Biology 211 Final Study Guide
Biology 211 Final Study Guide Biology 211
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This 19 page Study Guide was uploaded by Melissa on Wednesday March 9, 2016. The Study Guide belongs to Biology 211 at University of Oregon taught by Jana Prikryl in Fall 2015. Since its upload, it has received 68 views. For similar materials see Gen Biol I: Cells in Biology at University of Oregon.
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Bio 211 Final Study Guide ● Chemistry terms ○ Carbonyl group(aldehyde) ○ Carboxyl group: COOH; found in fatty acids which are bonded to a HC chain; the only polar part of a fatty acid ○ hydroxyl group: OH; very polar and interacts with water to form hydrogen bonds ○ Carbocyclic ○ Hydrogen and Covalent bonds ■ Covalent: chemical bond that involves the sharing of electron pairs between atoms ■ Hydrogen bond: charged based attraction between polar molecules that occurs when a hydrogen atom is bound to a highly electronegative atom like nitrogen or oxygen and experiences attraction to some other nearby highly electronegative atom ○ Functional groups: hydroxyl, carbonyl, and hydroxymethyl ● Macromolecules ○ Primarily made up of carbon. hydrogen, oxygen, and nitrogen ■ carbon makes up the backbone of these molecules and can form 4 covalent bonds ○ Monomers make up the polymers ○ Subunit:part of a larger molecule ■ subunits of polymers are monomers ○ Monomer: item that can form a polymer along with other similar monomers ■ connected by condensation reactions( dehydration) ○ Polymers are broken down into monomers by hydrolysis ○ Carbohydrates ■ Polar because they dissolve in water ■ Monomers: monosaccharide ● Ribose: C5H10O5 ● Glucose: C6H12O6 ○ Beta glucose is more abundant because it is more stable and found in cellulose; structural support ○ Alpha glucose is found in starch; energy storage ■ Disaccharide: Sucrose and lactose ■ Polysaccharides: polymers of the monomers ■ Oligosaccharide ■ Glycosidic Linkage links the hydroxymethyl groups between the two ringed structures ■ Functions ● Energy storage ○ Starch in plants ○ Glycogen in animals( a polymer) ● Structure ○ Cellulose in plant cell walls ○ Chitin in animals and fungi to build exoskeleton ○ Peptidoglycan in bacteria ● Cell to Cell Signaling ○ Oligosaccharides on glycoproteins ■ Glycoprotein: proteins that contain covalently linked oligosaccharides ● sugar and a protein ○ Lipids ■ made mostly of Carbon and Hydrogen ■ nonpolar, so they do not dissolve in water ● Hydrophobic ■ They do not form polymers ■ Fats and steroids ■ Functions: ● Long term energy storage: triglycerides ○ three fatty acids and a glycerol ● Structural: cholesterol and phospholipids ● CellCell signaling ○ Steroids and Glycolipids ■ Steroids ● Four ring structure and a functional group ○ Ex. Cholesterol component of animal cell membranes, has a hydroxyl group and a hydrocarbon chain(isoprene chain) ■ Adds density to hydrophobic part of the membrane which makes it less permeable ■ Absorbs movement of phospholipid tails ■ Fatty acids ● Saturated:no CC double bonds and all the carbons are saturated with hydrogen bonds ● Unsaturated: some CC double bonds and has a “kink” ● Made up of hydrocarbon chain and a carboxylic acid ● Length and saturation of hydrocarbon tails determines the fluidity ■ Phospholipid: ● amphipathic: both hydrophobic and hydrophilic ○ Head is hydrophilic ○ Tails are are hydrophobic and interact with each other ● Major component of cell membranes ● Constant lateral motion and do not flip to the other side due to their differences in polarity ■ Glycolipid: sugar and a lipid ○ Fluid Mosaic Model of membrane structure ○ ○ Hydrolysis and Condensation Reactions ■ Monomers are connected by condensation reactions which is when the loss of water molecules as two monomers are covalently bonded together ■ Hydrolysis breaks polymers into monomers; water breaks the two monomers covalently bonded together ■ Glucocerebrosideis a glycolipid ● Gaucher’s Disease is caused as a result of having too much glucocerebroside and not able to break it down at the same rate ■ Glucocerebrosidase: enzyme( protein) that breaks down glucocerebroside ● Uses hydrolysis to cleave the beta linkage of glucocerebroside ○ Proteins ■ made of carbon, hydrogen, nitrogen, oxygen, and sulfur ■ Monomers: Amino acids ■ Polymers: Polypeptides ■ Building blocks of amino acids ● contains an amino group, carboxyl group and an R group ○ Can have nonpolar, polar, or charged side chains ■ If nonpolar: amino acids will be found buried in the middle of the folded protein ■ If polar: found on the exposed