...CHAPTER 9: NUCLEIC ACIDS 9.1 Levels of Structure in Nucleic Acids Primary (1o) Structure – order of bases in the polynucleotide sequence Secondary (2o) Structure – 3D conformation of backbone Tertiary (3o) Structure – supercoiling of the molecule Quaternary (4o) Structure – interaction between DNA & proteins Two principle types of nucleic acids - DNA (deoxyribonucleic acid) - RNA (ribonucleic acid) How do DNA and RNA differ? Ribosomes: polypeptide-generating machinery of the cell Tobacco mosaic virus: nucleic acid strand winds through a cylinder of coat-protein subunits 9.2 The Covalent Structure of Polynucleotides Nucleotides: monomers of nucleic acids 1. Nitrogenous base 2. Sugar 3. Phosphoric acid residue Order of nucleic acids of DNA contains the information necessary to produce the correct amino acid sequence in the cell’s proteins What are the structures and components of the nucleotides? Nucleic acid bases (nucleobases): one or two-ring nitrogenous aromatic compound - Pyrimidines – single-ring aromatic compounds Cytosine – DNA & RNA Thymine – substitute for Uracil in DNA (sometimes in RNA) Uracil – RNA only - Purines – double-ring aromatic compounds Adenine – DNA & RNA Guanine – DNA & RNA Methylation can modify bases Nucleoside - base + sugar covalently bonded - lacks phosphate group - base forms a glycosidic linkage with sugar Ribonucleoside: β-D-ribose Deoxyribonucleoside: β-D-deoxyribose The glycosidic...
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...Stanford University STUDIES! Nucleic Acids, extremely complex molecules produced by living cells and viruses. Their name comes from their initial isolation from the nuclei of living cells. Certain nucleic acids, however, are found not in the cell nucleus but in cell cytoplasm. Nucleic acids have at least two functions: to pass on hereditary characteristics from one generation to the next, and to trigger the manufacture of specific proteins. How nucleic acids accomplish these functions is the object of some of the most intense and promising research currently under way. The nucleic acids are the fundamental substances of living things, believed by researchers to have first been formed about 3 billion years ago, when the most elementary forms of life began on earth. The origin of the so-called genetic code they carry has been accepted by researchers as being very close in time to the origin of life itself (see Evolution; Genetics). Biochemists have succeeded in deciphering the code, that is, determining how the sequence of nucleic acids dictates the structure of proteins. The two classes of nucleic acids are the deoxyribonucleic acids (DNA) and the ribonucleic acids (RNA). The backbones of both DNA and RNA molecules are shaped like helical strands. Their molecular weights (see Molecule) are in the millions. To the backbones are connected a great number of smaller molecules (side groups) of four different types (see Amino Acids). The sequence of these molecules on the strand determines...
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...Lecture 8 Nucleic Acid-Based Measurements Text Chapter 13 Wednesday, July 24, 2013 Total community DNA • Extract DNA from soil – – – – remove cells from soil separate cells from soil lyse cells separate DNA from cells – purify DNA • Extract DNA from soil – Extract DNA from cells in presence of soil • Bead-beating • chemical or enzymatic treatment – Sodium dodecyl sulfate or lysozyme Wednesday, July 24, 2013 DNA purification • Cesium chloride gradient centrifugation • Kits Low density DNA High density Wednesday, July 24, 2013 Visualizing nucleic acidsBlotting • Southern blotting – DNA • Northern blotting – RNA Wednesday, July 24, 2013 Agarose gel electrophoresis - Stain gel with ethidium bromide + Wednesday, July 24, 2013 DNA purification Agarose gel verification Wednesday, July 24, 2013 Gene Probes • Phylogenetic probes – 16S rRNA • Functional gene probes – dsr (bisulfite reductase) sulfate reduction – nirS (nitrate reductase) nitrate reduction Wednesday, July 24, 2013 16S rRNA gene probes • Oligonucleotide primers for PCR Target region cDNA 16S rDNA clone library • Oligonucleotide probes complementary to 16S rRNA molecule – no need for PCR because many copies in cells Wednesday, July 24, 2013 cDNA RNA ribosome Secondary Structure: 16S rRNA Different locations on the 16S rRNA molecule offer identity at different phylogenetic levels •Domain EU338 •Phylum •Class •Family •Group CF319a...
