Bio 211 Midterm 2 study guide
Bio 211 Midterm 2 study guide 21039
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This 9 page Study Guide was uploaded by Faith Leiva on Friday February 19, 2016. The Study Guide belongs to 21039 at University of Oregon taught by Dr. Jana Prikryl in Winter 2016. Since its upload, it has received 52 views. For similar materials see Biology 211 in Biology at University of Oregon.
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Date Created: 02/19/16
Biology Midterm Study Guide (Lectures 1018) Parts of the Chloroplast ● Thylakoid membrane: where electrons move down the ETC to ● Stroma:The fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water. pumps H+ into the thylakoid space creating a H+ gradient ● Thylakoid space: where H+ flows to the stroma through ATP synthase providing energy required to catalyze the reaction that produces ATP from ADP and pi H+ from water helps decrease pH (increase H+ concentration) in thylakoid space helping create PMF. ● Thylakoid lumen: an increase of the number of protons from the splitting of water occur here ● Inner membrane: The membrane of the mitochondria that is the site of electron transport and chemiosmosis., where the electron transport chain occurs, Where the electron transport chain of cellular respiration occurs ● outer membrane: the fluid filled space between the inner and outer mitochondrial membranes, the region between the inner membrane and the outer membrane of a mitochondrion or a chloroplast. The main function of the intermembrane space is nucleotide phosphorylation. ● Intermembrane space: the fluid filled space between the inner and outer mitochondrial membranes, the region between the inner membrane and the outer membrane of a mitochondrion or a chloroplast. The main function of the intermembrane space is nucleotide phosphorylation Light Reactions versus Calvin cycle Light reaction= H2O + Light →O2 Calvin cycle= O2→ Sucrose (export) ● ATP and NADPH produced in the light reactions are then used by the Calvin Cycle to provide energy for the reduction of Carbon dioxide to carbohydrates (G3P) ● ADP and NADP+ are regenerated by the calvin cycle and used again in the light reactions Electron Transport Chain ● transfer electrons from electron donors to electron acceptors via redox reactions, and couples this electron transfer with the transfer of protons (H ions) across a membrane. This creates an electrochemical proton gradient that drives ATP synthesis, or the generation of chemical energy in the form of adenosine triphosphate (ATP). PS II→ Pq→ Cyt→ Pc→ PS I→ Fd→ NADP+ reductase Roles for each complex: H2O: Energy process that drives photosynthesis (essential to ATP) CO2: absorbed through the calvin cycle which produces to oxygen NADPH= produced in the light reactions are then used by the Calvin cycle to provide energy for the reduction of carbon dioxide to carbohydrates NADP+= is regenerated by the Calvin cycle and used again in the light reactions Photophosphorylation= production of ATP (phosphorylation) by the transformation of light energy to chemical energy via PMF (photo). Can you compare this to Oxidative phosphorylation and substrate level phosphory Antenna Complex: (part of PSII PSI) absorbs light energy and excites electrons Pigment complex: energy is absorbed once the electrons have released energy from their past excited states Chlorophyll: responsible for capturing light energy: light energizes electrons that are along an electron transport chain Reaction center: where electrons are transferred to and passed to another molecule Absorption Spectrum of Chlorophyll: light absorbed by chlorophyll drives a transfer of electrons and hydrogen from water to an acceptor called NADP+ Calvin Cycle: Fixation: a carbon atom from CO2 is added to RuBP forming a 6 carbon molecule Reduction: 6 PGA is phosphorylated by ATP forming 6 BPG Regeneration: 5 G3P are rearranged to form 3 RuBP (cycle repeats) RuBisCO: catalyzes the first step of the Calvin cycle, the step that actually take inorganic carbon and adds it to an organic molecule, this process is called carbon fixation. DNA STRUCTURE: Qualities of hereditary material: 1) Must contain information on how to contain cell parts 2) Must be capable of variation 3) Must replicate accurately Chromosome: a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes. DNA: located the nucleus, the information conveyed to the ribosomes