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Becky Kriger

Introduction to DNA Structure - 0 views

www.blc.arizona.edu/...DNA_Tutorial.HTML

polynucleotides DNA

shared by Becky Kriger on 08 Dec 08 - Cached
  • Pyrimidine Bases Cytosine and thymine are pyrimidines. The 6 stoms (4 carbon, 2 nitrogen) are numbered 1-6. Like purines, all pyrimidine ring atoms lie in the same plane. Structure of C and T
  • DNA is a polymer. The monomer units of DNA are nucleotides, and the polymer is known as a "polynucleotide." Each nucleotide consists of a 5-carbon sugar (deoxyribose), a nitrogen containing base attached to the sugar, and a phosphate group. There are four different types of nucleotides found in DNA, differing only in the nitrogenous base.
  • Adenine and guanine are purines. Purines are the larger of the two types of bases found in DNA. Structures are shown below: Structure of A and G
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  • The 9 atoms that make up the fused rings (5 carbon, 4 nitrogen) are numbered 1-9. All ring atoms lie in the same plane.
  • The deoxyribose sugar of the DNA backbone has 5 carbons and 3 oxygens. The carbon atoms are numbered 1', 2', 3', 4', and 5' to distinguish from the numbering of the atoms of the purine and pyrmidine rings. The hydroxyl groups on the 5'- and 3'- carbons link to the phosphate groups to form the DNA backbone
  • A nucleoside is one of the four DNA bases covalently attached to the C1' position of a sugar.
  • Nucleosides differ from nucleotides in that they lack phosphate groups. The four different nucleosides of DNA are deoxyadenosine (dA), deoxyguanosine (dG), deoxycytosine (dC), and (deoxy)thymidine (dT, or T).
  • A nucleotide is a nucleoside with one or more phosphate groups covalently attached to the 3'- and/or 5'-hydroxyl group(s).
  • The DNA backbone is a polymer with an alternating sugar-phosphate sequence. The deoxyribose sugars are joined at both the 3'-hydroxyl and 5'-hydroxyl groups to phosphate groups in ester links, also known as "phosphodiester" bonds.
  • DNA is a normally double stranded macromolecule. Two polynucleotide chains, held together by weak thermodynamic forces, form a DNA molecule.
  • Two DNA strands form a helical spiral, winding around a helix axis in a right-handed spiral The two polynucleotide chains run in opposite directions The sugar-phosphate backbones of the two DNA strands wind around the helix axis like the railing of a sprial staircase The bases of the individual nucleotides are on the inside of the helix, stacked on top of each other like the steps of a spiral staircase.
  • Within the DNA double helix, A forms 2 hydrogen bonds with T on the opposite strand, and G forms 3 hyrdorgen bonds with C on the opposite strand.
Becky Kriger

Nucleotides, Polymerization of DNA - 0 views

users.rcn.com/...Nucleotides.html

polynucleotides DNA

shared by Becky Kriger on 08 Dec 08 - Cached
  • Nucleic acids are linear, unbranched polymers of nucleotides
  • Nucleotides consist of three parts:
  • two purines, called adenine (A) and guanine (G) two pyrimidines, called thymine (T) and cytosine (C) RNA contains: The same purines, adenine (A) and guanine (G). RNA also uses the pyrimidine cytosine (C), but instead of thymine, it uses the pyrimidine uracil (U).
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  • A five-carbon sugar (hence a pentose). Two kinds are found: Deoxyribose, which has a hydrogen atom attached to its #2 carbon atom (designated 2') Ribose, which has a hydroxyl group atom there
  • A nitrogen-containing ring structure called a base. The base is attached to the 1' carbon atom of the pentose. In DNA, four different bases are found:
  • The combination of a base and a pentose is called a nucleoside.
  • One (as shown in the first figure), two, or three phosphate groups. These are attached to the 5' carbon atom of the pentose.
  • The nucleic acids, both DNA and RNA, consist of polymers of nucleotides. The nucleotides are linked covalently between the 3' carbon atom of the pentose and the phosphate group attached to the 5' carbon of the adjacent pentose.
  • Most intact DNA molecules are made up of two strands of polymer, forming a "double helix". RNA molecules, while single-stranded, usually contain regions where two portions of the strand twist around each other to form helical regions.
Becky Kriger

