...1.1.2 Molecules Quiz 1. Explain why water is described as a dipolar molecule. -Water is described as a dipolar molecule because it has a negative end and it has a positive end also. The oxygen is more electronegative so it pulls the electron cloud away from the hydrogen’s. So the hydrogen’s become more positive and the oxygen more negative. (2) 2. Give examples of hydrogen bond formation contributing to the structure of molecules. - The structure is maintained through different groups of amino acid residues. Tertiary and Quaternary form bond between 4 water molecules. (1) 3. Explain why sodium chloride dissolves in water. -Sodium Chloride dissolves in water because the positive part of the water molecules attracts the negative chloride ions and the negative part of the water molecules attracts the positively sodium ions. The polarity of water molecules enables water to dissolve many ionically bonded substances. Polar molecule has an uneven charge distribution. (1) 4. Explain why some organic molecules, such as simple sugars and alcohols, form aqueous solutions but others, such as lipids, do not. - Simple sugars and alcohols have charged polar groups which can form hydrogen bonds with water molecules (1) 5. Why is water an important transport medium in animals? Write down as many examples of where water is important in transport as you can. - Water is an important transport medium in animals because substances such as polar...
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...Study Guide: Biochemistry A. Hydrophilic vs Hydrophobic. Since biological chemistry occurs largely in an aqueous environment, the interaction of a biological molecule with water is very important. That interaction is influenced by two primary causes: size and polarity (charge). The smaller a molecule is, the more likely it is to be willing to associate with water (dissolve). Also, the more polar and/or charged a molecule is, the more likely it is to be willing to associate with water. Since biological molecules are often very large, it is common for the different parts of the molecule to interact differently in water. For instance, a protein, which is composed of many different amino acids which have a large variety of characters, may be hydrophobic in part of its sequence and hydrophilic in other parts. Hydrophilic (hydro=water; philios=love): Hydrophilic molecules or parts of molecules will dissolve in (interact with) water. Hydrophobic (hydro=water; phobio=fear): Hydrophobic molecules or parts of molecules will refuse to interact with water. If sufficiently hydrophobic, a molecule or part of a molecule will actively repel or exclude water. Hydrophilic/phobic characters are not an all-or-none phenomenon. Molecules fall along a scale, somewhere between extremely hydrophobic and extremely hydrophilic. Changing the parts of a molecule will often shift it more toward the hydrophobic or the hydrophilic end of the scale (depending upon the change)...
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...covalently attach anions or cations onto it. Solute ions of the opposite charge in the mobile liquid phase are attracted to the resin by electrostatic forces. Molecular Exclusion Chromatography Also known as gel permeation or gel filtration, this type of chromatography lacks an attractive interaction between the stationary phase and solute. The liquid or gaseous phase passes through a porous gel which separates the molecules according to its size. The pores are normally small and exclude the larger solute molecules, but allows smaller molecules to enter the gel, causing them to flow through a larger volume. This causes the larger molecules to pass through the column at a faster rate than the smaller ones. Affinity Chromatography This is the most selective type of chromatography employed. It utilizes the specific interaction between one kind of solute molecule and a second molecule that is immobilized on a stationary phase. For example, the immobilized molecule may be an antibody to some specific protein. When solute containing a mixture of proteins are passed by this molecule, only the specific protein is reacted to this antibody, binding it to the stationary phase. This...
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...protein structure Analyze the given protein structure and predict the sites to be engineered for altering/introducing a specific property 2 Course Outline Unit 1 – Introduction (9 hrs) Unit 2 – Protein Sequences and Properties (9 hrs) Unit 3 – Conformation of Proteins (9 hrs) Unit 4 – Principles and Approach (9 hrs) Unit 5 – Probing Structure for Molecular Recognition (9 hrs) 3 Unit 1 Introduction (9 hrs) Amino acid structure and properties Detection of the size of proteins Covalent structures in proteins Overview of chemical and biosynthesis of proteins Topogenesis Post-translational covalent modification of polypeptide chains 4 Amino Acids Amino acids are molecules containing an amine group, a carboxylic acid group, and a side-chain that is specific to each amino acid The amino group is attached to the carbon atom immediately adjacent to the carboxylate group (the α– carbon ) In some amino acids, the amino group is attached to a different carbon atom; for example, in gamma-amino acids (such as gamma-amino-butyric acid) the carbon atom to which the amino group attaches is separated from the carboxylate group by two other carbon atoms The various alpha-amino acids differ in their side-chains (Rgroup) that is attached to their alpha carbon,...
