...POLYMERASE OR REPLICASE ENZYMES: A polymerase enzyme catalyses the formation of a polymer and cellular polymerase enzymes of genetic interest are those that bring about the synthesis of one polynucleotide chain that is copy of another. A polymerase enzyme is called replicase enzyme when the copy of the polynucleotide chain so produced is inherited by daughter cells or viruses, that is, when the enzyme brings about chromosomal replication. PROKARYOTIC DNA POLYMERASES: Three different DNA polymerases are known in E.Coli and other prokaryotes, of which DNA polymerase I and II are meant for DNA repair and DNA polymerase III is meant for actual DNA replication. 1. DNA polymerase I. This enzyme was isolated around 1960 by Arthur Kornberg and was the first enzyme suggested to be involved in DNA replication. It is also called Kornberg enzyme. DNA polymerase I enzyme is now considered to be a DNA repair enzyme rather than a replication enzyme. This enzyme is known to have five sites, namely, template site, primer site, 5’ 3’ cleavage or exonuclease site, nucleoside triphosphate site and 5’ 3’ cleavage site. DNA polymerase I is mainly involved in removing DNA primers from Okazaki or precursor fragments and filling the resultant gaps due to is 5’3’ polymerizing capacity. DNA polymerase I enzyme can also remove thymine dimmers produced due to UV- radiation and fill the gap due to excision. Both polymerization (chain elongation) and exonuclease activity of the enzyme are...
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...A) Lactose binds to the operator preventing the promoter from attracting RNA polymerase and preventing transcription. B) Lactose bind to RNA polymerase, which then binds to the promoter and transcribes the needed genes. C) Lactose binds to the repressor, which does not bind to the operator, and RNA polymerase transcribes the needed genes. D) Lactose binds to the operon, which attracts RNA polymerase, then transcription of the needed genes occurs. E) Lactose binds to the CAP site to prevent the CAP protein from binding Answer: C 2. Which of the following is likely to be expressed? A) euchromatin B) heterochromatin C) DNA without methyl groups D) DNA with many methyl groups E) euchromatin and DNA without methyl groups is more likely to be expressed Answer: E 3. Which of the following is a method of posttranscriptional control? A) transcription factors B) the life span of a mRNA molecule C) differential processing of mRNA D) how fast the mRNA leaves the nucleus E) both differential processing and how fast mRNA leaves the nucleus are involved in posttranscriptional control. Answer: E 4. Which gene in an operon is incorrectly matched with its function? A) promoter--where RNA polymerase first binds to DNA B) regulator--binds to the repressor protein ...
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...Thermophilic Bacteria of Yellowstone National Park CEE:5154 Environmental Microbiology Research Paper University of Iowa Department of Civil and Environmental Engineering December 14, 2015 Bruce McWilliams Amid the vast, sparsely populated regions of Northwest Wyoming, lies one of the most diverse and extraordinary ecosystems in the world, Yellowstone National Park. Yellowstone is one of the world's foremost sites for the study and appreciation of the evolutionary history of the earth. The park has a globally unparalleled assemblage of surficial geothermal activity, thousands of hot springs, mudpots, fumaroles, and more than half of the world’s active geysers (NPS, 2013). Yellowstone is located on top of the Yellowstone Caldera, which is a volcanic hot spot where hot, molten rock from the earth’s mantle rises toward the surface. Volcanic activity from the Caldera produces geothermal activity on the park’s surface that has drawn more than 3 million visitors to the park since 2000 (NPS, 2015). Geysers, hot springs, and mudpots are extremely toxic due to high concentrations of sulfuric acid (sulfate concentrations measure up to 925 ppm near vents) and, temperatures measuring over 100oC. Many have recorded inhabitable pH levels ranging from 2 to 9.8 (Rowe/Founder/Morey, 1973). While these colorful and wondrous hot springs may appear stagnant and devoid of life to the common park visitor, they are actually a complex, intricate habitat teeming with a diverse array...