surfaces of the proteins ● Synthesized from the amino to carboxyl terminus ■ Polymerize to form polypeptides ■ Sequence is written from the N terminus to the C terminus ■ 4 levels of protein structure ● Primary ○ The sequence of amino acids ■ determines the shape and the shape determines function ○ Proteins found in the cell membranes are the receptor proteins, transport proteins, and the signal proteins ● Secondary Structure ○ hydrogen bonds form between the backbone components ■ stabilization ■ bonds between H bond donor and H bond acceptor ○ Consists of the alpha helixes and beta sheets ● Tertiary Structure ○ 3 dimensional shape ○ How the alpha helices and beta sheets fit together ○ interactions between the side chains ■ Hydrogen bonds between the donors and acceptors ■ hydrophobic interactions between nonpolar groups ■ Covalent bonds ■ charged based interactions ○ Glucocerebrosidase is found here ● Quaternary Structure ○ how two or more polypeptides combine together to make a functional protein ○ protein is a tetramer or made up of four polypeptides ○ not every polypeptide contains both the alpha helix and the beta sheets ○ Nucleic Acids ■ Made up of carbon, hydrogen, nitrogen, oxygen, and phosphate ■ Monomers: Nucleotides ● Made up of sugar, nitrogenous base and phosphate ○ Phosphate group gives the DNA and RNA the negative charge ○ Sugar: Deoxyribose vs Ribose ○ Nitrogenous Base: DNA vs. RNA bases ○ Mutations occur in a change in the nucleotide sequence ● Polymerize to form nucleic acids ■ Polymers: Nucleic acids ■ Genetic material storage and processing ■ Functional units of DNA: genes ● Most genes code for proteins ● Polarity ○ Polardissolve in water because they are able to interact with water molecules ○ Hydrophilic: like water and will dissolve ○ Nonpolarunable to dissolve in water such as lipids ○ Hydrophobic: little or no affinity for water; will not dissolve ● Gaucher’s Disease ○ Individuals have a mutation in the gene that codes for glucocerebrosidase ■ autosomal recessive disease which means that it requires two copies of the mutated disease ■ Glucocerebrosidase is an enzyme while glucocerebroside is a lipid and a carbohydrate ● the enzyme is found within the lysosomes ○ Gaucher cells are found in the bone marrow ■ Macrophages are a type of WBC that cleans out the junk in the Gaucher cells by digesting the cells and degrading them inside cell compartments called lysosomes ● Phagocytosis ○ Plasma membrane detects a particle and the membrane then stretches around the particle forming a phagosome ■ The phagosome fuses with the lysosome where the particle is digested and then small molecules are released into the cell ○ Treatments ■ Enzyme replacement therapy using M6P so that the cells are targeted to the lysosome ■ Cell transplantation and gene therapy ■ Drug therapy using celastrol which up regulates expression of proteins that help mutant GCAse function ● Cells ○ Components ■ Plasma membrane: encloses the cell; selective barrier ● Phospholipids, cholesterol, protein, and oligosaccharides found here ■ Cytoplasm:regition between the nucleus and the membrane ● Cytosol liquid component of the cytoplasm ■ DNA: organized in chromosomes ■ Cytoskeletonprotein fibers that provide shape and allow movement ■ Actin: used for cell shape and important for cell division and moving things throughout the cell ■ Lysosome: important for breaking down and recycling cell parts ● Where Gcase functions ● found in animals ■ Peroxisome ● centers for oxidation reactions which oxidize toxins to detoxify the cell ● found in most eukaryotic cells ■ Mitochondria harvest energy from organic molecules ● takes products generated through the breakdown of glucose and uses them to make ATP ■ Ribosomes ● can either make protein into the ER lumen or make protein in the cytoplasm ● use RNA as a template to make protein ■ Endomembrane System ● includes the nuclear membrane, ER, Golgi, and the vesicles ○ nuclear envelope is a double bilayer that is continuous with the Endoplasmic Reticulum ■ has two phospholipid bilayers that enclose a lumen that is continuous with the lumen of the ER ● Smooth Endoplasmic Reticulum ○ Makes the lipids and cell membranes ○ Where glucocerebroside begins ● Golgi apparatus ○ modifies newly made proteins, lipids, and carbs and tags them for transport ○ The postal office ● Transmembrane protein: spans the whole membrane ○ glycoprotein ■ amino acids exposed to the lipid portion of the membrane are nonpolar which allows for the protein to stick in the membrane while the sugars are on the outside of the cell because they are nonpolar ■ made in the same