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...It is a large, asymmetric molecule, and has one long tail as well as two globular heads. If dissociated, it will dissociate into six polypeptide chains. Two of them are heavy chains which are wrapped around each other to form a double helical structure, and the other four are light chains. One main characteristic of myosin is its ability to bind very specifically with actin. When myosin and actin are combined together, that makes the muscle produce force. Proteins which have a 3D structure, tend to fall into two main groups, these are; Globular – globular proteins, form ball-like structures where hydrophobic parts are towards the centre and hydrophilic are towards the edges, these make them water...
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...transduction pathway is the route by which ligand-receptor interaction is translated into biochemical change inside the cell. This process is initiated by the binding interaction of complementary ligand and receptor during sufficient time and strength that bring a biochemical change in the receptor. The upstream components consist of elements closest to the receptor. The downstream components are closest to the effector molecule. 3. Describe Immuno-receptor Tyrosine Activation Motif (ITAM) and list some of the molecules associated with B- and T- cell antigen receptors. The ITAM is a pair of long cytoplasmic tail that is found on signaling proteins within the immune system. It contains tyrosine that is phosphorylated after signal transduction of associated receptors. The phosphorylation of ITAM facilitated the initiation of signaling cascade. Other molecules associated with B and T cell antigen receptors are CD19 /CD20 on B cells that bind to complement molecules attached to antigens and CD4 and CD8 on T cells that bind to regions of the antigen MHC molecule and help in signal transduction. C28 on naïve T-cells interact with ligands CD80 and CD86 for the activation of T-cell. 4. Describe lipid rafts and explain how the relation with B and T cell antigen receptors. Lipid rafts are specialized regions of lymphocyte membrane. They are ordered, detergent-insoluble, cholesterol- and sphingolipid-rich membrane...
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...Structure and Function The word protein was first coined in 1838 to emphasize the importance of this class of molecules. The word is derived from the Greek word proteios which means "of the first rank". This chapter will provide a brief background into the structure of proteins and how this structure can determine the function and activity of proteins. It is not intended to substitute for the more detailed information provided in a biochemistry or cell biology course. Proteins are the major components of living organisms and perform a wide range of essential functions in cells. While DNA is the information molecule, it is proteins that do the work of all cells - microbial, plant, animal. Proteins regulate metabolic activity, catalyze biochemical reactions and maintain structural integrity of cells and organisms. Proteins can be classified in a variety of ways, including their biological function (Table 2.1). Table 2.1 Classification of Proteins According to biological function. | Type: | Example: | Enzymes- Catalyze biological reactions | ß-galactosidase | Transport and Storage | Hemoglobin | Movement | Actin And Myosin in muscles | Immune Protection | Immunoglobulins (antibodies) | Regulatory Function within cells | Transeription Factors | Hormones | Insulin Estrogen | Structural | Collagen | How does one group of molecules perform such a diverse set of functions? The answer is found in the wide variety of possible structures for proteins. In the...