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...such fossils is questioned by some researchers -mainly in isolated pools whose high salt concentration exclude predators • Microfossils -the most convincing evidence for ealy microbial life is the visua appearance of microfossils which are microscopic fossils in which minerals have precipitated and filled in the form of ancient microbial cells -dated bythe age of the rock formation in which they are found, which is based on evidence like radisotope decay -convincing oned need to sho the 3-d patterns of cells that cannot be ascribed to abiotic causes -earliest convincing ones are from 2.0 Gyr • isotope ratios -may serve as a biosignature if the ratio between certain isotopes of a given element is altered by biological activity -enzymiatic rxns are so selective for their substrate that their rates may...
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...The ribosomal RNAs are folded into highly compact, precise three-dimensional structures that form the compact core of the ribosome and determine its overall shape and have the ability to position tRNAs on the mRNA, and its catalytic activity in forming covalent peptide bonds. The main role of the ribosomal proteins seems to be to stabilize the RNA core, while permitting the changes in rRNA conformation that are necessary for this RNA to catalyze efficient protein synthesis. The large and small ribosome subunits are assembled at the nucleolus, where newly transcribed and modified rRNAs associate with the ribosomal proteins that have been transported into the nucleus after their synthesis in the cytoplasm. These two ribosomal subunits are then exported to the cytoplasm, where they join together on an mRNA molecule, usually near its 5? end, to initiate the synthesis of proteins. The mRNA is then pulled through the ribosome, three nucleotides at a time. The small subunit provides...
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...Operons Control of Gene Activity in Prokaryotic Cells I. The activity of genes is controlled by the cell and the environment. A. Inducible genes are inactive unless circumstances cause them to be activated (“turned on”). B. Repressible genes are active unless circumstances cause them to be inactivated (“turned off”). C. Constitutive gene functions are active continually, with no control exerted. This is generally an abnormal situation. II. In prokaryotic cells (and viruses) the control of gene activity is often in the form of operons. A. Operons are a form of transcriptional control. B. An operon consists of the structural gene (or genes) which actually code for specific proteins and the controlling elements associated with the control of those genes. An operon typically contains several genes, all under the same control mechanism. C. Though rather similar controlling systems have been found for some eukaryotic genes, control mechanisms in eukaryotes are generally more diverse and more complex, and except for a few examples in simple eukaryotic organisms like yeasts, multiple genes are not found to function under a single control mechanism. In other words, eukaryotic cells do not have operons. III. The first operon investigated was the lac operon in E. coli. This work came from Jacob and Monod (1959 Journal of Molecular Biology V. 1). A. The primary carbohydrate source for the cell is the sugar glucose, but there...
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...Chapter 6 Blast program for sequence comparisons and blast p-values- test whether 2 or more sequences (protein or DNA) share a common evolutionary origin (p >10^-3 = due to chance) Lack of relationship between number of genes in a genome and its biological complexity 10-nm versus 30-nm chromatin fibers – condensed chromatin= 30nm wide, “beads-on-a-string” =10nm wide nucleosome core histone composition (2 each of H2A, H2B, H3, and H4) – Histones exists as octamers. Core is wrapped by 147 bp, about 2turns of DNA= CONSERVED IN ALL EUKARYOTES two turns of DNA around histone core (147 bp) variable size of DNA between nucleosomes (15-90 bp) – depends on species structure of 30 nm fiber and role of H1 histone – resting chromatin will be 30nm wide, H1 binds where DNA enters and exits nucleosome core histone tail modifications (acetylation, methylation, phosphorylation) – methylation & DEacetylation condensing of chromatin (30nm) acetylation DE-condensing of chromatin (10nm) phosphorylation & ubiquitination chromatin remodeling euchromatin versus heterochromatin chromosome scaffold – hold the 30nm chromatin loops attached, genes far apart on the chromosome are close at the base of the loops called SARS (Scaffold Associated Proteins) width of fully condensed metaphase chromosomes (500-750 nm) – 500-750nm wide chromosome banding and FISH (fluorescence in situ hybridization) – identification of karyotypes (chromosome composition) allows painting of each...
