of memory i. Sensory memory 1. Experience = if you pay attention it goes to short term memory ii. Short term memory (STM): aka working memory = what you are aware of now held for a short time 1. 7 +/- 2 items 2. Chunking 3. practice iii. Long term potentiation (LTP) = permanent connections in the brain iv. Memory does not equal learning 1. Learning = the use of memory to decrease likelihood of a negative outcome 2. You do better as a result of learning (natural selection) a. Ex. Eating something you are allergic to and then you remember not to eat it again v. Use of information is a sorting process 1. Used – important – retained 2. Not used – unimportant – discarded vi. STIMULUS CHART d. Long term potentiation i. LTP = encoding and re-encoding 1. Physical change in the brain Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 ii. (you get really good at accessing that memory) iii. It is a physiological change II. LECTURE 2 scientific method and chemistry A. Themes in biology a. Evolution i. Evolution = core theme of biology, the unity & diversity of organism 1. Living organisms are modified descendants of common ancestor b. Emergence i. Emergent properties: ii. Emergence = the whole is more than just the sum of its parts 1. Ex. Na + Cl = NaCl c. Levels of biological organization – a hierarchy i. Organelles 1. The nucleus ii. Cells 1. Human blood cells iii. Tissue 1. Human skin tissue iv. Organs & the organ system 1. Stomach in the digestive system v. Organisms, populations, and communities vi. Ecosystems vii. Biosphere B. Methods of investigating biology d. The scientific method i. Hypothesis = testable explanation for observations based on available data ii. Prediction = what you expect to see when you test your hypothesis iii. Theory = broad explanation with significant support iv. Law = statement of what always occurs under certain circumstance e. Steps of the scientific method i. Observation ii. Background iii. Hypothesis iv. Prediction v. Experiments vi. Evaluate C. Basic Chemistry f. Electrons i. 25 of 92 elements are essential to life ii. 4 = 96% of living matter (O,C,H,N) iii. Atoms = 3 subatomic particles (protons, neutrons, electrons) Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 1. Electron = a. 1 negative charge b. Moves rapidly c. Determines how atoms interact d. the further away the electron is from the nucleus the more potential energy the electron possesses e. if the electron becomes excited, it has a lot of energy 2. electron shell = an electrons potential energy 3. valence shell = (outmost shell) where bonds between electrons form g. formation of molecules i. chemical bonds = results from how atoms share electrons ii. energy = capacity to cause change iii. molecules = compounds with two or more atoms iv. emergent properties = many compounds have different properties than their elements h. chemical bonds i. electronegativity = affinity for electrons; tendency of an atom to attract an electron 1. oxygen is very electronegative ii. type of bond is determined by difference in electronegativity iii. two types: 1. covalent bonds = occur when the electronegativity difference between two atoms is less than two a. sharing a pair of valence electrons by two atoms b. strong bond in perspective of the cell Non-polar covalent Polar covalent - same electronegativity - less than two electronegativity - share electrons equally - electrons shared unequally 2. ionic bond = occur when the electronegativities are than two apart a. greater than two difference in electronegativity b. one atom steals electrons from the other c. bond formed by attraction between anions and cations 3. interactions between molecules: van der waals interactions a. develop because electrons are in constant motion 4. hydrogen bonds = really strong dipole-dipole interaction D. Emergence properties of water i. Hydrogen bonds i. Water is polar ii. Forms hydrogen bonds with other water molecules j. Cohesive behavior Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 i. Cohesion = water molecules stick to each other ii. Adhesion = water molecules stick to other polar things iii. Surface tension = a measure of how hard it is to break the surface of a liquid k. Moderates temperature i. Waters high specific heat – hard to change water temperature 1. The higher the specific heat the longer it takes to change temperature ii. High heat of vaporization – hard to change state 1. Water is a stable environment l. Expansion upon freezing i. Ice floats: hydrogen bonds in ice are more “ordered” and makes air pockets 1. Ionic bonds between adjacent molecules result in a crystal structure ii. Water reaches its greatest density at 4 degrees Celsius m. Versatility as a solvent i. Substances can be 1. Hydrophilic a. Ions, salts, polar 2. Hydrophobic a. Lipids, non-polar III. LECTURE 3 biological molecules A. Importance of Carbon a. Introduction to carbon i. Organic compounds = contain carbon bonded to C or H ii. Carbon chains = skeletons of organic molecules 1. Carbon – 4 single valence electrons – tetravalent iii. Structure is key to molecular function iv. Functional groups = R b. Hydrocarbons i. Hydrocarbons = carbon and hydrogen (methane = CH4) 1. Nonpolar and uncharged = hydrophobic = insoluble in H2O ii. Differential function groups can change molecular function (change in functional group = change in function) Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 c. Functional groups Group Compound name Structure Polar or non- Hydrophobic Base or polar or hydrophilic acid Hydroxyl group Alcohol (ends in Look at paper polar hydrophilic neutral -ol) version Carbonyl group Aldehyde/ketone polar hydrophilic neutral (depends on location of C = O) Carboxyl group Carboxylic acids polar hydrophilic acid (H+ easily released) (R- COOH) Amino group Amines (H+ Polar hydrophilic base easily accepted) (R-NH2) Sulfhydryl Thiols (R-SH) Polar (less hydrophilic Slightly Group polar than acidic hydroxyl) Phosphate Organic polar hydrophilic acid group phosphate (R Methyl group Methyl Non-polar hydrophobic neutral hydrocarbon (R- CH3) phosphate group – often