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...BIOL2103 Biological Sciences Laboratory Course Practical 3 Laboratory manual Isolation of nucleic acid and spectrophotometry Introduction: The ability to isolate and quantify nucleic acids accurately and rapidly is a prerequisite for many of the methods used in biochemistry and molecular biology. The concentration of DNA or RNA in a sample, and its condition, are often estimated by running the sample on an agarose gel. Such concentration estimates are semiquantitative at best and are time-consuming. For a more accurate determination of the concentration of DNA or RNA in a sample, a UV spectrophotometer is commonly used. Spectrophotometry uses the fact that there is a relationship between the absorption of ultraviolet light by DNA/RNA and its concentration in a sample. The absorption maximum of DNA/RNA is approx 260nm. The purity of a solution of DNA can be determined using a comparison of the optical density values of the solution at various wavelengths. For pure DNA, the observed A260/A280 ratio will be near 1.8. Elevated ratios usually indicate the presence of RNA. The A260/A280 ratio is used to assess RNA purity. An A260/A280 ratio of 1.8-2.1 is indicative of highly purified RNA. The 260/280 ratio below 1.8 often signal the presence of a contaminating protein or phenol. Alternatively, protein or phenol contamination is indicated by 230/260 ratios greater than 0.5. Workflow Time 2 days before the lab session During lab session 1:30 pm Task Cell...
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...Nucleic Acids Competency 208.5.1 Melissa Kelleher, RN The Structure of DNA • DNA is composed of units called nucleoCdes, (Wolfe, 2000). • NucleoCdes are composed of a phosphate group, a deoxyribose sugar, and a nitrogenous base, (Wolfe, 2000). – Purines – nitrogenous bases that composed of two rings, (Wolfe, 2000). – Pyrimadines – nitrogenous bases composed of one ring, (Wolfe, 2000). The Structure of DNA • DNA is a double helix structure of nucleoCdes wound together in an anCparallel direcCon, (Wolfe, 2000). – Hydrogen bonds form between the nitrogenous bases, (Wolfe, 2000). – Base pairs only bond in specific pairs, (Wolfe, 2000). • Adenine bonds only with thymine, (Wolfe, 2000). • Guanine bonds only with cytosine, (Wolfe, 2000). • Deoxyribose sugars line up in one direcCon, considered the 51 to 31 direcCon, in one strand of DNA, and in the opposing direcCon, considered the 31 to 51 direcCon...
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...What biological principle is illustrated by the Heike crabs? Selection by humans Sagan says that if artificial selection can produce vast changes in a short period of time, then what must nature be able to do, given the age of the ear (4.5 billion years or so)? Don't just quote the video here. Explain what he means! Nature must be able to produce and create. What are the basic “steps” in natural selection as Sagan describes them? What questions does he raise for you? Natural Selection happens when human’s changes have created other changes without humans directly deciding to do so. Sagan describes the basic steps as there are more creatures then can survive. Less adapted have a less chance of surviving and producing off spring. Sudden changes in heredity can be pushed on to the off springs. Environmental changes can have an impact on what mutations will help survival. Thus, slow changes produce new species. Natural Selection was discovered by Charles Darwin and Alfred Russel Wallace. Explain the Watchmaker Hypothesis as an argument against natural selection. How does Sagan address it? “Our ancestors looked at the intricacy and the beauty of life and saw evidence for a great designer. The simplest organism is a far more complex machine than the finest pocket watch. And yet, pocket watches don’t spontaneously self-assemble or evolve in slow stages on their own from say, grandfather clocks”. (Sagan, C) It’s impossible to just look at something and understand...
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...g A New Molecule of Life Life as we know it is far more complex than one can imagine. The smallest molecule in human body can play a large role in determining the genetic outcome or the overall well being of a person. In Peter Nielsen’s “Designing a New Molecule of Life”, he speaks of a molecule that hopefully one day will create a scientific and medical breakthrough. In this essay you will read a summary of Peter Nielsen’s article and the research he has done with this molecule. Peter Nielson, along with many other scientists, have spent years creating and experimenting with a synthetic molecule called peptide nucleic acid (PNA). PNA is an artificial polymer that has many similarities to deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). It has the same storing features as DNA and RNA while being built on a protein based backbone therefore making it sturdier and simpler than the sugar phosphate-backbone. The molecule was created in hopes of having an immediate affect by pursuing a drug that would target DNA’s composing specific genes, to either enhance or block the gene’s expression. This new drug would be in efforts to interfere with the production of disease producing proteins. Although this molecule has produced highly anticipated medical research, it has also lead to speculations of being the origins of life. In his years of research, Peter Nielsen and his colleagues wanted to achieve the ability of PNA recognizing double-stranded or duplex DNA having specific...