that will make proteins RNA: Made in the nucleus using DNA as a template, then the RNA leaves the nucleus and finds a Ribosome and then protein can be made. Nucleotide: Parts, differences, similarities, directionality (5’ and 3’ ends) Contains the base, sugar, and phosphate Nucleic acid structure: One strand runs 5’ to 3’ and the complementary runs 3’ to 5’ (seen with any double stranded nucleic acid A is complementary to T and C is complementary to G which are held together by hydrogen bonds covalent bonds attach 3’ carbon of one nucleotide and the phosphate group attached to the 5’ carbon of another nucleotide The covalently bonded run of sugar and phosphate that makes up each strand is called the “sugar phosphate group Ribose and deoxyribose: Secondary structure: The double helix has major and minor grooves Major groove allows more access to the base pairs in the middle Proteins usually bind to the major groove of the DNA and might be involved in regulating gene expression by binding to specific sequence Alpha Helices: protein secondary structure in which the polypeptide backbone coils into a spiral shape stabilized by by hydrogen atoms between atoms Beta pleated sheets: A protein secondary structure in which the polypeptide backbone folds into a sheet like shape stabilized by hydrogen bonding. DNA Replication Semiconservative: Each replicated DNA molecule is made up of one new strand and one old strand Origin of replication: is the particular sequence in a genome at which replication is initiated. DNA synthesis proceeds in two directions The DNA fragments that are synthesized on the lagging strand are called Okazaki fragments. These fragments are joined by ligase. Ligase makes a covalent bond between the phosphate of one fragment and the 3’ OH of the other. This is a process called litigation (hence the enzyme name: ligase) Also notice that the lagging strand fragments are made in the opposite direction from the replication fork movement. The polymerase is synthesizing the new strand right to left, it only adds nucleotides to the 3’ end. This means that the left side of the new (top) strand must be the 3’ end. Because the strands are antiparallel, the bottom, template, strand must be running 5’ to 3’ (left to right) Ploidy: the number of sets of chromosomes an organism has Haploid: the cell only has one of each chromosome Diploid: the cell has two of each chromosome Triploid: Three x the set of chromosomes Somatic versus germ cells Homologous chromosomes: Contain the same genes though the gene alleles may be different Sister chromatids: chromosomes that are exact copies of another generated during DNA replication Allele: one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome. centromere: Structure that joins sister chromatids together DNA molecule vs. chromosome Chromosome: consists of two chromatids DNA molecule: a single chromosome Karyotype: the number and visual appearance of the chromosomes in the cell nuclei of an organism or species. Cell cycle Interphase: G1: gap 1: cell grows, gets ready for Sphase Sphase: S=snythesis: DNa is replicated G2: gap 2: cell grows , gets ready for mitosis Centrosomes: organize the formation of the mitotic spindle Mitosis: microtubules: long fibers that control movement of chromosomes Prophase: chromosomes condense mitotic spindle forms Prometaphase: nuclear envelope breaks down; spindle fibers (microtubules) connect to chromosome Metaphase: chromosomes line up in middle of cell anaphase: sister chromatids separate; chromosomes are pulled apart to opposite poles of cell telophase: nuclear envelope reforms; spindle apparatus breaks down; chromosomes begin to decondense Cytokinesis: cytoplasm is divided and two new daughter cells forms Three main checkpoints normally control cell division G1: Pass this checkpoint if nutrients are sufficient growth factors cell size is adequate DNA is undamaged G2: Pass this checkpoint if chromosome replication is successfully completed no DNA damage activated MPF present Metaphase checkpoint all chromosomes are attached to mitotic spindle ● Cancer is unregulated cell growth in which cells divide and grow uncontrollably ● Since cancer is uncontrolled cell division, understanding the cell cycle can allow us to come up with cancer therapies Chemotherapies paclitaxel → interferes with depolymerization of microtubules Cyclophosphamide → keeps replication enzymes from getting access