contributes negative charge methyl group – control of gene expression; shape and function of sex hormones B. Biological macromolecules d. Macromolecules i. Monomers = building blocks of macromolecules ii. Join monomers together to get polymers iii. 3 out of 4 biological molecules are polymers 1. Carbohydrates 2. Proteins 3. Nucleic acids iv. Lipids are biological molecules but never polymers v. Monomers are joined together through dehydration synthesis Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 1. Dehydration synthesis means you remove a water to join monomers together vi. Monomers joined together are broken by hydrolysis 1. Hydrolysis means you add a water and it breaks vii. Enzymes used are hydrolases Types of bonds Type Strength electronegativity Interaction Inter or of (biology w water intramolecular bond ) Intra = within molecules Inter = between molecules e. Carbohydrates i. CH2O (mostly CHON) ii. Monomer = 1. sugars (monosaccharides) 2. glucose (C6H12O6) 3. Fueling and building material iii. Glucose is in linear and ring form – ring form more common iv. Covalent bond between monosaccharides = glycosidic linkage v. Sucrose = glucose + fructose vi. Polysaccharides = sugar polymers 1. Structure and function = COME BACK TO LECT 9/11 f. Lipids i. Not true polymers ii. Hydrophobic: mostly hydrocarbons iii. 3 families 1. Fats a. Function = store energy b. Consists of glycerol (3 carbon alcohol w 3 -OH) and 1, 2, or 3 fatty acids Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 c. Dehydration synthesis – covalent bond = ester linkage d. Triglyceride = storage form of fat e. Presence of double bonds determine if the fat is i. Saturated fatty acid – animal fats and coconut ii. Unsaturated fatty acid – vegetable oils iii. Trans fatty acid – not naturally occurring 2. Phospholipids = cell membranes a. Amphipathic = i. glycerol and two fatty acids (hydrophobic) ii. phosphate group (hydrophilic) 3. Steroids = 3 rings of 6 C and 1 ring of 5 C a. Side chains of functional groups vary b. Cholesterols in animals – communication, cell membrane structure c. Cortisol = stress hormones g. Proteins i. Proteins have many functions/structures ii. Monomer = amino acid (20 types) iii. Polymer = protein of polypeptide iv. Know the structure of an amino acid v. R groups determine the function, acidity, and polarity vi. Peptide bonds between amino acid vii. Polypeptide is a sequence of amino acids Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 1. Each amino acid is bound to the next with a peptide bond but must be folded into correct 3D shape to become a protein viii. Primary structure 1. Sequence of amino acids join by peptide bonds in polypeptide chain ix. Secondary structure 1. Within a single polypeptide 2. Hydrogen bonds stick amino acids together a. Amino group b. Carboxyl group 3. R-groups do not participate 4. Hydrogen bonds consist of helix (coil) and pleated sheet x. Tertiary Structure 1. Within a single polypeptide R-groups interact 2. Folds into a particular 3D shape 3. All types of bonds xi. Quaternary structure 1. Multiple polypeptide chains form one macromolecule (no more folding) xii. Denaturation = the loss of proteins 3rd or 4th structure 1. A denatured protein is biologically inactive 2. pH, salt concentration, and temperature h. nucleic acids i. monomers are nucleotides ii. 2 classes 1. DNA = deoxyribonucleic acid 2. RNA = ribonucleic acid iii. Transmits hereditary information and determines protein production iv. Monomers are held together with phosphodiester bonds (this will be more discussed in the genetics lecture) IV. LECTURE 4 origin of life A. 4 steps of abiogenesis a. Abiotic synthesis of monomers i. Little or no free oxygen 1. Oxygen breaks bonds (oxidizes) ii. Source of energy: builds biological molecules iii. Presence of chemical building blocks (CHON) Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 1. Water 2. Dissolved inorganic materials 3. Atmospheric chemicals iv. Time: for molecules react with one another 1. Earth is about 4.6 billion years old 2. Life on earth started about 3.5 billion years ago v. Prebiotic soup hypothesis: life formed near earths surface, spontaneous formation of monomers 1. Miller and Urey: 1953, tested prebiotic soup hypothesis a. Formed amino acids and other organic molecules b. Didn’t create life in a lab, Miller just showed that molecules like amino acids can be created without living beings creating them vi. Iron-sulfur world hypothesis: life formed at cracks of the ocean floor – hydrothermal vents 1. H2O, CO, HO something, and other minerals released 2. Iron (Fe) = catalyst to build molecules b. Synthesis of macromolecules i. Formation of polymers from monomers (protein or RNA) ii. Monomers polymerize on hot sand or rock iii. Negative ions bind monomers c. Formation of protocells i. Lipids spontaneously form vesicles (containers) ii. Organic polymers exhibit attributes of living cells 1. Osmosis 2. Homeostasis 3. Divide iii. But no mechanisms of heredity d. Appearance of self-replication i. RNA = nucleic acid in protocells ii. RNA is capable of self-replication and catalyzing protein synthesis: Ribozymes iii. DNA evolved later 1. Double stranded 2. More stable B. History of life e. Early life i. 3.5 billion years ago – prokaryotes ii. All heterotrophic bacteria iii. 1st heterotrophs 1. Use fermentation (anaerobic) nd iv. 2 : photosynthetic autotrophs appear 1. Energy from sunlight Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 2. They release O2 3. Then – rise of atmospheric oxygen rd v. 3 : aerobic bacteria 1. Uses O2 – more atp 2. The archaea arose from aerobic bacteria f. Origin of eukaryotes i. Eukarya arise from archaea and bacteria ii. A symbiotic relationship iii. Endosymbiont theory iv. Oldest fossils: 1.8 billion years v. The endosymbiont theory: 1. Mitochondria and chloroplasts were bacteria vi. Key Events in the history of life 1. Abiotic synthesis (early earths conditions) – monomers 2. Abiogenesis: monomers -> polymers -> protocells -> self- replication, life 3. Heterotrophic anaerobic bacteria (no O2) 4. Photosynthetic