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..._ However, the helix structure (to be more specificly, the glycosidic bonds) is easily wrecked by heat (boiling temperature of water) and acid treatment (HCl). Once the helix structure of homopolycarbohydrate is broken, the conformation with iodine no longer exists. It leads to the gradual loss of blue color. | 2 | | | 4 | | | 6 | | | 8 | | | 10 | | | | No color change | | Color of Lugol | | | 2.PROTEINS 2.2.2. Task-Qualitative Detection of Proteins Protein solution | Original color | After 10% NaOH | After 0.5% CuSO4 | 1. Egg albumin | Colorless | Colorless | Blue->purple | 2. Fresh cow milk | White | White | Blue->purple | Explanation: NaOH doesn’t react with Proteins, so there’s no change to the protein solutions Next, when CuSO4 is added, it reacts with NaOH to form Cu(OH)2 (blue) first. 2NaOH+ CuSO4 -> Cu(OH)2(s) + Na2SO4 Then Cu(OH)2 and Proteins together form the complex, which gives out the purple color. This reaction (called biuret reaction) is useful to detect the protein presence. (write down the chemical equation, GOOGLE) 3. LIPIDS 4. NUCLEIC ACIDS 4.1.General Introduction Nucleic acids are large biological molecules essential for all known forms of life. They include DNA (deoxyribonucleic acid) and RNA(ribonucleic acid). Together with proteins, nucleic acids are the most important biological macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting...
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...Leila Halaby Biochemistry 208.5.1 09/11/14 The Process of DNA Replication Western Governors University The Process Of DNA Replication The process of DNA replication at the biochemistry level starts with DNA to RNA and RNA to protein. DNA is “The Master” molecule of every cell. It contains vital information that is passed onto every generation. It has information on how to make itself as well as other molecules. DNA is the key to life. RNA leaves the nucleus of the cell and makes proteins. (Sally Seller December 2013) http:/ /www.cytochemistry.net/cell-biology/ ribosome.htm The process by which both strands are replicated starts with the strands being separated and unwound by DNA Helicase. DNA polymerases, an enzymes which catalyze the synthesis of new complementary strands will add nucleotides to the 3’ end of the growing nucleotide strand. An RNA primer is needed to start the synthesis of a new strand to make the first 3’ end the enzyme needs. After that, the RNA is taken out and replace with DNA. The synthesis of both complementary strands start in the 5’ to 3’ direction. The leading strand will then grow continuously in the direction of the replication fork. On the leading strand, RNA primase comes in and add RNA primer. ! ! (thinkwell biochemistry 6.4.2) Newly synthesized DNA The lagging strand will point away from the opening of the fork. RNA primase will constantly add RNA primer as the strand opens up On the leading strand, DNA polymerase III...
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...medicine Declaration 1. I know that plagiarism is wrong. Plagiarism is to use another person’s work and present it as one’s own. 2. Each significant contribution to, and quotation in this report that I have taken from the work (s) of other people has been attributed, and has been cited and referenced. 3. This report is my own. 4. I have not allowed, and will not allow anyone to copy my work with the intention of passing it off as his/her own work. Signature date Question: Discuss what are the nucleotides and nucleic acids in human health and disease Almost all living cells contain two very important substances, deoxyribonucleic acid or DNA and ribonucleic acid or RNA. These molecules carry instructions for making proteins. The help specify the amino acid sequence and thus which proteins will be made. When nucleotides join together they form the functional units of the structure of DNA and RNA where DNA contains one less hydroxyl group than RNA. Nucleotides serve as a source of energy therefore playing an important role in metabolism, for example mitochondria produce ATP or Adenosine triphosphate. They also serve as co-factors in enzymatic reactions and participate in cell signalling for example as Camp messengers. A single nucleotide is made up of three smaller molecules, a phosphate group which helps to form the sugar phosphate backbone via phosphodiester bonds...
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...water molecule is caused by an uneven distribution of electrons between the oxygen and hydrogen atoms. 9. the concentration of H+ ions determines whether a solution is acidic or basic 10. Capillary action is the effect of water rising in a narrow tube against the force of gravity. 11. Two types of mixtures are solutions and suspensions 12. A base is a compound that can form a basic solution when dissolved. 13. Acidic solutions have a lower pH than pure water. This is due to the greater concentration of H+ ions than pure water. 14. Strong acids and bases are dangerous to cells. Buffers are dissolved compounds that help prevent sharp, sudden swings in pH. Section Review 2-3 1. Carbohydrates 2. Proteins 3. Lipids 4. Nucleic Acids 5. Proteins 6. Proteins 7. Carbohydrates 8. Nucleic Acid 9. Glycerol 10. Monosaccharides 11. Ribonucleic Acid (RNA), Deoxyribonucleic Acid (DNA) 12. Proteins 13. Saturated 14. Carbon atoms have 4 valence electrons and therefore can form 4 strong, stable, covalent bonds. 15. Both plastics and polysaccharides are organic...