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...Contents Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Chapter 6 Chapter 7 Chapter 8 Chapter 9 Chapter 10 Chapter 11 Chapter 12 Chapter 13 Chapter 14 Chapter 15 Chapter 16 Chapter 17 Chapter 18 Chapter 19 Chapter 20 Chapter 21 Chapter 22 Chapter 23 Introduction to Biochemistry Water Amino Acids and the Primary Structures of Proteins Proteins: Three-Dimensional Structure and Function Properties of Enzymes Mechanisms of Enzymes Coenzymes and Vitamins Carbohydrates Lipids and Membranes Introduction to Metabolism Glycolysis Gluconeogenesis, The Pentose Phosphate Pathway, and Glycogen Metabolism The Citric Acid Cycle Electron Transport and Oxidative Phosphorylation Photosynthesis Lipid Metabolism Amino Acid Metabolism Nucleotide Metabolism Nucleic Acids DNA Replication, Repair, and Recombination Transcription and RNA Processing Protein Synthesis Recombinant DNA Technology 1 10 27 46 65 85 104 119 137 153 169 185 199 213 227 241 256 269 284 300 315 330 348 Chapter 1 Introduction to Biochemistry 1) Which elements account for more than 97% of the weight of most organisms? A) C, H, N, Mg, O, S B) C, H, N, O, P, S C) C, H, N D) Fe, C, H, O, P E) Ca2+ , K+ , Na+ , Mg 2+ , ClAnswer: B Page Ref: Section 2 2) Proteins in biological membranes may be A) porous. B) attached to the membrane surface. C) span the membrane. D) All of the above E) B and C only Answer: D Page Ref: Section 3 3) Which statement...
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...early geneticists that they might harbor the genetic material? What experiments confirmed these suspicions? Chromosomes was known to possess deoxyribonucleic acid. The genetical material was expected to have the stability but still capable of accepting sudden and permanent changes to adapt to evolution. Experiments that confirmed the suspicions were done by: • Griffith- demonstrated non-virulent strains of bacteria turned virulent when mixed with heat-killed pathogenic bacteria • Avery and colleagues- showed that deoxyribonuclease leads destruction of transforming activity • Hershey and Chase- used radioactive labels and bacteriophages to show that only nucleic acid was passed onto progeny not protein B)...
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...PYF12 3/21/05 8:04 PM Page 191 Chapter 12 Gene expression and regulation Bacterial genomes usually contain several thousand different genes. Some of the gene products are required by the cell under all growth conditions and are called housekeeping genes. These include the genes that encode such proteins as DNA polymerase, RNA polymerase, and DNA gyrase. Many other gene products are required under specific growth conditions. These include enzymes that synthesize amino acids, break down specific sugars, or respond to a specific environmental condition such as DNA damage. Housekeeping genes must be expressed at some level all of the time. Frequently, as the cell grows faster, more of the housekeeping gene products are needed. Even under very slow growth, some of each housekeeping gene product is made. The gene products required for specific growth conditions are not needed all of the time. These genes are frequently expressed at extremely low levels, or not expressed at all when they are not needed and yet made when they are needed. This chapter will examine gene regulation or how bacteria regulate the expression of their genes so that the genes that are being expressed meet the needs of the cell for a specific growth condition. Gene regulation can occur at three possible places in the production of an active gene product. First, the transcription of the gene can be regulated. This is known as transcriptional regulation. When the gene is transcribed and how much it is...
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...from mitochondria and chloroplasts. Unicellular types came from simple multicellular forms metazoans; significance of cyanobacterial ancestors * presence of cyanobacteria-like chains of cells in stomatolite fossils represent growth of cyanobacteria * cyanobacteria photosynthesize like plants; they use H2O to synthesize O2. d. Microbial taxonomy & phylogeny (3 domains: Archaea, Bacteria, & Eukarya ) * the 3 domains (bacteria, archaea, and eukaryotes) evolved from a common cell * Archaea and bacteria include prokaryotes * Eukarya includes algae, plants, fungi, animals, and protists eukaryotes * Monera includes all 3 domains i. Taxonomic groupings: microbes in the different kingdoms of those domains ii. Similarities & differences: eukaryotic & prokaryotic cells; genomes iii. Metagenomics e. Who are the microbes: bacteria/archaea/fungi/protists/viruses; characterize/describe these * Bacteria: cells lacking a nucleus * Fungi: are in eukarya domain. A heterotrophic eukaryote with chitinous cell walls. * Protist: single-celled eukaryotic microbe, usually motile. Not a fungus * Virus: consists of a noncellular particle containing genetic material that takes over the...