bacteria (atmospheric O2) 5. Archaea 6. Endosymbiosis leads to the Eukarya V. LECTURE 5 cell structure A. Cellular diversity and characteristics a. Classification by structure/morphology i. Prokaryotic cells: bacteria and archaea 1. Tiny-typical size = 1-10 micrometers 2. No nucleus -> nucleoid (DNA unbound) 3. DNA is in one circular strand 4. Ribosomes in the cytosol 5. No organelles 6. Plasma/cell membrane 7. Cell wall 8. Divide by binary fission ii. Eukaryotic cells: typically larger (10-100 micrometers) 1. DNA as linear chromosomes inside nucleus membrane – bound organelles like a. Mitochondrial/chloroplast and parts of the endomembrane system 2. Ribosomes in cytosol or membrane bound 3. Some have a cell wall 4. Divide by mitosis b. Common features of cells Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 i. Smallest unit of life ii. Multicellular organisms = cooperative specialized cells iii. Cell theory states 1. All life is made of cells 2. All cells have 4 common features 3. All cells have a common evolutionary ancestor iv. Basic cell structure – all cells have: 1. Plasma membrane = phospholipid bilayer 2. Cytosol/cytoplasm = semifluid substance 3. Chromosomes = carry genes, made of DNA 4. Ribosomes = makes polypeptides, made of RNA c. Cell size i. Why are cells so small? 1. Plasma membrane = selective barrier 2. O2 nutrients and waste 3. Surface area to volume ratio 4. Bigger? – compartments or multicellular B. Components of Eukaryotic cells d. Nucleus i. Structure: surrounding membrane = nuclear envelope ii. Inside: 1. DNA organized in many linear chromosomes a. DNA + proteins = chromatin 2. Nucleolus – makes ribosomes 3. RNA and proteins 4. No membrane iii. Nuclear envelope 1. 2 membranes – both lipid bilayers 2. Inside linked by nuclear lamina a. Proteins b. Maintains nucleus shape 3. Transport regulated by nuclear pores e. Mitochondria and chloroplasts i. Theory of endosymbiosis 1. Mitochondria and plastids: similar to prokaryotic cells a. Membranes b. Have own DNA c. Have own ribosomes d. Undergo binary fission e. BUT: both surrounded by a eukaryotic membrane Prokaryotes vs Eukaryotes Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 Prokaryotes Eukaryotes Structure Simple Complex Evolution From S.R. and protocells Endosymbiosis; Proterozoic Size Small – 1-10 micrometers Larger 10-100 micrometers Domain Bacteria, archaea eukaryota Organelles No ‘true’ nucleus True nucleus; mitochondria Examples Bacteria: e. coli, salmonella Ostrich, human, yeast f. Ribosomes i. All cells have ribosomes ii. Structure: 1. Non membrane-bound: not organelles 2. Made of ribosomal RNA (rRNA) and proteins iii. Functions 1. Synthesize primary polypeptides. (lectures 14-17) 2. Free ribosomes – all cells (and mitochondria and chloroplasts) 3. Bound ribosomes – attached to rough endoplasmic reticulum (ER) g. Endomembrane system i. Phospholipid bilayers inside (endo) cell ii. No free ends: closed compartments iii. Separates internal and external iv. Lumen – inside space v. Structure 1. Phospholipid bilayer either: a. Continuous: one long structure b. Connected via vesicles: transfer membrane segments vi. Functions 1. Regulates protein folding/ movement 2. Metabolic functions vii. Plasma membrane 1. All cells – encloses cell contents, does not equal cell wall 2. Selectively permeable 3. Regulates what and how much 4. Passes through membrane viii. Nuclear envelope 1. Encloses DNA 2. Instructions for a protein (mRNA) 3. Leave through nuclear pores a. Ribosomes i. Primary polypeptide ix. Endoplasmic reticulum (ER) 1. ER continuous with nuclear envelope Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 2. Two regions a. Smooth ER: no ribosomes b. Functions i. Synthesizes lipids ii. Metabolizes polysaccharides (breaks down glycogen) iii. Detoxifies drugs and poisons iv. Stones calcium ions Ca^2+ c. Rough ER: surface has ribosomes d. Functions i. Proteins folded and modified ii. Secrete glycoproteins (proteins binded carbohydrates) iii. Distributes transport vesicles iv. Cell membrane factory x. Golgi Apparatus 1. Structure= stacks of membranous sacs = cisternae a. Not continuous with ER b. Cis face = “receiving” side from ER c. Trans face = “shipping” side 2. Functions a. modifies ER products b. Sorts and packages c. Manufactures some macromolecules d. Shipping product using transport vesicles xi. Lysosomes 1. Sacs of hydrolytic enzymes 2. “cell stomach” 3. Primary lysosome: buds off golgi – no food yet 4. Food enters in vacuole -> fuses with lysosome -> forms 5. Secondary lysosome breaks down complex molecules xii. Vacuoles: maintenance compartment 1. Structure a. Membrane – bound containers from ER and golgi apparatus 2. Functions: vary cell by cell a. Food vacuoles = store food b. Contractile vacuoles = pump out water c. Central vacuoles = (plant cells) hold water VI. LECTURE 6 membrane and transport A. Membrane structure a. Membrane components Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 i. How do phospholipid bilayer form? 1. Spontaneously due to amphipathic structure ii. Amphipathic = polar/non-polar sides iii. Membrane proteins 1. Determines many membrane functions 2. Can move laterally – can’t flip 3. Integral – span membrane, amphipathic 4. Peripheral proteins – can be polar or non-polar iv. Membrane protein functions = 1. Focus on: a. Transport b. Enzymes c. Signal transduction 2. Others are: a. Cell-cell recognition b. Intercellular joining c. Attachment to the cytoskeleton and extracellular matrix (ECM) v. Carbohydrates 1. Polysaccharides attached to protein (glycoprotein) or lipid (glycolipid) 2. Cell identification (blood type (A, B, O, etc.) 3. Membrane components can move laterally within 1 layer of the membrane a. Lipids b. Proteins c. Carbs b. Fluid mosaic model i. Fluidity depends on 1. Temperature 2. Lengths of tails 3. Bends in tails (saturation) 4. Amount of cholesterol a. Acts as a spacer ii. Plasma membrane is selectively permeable iii. 2 basic types of transport 1. Passive transport = doesn’t use metabolic energy (ATP) and moves with the gradient 2. Active transport= does