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...Pre-AP Biology Chapter 2 Test Chemistry of Life Multiple Choice (1 point each) Identify the choice that best completes the statement or answers the question. ____b 1. The space surrounding the nucleus of an atom contains |a. |protons. |c. |neutrons. | |b. |electrons. |d. |ions. | ____c 2. If an atom contains 3 protons, 4 neutrons, and 3 electrons, its mass number would be |a. |3. |c. |7. | |b. |4. |d. |11. | c____ 3. Isotopes are atoms of the same element with the same number of protons and |a. |a different number of |c. |a different number of neutrons.| | |electrons. | | | |b. |a different number of |d. |the same number of neutrons. | | |molecules. | | | ___d_ 4. Which of the following is...
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...BIO Week 1 Assessment * Question 1 8 out of 8 points | | | Which of the following is an appropriate scientific hypothesis? | | | | | Selected Answer: | People catch colds because of exposure to cold temperature. | Correct Answer: | People catch colds because of exposure to cold temperature. | | | | | * Question 2 8 out of 8 points | | | When a sodium atom gives up an electron to a chlorine atom, what type of bond is formed? | | | | | Selected Answer: | Ionic | Correct Answer: | Ionic | | | | | * Question 3 0 out of 8 points | | | A solution with a pH of 2 is considered to be a: | | | | | Selected Answer: | weak acid | Correct Answer: | strong acid | | | | | * Question 4 8 out of 8 points | | | Sally is trying to eat healthier and watch her intake of saturated fats. Which of the following oils would be the best choice for Sally to use when she cooks? | | | | | Selected Answer: | Olive oil | Correct Answer: | Olive oil | | | | | * Question 5 8 out of 8 points | | | Nonliving things include fire, water, and viruses. Many features of living things are also found in nonliving things. Of the following features, which is most likely to be ABSENT in nonliving things? | | | | | Selected Answer: | Homeostasis | Correct Answer: | Homeostasis | | | | | * Question 6 56 out of 60 points | | | Match the following term to its...
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...The Energy Document “Be humble, for you are made of earth. Be noble, for you are made of stars.” -Serbian Proverb Science can only talk about what it can measure and it cannot measure thoughts, love, spirit, or God; therefore, it cannot scientifically talk about those things. Science measures the physical make-up of the universe and talks about how it happened, not who made it. An obvious example of this is the illusion of conflict between creationist and evolutionist. They argue as if they are talking about the same thing when they are not. Creationist have no idea how it was done, they only know that God did it. Evolutionist are not at all interested in who did it, they are exploring all the possibilities from physical and mathematical evidence of how one thing led to another. Hydrogen is found to be the most abundant element in the universe (97%) and comprises the core of most stars. Stars are seen as fusion furnaces forming (creating), at the least, the elements of the periodic table up to iron. Science finds that 99.6% of the human body is comprised of 11 elements. 54 trace elements make up the rest of the body. We are made of star dust. Each atom in our bodies is at least 5 billion years old. I wonder where all they have been in that time. This is one big reason to start teaching the Periodic Table of Elements in the 1st Grade. Start with 5 elements that they encounter everyday: Oxygen (air) and Hydrogen (water); add Carbon and make carbon dioxide,...
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...States of Matter Gases, liquids and solids are all made up of microscopic particles, but the behaviors of these particles differ in the three phases. The following figure illustrates the microscopic differences. | | | Microscopic view of a gas. | Microscopic view of a liquid. | Microscopic view of a solid. | Note that: * Particles in a: * gas are well separated with no regular arrangement. * liquid are close together with no regular arrangement. * solid are tightly packed, usually in a regular pattern. * Particles in a: * gas vibrate and move freely at high speeds. * liquid vibrate, move about, and slide past each other. * solid vibrate (jiggle) but generally do not move from place to place. Liquids and solids are often referred to as condensed phases because the particles are very close together. The following table summarizes properties of gases, liquids, and solids and identifies the microscopic behavior responsible for each property. Some Characteristics of Gases, Liquids and Solids and the Microscopic Explanation for the Behavior | gas | liquid | solid | assumes the shape and volume of its container particles can move past one another | assumes the shape of the part of the container which it occupies particles can move/slide past one another | retains a fixed volume and shape rigid - particles locked into place | compressible lots of free space between particles | not easily compressible little...
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