Polypeptides and Proteins - 0 views

student.ccbcmd.edu/...protein.html

Protien polypeptides

shared by Becky Kriger on 08 Dec 08 - Cached
  • A peptide (def) is two or more amino acids joined together by peptide bonds, and a polypeptide (def) is a chain of many amino acids. A protein contains one or more polypeptides. Therefore, proteins (def) are long chains of amino acids held together by peptide bonds.
  • The secondary structure (def) of the protein is due to hydrogen bonds that form between the oxygen atom of one amino acid and the nitrogen atom of another. This gives the protein or polypeptide the two-dimensional form of an alpha-helix or a beta-pleated sheet (see Fig. 4).
  • Amino acids (def) are the building blocks for proteins. All amino acids contain an amino or NH2 group and a carboxyl (acid) or COOH group. There are 20 different amino acids commonly found in proteins
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  • To form polypeptides and proteins, amino acids are joined together by peptide bonds (def), in which the amino or NH2 of one amino acid bonds to the carboxyl (acid) or COOH group of another amino acid as shown in (see Fig. 2). Animation showing the formation of a peptide bond.
  • The actual order of the amino acids in the protein is called its primary structure (def) (see Fig. 3) and is determined by DNA.
  • it is commonly said that the order of deoxyribonucleotide bases (def) in a gene determines the amino acid sequence of a particular protein. Since certain amino acids can interact with other amino acids in the same protein, this primary structure ultimately determines the final shape and therefore the chemical and physical properties of the protein.
  • In globular proteins such as enzymes, the long chain of amino acids becomes folded into a three-dimensional functional shape or tertiary structure (def).
  • In some cases, such as with antibody molecules and hemoglobin, several polypeptides may bond together to form a quaternary structure (def) (see Fig 6).
Becky Kriger

