Bio 211 Midterm 2 Study Guide
Bio 211 Midterm 2 Study Guide Biology 211
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This 9 page Study Guide was uploaded by Melissa on Thursday February 18, 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 107 views. For similar materials see Gen Biol I: Cells in Biology at University of Oregon.
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Date Created: 02/18/16
Bio 211 Midterm 2 Study Guide **Lectures 1018 and Labs 47 Quizlet linhttps://quizlet.com/_1zhcff Password provided after purchase! Aerobic vs. Anaerobic Harvest ● Aerobic ○ Happens in the mitochondria and site of cellular respiration ○ Pyruvate Processing: No ATP produced, 2 CO2, and 2 NADH, and 2 Acetyl CoA ■ Put in: 2 NAD+, 2 COA, 2 pyruvate ○ ETC: No ATP; no CO2, 10 NADH used up ■ 2 NAD+ and 2 FAD ○ Krebs Cycle: 2 ATP produced, 4 CO2, and 6 NADH, 2 FADH2 ○ Glycolysis: ■ In: 4 ADP, 2 NAD+, and 2 ATP ■ Out: 4 ATP, 2 NADH, 2 pyruvate ● Anaerobic ○ NO ATP ○ 2 CO2 produced while 2 NADH is used up ○ In humans: lactic acid formation ■ Get out 2 lactate and 2 NAD+ ○ Alcoholic Fermentation ■ Get out 2 ethanol, 2 CO2 and 2 NAD+ ○ grow much slower because they produce no ATP Redox Reactions ● Pyruvate Processing ○ Pyruvate undergoes OXIDATION ○ NADH is undergoing reduction because it accepts the electron from pyruvate ● Oxygen undergoes reduction in the mitochondria 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+ ○ 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 radioactiity 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 biproduct ○ 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→ mRNA→ protein→ traits ● 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 ● 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 ○ A and T or A and U, C and G pairs DNA Replication ● Semiconservative 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 ● Helicase: unwinds the DNA ● Primase: 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 ● 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 ○ Tumor suppressor genes inhibit cell division ■ Apoptosis: cell death, blocked division ○ 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 facto s ○ 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 ● Phenotype: 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 ■ 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 step:TRANSLATION 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 ● Aminoacily site ● Peptidyl site ● Exit Site ■ tRNA: single RNA strand ● anticodon forms base pair with mRNA codon ● amino acids attatch to the 3’ end ● Codon sequence runs antiparallel to the anticodon ● If charged with an amino acid it is minoacyl 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 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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