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...Structure and Significance of Human Serum Albumin in Blood MJ May 11, 2013 Abstract Human Serum Albumin (H.S. Albumin) is the most common transporting protein found in blood plasma. Its Y-shaped molecule is mostly build of α-helix configurations that are perfect sites for carrying hydrophobic organic compounds. The human organism highly depends on the proper functioning of H. S. Albumin, thus its function and nature have been extensively studied. This article briefly describes H. S. Albumin structural features and how they influence albumin’s transposing mechanism. Introduction Proteins are large polypeptide molecules consisting of chains of amino acids. The order of amino acids in each protein is determined by the codon of the nucleotide acid sequence that is encoded within the organism’s genetic material. The combination of amino acid sequence influences how the protein will fold into its specific, three-dimensional structure. In turn, the protein’s three-dimensional structure will highly influence the physical and chemical activity of that protein. Proteins perform all major functions within living organisms. One of these functions is transportation of molecules from one location to another. Human serum albumin is a common protein in human blood responsible for transporting metabolite products, lipids and drugs. Human serum albumin makes total of 62% of all proteins in blood plasma[i], and belongs to serum...
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...adsorption, the enzymes are attached to the matrix through hydrogen bonding, van der Waals forces, or hydrophobic interactions; whereas in ionic bonding the enzymes are bound through salt linkages. This method is the easiest method of preparing immobilized enzymes, being based on the physical adsorption of the enzyme molecules onto the surface of solid matrices. Ionic binding Ionic binding provides a slightly more specific way of attaching an enzyme to a carrier: many ion exchange resins, example DEAE-...
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...of Biosynthesis, Oxford Science Publications, pp. 10-18 Loudon, M. Organic chemistry Solomons, G. Organic Chemistry Occurrence of fatty acids in Nature • Fatty acids are seldom encountered in free form, and are usually found to be esterified with glycerol • Some plants of the Crucifer (mustard) family (which includes cabbages, broccoli, Brussel sprouts) store fatty acids in free, unesterified form. However, this is rare in Nature • Fats and oils are triacylglycerides whereby all of the three hydroxyl groups of glycerol are esterified • Membrane lipids are phospholipids in which two hydroxyl groups of glycerol are esterified with fatty acids, and one hydroxyl group is modified by phosphorylation which forms the polar (hydrophilic) portion of the molecule The fatty acid synthase complex - Bacterial fatty acid synthases are aggregates of 6-7 enzymes while in plants and animals this synthase is a dimeric complex of two multifunctional protein which possess seven catalytic sites. Another enzyme, thioesterase which catalyses the release of the fatty - The functional groups responsible for binding to acetyl coA or malonyl CoA are thiol groups belonging either to cysteine (cys) or 4-phosphopantetheine (pant), the structure of which is similar to that of coenzyme A. Phosphopantetheine is attached to serine. -The cysteine active site is located on acyl carrier protein (ACP) while the 4-phosphopantetheine is located on ketoacyl synthase. Simplified scheme for the reactions of...
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...Experiment 7: Lipid Extraction I. Abstract Lipids are biomolecules that are used primarily for structural components of the cell, signaling molecules and energy storage purposes. Lipids are naturally occurring esters of long chain fatty acids with both hydrophobic chains, which is insoluble to polar organic solvents and hydrophilic chains which is soluble to polar organic solvents. Because of this conformation, they can assume a wide range of complex structures including fused rings. Lipids can be isolated from cells through different techniques and their presence can be tested through different qualitative tests. The sample choice is egg yolk and was used as a source of lipids in the experiment. Liquid-liquid extraction, separation of the organic and aqueous layer was used to extract the supernatant or extract. Also, thin layer chromatography or TLC was used to separate the different lipid components by using the Rf values computed. The farther the distance traveled by the compound (higher Rf), the more nonpolar the component, while the smaller the distance traveled, the more polar the component (lower Rf). Lecithin and cholesterol was not able to travel the plate. After, the isolated lipid was subjected to qualitative tests such as Acrolein test, test for phosphates, Leibermann-Burchard test and test for unsaturation. Acrolein tests determine the presence of glycerin; the test for phosphate detects phosphate groups in the structure of the lipid, Leibermann-Burchard uses cholesterol...