Carbohydrates and Polysaccharides - 0 views

www.rsc.org/...carbohydrates.htm

Carbohydrates polymers Polysaccharides

shared by Becky Kriger on 08 Dec 08 - Cached
  • Disaccharide Monosaccharides sucrose from α-glucose + α-fructose maltose from α-glucose + α-glucose α-lactose * from α-glucose + β-galactose * Lactose also exists in a beta form, which is made from β-galactose and β-glucose
  • A condensation reaction takes place releasing water. This process requires energy. A glycosidic bond forms and holds the two monosaccharide units together.
  • Carbohydrates (also called saccharides) are molecular compounds made from just three elements: carbon, hydrogen and oxygen. Monosaccharides (e.g. glucose) and disaccharides (e.g. sucrose) are relatively small molecules.
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  • a source of energy
  • building blocks for polysaccharides (giant carbohydrates
  • components of other molecules eg DNA, RNA, glycolipids, glycoproteins, ATP
  • Monosaccharides are the simplest carbohydrates and are often called single sugars.
  • Monosaccharides have the general molecular formula (CH2O)n, where n can be 3, 5 or 6.
  • n = 3 trioses, e.g. glyceraldehyde n = 5 pentoses, e.g. ribose and deoxyribose ('pent' indicates 5) n = 6 hexoses, e.g. fructose, glucose and galactose ('hex' indicates 6)
  • Molecules that have the same molecular formula but different structural formulae are called structural isomers.
  • Monosaccharides containing the aldehyde group are classified as aldoses, and those with a ketone group are classified as ketoses. Aldoses are reducing sugars; ketoses are non-reducing sugars.
  • in water pentoses and hexoses exist mainly in the cyclic form, and it is in this form that they combine to form larger saccharide molecules.
  • There are two forms of the cyclic glucose molecule: α-glucose and β-glucose.
  • Two glucose molecules react to form the dissacharide maltose. Starch and cellulose are polysaccharides made up of glucose units.
  • Galactose molecules look very similar to glucose molecules. They can also exist in α and β forms. Galactose reacts with glucose to make the dissacharide lactose.
  • However, glucose and galactose cannot be easily converted into one another. Galactose cannot play the same part in respiration as glucose.
  • Fructose reacts with glucose to make the dissacharide sucrose.
  • Ribose and deoxyribose are pentoses. The ribose unit forms part of a nucleotide of RNA. The deoxyribose unit forms part of the nucleotide of DNA.
  • Monosaccharides are rare in nature. Most sugars found in nature are disaccharides. These form when two monosaccharides react.
  • The three most important disaccharides are sucrose, lactose and maltose.
  • Disaccharides are soluble in water, but they are too big to pass through the cell membrane by diffusion.
  • This is a hydrolysis reaction and is the reverse of a condensation reaction. It releases energy.
  • Monosaccharides are converted into disaccharides in the cell by condensation reactions. Further condensation reactions result in the formation of polysaccharides. These are giant molecules which, importantly, are too big to escape from the cell. These are broken down by hydrolysis into monosaccharides when energy is needed by the cell.
  • Monosaccharides can undergo a series of condensation reactions, adding one unit after another to the chain until very large molecules (polysaccharides) are formed. This is called condensation polymerisation, and the building blocks are called monomers. The properties of a polysaccharide molecule depend on: its length (though they are usually very long) the extent of any branching (addition of units to the side of the chain rather than one of its ends) any folding which results in a more compact molecule whether the chain is 'straight' or 'coiled'
  • Starch is often produced in plants as a way of storing energy. It exists in two forms: amylose and amylopectin
  • Amylose is an unbranched polymer of α-glucose. The molecules coil into a helical structure. It forms a colloidal suspension in hot water. Amylopectin is a branched polymer of α-glucose. It is completely insoluble in water.
  • Glycogen is amylopectin with very short distances between the branching side-chains.
  • Inside the cell, glucose can be polymerised to make glycogen which acts as a carbohydrate energy store.
  • Cellulose is a third polymer made from glucose. But this time it's made from β-glucose molecules and the polymer molecules are 'straight'.
  • Cellulose serves a very different purpose in nature to starch and glycogen. It makes up the cell walls in plant cells. These are much tougher than cell membranes. This toughness is due to the arrangement of glucose units in the polymer chain and the hydrogen-bonding between neighbouring chains.
  • Cellulose is not hydrolysed easily and, therefore, cannot be digested so it is not a source of energy for humans.
Becky Kriger

Polynucleotides - 0 views

www.3rd1000.com/...chem302v.htm

shared by Becky Kriger on 08 Dec 08 - Cached
  • A polymer of mononucleotides is called a polynucleotide. In polynucleotides, only one phosphoric acid is present on each ribose sugar so hydrolysis of polynucleotides produces equimolar solutions of nitrogenous base, ribose sugar, and phosphate. The phosphoric acid component of polynucleotides readily loses a proton and so polynucleotides are also called nucleic acids.
  • Polynucleotides, both DNA and RNA, are the information carriers of living organisms and play the central role in reproduction.
Becky Kriger

Polypeptides - 0 views

users.rcn.com/...Polypeptides.html

polymers biopolymers protein

shared by Becky Kriger on 08 Dec 08 - Cached
  • Polypeptides are chains of amino acids. Proteins are made up of one or more polypeptide molecules.
  • One end of every polypeptide, called the amino terminal or N-terminal, has a free amino group. The other end, with its free carboxyl group, is called the carboxyl terminal or C-terminal.
  • he sequence of amino acids in a polypeptide is dictated by the codons in the messenger RNA (mRNA) molecules from which the polypeptide was translated. The sequence of codons in the mRNA was, in turn, dictated by the sequence of codons in the DNA from which the mRNA was transcribed. The schematic below shows the N-terminal at the upper left and the C-terminal at the lower right.
Becky Kriger

