...1.A. Original model of an essential amino acid Phenylalanine. This shows the atoms and bonds in both the backbone and the side chain. B. Original diagram of the different levels of protein structure (i.e., primary, secondary, tertiary, and quaternary). C. An original diagram, that demonstrates how a peptide bond is made through dehydration, using a complete chemical equation. Citation: Hudon-MIller, S. (2013). D. An original diagram, that demonstrates how a peptide bond is broken through hydrolysis, using a complete chemical equation. Citation: Hudon-MIller, S. (2013). E. The four forces (i.e., bonds or interactions) that stabilize a protein’s structure at the tertiary level. Hydrogen Bond this is a relatively weak bond stronger than hydrophobic bonds. Hydrogen bonds occur between one of the hydrogens on the Nitrogen molecule end of one amino acid and the oxygen molecule from the carboxylic acid end of another amino acid. The Ionic bonds are strong bonds which occur between positive and negatively charge ions of separate amino acids. Hydrophobic bonds are the weakest bonds which occur between two non-polar molecules when they come together into the interior of the structure to minimize contact with water. As the hydrophobic R groups pack together other molecules form Van der Waals...
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...Biochemical Engineering Journal 13 (2003) 169–179 Bioconversion of lignocellulose in solid substrate fermentation R.P. Tengerdy a,∗ , G. Szakacs b b a Department of Microbiology, Colorado State University, Technical University, Fort Collins, CO 80523-1677, USA Department of Agricultural Chemical Technology, Technical University of Budapest, 1111 Budapest, Gellert ter 4, Hungary Received 15 November 2001; accepted after revision 24 July 2002 Abstract In this review the state of the art of lignocellulose bioconversion by solid substrate fermentation (SSF) is presented. The most important lignocellulolytic fungi and their properties are described, and their application in novel solid state bioreactors with on-line process control is discussed. The most important bioconversion products, biofuels, enzymes, animal feeds, biofertilizers, biopesticides, biopromoters, secondary metabolites, and the economy of their production by SSF is discussed. The use of SSF in the pulp and paper industry and in integrated crop management is illustrated. © 2002 Elsevier Science B.V. All rights reserved. Keywords: Lignocellulose; Bioconversion; Solid substrate fermentation 1. Introduction Lignocellulose composes more than 60% of plant biomass produced on earth. This vast resource is the potential source of biofuels, biofertilizers, animal feed and chemical feedstocks. Lignocellulose is also the raw material of the paper industry. To fully utilize the potential of lignocellulose, it has...
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...REVIEW Understanding Structural Features of Microbial Lipases—An Overview John Geraldine Sandana Mala 1 and Satoru Takeuchi 2 1 SANDANA FLORALS, Module-7, Golden Jubilee Biotech Park for Women Society, In SIPCOT-IT Park, Old Mahabalipuram Road, Siruseri, Navalur P.O., Kanchipuram District-603103, Tamilnadu, India. 2 Factory of Takeuchi Nenshi, TAKENEN, 85 NE, Takamatsu, Kahoku, Ishikawa 929-1215, Japan. Abstract: The structural elucidations of microbial lipases have been of prime interest since the 1980s. Knowledge of structural features plays an important role in designing and engineering lipases for specific purposes. Significant structural data have been presented for few microbial lipases, while, there is still a structure-deficit, that is, most lipase structures are yet to be resolved. A search for ‘lipase structure’ in the RCSB Protein Data Bank (http://www.rcsb.org/pdb/) returns only 93 hits (as of September 2007) and, the NCBI database (http://www.ncbi.nlm.nih.gov) reports 89 lipase structures as compared to 14719 core nucleotide records. It is therefore worthwhile to consider investigations on the structural analysis of microbial lipases. This review is intended to provide a collection of resources on the instrumental, chemical and bioinformatics approaches for structure analyses. X-ray crystallography is a versatile tool for the structural biochemists and is been exploited till today. The chemical methods of recent interests include molecular modeling...
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...Andrei Vasiliev 01040632 PTC Genotype Determination basing on DNA Samples (Obtained From Individuals with known PTC Test result) that are incubated with Restriction Enzyme (Hae III) Abstract: The ability to taste the bitter compound phenylthiocarbamide (PTC) and related chemicals is bimodal, and all human populations tested to date contain some people who can and some people who cannot taste PTC. Why this trait has been maintained in the population is uncertain but this polymorphism may influence food selection, nutritional status or thyroid metabolism. The gene product that gives rise to this phenotype is unknown, and its characterization would provide insight into the mechanism of bitter taste perception. Although this trait is often considered a simple Mendelian trait, i.e. one gene two alleles, a recent linkage study found a major locus on chromosome 5p15 and evidence for an additional locus on chromosome 7. The development of methods to identify these genes will provide a good stepping-stone between single-gene disorders and polygenic trait. [5. Guo SW, Reed DR.Department of Pediatrics, Medical College of Wisconsin, Milwaukee, USA.] Introduction:The genetic taste phenomenon of PTC was discovered in 1931 when a DuPont chemist named Arthur Fox accidentally released a cloud of a fine crystalline PTC. Standing by his side colleague complained about the bitter taste, while Dr. Fox, who was closer and should have uptaken a strong dose, tasted nothing. Fox then continued...