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...municipalities have specific teams and public policies engaged in dealing with the waste. When it is not treated, waste becomes a serious sanitary problem, since it exposes the community to illnesses like diarrhea, amebiasis, and parasitosis, apart from contaminating the soil, waters and water tables. Among solutions, there are the creation of sanitary landfills in appropriate places, adoption of selective collecting and recycling programs, conducting of campaigns with the aim of both making society conscious about the problem and demanding a greater participation of government authorities (Editora Abril, 2002). The manufacturing of biodegradable material offers an interesting solution for plastic materials. Like it happens with organic residues, such as foodstuff, elimination of biodegradable materials is not automatic and is considered as a recycling process by many experts. Biodegradable materials go through a composting process, for the obtaining of a stable compound, considered the final product of recycling. The bioplastics found in the market are made mainly from starch. Starch-based bioplastics represent from 85% to 90% of market’s bioplastics (Bastioli, 2000). Among starch...
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...Chromatography INTRODUCTION IN THIS LAB, WE WILL BE EXPRESSING THE GREEN FLUORESCENT PROTEIN (GFP) IN BACTERIA AND PURIFYING IT USING COLUMN CHROMATOGRAPHY. THE SPECIFIC TYPE OF CHROMATOGRAPHY WE WILL BE USING IS HYDROPHOBIC INTERACTION CHROMATOGRAPHY (HIC). THE FOLLOWING IS INFORMATION FROM BIO-RAD INC., THE SUPPLIER OF THE REAGENTS: GFP has several stretches of hydrophobic amino acids, which results in the total protein being very hydrophobic. When the supernatant, rich in GFP, is passed over a HIC column in a highly salty buffer (Binding Buffer), the hydrophobic regions of the GFP stick to the HIC beads. Other proteins which are less hydrophobic (or more hydrophilic) pass right through the column. This single procedure allows the purification of GFP from a complex mixture of bacterial proteins. Loading the GFP supernatant onto the chromatography column When students load the GFP supernatant onto their columns, it is very important that they do not disturb the upper surface of the column bed when performing the chromatography procedure. The column matrix should have a relatively flat upper surface. A slightly uneven column bed will not drastically affect the procedure. However, subsequent steps of loading, washing, and eluting should minimize disrupting the column such that beads "fluff up" into the buffer. When loading the GFP supernatant onto the column, the pipette tip should be inserted into the column and should rest against the side of the column...
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...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 about cellulose is false? A) It is the most abundant polysaccharide in nature. B) Its monomers are joined by glycosidic bonds. C) It is present in the stems of flowering plants. D) The hydroxyl groups of neighboring cellulose molecules interact to form strong, insoluble fibers. E) It is a branched polymer of glucose. Answer: E Page Ref: Section 3 1 4) When Keq of a reaction...
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...The Raw Materials of Biotechnology The Molecules of Cells Entire organism System Tissue Cells Organelle Molecules Atoms Molecular/atoms lowest level of organization Organic chemistry Chemistry of Carbon CHNOPS ◦ ◦ ◦ ◦ ◦ ◦ ◦ Carbon Hydrogen Nitrogen Oxygen Phosphorus Sulfur Several Trace Minerals Forms a bond with 4 other atoms in which electrons are shared forming a covalent compound C H C H H H CH4 \ H C H H OH CH3OH H H H C C OH H H CH3CH2OH O H C H CH2O All are polymers All are organic (C) compounds Carbohydrates Proteins Lipids Nucleic Acids Differ in terms of composition and function Carbohydrates……. Energy, support and recognition Proteins……………..Enzymes, structure, recognition, transport pigments, signals, mov’t Lipids………………..Cell membrane structure energy storage, signals cellular metabolism (VitK..) Nucleic Acids……….Hereditary and protein information, energy, signals Carbohydrates……. Polysaccharide..of simple sugars Proteins……………..Polypeptide..of amino acids Lipids………………..Insoluble in water..although common polymer glycerol and fatty acid Nucleic Acids……….Polynucleotide..of nucleotides -OH Several OH (alcohol) groups This group LOVES water Makes sugars solids and water soluble C with a double bond to an oxygen Aldehyde or ketone Joins w/an –OH to form a cyclic structure The resulting C (C-1) has...
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