Biopolymers and Bioplastics - 0 views

www.biobasics.gc.ca/...View.asp

shared by Becky Kriger on 08 Dec 08 - Cached
  • Biopolymers are polymers which are present in, or created by, living organisms. These include polymers from renewable resources that can be polymerized to create bioplastics. Bioplastics are plastics manufactured using biopolymers, and are biodegradable.
  • There are two main types of biopolymers: those that come from living organisms; and, those which need to be polymerized but come from renewable resources. Both types are used in the production of bioplastics
  • Biopolymer Natural Source What is it? Cellulose Wood, cotton, corn, wheat, and others This polymer is made up of glucose. It is the main component of plant cell walls. Soy protein Soybeans Protein which naturally occurs in the soy plant. Starch Corn, potatoes, wheat, tapioca, and others This polymer is one way carbohydrates are stored in plant tissue. It is a polymer made up of glucose. It is not found in animal tissues. Polyesters Bacteria These polyesters are created through naturally occurring chemical reactions that are carried out by certain types of bacteria.
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  • Biopolymer Natural Source What is it? Lactic Acid Beets, corn, potatoes, and others Produced through fermentation of sugar feedstocks, such as beets, and by converting starch in corn, potatoes, or other starch sources. It is polymerized to produce polylactic acid -- a polymer that is used to produce plastic. Triglycerides Vegetable oils These form a large part of the storage lipids found in plant and animal cells. Vegetable oils are one possible source of triglycerides that can be polymerized into plastics.
  • Using Fermentation to Produce Plastics Fermentation, used for hundreds of years by humans, is even more powerful when coupled with new biotechnology techniques.
  • Today, fermentation can be carried out with genetically engineered microorganisms, specially designed for the conditions under which fermentation takes place,
  • Fermentation, in fact, is the process by which bacteria can be used to create polyesters. Bacteria called Ralstonia eutropha are used to do this. The bacteria use the sugar of harvested plants, such as corn, to fuel their cellular processes. The by-product of these cellular processes is the polymer.
  • Lactic acid is fermented from sugar, much like the process used to directly manufacture polymers by bacteria. However, in this fermentation process, the final product of fermentation is lactic acid, rather than a polymer. After the lactic acid is produced, it is converted to polylactic acid using traditional polymerization processes.
  • Plants are becoming factories for the production of plastics. Researchers created a Arabidopis thaliana plant through genetic engineering. The plant contains the enzymes used by bacteria to create plastics. Bacteria create the plastic through the conversion of sunlight into energy. The researchers have transferred the gene that codes for this enzyme into the plant, as a result the plant produces plastic through its cellular processes. The plant is harvested and the plastic is extracted from it using a solvent. The liquid resulting from this process is distilled to separate the solvent from the plastic.
  • Currently, fossil fuel is still used as an energy source during the production process. This has raised questions by some regarding how much fossil fuel is actually saved by manufacturing bioplastics. Only a few processes have emerged that actually use less energy in the production process.
  • Energy use is not the only concern when it comes to biopolymers and bioplastics. There are also concerns about how to balance the need to grow plants for food, and the need to grow plants for use as raw materials. Agricultural space needs to be shared. Researchers are looking into creating a plant that can be used for food, but also as feedstock for plastic production.
  • Biopolymers and bioplastics are the main components in creating a sustainable plastics industry. These products reduce the dependence on non-renewable fossil fuels, and are easily biodegradable. Together, this greatly limits the environmental impacts of plastic use and manufacture. Also, characteristics such as being biodegradable make plastics more acceptable for long term use by society. It is likely that in the long term, these products will mean plastics will remain affordable, even as fossil fuel reserves diminish.
Becky Kriger