use metabolic energy (ATP) and moves against the gradient II. Membrane transport a. Passive transport 1. Simple diffusion Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 2. Osmosis 3. Facilitated diffusion ii. Net momentum is down concentration gradient iii. No ATP required – spontaneous iv. Results in dynamic equilibrium v. Diffusion 1. Tendency for molecules of a substance to fill available space 2. Small gases: O2, CO2, N2 – tend to do this (diffusion) 3. Small non-polar molecules – including hydrocarbons 4. Small polar uncharged molecules – including H2O vi. Osmosis 1. Diffusion of water across selectively permeable membrane 2. Water diffuses from lower to higher (solute) vii. Solvent = a substance capable of dissolving water (water is the mostly universal solvent) viii. Solute = a dissolved substance ix. Ex. Sugar x. Water moves toward higher concentration of solute 1. Always about water moving xi. Osmosis tonicity = ability of a solution to cause a cell to gain or lose water xii. Isotonic solution = equal, iso mean same xiii. Hypertonic solution = [solute] outside cell > [solute] inside cell xiv. Hypotonic solution = [solute] outside cell < [solute] inside cell xv. Facilitated diffusion 1. Large molecules or ions (H+,Ca^2+, Na +) 2. Transport proteins – (integral proteins) b. Active transport i. Works against gradient ii. Large polar molecules iii. Requires ATP iv. Facilitated by proteins (carriers or pumps) or bulk transport v. Pumps/carrier: integral membrane protein that changes shape vi. Requires ATP vii. Works against gradient viii. Bulk transport = large number of molecules at once 1. Not carrier mediated 2. Formation of vesicles ix. Active means always requires ATP x. Does not pass through plasma membrane B. Bulk transport c. Exocytosis “out” i. Waste, proteins, and secretory products ii. Vesicles fuse with plasma membrane iii. Releases contents from cell Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 iv. Vesicle fuses with plasma membrane -> primary mechanism for growing plasma membrane d. Endocytosis “in” i. Material taken into cell by forming vesicles derived from plasma membrane ii. 3 types 1. Phagocytosis “cellular eating” a. Cell engulfs large particle b. Non-specific 2. Pinocytosis “cellular drinking” a. Ingestion of fluid and dissolved material b. Non-specific 3. Receptor mediated endocytosis a. Receptor proteins in plasma membrane bind specific macromolecules outside cell b. Form coated pits c. Fold inward to form vesicles d. Main mechanism for uptake of macromolecules e. Specific VII. LECTURE 7 metabolism A. Metabolism and energy change a. Metabolism basics 1. Metabolic pathways begin with a specific molecule and ends with a product 2. Each step is catalyzed by a specific enzyme ii. Catabolic pathways 1. Breaking down complex molecules 2. Releases energy a. ex. cell respiration iii. Anabolic pathways 1. Builds complex molecules 2. Requires energy a. Ex. synthesis of protein from amino acids b. Free-energy change in chemical reactions i. Energy = capacity to cause change do to work ii. Kinetic = energy of motion iii. Potential = stored energy -> has not yet been used iv. Thermodynamics = study of energy transformations 1. First law of thermodynamics = energy cannot be created nor destroyed, only converted Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 2. Second law of thermodynamics = every energy transformation is an increase in entropy v. Entropy = a measure of disorder 1. The more energy that a system loses to its surrounding, the less ordered and more random of a system vi. Light energy enters an ecosystem vii. Heat energy exits viii. Energy conversion is never 100% ix. Total energy in the universe is constant x. Gibbs free energy = the energy available to do work cannot measure G but you can see how G changes during a reaction (deltaG) 1. If deltaG is less than zero, energy is released from reaction 2. If deltaG is equal to zero, chemical process is at equilibrium 3. If deltaG is greater than zero, energy is added to cause a reaction and it is nonspontaneous Exergonic Endergonic Negative deltaG Positive deltaG Energy released Energy stored Spontaneous Nonspontaneous c. ATP i. Cells use atp to carry energy ii. ATP (adenosine triphosphate) structure: 1. Ribose (5 C sugar) 2. Adenine (nitrogenous base) 3. 3 phosphate groups 4. Diagram of ATP: iii. Coupled reactions 1. Pair: exergonic reaction (provides energy) with endergonic reaction (requires energy) 2. Hydrolysis of ATP is exergonic 3. ATP drives endergonic reactions by phosphorylation 4. Phosphate group transferred to molecule, molecule now a new shape Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 5. Reactant now = phosphorylated intermediate 6. ATP is hydrolyzed into ADP and P 7. P group binds to protein or a reactant which causes a conformational shape or change in function B. Enzymes d. Characteristics of enzymes i. Enzymes speed up reactions by lowering energy barriers ii. Activation energy = initial energy needed to start a reaction iii. Enzymes act on a specific substrate 1. Active site = cleft or groove for substrate binding 2. Substrate = reactant that an enzyme acts upon 3. Change of shape: facilitates breaking of bonds e. Factors affecting enzyme activity i. Temperature and pH ii. Enzyme has optimal temperature 1. Ex: human optimal temp (35-40 degrees C) iii. Denaturation 1. High temp: even short exposure it denatures enzymes 2. Low temp: enzyme reaction -> slows or not at all iv. Enzyme helpers’ cofactors 1. Inorganic a. Often metals (iron or zinc) 2. Organic coenzyme a. NAD+ and FAD+ b. Vitamins v. Reversible or irreversible inhibition 1. Inhibitors a. Competitive: bind to the active site and compete with substrate-penicillin b. Non-competitive: bind elsewhere and changes shape of active site -cyanide C. Redox reactions f. Characteristics of redox reactions i. Redox reaction = transfer of electrons between reactants oxidation- reduction reaction ii. Oxidation = loss of electron (one or more) -> is oxidized iii. Reduction = gains electron -> is reduced iv. OILRIG 1. Oxidation Is Losing