way as soluble proteins but a part of the protein is left in the RER when ribosome is done translating ○ Prokaryotes ■ bacteria and archaea ■ DNA is free in the cytoplasm ■ No membrane bound nucleus or organelles ■ Most have a cell wall ■ Single cellular ○ Eukaryotes ■ Membrane bound organelles and nucleus ■ Protists, plants, fungi, and animalia ○ Protein Synthesis ■ Always starts on free ribosomes in the cytoplasm but some are completed in the cytoplasm while others are completed in the RER ■ Pathway for protein made on ribosome free in the cytoplasm ● Protein is encoded in the nucleus which is used to make mRNA and then synthesized on the ribosome and once complete, attaches to the outside of the Rough Endoplasmic Reticulum. Once on the outside, part of the RER pinches off and attaches to the golgi apparatus. The golgi processes the ribosome and then pinches off to form a vesicle where it will then fuse with the cell membrane ○ If the protein was encoded in such a way that the protein would need to reenter the RER, it would require an SRP and the protein would need to fold up and be inserted into the RER ■ If a lipid such as glucocerebroside is made, it will start in the smooth endoplasmic reticulum and then pinch off to the golgi apparatus and then go to the cell membrane ■ Production of GCASE ● gene used to make mRNA in the nucleus ● RNA joins the free ribosomes in the cytoplasm and protein synthesis begins ● Ribosomal complex moves to the ER where protein synthesis is completed on the RER ● Protein is now inside the ER ● Vesicle containing the protein pinches off from RER and transported to the Golgi ● M6P tags the protein to go to the lysosome ■ M6P or Mannose6Phosphate is a targeting signal for digestive enzymes that are destined for transport to the lysosomes ○ Energy to do work ■ Kinetic and Potential ■ Laws of thermodynamics ■ 1st law: energy cannot be created or destroyed ■ 2nd law: some energy is lost as unusable heat ■ Gibbs Free energy: portion of a system's potential energy that can perform work ● In a spontaneous process, the free energy of the system decrease( Delta G will be negative) ● Exergonic energy releasing and negative ● Endergonic: energy absorbing and positive ■ Even if cells have high potential energy they require activation energy ● Enzymes ○ speed up favorable reactions ○ couple favorable reactions with unfavorable ○ not used up in reactions ○ lower the activation energy required ○ Lock and Key model ■ Active site: site on the enzyme where the reaction takes place ■ Substrate: reagent that is going to be converted to product by the enzyme ■ Enzymesubstrate complex: complex that forms when the substrate and the enzyme come together ○ Catalyzation ■ stress bonds between the substrates ■ put substrates in proper orientation ■ provide favorable microenvironment ■ form brief covalent bonds with the substrate ■ Can only catalyze a reaction with a negative double G ■ They catalyze using ATP ○ Enzymes couple endergonic and exergonic reactions together so that energy releasing reactions provide the oomph to make energy absorbing reactions work ○ Factors that affect enzymes ■ Substrate Concentration ● How well the enzyme binds the substrate and how quickly it can catalyze the reaction ○ Rate is limited by how quickly the enzyme can find and bind the substrate ■ High affinity means the rate will be faster ● As substrate concentration increases, rate increases because the enzyme can more easily find a new substrate molecule after finishing a reaction ○ After a certain point where the substrate concentration is too high, adding more substrate will not increase the reaction ■ Temperature ● As temperature increases, substrate molecules collide with active sites more frequently ● If too high, the enzyme becomes denatured and begins unfolding and thus the enzyme cannot work properly anymore ● ■ PH ■ Other Chemicals ● Cells must regenerate ATP from ADP and Pi in order to continue functioning ■ Adenosine Triphosphate (ATP) ● Currency of energy in cells ● Phosphates are covalently bonded to one another so when one whey are broken apart, a lot of energy is released due to hydrolysis ● a nucleotide ● Energy Harvest ○ Molecules that make good food will have ■ more potential energy ■ electrons are not held tightly so they are equally shared ■ molecules that are highly ordered ■ There is a lot of potential energy in glycolysis but as it goes through the aerobic processes, it slowly loses potential energy because it is being converted to useful energy ● The products will have higher potential energy than the glucose ○ Reduction/Oxidation Reactions ■ OIL RIG ● Oxidation is LOSS, Reduction is GAIN ■ Oxidation: loss of electrons ■ Reduction: gain of electrons ■ If something is being oxidized, it is reducing another molecule ■ Glucose is oxidized during cellular respiration and fermentation because it is used to make ATP ■ ● When it says that glucose becomes oxidized, it means that is it is losing its electrons to carbon dioxide ● The electrons that come off of glucose are added to oxygen to make water ● This redox reaction generates energy that can be used to make ATP because the products have less PE than the reactants ● Electron donor: Glucose ● Electron acceptor: oxygen ■ Oxidative Phosphorylation ● when the energy is used for phosphorylation comes from the oxidation of high energy molecules ● Chemiosmosis and the ETC ● While substrate phosphorylation occurs in glycolysis ○ The Aerobic Pathway ■ Oxygen is the terminal electron acceptor ■ Glucose + 6 Oxygen→ 6 Carbon Dioxide + 6 Water ● reducing glucose and make ATP ■ More energy is released during this process ■ Glycolysis( beginning step of both the aerobic and anaerobic processes!!) ● occurs in the cytoplasm ● makes the ATP and the NADH ■ The Process 1. Glycolysis a. 2 ATP in to make 2 ADP which make two G3P b. The 2 G3P use 4 ADP and 2 NAD+ to make 4 ATP and 2 NADH, resulting in 2 pyruvate i. PRODUCTS: 4 ATP, 2 NADH, 2 Pyruvate c. Glucose→ pyruvate: OXIDATION NAD+ → 2 NADH: Reduction 2. Pyruvate Processing a. No ATP is produced i. Used up: 2 pyruvate, 2 NAD+, 2 COA ii. Products: 2 CO2, 2 NADH, 2 Acetyl CoA 3. Krebs Cycle a. Products: 2 ATP, 4 CO2, 6 NADH, and 2 FADH2 4. Electron Transport Chain a. NO ATP or CO2 b. 10 NADH are used up c. Products: 2 NAD+ and 2 FAD 5. Chemiosmosis ● What occurs at each of the complexes of the ETC ○ NADH is oxidized to NAD+ at complex 1→ protons go into intermembrane space while the electrons are picked up by Q→ FADH2 oxidized to FAD at complex 2 and electrons are given to Q→ Q carries electrons to Complex 3 and to Cytochrome C which then provides the electrons for Complex 4 where oxygen is reduced to H2O ■ These processes create the proton motive force which allows for the the ATP synthase to work during chemiosmosis ■ ○ Anaerobic Pathway( Fermentation) ■ Two possibilities depending on if it is occurring in humans or other species ● Both have lots of potential energy ● Humans: Glucose + pyruvate→ pyruvate + lactate ● Other: Glucose + Acetaldehyde → Acetaldehyde + Ethanol ■ Does not make ATP; but it does oxidize NADH back to NAD+ ■ 2 pyruvate→ 2 lactate: REDUCTION ■ 2 NADH→ 2 NAD+ : OXIDATION ■ The Process ● regeneration of NAD+ ● Lactic Acid ○ 2 NADH in, 2 NAD+ and 2 Lactate Out ● Alcohol fermentation in yeast ○ Out: 2 ethanol, 2 CO2, 2 NAD+ ○ Important Molecules ■ NAD+: accepts 2 electrons during energy harvest ■ NADH: carries electrons to next reactant ■ NAD+ → NADH : NADH is reduced ○ Terminal electron acceptor of the ETC is oxygen which allows for the production of water ● Kristine’s case involved her ETC ○ Her Complex 3 was blocked so complex 1 was forced to remain in a reduced state ■ To overcome this, need to take Vitamin K and Vitamin C Energy harvest Chart for both Plants and Humans Molecules put in Products How much ATP Location Produced Glycolysis 2 ATP, 4 ADP, 2 G3P, 2 4 ATP, 2 NADH, 2 4 ATP Cytoplasm NAD+ pyruvate Pyruvate Processing 2 NAD+, 2 COA, 2 2 CO2, 2 NADH, 2 none mitochondrial matrix pyruvate AcetylCoA Krebs Cycle 4 CO2, 6 NADH, 2 2 mitochondrial matrix FADH2 Human ETC 10 NADH used up none inner membrane of the mitochondria Lactic Acid 2 NADH 2 lactate, 2 NAD+ none Cytoplasm Fermentation Alcoholic fermentation 2 NADH 2 ethanol, 2 CO2 and 2 none Cytoplasm NAD+ Calvin Cycle 18 ATP, 12 NADPH, 6 12 G3P, 18 ADP, 12 18 stroma of the chloroplast CO2 NADP+ ETC of the plant 9 ADP, 9 NADP+ 9 ATP, 6 NADPH 9 thylakoid membrane Molecules Photosynthesis ● Parts of the chloroplast ○ Inner and outer membranes ○ Granum: stacks of thylakoids ■ Within the thylakoid is the thylakoid lumen and thylakoid membrane ● ETC takes place in the thylakoid membrane ○ Stroma: space where the granum are located ○ Intermembrane space: space in between the outer and inner membranes ● Light Reactions ○ Water enters the chloroplast through the stomata of the leaves and sunlight is absorbed by chlorophyll which drives the transfer of electrons and hydrogen ions from water to the acceptor NADP+ because of NADP reductase ○ Light excites the electrons on PS2 by oxidizing water and those electrons are carried to Pq. The Hydrogen ions are used in the PMF ○ Energy is stored in energy carriers and the high energy electron is passed