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...GRT task 2: Biochemistry (V. Undergrad-0814) Proteins are made up of smaller units called amino acids. Hundreds or thousands of amino acids in long chains form a protein molecule. There are 20 different types of amino acids that combine to make a protein. Amino acids are classified into three groups: essential amino acids, non-essential amino acids, and conditional amino acids. Essential amino acids cannot be made by the body and must come from food. Non-essential amino acids can be produced by the body even if not obtained through food ingested (Wolfe,2000). Conditional amino acids are needed at times of stress, like an illness. Proteins can be described as polar and non-polar depending on how they interact in the environment. Polar and non-polar chemical trait allows for the amino acid to direct themselves toward water (hydrophilic) or away from water (hydrophobic). Valine is an essential amino acid that enables chemical messages to be transmitted from the brain. Valine’s chemical structure is C5H11NO2 and is a branched chain amino acid. Valine is non-polar in nature so it is not a charged molecule. Valine is hydrophobic and if found deep inside the structure for this reason. Valine is important to muscle function as the muscle recovers from strenuous activity. The amino acids sequencing of a protein decides its structure and function. Protein function is also dependent on its structure but some changes can disrupt the structure. When a protein loses function it...
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...Travis Block Dominic Marino BME 262 – Cell and Tissue Engineering Professor Hani Awad Cellular Therapy for the Treatment of Moderate to Severe Traumatic Brain Injury Introduction: Traumatic brain injuries occur when external forces cause traumatic injury to the brain. They directly affect 1.5 million Americans annually, and annually result in 100,000 cases of life-long impairment with substantial loss of function. Today there are 3.2 million Americans living with long-term disability as a result of brain injury (Congressional Brain Injury Task Force, 2012). It is estimated that 2.5 to 6.5 million individuals live with consequences of TBI (National Institue of Health). In addition to the devastating effects on the families and friends of those injured due to cognitive, social, emotional, and behavioral effects; TBIs are also responsible for significant economic cost to society. Annual societal economic impact of TBIs has been estimated at $60 billion. This cost accounts for 29% of the total cost of all injuries in the United States (Max, MacKenzie, & Rice, 1991). Even though the NIH considers the burden of disease when allocating funding, acute treatments for TBI are still limited to attempting to control intracranial pressure and optimizing cerebral perfusion to prevent further edema, inflammation and cell death, and chronic treatment is limited to motor, cognitive, and behavioral rehabilitation (Varmus, 1999). While these treatments are limited...
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...Pepper Seed DNA Extraction Biochem lab: CHE 452L marisol gomez Pepper Seed DNA Extraction Biochem lab: CHE 452L marisol gomez 2015 2015 INTRODUCTION The jalapeno is a member of the capsicum family, along with many other peppers. The usual methods for characterization of different pepper species are based on their morphological and physiological traits, however this many not always be enough. For peppers, their traits are influenced by things like their genotype or their specific environment. Genomic markers can allow for a more direct comparison of closely related individuals (Ansari and Khan, 2012). In our case we focus on DNA extraction. The two basic parts of a DNA extraction procedure include the breaking of the cell walls to expose the DNA and the use of enzymes to remove contaminants. The DNA is analyzed for purity by taking the absorbance. The pure DNA is then visualized by gel electrophoresis. The DNA extraction of plant seeds is difficult because of their cell wall. The method used to break the cell wall includes grinding the seeds with liquid nitrogen. The addition of DNAzol is used to isolate genomic DNA (Chomczynski et al. 1997). Restriction enzymes are necessary to fragment patterns of the DNA and in turn making it easier to analyze the DNA through gel electrophoresis. BACKGROUND The purpose of our experiment is to extract the DNA from pepper seeds to be able to compare and contrast the similarities in their DNA. The extraction of DNA from a plant...