Reduction Is Gaining v. Reducing agent = electron donor, loses an H 1. Oxidized in a redox reaction 2. Ex. NADH -> NAD+ + H + e- (NADH is oxidized) vi. Oxidizing agent = electron acceptor, gain an H Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 1. Reduced in a redox reaction electron carriers 2. Ex. NAD+ + H + e- -> NADH (NAD+ is reduced) g. NAD+: electron acceptor i. NADH represents stored electrons that will be used to make ATP ii. Dehydrogenases 1. Remove 2 of H atoms (2 electrons and 2 protons) + oxidation VIII. LECTURE 8 photosynthesis A. Introduction to photosynthesis a. Ecological importance i. Photoautotrophs = fix inorganic carbons (CO2) producers ii. Heterotrophs = obtain their carbon material from organic sources (other organisms); consumers iii. Redox: H2O is oxidized and CO2 is reduced iv. Endergonic process -> energy boost from light energy deltaG + b. Nature of light i. Light = form of electromagnetic energy ii. All radiation travels in waves iii. Photon = small particles of light energy iv. Energy in photon = 1. Shorter wavelength = more energy/photon 2. Longer wavelength = less energy/photon c. Effects of photons on electrons i. Molecule absorbs a photon of light energy ii. Electron becomes energized -> shifts to higher energy iii. Can: 1. Return to lower energy orbital or 2. Leaves atoms -> captured by an electron acceptor -> acceptor is reduced B. Structures in photosynthesis d. Plant organization i. Plant absorbs visible light ii. Leaves are green because chlorophyll reflects and transmits green light iii. Chloroplasts = photosynthetic organelle e. Structures of chloroplasts i. Two outer membranes in a chloroplast ii. Chloroplast is located in the thylakoid membrane iii. Should recognize basic structure Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 f. Photosynthetic pigments i. Chlorophyll is a pigment: “read” absorbs visible light ii. Chlorophyll is embedded in thylakoid membrane II. The process of photosynthesis a. Overview of photosynthesis i. Endergonic +deltaG reaction b. Light dependent reactions i. The light reactions (in the thylakoid) 1. Split H2O and release O2 2. Reduce NADP+ to NADPH 3. Generate ATP from ADP ii. How? On thylakoid membrane iii. Two photosystems (PSII & PSI) 1. Trap sun energy and 2. Convert it to NADPH ATP iv. Most reactions use linear electron flow v. Linear electron flow 1. Light dependent 2. PSII then PSI 3. Produces ATP (PSII) and NADPH (PSI) and O2 4. More recent – cause of O2 rev vi. FYI: 1. Cyclic electron flow 2. Produces only ATP 3. Older – predates O2 rev vii. Photosystem parts 1. 2 light harvesting complexes: photosystems II & I 2. Capture light and produce ATP and NADPH 3. (look in textbook) 4. PSII has wavelength P680 and PSI have wavelength P700 5. Each photosystem has a pigment (P680 or P700) that captures a specific wavelength Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 6. 2 electron transport chains a. Protein chain – passes electron from 1 protein to the next each time electron some of the excited electron is used some is lost PSII ETC PSI ETC - Uses electrons to pump H+ and fill - Catalyzes building NADPH thylakoid with H+ viii. Photosystem parts 1. ATP synthase: protein – proton channel (H+) and as the H+ flow 2. Catalyzes: ADP + Pi -> ATP 3. Light reactions result in building two molecules a. ATP – cellular energy and b. NADPH – an electron carrier ix. Linear electron flow 1. Both photosystems involved, same three things happen in each: a. Excite electron b. Use energy in electron c. Replace electron 2. Many steps involve redox reactions a. Boost PSII electron (no official name for each step) i. Photon hits pigment in PSII ii. Energy is passed to P680 (reaction center) iii. P680 is oxidized to P680+ iv. Primary electron acceptor (redox reaction) b. Use energy in electron passed down ETC (to make ATP) i. Electron from primary electron acceptor goes through electron transport chain ii. Passes from protein to protein and this causes H+ to be pumped into the thylakoid (generates H+ gradient inside thylakoid space) iii. H+ diffuses through ATP synthase (facilitated diffusion) 1. ATP synthesis c. Replace PSII electron (from H2O) i. P680+ is an extremely strong oxidizing agent -> H2O is oxidized (photolysis) ii. Electron transferred to P680+ iii. P680+ is reduced back to P680 iv. O2 is released as by product 1. This is where atmospheric O2 comes from d. Boost PSI electron i. Light energy excites electron in pigments 1. Excites P700 Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 2. Oxidizes to P700+, primary electron acceptor reduced e. Use energy in electron to make NADPH i. Electron transferred to the enzyme NADP+ reductase NADP+ + e- + H+ -> NADPH ii. Electron moved through PSI ETC to ferredoxin (FD) f. Replace PSI electron (with PSII electron) i. After PSII electron travels down ETC, energy has been used ii. Now low energy electron donated to PSI -> replaces lost electrn c. Carbon fixation reactions i. Where? Abiotic sy ii. Why? Reduce CO2 into sugar using NADPH and ATP iii. Three stages – Calvin cycle 1. Carbon fixation 2. Carbon reduction 3. Regeneration iv. Phase 1: carbon fixation 1. 3 carbons enter cycle as CO2 a. CO2 + RuBP 2. Catalyzed by RuBisCo and forms 6 PGAs (phosphoglycerates) 3 carbon each v. Phase 2: reduction 1. 6 PGA (3 carbon each) 2. Using 6 ATP -> biphosphoglycerate 3. Then reduced using 6 NADPH a. -> 6 G3P b. One G3P leaves cycle to become a sugar 4. 5-3 carbon G3P 5. Converted to 3 molecules of 6 carbon RuBP using ATP IX. LECTURE 9 respiration A. Introduction to cell respiration a. Overview of eukaryotic respiration i. Redox reactions: follow the H 1. Transfer of electrons from sugar to O2 ii. Where? Cytosol of cell and in mitochondria iii. Function? Oxidize a glucose -> a lot of ATP (moving e- + H+) iv. NAD+ + 2e- + H+ = NADH -> electron carrier v. FAD + 2e- + 2H+ = FADH2 -> another electron carrier vi. NADH and FADH2 = store energy to make ATP Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 B. The stages of cellular respiration b. Glycolysis i. Where? Cytosol of cell ii. Function? Convert 1 glucose to 2 pyruvates and 2 net ATP iii. Two stages: investment and pay off iv. Glucose enters cells: (mammals) via facilitated diffusion by GLUT1 v. No oxygen required (anaerobic) vi. Stage 1: energy investment phase 1. Needs 2 ATP (endergonic) 2. +deltaG (not spontaneous) vii. Stage 2: energy payoff phase 1. -deltaG (spontaneous) 2. 