along the reaction centers. As they travel, they lose energy ○ Then PS1: also absorbs light energy from the antenna complex which excites electrons as well; here pheophytin is the electron acceptor. Once it has the electrons needed it reduces NADP+ to NADPH ○ ATP is produced during this cycle because the hydrogen ions from the PMF provide the energy required to catalyze the reaction that produces ATP from ADP and Pi ○ Products: O2, ATP, and NADPH ● Calvin Cycle ○ Uses the ATP and NADPH from the light reactions to provide energy for the reduction of CO2 to G3P ○ ADP and NADP+ are regenerated by the Calvin Cycle and used again in the light reactions ○ 3 steps ■ Fixation: carbon dioxide reactions with RuBP and produces 3PGA ■ Reduction: 3PGA is phosphorylated by ATP and then reduced by electrons from NADPH which produces G3P ■ Regeneration: G3P acts as a substrate for reactions that use additional ATP in regeneration of RuBP ○ Inputs per glucose: 18 ATP, 12 NADPH, 6 CO2 ○ Products: 2 G3P, ADP, NADP+ (From “intro to photosynthesis”) ● Photophosphorylation ○ production of ATP by transformation of light energy to chemical energy via PMF ○ Includes the steps of the ETC ● The different photosystems ○ Antenna complex, pigment molecules, pigment molecules, chlorophyll, and reaction centers\ ○ ● Absorption spectrum of chlorophyll ○ Absorbs red and blue and reflects green and yellow ● What happens if a herbicide prevents electrons from being transferred from photosystem 2 to the electron carrier? ○ no ATP can be made ○ light reactions will not occur so no production of NADPH, thus causing the end of photosynthesis ● If two scientists are studying radioactivity of plant cells and one group is labeled as an oxygen atom and the second group has cells growing with carbon dioxide with two radioactive oxygen, where should the scientists look to find the radioactive oxygens in group 1? ○ in the oxygen gas given off. ater is split during the lightcapturing reactions and oxygen gas is given off as a byproduct ○ Where should they look to find the radioactive oxygens in group 2? ■ in the carbs made during the calvin cycle because a 5 carbon is reduced to produce sugars Genetic Structure ● Central Dogma of Molecular Biology: DNA→ pre mRNA→ mRNA→ translated proteins ● Qualities of hereditary material ○ contains info for organism’s cell structure, function, development, and reproduction ○ capable of variation so some mutation is acceptable ○ must replicate accurately so not too much mutation ○ In Eukaryotes: contained in the nucleus and proteins are made in the cytoplasm; RNA is also made in the nucleus ● Chromosomes are made up of DNA and proteins(histones) DNA vs. RNA Material Sugar Bases Structure H or OH DNA Deoxyribose A,T,C,G double strand H RNA Ribose A,U,C,G single strand OH ● DNA ○ hydrogen bonds between base pairs ○ covalent bonds between 3’ end of one nucleotide and the 5’ of the other ○ strands run antiparallel ○ negatively charged ○ Major and Minor grooves ■ Major groove provides more access to proteins ○ If given a DNA strand with the sequence 5’ AATTCGCA 3’ ■ It’s complementary strand written 5’ to 3’ would be 5’ TGCGAATT 3’ ○ 5’ end occurs at the phosphate side while the 3’ is where the OH or H molecule is located ○ DNA polymerase gets energy from removal of 2 phosphates during hydrolysis ● RNA ○ AZT ■ has extra phosphate group and 3 Ns double bonded to each other ■ Stops DNA synthesis because the AZT cannot form the phosphate link between the nucleotides ○ Single stranded ○ Contains Uracil rather than Thymine ● The Bases ○ A and G are purines two ringed structures ○ C, T, and U are pyrimidines 1 ring ■ “Ur The Coolest Pyramid ○ A and T or A and U, C and G pairs DNA Replication ● Semiconservativ made up of one new strand and one old; strands separate and then each strand is used as a template for synthesis of a new daughter strand DNA synthesis ● new nucleotides are added to the 3’ end ○ energy comes from hydrolysis of the 2 end phosphates that are incoming ● DNA polymerase makes DNA in the 5’ to 3’ direction ○ enzyme ● Replication fork ○ where the strands form an opening and allows for replication in both directions ○ Moves in opposite direction of the polymerase ● Leading strand: made continuously from 5’ to 3’ ● Lagging strand: made in pieces but also 5’ to 3’ ○ known as the okazaki fragments ○ made in opposite direction of the replication fork ● To bring together the lagging strand, ligase is used to make a covalent bond between phosphate of one fragment and the 3’ OH of the other ● Helicas unwinds the DNA ● Primas: makes RNA primer to prime DNA synthesis ● DNA