Doxorubicin→ interferes with topoisomerase also blocking S-phase Methotrexate →competes with folic acid for enzyme active site Protooncogenespromote cell division or cell survival Oncogenes: Mutation that increases function Tumor suppressor genes genes whose normal alleles inhibit inappropriate cell division or cell survival Apoptosis (blocked division, cell death) Dominant, gainoffunction mutations that cause inappropriate activity of these genes turns them into ONCOGENES that lead to cancer Loss of function mutations in tumor suppressor genes are associated with cancer Herceptin: is a monoclonal antibody that interferes with the HER2/neu (Human Epidermal Growth Factor Receptor 2) receptor. Its main use is to treat certain breast cancers. Protein Synthesis Cystic fibrosis is the most common genetic disease of people of European descent characteristics mucus buildup in the lungs male sterility salty sweat trouble digesting foods infections death by 30 or by twenties Genotype and phenotype Genotype is genetic makeup Phenotype are characteristics that arise because of the genetic makeup and the environment CFTR: This protein functions as a channel across the membrane of cells that produce mucus,sweat, saliva, tears, and digestive enzymes. The channel transports negatively charged particles called chloride ions into and out of cells. The transport of chloride ions helps control the movement of water in tissues, which is necessary for the production of thin, freely flowing mucus. Mucus is a slippery substance that lubricates and protects the lining of the airways, digestive system, reproductive system, and other organs and tissues. Transcription and Translation Transcription: DNA to RNA to make a RNA copy of a gene, allows DNA to stay in nucleus, amplifies protein production located in the nucleus in eukaryotes and cytoplasm in prokaryotes Initiation:RNA polymerase binds to DNA; DNA unwinds Elongation: complementary RNA nucleotides bind to one DNA strand, adjacent RNA nucleotides join forming single strand of RNA, RNA is made in 5’ to 3’ direction termination. Termination: RNA transcript is released Promoter: sequence that tells RNA polymerase where to bind and which way to go Regulatory regions: help recruit polymerase to promoter (also not transcribed) Transcription unit: part that is transcription unit *** RNA is synthesized 5’ to 3’ *** Template DNA is read 3’ to 5’ direction Transcription bubble: when the DNA double strand is unwound and RNA polymerase may then bind to the exposed DNA and begin synthesizing a new strand of RNA Coding strand: (nontemplate strand) runs 5’ to 3’ and has the same sequence as the RNA strand that is being made (also running 5’ to 3’ sequence written in above coding strand), except that the T’s are replaced with U’s in the RNA. Splicing: Where introns must be removed and exons are covalently joined to one another as part of generating the mature messenger RNA Exons: Regions of gene that are part of the mature mRNA; coding regions Introns: regions of a gene that are not part of the mature mRNA; noncoding regions Poly A tail: is added by a special polymerase called A polymerase Regulator regions: sections of DNA that are involved in controlling the activity of genes (when and where a gene is turned on) Coding region: part of RNA that is translated UTR: untranslated part of mature mRNA Translation: mRNA to protein make protein (polypeptide from mRNA) on ribosomes in the cytoplasm mRNA, tRNA, ribosomes, amino acids, aminoacyl tRNA synthetases are involved Start Codon: sets the reading frame for the ribosomes Reading frame: consecutive, nonoverlapping, triplets of nucleotides Ribosomes: complex of rRNA and proteins consist of the small subunit and large subunit Catalyzes translation w/ help of tRNA aminoacyl tRNA synthetase: joins a specific amino acid to tRNA aminoacyl tRNA: tRNA molecule linked to an amino acid mRNA start codon: AUG tRNA anticodon: 5’ UUC 3’ Translation: Elongation Peptide bond formation: peptide bond forms between the new amino acid in the A site and the growing polypeptide in the P site Genomic DNA: is the DNA as it is found in the organism , including introns and regulatory regions Complementary DNA(cDNA): this is a DNA representation of the mature mRNA sequence: No introns, no promoters, no regulatory regions: JUST EXONS often written as coding strand from 5’ to 3’
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