2 G3P converted to 2 pyruvate, 2 NADH, and 4 ATP 3. Phosphate groups removed and transferred to ADP a. Forms new substrate level phosphorylation viii. Summary 1. Glucose: glucose enters cell via facilitated diffusion a. Investment phase – “pay” two atp 2. 2 G3P: results in two G3P molecules a. Payoff phase – oxidizes 2 G3P and creates two NADH; uses enzymes build 4 atp 3. 2 pyruvate: glucose has been oxidized to 2 pyruvate, 2 NADH, and we have made 2 net ATP c. Pyruvate oxidation i. Oxidation of pyruvate to acetyl CoA Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 ii. What are the parts of a mitochondria? iii. Outer mitochondrial membrane – diffusion through small pores iv. Inner mitochondrial membrane – carrier protein v. Each pyruvate is converted to acetyl coenzyme A vi. Catalyzed by pyruvate dehydrogenase 1. Removes an H+ 2. Builds NADH vii. No ATP d. Citric acid cycle (CAC) i. Where? Inside cytosol of mitochondria – mitochondrial matrix ii. Why? To break down acetyl CoA as efficiently as possible iii. Goal = to build electron acceptors to give to ETC iv. 1 glucose is 2 turns (1 turn per acetyl CoA) 1. Oxaloacetate (4C) waits in matric 2. Enzyme joins oxaloacetate and 2C acetyl group 3. Cycle tears apart citrate -> electron (H) in sugar to electron acceptors NAD+ and FAD 4. NADH and FADH2 5. Glucose completely oxidized -> CO2 a. One little generated ATP e. Oxidative phosphorylation i. Where? Proteins imbedded in the inner mitochondrial membrane cristae ii. Why? To make lots of ATP 1. Converts energy in NADH & FADH2 to ATP Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 iii. Energy from glucose molecule is now: 1. In excited electrons in NADH and FADH2 (now electron carriers) iv. We want more of 1. Electron transport chain (ETC) and 2. Chemiosmosis v. Oxidation phosphorylation = ETC + chemiosmosis vi. Goal = take excited electron carriers and use it to build lots of ATP vii. How? 1. First break up NADH and FADH2 2. Pull off electrons (O2 will help) 3. Then electron energy to 4. Pull it + off carriers and dam it up viii. This is a set up to power ATP synthesis ix. First use electron transport chain (ETC) more elections from increase to decrease x. ETC is made of proteins I II III and IV xi. Electrons pulled by O2 xii. Proteins are each eletron carriers xiii. I & II hydrolyze electron carriers xiv. I III and IV pump H+ into intermembrane space xv. IV passes electrons to O2 forms H2) w addition of 2 H+ xvi. Electrons transfer in ETC causes proteins to pump H+ to the intermembrane space -> create H+ gradient 1. ETC makes no ATP xvii. Water is produced xviii. Water is the final acceptor of electrons in this process xix. To make ATP -> ATP synthase xx. Chemiosmosis = uses H+ gradient to drive cellular work xxi. How? 1. ATP synthase = molecular mill: inner membrane enzyme xxii. ETC set up an H+ gradient 1. H+ = ion xxiii. H+ diffuses through back to matric: through ATP synthase -> it rotates xxiv. Drives phosphoralation 1. ADP + Pi -> ATP 2. About 28 ATP per glucose Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 CELLULAR RESPIRATION – HANK GREEN NOTES 1 Glycolysis 2 Krebs citric acid cycle 3 electron transport chain I. Glycolysis a. Breaking down of sugar i. Glycolysis is the breaking up of glucose’s 6 carbon ring into two 3 carbon molecules called pyruvic acids b. Glycolysis needs the investment of 2 ATPS in order to work i. Ends with 4 ATPs and 2 pyruvates and 2 NADH c. Anaerobic – does not require oxygen d. Occurs in the cytoplasm II. Krebs CAC a. Aerobic process – requires oxygen b. Occurs across the inner membrane of the mitochondria i. One of the pyruvates is oxidized ii. One of the carbons off the 3 carbon chain bonds with an oxygen molecule and leaves the cell as CO2 1. What is left is a two carbon compound called acetyl CoA iii. Another NAD+ comes along and picks up a hydrogen and becomes NADH DIRTY MEDICINE NOTES C. Electron transport chain c. Aerobic process – requires oxygen d. Goal is to couple energy stored in electron acceptors to a proton gradient that drives ATP synthesis Electron transport chain Photosynthesis vs Respiration Other: Binary fission = Binary fission, asexual reproduction by a separation of the body into two new bodies. In the process of binary fission, an organism duplicates its genetic material, or deoxyribonucleic acid (DNA), and then divides into two parts (cytokinesis), with each new organism receiving one copy of DNA Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 X. LECTURE 10 cell cycle A. Organization of genetic material a. Introduction 1. Cell division is an integral part of the cell cycle 2. What are the three functions of cell division? 1. Reproduction 2. Growth and development 3. Tissue renewal b. Genetic material of the cell 1. Genome = all DNA in cell (gene instruction) 2. Prokaryotic cells = single circular DNA molecule 3. Eukaryotic cells = several linear DNA molecules 1. Chromatin = lose DNA and proteins 2. Chromosomes = DNA = proteins packaged tight 4. Eukaryotic chromosomes 5. Condenses during cell division DNA wound around histore proteins into nucleus c. Chromosome number 1. Humans = 46 chromosomes 2. Every eukaryotic species has a characteristic number of chromosomes in each cell nucleus 3. Ploidy = number of sets of chromosomes 4. Haploid cell (n) 1. 1 full set of each gene 2. 1 full set of chromosomes 5. Gametes = sex cells (n) Or 6. Diploid cells (2n) 1. 2 sets of each gene 2. 2 full sets of chromosomes 7. Somatic cells = body cells (2n) 8. Chromosome structure 9. Genes (instruction for a protein) 10. Centromere = pinched part 11. Prior to mitosis, DNA is doubled 1. Sister chromatids form 2. Ploidy does not change 3. Same genetic info just 2x mass B. Phase of cell cycle d. Introduction 1. All cells must divide 2. Goal = make identical copies 3. During cell: starting ploidy = ending ploidy Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 4. So 1. nn 2. 