polymerase: makes new strand starting at the primer, removes the primer in the front ● Singlestrand binding proteins: binds singlestranded DNA and keeps it stable Mitosis and Chromosome Structure ● Ploid: the number of sets of chromosomes ○ Haploid is represented by N; diploid by 2N, and triploid by 3N and so forth ■ In a haploid cell where N=4, that means there is only one set of four ■ In a diploid cell if 2N=6, that means there are two groups of 3 chromosomes ○ Haploid cells are found in prokaryotes and germ cells; diploid in somatic cells of eukaryotes ○ This is triploid because it has 3 different color types when n=3 so it should have 9 chromosomes total ● Homologous chromosomes: identical in size, shape, and gene content ○ diploid chromosomes are homologous but even though they are homologous they made have alleles that code for different genes ● Sister Chromati: DNA molecules that are exact copies of one another due to DNA replication ○ this would occur in the S phase ○ Sister chromatids separate during M phase to become individual chromosomes ○ each have their own DNA molecule ○ A single chromatid is one stand of replicated chromosome ● Centromere structure that joins sister chromatids together ● Karyotype ○ Representation of our chromosomes from the M phase because chromosomes are condensed ● Centrosomes: organize the formation of the mitotic spindle ● Cell cycle ○ Interphase ■ G1, S, G2, Go, and Terminal Differentiation ● G1: The growth period; DNA not yet replicated ○ Each chromosome is one DNA molecule and DNA is not condensed ● Go: only for cells that do not continue to divide ○ cell is terminally differentiated or done dividing ■ Ex. neurons ● S: Synthesis, DNA is replicated( still uncondensed) ● G2: Each chromosome consists of 2 DNA molecules; still uncondensed ○ sister chromatids ○ M Phase ■ Mitosis ● Condensed and replicated DNA ● PPMATC Please Prepare Macaroni And Triple Cheese ○ Prophase, Prometaphase, Metaphase, Anaphase, Telophase, Cytokinesis ○ Prophase: Chromosome condenses and the mitotic spindle forms; appears like a spaghetti bowl ○ Prometaphase: Nuclear envelope breaks down and the spindle fibers connect to the chromosome ○ Metaphase: Chromosomes line up in the middle of the cell forming what looks like a plate ○ Anaphase: Microtubules attach to the centromeres and pull the sister chromatids apart, pulling each one to different sides ○ Telophase: Nuclear envelope reforms and the chromosomes begin decondensing ○ Cytokinesis: Cytoplasm is divided and two new daughter cells form ● Cell Division checkpoints ○ Controlled by genes ○ some block while others promote cell cycle progression ○ G1 checkpoint: passes if the nutrients are sufficient, presence of growth factors, adequate cell size, and DNA is undamaged ○ G2: Passes if there is successful chromosome replication, no DNA damage, and activated MPF is present ■ MPF: protein that stimulates the mitotic phase of cell cycle ● promotes entrance into M phase by phosphorylating multiple proteins needed during mitosis ○ Metaphase checkpoint: if all chromosomes successfully attach to the mitotic spindle ● Cancer’s Relationship to the Cell Cycle ○ Cancer cells divide and grow uncontrollably ■ interferes with cells that work to promote cell division or inhibit cell division ● Normal functions ○ Protooncogenes: promote cell division ■ Require 1 bad copy ○ Tumor suppressor genes inhibit cell division ■ Apoptosis: cell death, blocked division ■ Require 2 bad copies ○ Dominant gain of function mutations cause activity of protooncogenes to become oncogenes that lead to cancer ○ If cells are unable to die, this leads to cancer ○ Cancer typically caused by one oncogene and several mutations in the tumorsuppressor genes ● Growth Factors ○ proteins that bind to the cell membrane that regulate replication and growth ○ Diffuse through body ○ act by binding receptors ■ receptors bind to different growth fa tors ○ HER 2 is a gene involved in aggressive forms of breast cancer ■ Herceptin is used as an antibody that interferes with the growth factor receptor; triggers an immune reaction that targets the cells with the antibodies Protein Synthesis ● Genotype:genetic makeup ○ sequence of nucleotides accounts for the differences in characteristics of individual organisms ● Phenotyp: physical characteristics ● Cystic Fibrosis ○ Mucus buildup in the lungs ○ Infections ○ Salty sweat because sodium and chloride ions are not reabsorbed ○ males are sterile because vas deferens does not form properly ○ trouble digesting food ○ early death ○ CFTR is the protein that codes for CF ■ transmembrane protein ■ loss of