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...from a smaller number of genes in humans. In fact, Walter Gilbert had expressed that a variety of mRNA isoforms of one gene arises from different combinations of exon-splicing known as alternative splicing (Modrek & Lee, 2002). Alternative splicing can be classified into several types, with each type being different among species. Exon skipping is a type wherein a cassette exon and its bordering introns are spliced out of the transcript. This type is prevalent in higher eukaryotic forms. Two other types of alternative splicing are alternative 3’ splice site (3’ SS) and 5’ SS selection in which two or more splice sites are identified at one end of an exon. These two types account for a small percentage of alternative splicing in higher eukaryotes. Another type of alternative splicing is intron retention, characterized by an intron persisting in the mature mRNA transcript. It is the rarest type of alternative splicing in both vertebrates and invertebrates, but the most prevalent in plants, fungi, and protozoa (Keren et al., 2010). In the wake of discovering these alternative mRNA forms that diversify protein functions of the same gene, there, however, exists a problem of how to differentiate truly functional forms from those that are not, biologically or otherwise, which further opens up an avenue towards the risk of outright designating a discovered form as functionless mainly because it is perceived to have no obvious function. In this instance, it may be entirely possible...
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...Biology: Concepts and Connections, 5e (Campbell) Chapter 11: The Control of Gene Expression 1) Which of the following are problems created by cloning? A) Cloning endangered species may de-emphasize the need to preserve critical natural habitats. B) Cloning does not increase genetic diversity in the cloned species. C) Cloned animals are less healthy than animals created by natural methods. D) All of the choices are problems created by cloning. E) None of the choices are problems created by cloning. Topic: Introduction Skill: Factual Recall 2) The ability to use the nucleus from an adult somatic cell to create all of the cell types in a new organism demonstrates that development depends upon A) the control of gene expression. B) the timing of mitosis and meiosis. C) the timing of meiosis and cell migrations. D) the deposition of materials in the extracellular matrix. E) the position of cells within an embryo. Topic: Introduction Skill: Conceptual Understanding 3) The term gene expression refers to the A) fact that each individual of a species has a unique set of genes. B) fact that individuals of the same species have different phenotypes. C) process by which genetic information flows from genes to proteins. D) fact that certain genes are visible as dark stripes on a chromosome. E) flow of information from parent to offspring. Topic: 11.1 Skill: Conceptual Understanding 4) In a prokaryote, a group of genes with related functions, along...
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...and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by posttranslational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only...
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...contain genes for synthesis of envelope proteins * viral genomes= virus-specific enzymes (nucleic acid replication) * non-living organism/not “alive” - lack that properties of life (no independent reproduction, no metabolic system= no energy, dependent on host cells 2. Why viral infections are usually difficult to treat with drugs, and exceptions to this general principle. * viruses= hidden in host cells, use host cell machinery to replicate (no obvious viral product to be targeted by drugs/antibiotics - not like bacteria) * symptoms can only be relieved not treated - natural immune function treats — some viruses deadly symptoms= prevention w/ vaccinations (e.g. measles, polio) * Viruses using own polymerases (e.g. RNA viruses - influenza)= more obvious targets - antiviral drugs to treat 3. Whether viruses are always pathogenic. * not all viruses= pathogenic - some benefit hosts e.g. some non-pathogenic viruses protect humans from pathogenic viruses * “protective” viruses - interfere with replication/functions of pathogenic viruses * some viruses defend host cells (e.g. bacteriophages/phages control bacteria growth) * viruses= vital to ecosystems (may be dominant...
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