Plastics - 0 views

nobelprize.org/...readmore.html

shared by Becky Kriger on 08 Dec 08 - Cached
  • lastics are synthetic materials, which means that they are artificial, or manufactured.
  • he building blocks for making plastics are small organic molecules - molecules that contain carbon along with other substances. They generally come from oil (petroleum) or natural gas, but they can also come from other organic materials such as wood fibers, corn, or banana peels! Each of these small molecules is known as a monomer ("one part") because it's capable of joining with other monomers to form very long molecule chains called polymers ("many parts")
  • 1. Crude oil, the unprocessed oil that comes out of the ground, contains hundreds of different hydrocarbons, as well as small amounts of other materials. The job of an oil refinery is to separate these materials and also to break down (or "crack) large hydrocarbons into smaller ones. 2. A petrochemical plant receives refined oil containing the small monomers they need and creates polymers through chemical reactions. 3. A plastics factory buys the end products of a petrochemical plant - polymers in the form of resins - introduces additives to modify or obtain desirable properties, then molds or otherwise forms the final plastic products.
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  • One such molecule is the ethylene monomer, the starting point for a variety of plastics. Ethylene is a small hydrocarbon consisting of four hydrogen atoms and two carbon atoms.
  • Polymerization is often started by combining the monomers through the use of a catalyst - a substance that aids a chemical reaction without undergoing any permanent chemical change itself. During the chemical reaction, hundreds or thousands of monomers combine to form a polymer chain, and millions of polymer chains are formed at the same time. The mass of polymers that results is known as a resin.
  • Polyethylene is made from just ethylene monomers - but it's also possible to create polymers from two or more different monomers. You can make hundreds of different polymers depending on which monomers and catalysts you use.
  • Cellulose, the basic component of plant cell walls is a polymer, and so are all the proteins produced in your body and the proteins you eat. Another famous example of a polymer is DNA - the long molecule in the nuclei of your cells that carries all the genetic information about you.
  • lastics are classified into two categories according to what happens to them when they're heated to high temperatures. Thermoplastics keep their plastic properties: They melt when heated, then harden again when cooled. Thermosets, on the other hand, are permanently "set" once they're initially formed and can't be melted. If they're exposed to enough heat, they'll crack or become charred.
  • Thermoplastics have long, linear polymer chains that are only weakly chemically bonded, or connected, to each other. When a thermoplastic object is heated, these bonds are easily broken, which makes the polymers able to glide past each other like strands of freshly cooked spaghetti. That's why thermoplastics can readily be remolded. The weak bonds between the polymers reform when the plastic object is cooled, which enable it to keep its new shape.
  • The linear chains are crosslinked - strongly chemically bonded. This prevents a thermoplastic object from being melted and reformed.
  • The most common method for making plastics is molding. To make a thermoplastic object, plastic granules known as resin are forced into a mold under high heat and pressure. When the material has cooled down, the mold is opened and the plastic object is complete. When making plastic fibers, the molten resin is sprayed through a strainer with tiny holes.
  • Thermosets are produced in two steps: 1. Linear polymers are formed. 2. The linear polymers are forced into a mold where "curing" takes place. This may involve heating, pressure, and the addition of catalysts. During this process, a cross-linked or networked structure forms, creating a permanently hard object that is no longer meltable or moldable.
  • For most applications, the ideal polymer is a long, straight chain with a highly regular molecular structure. Early synthetic polymers, however, often exhibited odd little branches and other irregularities. In the 1950s, German chemist Karl Ziegler (1898–1973) discovered that an entirely different type of catalyst - a combination of aluminum compounds with other metallic compounds - could solve some of these annoying problems and increase the length of a polymer chain, producing superior plastics.
  • olymers often have short side chains, which can occur on either side of the main chain. If side branches occur randomly to the left or right, the polymer has an irregular structure. Italian chemist Giulio Natta (1903–1979) discovered that some Ziegler catalysts led to a uniform structure in which all the side branches are on the same side.
  • Firstly, there is an environmental impact from plastics production; however the plastics industry has worked hard to reduce energy and water use, as well as waste generation during the manufacturing processes.
  • Secondly, during their lives, plastic products can save energy and reduce carbon dioxide emissions in a variety of ways. For example, they're lightweight, so transporting them is energy efficient. And plastic parts in cars and airplanes reduce the weight of those vehicles and therefore less energy is needed to operate them and lower emissions are created.
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