function gene tumor suppressant ■ functions as channel across membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes ■ transports negatively charged chloride ions ■ controls movement of water which is a huge component of mucus ● Nucleotide vs. Nucleoside ○ Nucleoside: the bases ○ Nucleotide: sugar, phosphate, and base ● Transcription: DNA → mRNA ○ Prokaryotes: transcription and translation both happen in the cytoplasm ■ RNA transcribed 5’ to 3’ ■ DNA template read 3’ to 5’ in transcription ○ Eukaryotes: ■ Transcription and RNA processing in the nucleus ■ Translation in the Cytoplasm ○ Steps for DNA to premRNA ■ Initiation ● RNA polymerase causes DNA to unwind and the strands separate ■ Elongation ● Complementary RNA nucleotides bind to one DNA strand and adjacent RNA nucleotides join forming single strands of RNA ○ RNA is made in 5’ to 3’ direction ■ Termination ● RNA transcript is released ○ Next:RNA processing of premRNA to mature mRNA ■ only occurs in eukaryotic cells ■ Protects RNA from RNAses, helps recruit ribosomes once RNA is in cytoplasm, removes RNA that shouldn't be translated ■ Addition of 5’ cap to the 5’ end of a nucleotide ■ Splicing: introns removed ● Exons are translated ○ Exons are both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts ■ Addition of the polyA tail to 3’end ● not encoded by DNA ● increases ribosome recruitment and translation and prevents degradation of the 3’ end by RNAse ● added by the Poly A Polymerase ● Next stepTRANSLATION of mRNA to protein ○ The promoter: sequence that tells RNA polymerase where to bind and which way to go ○ Regulatory regions: help recruit polymerase to the promoter ○ Codons ■ Start Codon: AUG ■ STOP Codon: UGA, UAA, and UAG ■ group of 3 bases that specify a particular amino acid ○ Ribosomes ■ complex of rRNA and proteins ● small and large subunit and in between that is the tRNA ■ 3 sites ● Aminoacyl site ● Peptidyl site ● Exit Site ■ tRNA: single RNA strand ● anticodon forms base pair with mRNA codon ● amino acids attached to the 3’ end ● Codon sequence runs antiparallel to the anti odon ● If charged with an amino acid it iaminoacyl tRNA ● Aminoacyl tRNA synthetase joins a specific amino acid to tRNA ○ tRNA brings the correct amino acids to the mRNA ○ Steps ■ Initiation ● mRNA recruits small ribosomal subunits via the 5’ cap ● ribosome scans for start codon AUG via attached MettRNA ● large ribosomal subunit arrives ● a site is available to the tRNA with next amino acid ● This is the only time that the aminoacyl tRNA is directly next to the P site ■ Elongation ● tRNAs deliver amino acids to growing polypeptide ○ Peptide bond formation ■ peptide bond forms between the new amino acid in the A site and the growing polypeptide in the P site ■ Termination ● when a stop codon is reached on the mRNA, a release factor is accepted in the A site ● release factor hydrolyzes the completed polypeptide from the tRNA in the P site ● two ribosomal subunits disassemble ● Genomic vs. Complementary DNA ○ Genomic: DNA as it is found in the organism, including introns and regulatory regions ○ Complementary: DNA representation of the mature mRNA sequence ■ no introns, promoters, or regulatory regions; just exons and UTR ● Down Syndrome ○ occurs from an error in Meiosis where there is a trisomy on chromosome 21; typically diagnosis based on phenotype ■ Occurs because of nondisjunction ○ Typically, the more genes that are affected, the higher the risk of severe developmental problems that cause the developing embryo to abort itself ○ the extra chromosome typically comes from the mother ● 3 Sources of Genetic Variation in Meiosis ○ Independent assortment: metaphase 1 where the homologous chromosomes align independently ○ Fertilization: union of egg and sperm ■ gametes are haploid ○ Crossing over or Recombination: homologous chromosomes exchange parts early in Meiosis 1 ■ exchange of NONsister chromatids ● Nondisjunction ○ homologous chromosomes fail to separate in anaphase 1 or sister chromatids fail to separate in anaphase 2 ■ ■ Differences in nondisjunction occurring in Meiosis 1 vs Meiosis 2 ● Oogenesis ○ there are preegg cells present in girls before they are born ○ At ovulation, the primary oocyte finishes meiosis 1 and the sperm triggers the completion of meiosis 2 ○ Each meiosis cycle results in one egg and 3 polar bodies ● Spermatogenesis ○ sperm formation starts at puberty and continues throughout life ○ each cycle results in 4 sperm ● Mendel ○ 1st law: principle of segregation or the law of inheritance ■ ½ the gametes carry one allele, the other carries the other ■ If homologous, they will carry both ■ Occurs because in meiosis, the alleles separate during anaphase ○ Diploid organisms can have two alleles but haploid can only have one ○ Homozygous: both alleles are the same and thus considered true breeding ■ C^P/C^P ■ In plants, self pollination always leads to progeny with the same phenotype ○ The Chi square value measures how well our observed number matches the expected number ■ the higher the number, the less of a match ■ Then use this number to find the P value. If the P value is above .5, we reject the hypothesis ○ Mendel’s Second Law ■ principle of independent assortment ● Ratios depend on what is being crossed ● If crossing double homozygous recessive with double heterozygous 1:1:1;1 ● 9:3:3:1 fpr genes that are not linked and must be a dihybrid cross between two heterozygous parents ○ Test cross: crossing to a fully homozygous recessive ■ offspring will have phenotype similar to the parent genotype ○ Effect of distance ■ if genes were on opposite ends, they would not segregate together because there would be the possibility of crossing over ■ Recombination can cause these genes to segregate independently ● further apart they are, the more likely for independent segregation ■ If genes are extremely far apart, multiple recombinations will occur so the genes will segregate independently ■ At 50% the genes assort independently ○ Linked genes are genes on the same chromosome and are close enough to one another that the probability of recombination between them is less than 50% ■ The proportions of offspring will be similar but not identical ● Inactivation of the X chromosome ○ so that we have the correct dosage of genetics for sex chromosomes ■ occurs early on in female development ○ Cats can have calico fur color because the x chromosome is inactivated , so some cells that represent the colors that are needed to be exhibited are no longer available ● Barr Body: Chromosomal material along the nuclear envelope in body cells in interphase ● What occurred in Maria? ○ She did not have Barr bodies ○ had a genotype of xy but a phenotype that resembled a female ■ This is because she did not have the sex determining region on her y chromosome ● Can occur in males as well except it is known as the xx syndrome where males have the sexdetermining region on one or both x chromosomes which is moved there by translocation ● Sex determining region is necessary for development of the testes and turns on certain genes in other chromosomes ■ Her body makes the SRY gene but does not make the receptor necessary for binding ■ She has androgen insensitivity syndrome which is the lack of the testosterone binding protein ● Male Development ○ Sex determining region→ testes form→ testosterone→ male phenotype ● Pedigrees ○ Unaffected individual cannot have any alleles of a dominant trait ○ Individuals marrying into the family are assumed to have no disease alleles because the trait is rare ○ Unaffected individuals can be a carrier of a recessive trait ○ When trait is xlinked, a single recessive allele is sufficient for a male to be affected ○ Father transmits his allele of xlinked genes to his daughters but not sons ○ Mother transmits an allele of xlinked genes to both daughters and sons ○ Autosomal recessive ■ both sexes with equal frequency ■ skips generations ■ affected offspring come from unaffected parents ○ Autosomal Dominant ■ both with equal frequency ■ doesn’t skip a generation ■ affected offspring must have an affected parent ○ Xlinked dominant ■ mostly female but males can have as well ■ Doesnt skip generations ■ Affected sons must have an affected mom ■ Affected daughter can have either ■ Affected dada passes to all daughters ○ Xlinked Recessive ■ more likely in males ■ Affected sons usually have an Unaffected mom ■ skips generations ■ if mom is carrier, usually ½ of sons are affected ■ does not pass from dad to son ■ all daughters of affected fathers are carriers ○ Ylinked ■ only males and doesn't skip a generation ○ Mitochondrial Inheritance ■ comes from mom ■ all children can be affected ● Beyond Basic Mendelian Genetics ○ Incomplete dominance ■ often in pigmentation ■ Occurs when you get a 3rd phenotype in your offspring ○ Codominance ■ heterozygotes express both alleles separately HW Example: Electrons that enter the light reactions of photosynthesis can be traced through all the photosynthesis processes ending up in a molecule that can be later used in respiration. These same electrons can then be tracked through the processes of respiration. H20> PS2> PS1> NADPH>G3P> NADH> Complex 1> ubiquinol> H20
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