2n2n 3. 100n100n 5. Prokaryotes (what two domains) 1. Binary fission – double in size and split 2. Why? a. 1 circular chromosome b. No nucleus 6. Eukaryotes 1. Interphase (growth and DNA replication) 2. Mitotic (M) phase (mitosis and cytokinesis) e. Events of interphase 1. G1 phase 1. 90% of cells life 2. No DNA synthesis 3. Cell functions, communication 4. Protein manufacture 5. 4 chromosomes (2 from mom 2 from dad) 2. S phase 1. Chromosomes duplicate (2n2n) 2. Firm identical sister chromatids 3. Diagram 4. Held together at centromere a. By cohesion proteins 5. Kinetochores (protein handles) will grow from centromere 3. G2 phase 1. Centrosomes duplicate 2. 2 centrioles per centrosome 3. Function = more chromosomes f. Events of M phase 1. PMAT (diagrams) 1. Prophase a. Chromosomes condense mitotic spindle forms b. Centrosomes to opposite poles c. Nuclear envelope breaks down d. Spindle fibers attach to kinetochore handles 2. Metaphase a. Longest stage of mitosis b. Chromosomes align on metaphase plate 3. Anaphase a. Shortest stage of mitosis b. Cohesion proteins cleared by an enzyme – disjunction c. Chromosomes begin to move to opposite sides Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 d. How have complete sets of chromosomes 4. Telophase a. 2 new daughter cells form b. Nuclear envelope reforms c. Cytokinesis will divide d. Cytoplasm 2. Cytokinesis 1. Not part of mitosis 2. Cytoplasm divides 3. How? a. Animals form a cleavage furrow b. Plants for a cell plate 4. Each daughter cell gets: a. Full set chromosomes organelles 5. Then return to interphase XI. LECTURE 11 meiosis A. Introduction to heredity a. Asexual reproduction i. One parent ii. Mitosis iii. Clones iv. Advantages 1. Always the same v. Disadvantages 1. Always the same 2. Mutations can take a toll b. Sexual reproduction i. Two parents ii. Meiosis iii. Variable iv. Advantages 1. Genetic variations v. Disadvantages 1. Hard to find a partner c. Types of chromosomes (humans) i. In somatic cells: diploid (2n) 1. 46 chromosomes = 23 pairs of homologs ii. 1 pair sex chromosomes (XX or XY) iii. 22 pairs autosomes: (body chromosomes) iv. Gametes: haploid cells (n)  23 chromosomes 1. 1 sex chromosome Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 2. 22 autosomes B. Life cycles of different organisms d. Human life cycle i. Life cycle is from conception to production of own offspring ii. Fertilizations and meiosis 1. Sexual reproduction 2. Makes sure each offspring has same number of chromosomes 3. Haploid and diploid alternate during life cycle iii. Fertilization n+n=2n 1. Results in zygote 2. Grows into a multicellular organism iv. Meiosis 2nn 1. Single cell gametes (egg/sperm) e. Three types of sexual life cycles i. Plants – alternation of generations 1. Fertilization n+n=2n 2. Results in a zygote that grows into a multicellular diploid organism ii. Meiosis 2nn 1. Single cell 2. Also grows into a multicellular haploid iii. Fungus and many protists 1. Dominant stage is haploid iv. Fertilization n+n=2n 1. Results in a zygote, immediately goes through v. Meiosis 2nn 1. Single cell haploid 2. Grows into a multicellular (haploid) organism C. 4 stages of meiosis f.DNA replication before meiosis i. Not a cycle g. Results in: i. 4 daughter cells ii. Unique iii. Haploid h. 4 stages: i. Interphase (G1, S, G2) ii. Meiosis I (PMAT) iii. Interkinesis iv. Meiosis II (PMAT) a. Interphase a. Same as mitosis: G1, S, G2 i. S: chromosomes duplicate b. Each chromosome now composed of 2 sister chromatids Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 i. G2: centrioles replicate c. Humans = 46 = 2n d. 92 chromatids i. pairs ii. Diploid organisms have 2 sets of chromosomes – matched pairs are homologous chromosomes b. Meiosis I a. Goal = separate homologous pairs b. Results in: two haploid (n) daughter cells 2n2 x n i. Ploidy halves in Meiosis I c. Prophase I = longest stage of meiosis i. Chromosomes condense ii. Homologous chromosome pairs align by gene d. Synapsis = process of homologous chromosome pair up, forms a tetrad (4 sisters) e. (also) i. nuclear envelope disappears ii. Organelles move out of the way iii. Mitotic spindle appears iv. Spindle attaches to kinetochores 1. Crossing over = non sisters “swap genes” 2. Chiasmata – location (x’s) where genes cross v. Why? Genetic variability f. Metaphase I i. Homologous pairs line up at the metaphase plate (still crossing over) ii. Alignment is random (random assortment) iii. Why? Genetic variability iv. Spindle fibers maneuver homologous tetrads v. As soon as they line up g. Anaphase I i. Homologous chromosomes separate (disjunction) ii. chromatids stay together – but not homologous iii. Ploidy changes h. Telophase I and cytokinesis i. Each chromosome has sister chromatids ii. Homologous pairs have been separated iii. Cytokinesis occurs simultaneously c. Interkinesis a. No chromosome replication occurs i. Because the chromosomes are already replicated ii. Does not go through S phase again d. Meiosis II i. How we basically do mitosis (literally just mitosis notes again) ii. Prophase, Metaphase, Anaphase, Telophase Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 iii. No ploidy changes iv. Separate sister chromatids j b. Prophase II i. Spindle forms, nuclear envelope disappears ii. Chromosomes = pairs of sister chromatids 1. No crossing over iii. Kinetochores attach to microtubules c. Metaphase II i. Sister chromatids line up at the metaphase plate d. Anaphase II i. Sister chromatids separate ii. No ploidy change e. Telophase II and cytokinesis i. Chromosomes arrive at opposite poles ii. Cytokinesis occurs concurrently f. Four daughter cells, each w a haploid set of chromosomes i. Each daughter cell is genetically distinct XII. LECTURE 12 mendel A. Mendel’s Experimental Approach a. Background i. Gregor Mendel (1822-1884) ii. Why pea plants? (what makes a good test organism?) 