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...Biochemistry Task Two Sarah Taylor 000504232 9/11/2015 Task 2: Protein Structure Introduction: Bovine spongiform encephalopathy (BSE), also known as mad cow disease, is a worldwide problem. While the United States and many countries in the European Union have regulatory legislation in place to combat the spread of BSE, many other countries do not yet have the ability to enact such regulations, making the import and use of possibly tainted beef a health risk. You should compile your work for this task in a single document (e.g., Microsoft Word, Google Document) that will include diagrams, models, text explanations, and references. If a requirement asks for an explanation, you should provide a written response in a narrative style (i.e., complete sentences rather than bullet points). Note: Multimedia presentations (e.g., PowerPoint, Keynote) will not be accepted due to potential originality concerns. Note: Please save submission documents as *.doc, *.docx, *.rtf, or *.pdf files. If you are using Google Documents, you must save the file in *.pdf format and upload the *.pdf file. Scenario: As a specialist in biochemistry, you have been asked to be part of a team that will assist a country that currently does not have regulatory legislation. You will help the other workers in understanding BSE at a chemical level. Because these workers are unfamiliar with the basic biochemistry concepts necessary...
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...The usefulness and potential of artificial/non-caloric sweeteners as weapons to reduce or control obesity in the general population Abstract Obesity is a growing global health problem in the work. Many are increasing in weight and seeking ways to reduce weight or solution to stop matter from getting worse. Over a century ago many accidental discovery of sweetening agent which called artificial sweeteners with low or zero calories ought to be able to assist with obese and overweight issues. Many research have been done to find the actually benefit of artificial sweeteners. Sweeteners benefit from being much sweeter than normal sugar and could reach up to 600 times sweeter than sugar which industries took advantage in cutting cost of their product and heavily promote the benefit side of artificial sweeteners. Studies shows that artificial sugar does help to cut sugar calories low but on the other the population is getting more over weight on correlation with the use of artificial sugar. People tend to consume more calories from other food instead. Real sugar allows your body to accurately determine that it has received enough calories, thereby activating satiety signaling. Without the calories, your appetite is activated by the sweet taste, but as your body keeps waiting for the calories to come, sensations of hunger remain. Nonetheless many have criticized artificial sugar but it does help to reduce tooth decay and give the privilege of diabetes to satisfy the sweet tooth...
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...Bryant Irawan Dr. Brutlag BIOCHEM 158 Due April 08, 2013 Mendelian Disease Case Project 1. The genetic disease I have chosen is narcolepsy. The OMIM url can be found here: http://www.omim.org/entry/161400. 2. 1,2Narcolepsy is a neurologic sleep disorder characterized by excessive daytime drowsiness and the inability to properly regulate sleep cycles. Thus, narcoleptics experience REM sleep, the deepest stage of sleep when dreaming occurs, within five minutes of sleep onset. Narcoleptics may also experience cataplexy, sudden loss of muscle tone, when experiencing strong emotions including laughter, fear, excitement, etc. When waking up or during sleep onset, narcoleptics often experience sleep paralysis, a temporary state of complete loss of muscle control. Sleep paralysis occurs when the brain believes REM sleep is occurring even though one is already awake or just about to sleep so it is easy to see how narcoleptics who have trouble regulating sleep cycles also frequently experience sleep paralysis. Besides sleep paralysis, hallucinations are also common during waking up or sleep onset. For almost all cases, narcolepsy is caused by the lack of a brain neurotransmitter called hypocretin. The shortage then causes a shorter, improperly controlled sleep cycle. 3. Diagnosis of narcolepsy may seem simple enough because of its characteristic cataplexy symptom. However, while almost all cases of cataplexy are tied with narcolepsy, not all cases of narcolepsy are...
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...Recent genetic analyses have clearly demonstrated the crucial role of the hippocampal synaptic plasticity in memory formation (10–11). Despite the significance of the hippocampus in learning and memory, our understanding of the genetic programs underlying the developing hippocampus is quite limited. Cyclooxygenase (COX)-1 and COX-2 fabricate prostanoids starting arachidonic acid and are consideration to have significant yet different roles in customary brain task. Removal of COX-1 or COX-2 outcome in philosophical differentiations both in brain heights of prostaglandin E2 and in commencement of the copy factor, advise that COX-1 and COX-2 play different roles in brain arachidonic acid metabolism and regulation of gene expression. Prostaglandin H synthase, or else known as cyclooxygenase (COX), catalyzes the first metabolic step in the transformation of arachidonic acid (AA) to the bioactive harvest prostaglandins and thromboxanes [10]. The continuation of two isoforms of prostaglandin H synthase, namely COX-1 and COX-2, has been incorrigible in several organs, together with brain [12, 13]. Mice...
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...THESIS WRITING ( LSM4199 (Version V) Order of presentation The order of contents should be as below: Title Page Acknowledgements Table of Contents Abstract Introduction (including Literature Review) Materials & Methods Observations and/or Results Discussion (Results and Discussion can also be combined as one section) [A short section on General Conclusion(s) can also be included] References Appendices (if there is any) Pagination All sections before the Introduction (except the Title Page) should be numbered in Roman numerals (i, ii, iii, iv, etc.) at the bottom centre of the page. All other pages should be numbered with Arabic numbers (1, 2, 3, 4, etc.) Appendices will not be paginated. Length of Thesis The maximum length of the thesis text is 15,000 words. A length of 100 pages from the Introduction to References is recommended. Please do not ‘pad’ your thesis and reach this suggestion. This is detrimental! Typing The entire thesis must be typed on white A4 paper with double spacing, using Times New Roman font and font size of 12 points and with 3.5 cm left margin, and 2.5 cm margins on all other sides. The contents in the References section of thesis may be typed with single spacing. Submission Date & Format Two hardcopies of the thesis (ring-bound; both single-sided and double-sided printings are acceptable) as well as a softcopy (in PDF format)...
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...Vyvanse: An Investigation of the New Breed of ADHD Treatment By Craig Leopold Psychopharmacology Dr. Zoladz 9 May 2011 On April 23, 2008, Vyvanse (lisdexamfetamine) received FDA approval for the adult population. The approval of this drug marked a new era in evolution of Attention Deficit Hyperactivity Disorder treatments. After decades of criticism on the rampant abuse and alleged overprescribing of amphetamine ADHD medications New River Pharmaceuticals responded by developing lisdexamfetamine, a compound that is inactive until converted to dextroamphetamine by the gastrointestinal tract. This means that Vyvanse is only effective when taken orally, reducing the potential for abuse. Moreover, that Vyvanse lasts much longer than typical amphetamine ADHD medications. One administration of the drug lasts throughout an entire day. Although this drug removes a few issues pertaining to amphetamine treatment of ADHD, there has been questioning as to its efficacy in treating the full range of symptoms caused by ADHD because it is broken down into dextroamphetamine alone instead of a combination of amphetamines such as Adderall. Nevertheless, Vyvanse has been established as efficacious in the treatment of ADHD symptoms. In order investigate this new breed of ADHD treatment more completely one must understand the neurobiology of ADHD, the pharmacodynamics and pharmacokinetics of lisdexamfetamine, and what the empirical evidence on Vyvanse suggests. Before...
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...579 Atomic force microscopy and other scanning probe microscopies Helen G Hansma and Lía Pietrasanta The highlight of the past year is the unfolding and refolding of the muscle protein titin in the atomic force microscope. A related highlight in the intersection between experiment and theory is a recent review of the effects of molecular forces on biochemical kinetics. Other advances in scanning probe microscopy include entropic brushes, molecular sandwiches and applications of atomic force microscopy to gene therapy. Address Department of Physics, University of California, Santa Barbara, CA 93106, USA Current Opinion in Chemical Biology 1998, 2:579–584 http://biomednet.com/elecref/1367593100200579 © Current Biology Ltd ISSN 1367-5931 Abbreviations AFM atomic force microscopy/microscope SFM scanning force microscopy/microscope SICM scanning ion conductance microscopy/microscope SPM scanning probe microscopy/microscope STM scanning tunneling microscopy/microscope A new journal, Probe Microscopy, was launched in 1997 as a forum specifically devoted to the science and technology of SPM. AFM and SFM have been also newsworthy items in Science and Nature in the past year [14••,15•–17•,18••,19]. An introduction to AFM is covered well in a recent issue of Current Opinion in Chemical Biology, which describes and illustrates the design and mode of operation of AFM [4••]. The AFM images sample surfaces by raster-scanning a sharp tip back and forth over the surface. The tip is on...
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...Physiology, Yale University School of Medicine, New Haven, Connecticut, USA Address correspondence to: Gerald I. Shulman, Howard Hughes Medical Institute, Yale University School of Medicine, 254C Boyer Center for Molecular Medicine, 295 Congress Avenue, New Haven, Connecticut 06510, USA. Phone: (203) 785-5447; Fax: (203) 737-4059; E-mail: gerald.shulman@yale.edu. It is estimated that by the year 2020 there will be approximately 250 million people affected by type 2 diabetes mellitus worldwide (1). Although the primary factors causing this disease are unknown, it is clear that insulin resistance plays a major role in its development. Evidence for this comes from (a) the presence of insulin resistance 10–20 years before the onset of the disease (2, 3); (b) cross-sectional studies demonstrating that insulin resistance is a consistent finding in patients with type 2 diabetes (3–6); and (c) prospective studies demonstrating that insulin resistance is the best predictor of whether or not an individual will later become diabetic (2, 3). Here, I focus on some recent advances in our understanding of human insulin resistance that have been made using nuclear magnetic resonance spectroscopy (NMR). This technique takes advantage of the spin properties of the nuclei of certain isotopes, such as 1H, 13C, and 31P, which endow the isotopes with a magnetic component that can be used to measure the concentration of intracellular metabolites noninvasively and to assess biochemical differences between...
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