1. Inexpensive 2. Many varieties 3. Easy to grow, short generation time 4. Lots of offspring 5. Clearly identifiable traits 6. Easy to control pollination b. Testing blending hypothesis i. Testing the blending inheritance hypothesis: Mendel crossed true- breeding plants with contrasting ii. Mendel’s control: pollination 1. Crossing two different flowers in P (parent) generation results in first generation (F1) iii. True breeding = all individual of line have the same characteristics iv. Crossed purple and white 1. F1 generation was 0% white and 100% purple 2. F2 generation was 25% white and 75% purple a. This disproved blending hypothesis v. No intermediate phenotypes appeared vi. Lost phenotypes reappear vii. Blending of fluids cannot explain either observation Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 c. Mendel’s model i. New hypothesis = particulate inheritance ii. “heritable factors discrete units (gene) determine characters iii. Each character is controlled by 2 factors (genes) from parents iv. Mendel’s particulate inheritance model explains the 3:1 inheritance pattern in F2 offspring v. 4 related concepts make up this model 1. Alleles are discrete units of information 2. 2 alleles from each parent (2n) 3. Dominant and recessive alleles 4. Mendel’s two laws of inheritance vi. Concept 1: alleles 1. Alleles = alternative versions of genes (2n means 2 of each allele) a. Each allele at same locus (location) on homologous chromosomes vii. Concept 2: two alleles – 1 from each parent 1. The 2 alleles: a. May be identical  (like P generation) = homozygous b. Or different  (likeF1, hybrids) heterozygous viii. Concept 3: dominant and recessive alleles 1. If an organism is heterozygous a. Dominant alleles determine the organisms’ appearance b. The recessive allele has no effect on appearance ix. Concept 4: Mendel’s two laws 1. Law of segregations a. Each gamete gets one of each allele b. The two copies of each gene (alleles) segregate (separate) during Meiosis c. Egg or sperm gets only 1 of the 2 alleles 2. Law of independent assortment (action of sorting) a. Genes on different chromosomes assort randomly and independently during gamete formation b. Due to random orientation of tetrads during metaphase II i. each are equally likely, and this leads to genetic recombination and more variation B. Genetic crosses d. Introduction i. Punnett squares -- illustrates Mendel’s laws 1. Show possible babies ii. Phenotype = physical/expressed type (yellow or green) iii. Genotype = genetic type (YY, Yy, yy) iv. Monohybrid cross = cross of one character/allele e. Monohybrid cross Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 i. Let’s cross two pea plants: Homozygous yellow (D) and Homozygous green (R) Dominant – upper case Y Recessive = lower case y Homozygous yellow=Y Homozygous green=y Y Y y Yy Yy y Yy Yy All are going to be yellow but hiding green Now breed again Yy and Yy Y y Y YY Yy y YY yy 75% yellow, 25% green Practice: the monohybrid testcross: B = black, b = brown We have a black dog so he could be BB or Bb If you pick a brown dog to breed with then you can test to see if it also has the Brown (a testcross crosses an unknown genotype with an individual of the recessive genotype) C. Probability in genetics f. Introduction i. Probability = use math to solve squares faster genetic ratios expressed probability ii. Event is certain to occur 1. Probability is 1 iii. Event is certain not to occur 1. Probability is 0 iv. Event occurs 50% of the time 1. Probability is 0.5 g. Multiplication rule Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 i. Predicts combined probability of independent events ii. Independent events = one event does not affect probability of other 1. P(this) ad P(that) 2. Word ‘and’ means to multiply separate probabilities iii. Ex. So tonight I hope to have chicken and beer 1. P(eating chicken) = 50% 2. P(drinking beer) = 25% 3. Both 0.5*0.25 = 0.125  12.5% probability h. Addition rule i. Predicts combined probability of mutually exclusive events 1. Mutually exclusive events = cannot occur simultaneously ii. Stated as 1. P(this) or P(that) 2. Work ‘or’ in equation means to add separate probabilities XIII. LECTURE 13 chromosomes A. Chromosomal theory of inheritance a. Morgan and D. melanogaster i. Mendel’s “hereditary factors” were abstract ii. 1902: Scientists began to develop the “chromosome theory of inheritance” 1. Genes have specific loci on chromosomes 2. Chromosomes undergo segregation & independent assortment iii. Thomas Hunt Morgan 1. Evidence that chromosomes are the location of Mendel’s “heritable factors” iv. Drosophila melanogaster: a convenient organism for genetic studies 1. 100’s offspring 2. Eggs every two weeks 3. Four pairs of chromosomes a. 3 pairs of autosomes b. 1 pair of sex chromosomes v. Trait is named after mutation 1. Wild type a. Phenotype most in population b. Ex. red eyes  red eyes = w+ 2. Mutant phenotype a. Alternative to wild type b. Ex. white eyes (first mutant found in male)  w b. Correlating allelic and chromosome behavior i. Morgan’s experiment: white eyes female (w) X red eyed male (W+) W+ W+ w W+ W+ Downloaded by Tina Zhu ([email protected]) lOMoARcPSD|46266463 w w w W+ W+ w w Red eyes 100% prediction but in reality, came out 50% 50% - Concluded that these genes have something to do with sex - Male flies XY, female flies XX o Result: sex linked inheritance pattern - Put alleles on the X chromosome o W+ = red eyes o w = white eyes - discovered eye color is only on the X Xw Yw Xw XwXw XwYw Xw XwXw XwYw B. inheritance patterns of sex chromosomes c. sex chromosomes i. quick chromosome review 1. autosomes: 22 pairs (in humans) a. homomorphic = same shape 2. sex chromosomes: 1 pair a. heteromorphic = not morphologically similar meiosis some regions synapse ii. sex linked genes on either sex chromosomes iii. humans 2 sex chromosomes: X and Y 1. male = heterogametic a. xy genotype b. sperm: ½ get x ½ get y 2. females = homogametic a. xx genotype b. so all eggs have an x iv. alternate systems of sex determination 1. Z-W system – reptiles a. Chickens

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