BIO 281 Week 2 Notes, Chapter 2-Chapter 3.1 & Lecture Notes
BIO 281 Week 2 Notes, Chapter 2-Chapter 3.1 & Lecture Notes BIO 281
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Lecture 8/25 DNA & Evolution Thursday, August 25, 2016 10:32 AM Stanley Miller's experimentcreated a system which was supposed to represent molecules in the early earth's atmosphere. After later research, it was found this was not an accurate representation of early earth's atmosphere. Pyrimidine bases- Cytosine, Thymine, Uracil Purine bases- Guanine, Adenine Could DNA been formed early in the developmentof earth? Carbons are numbered 1' -5' Key points- DNA has directionality or polarity -OH group on 3' C -Phosphate group on 5'C DNA is anti-parallel Complementarybase pairing -A:T -C:G Are nucleotides hydrophilic or hydrophobic? Both Nitrogenous bases are hydrophobic and hydroxl group and phosphate group are hydrophilic Water is a polar moleculesbecause of differences in oxygen being electronegative. How will a moleculeslike H 2 interact with water? Key point: Because water is polar it can form hydrogen bonds with itself or other molecules Key point: moleculesare classified based on how they react with water Hydrophilic Hydrophobic Notes from the reading: 2.1 Properties of Atoms Each element contains only one type of atom, the basic unit of matter. Elements are often indicated by a chemical symbol that consists of a one- or two-letterabbreviation of the name of the element. For example: carbon is represented by C, helium by He The atom contains a dense central nucleus made up of positively charged protons and electrically neutral particles called neutrons. A third type of particle, the negatively charged electron, movesaround the nucleus. Protonsand neutrons determine the atomic mass Bio 281 Lecture Page 1 Protonsand neutrons determine the atomic mass Isotopes are atoms of the same element that have different numbers of neutrons. Electrically charged atoms are called ions. Electrons movearound the nucleus in a region called an orbital. The maximum number of electrons in any orbital is two. Orbitals differ in size and shape. Electrons in orbitals close to the nucleus have less energy than those farther away. Several orbitals can exist at a given energy level or shell. Elements are often arranged in a tabular form known as the periodic table of the elements, generally credited to Dmitri Mendeleev. Elements in a vertical column are called a group or family. Membersof a group have the same number of valence electrons. Elements in a row have the same number of shells and number and type of orbitals. 2.2 Molecules and Chemical Bonds Atoms combine to form molecules Atoms interact through a chemical bond The ability of atoms to combine with other atoms is largely determined by the electrons furthest from the nucleus which are called valence electrons. When atoms combine they share valence electrons with each other. The merged orbital is called a molecular orbital and each shared pair of electrons constitutes a covalent bond that holds the atoms together. A covalentbond is formed when two atoms share a pair of electrons in a molecular orbital, easily identified by two non-metallic atomsforming a molecule. For example: H 2 Two adjacent atoms can sometimesshare two pairs of electrons,forming a double bond denoted by a double line connecting the two chemical symbols for the atoms. A polar covalent bond is characterizedby unequal sharing of electrons A notable example of this is the bonds in the water molecule. The unequal sharing of electrons results from a difference in the ability to attract electrons,also known as electronegativity. Electronegativityincreases across a row and up a column. Oxygen is more electronegativethan hydrogen, thereforein a moleculeof water, oxygen has a slight negative charge and hydrogen has a slight positive charge. Bio 281 Lecture Page 2 When electrons are shared unequally between two atoms, the interaction result is a polar covalent bond. A covalentbond between atoms that have the same or similar electronegativityis a nonpolar covalent bond. Examples are: H 2,a2 well as carbon-carbon, (C-C) and carbon hydrogen (C-H). MOLECULES HELD TOGETHERBY NONPOLARCOVALENT BONDS DO NOT MIX WELL WITH WATER An ionic bond forms between oppositely charged ions An atom that lost an electron has a positive charge and is a positive ion. Likewise if an atom gains an electron it has a negative charge and is a negative ion. These two ions are not covalentlybound, but because opposite charges attract they associate with an ionic bond(Metallic ion and non-metal ion) When sodium chloride is placed in water, the salt dissolves to form sodium ions and chlorine ions and in solution, they are pulled apart and surrounded by water molecules. In a chemical reaction there are reactants, the moleculesthat transform into different molecules,which are called products. 2.3 Water: The medium of life Moleculesor different even different regions of the same molecule fall into two general classes, depending on how they interact with water: hydrophilic and hydrophobic. Hydrophilic compounds are polar; they dissolve readily in water. That is, water is a good solvent, capable of dissolving many substances. Hydrophobic compounds are nonpolar, they do not have regions of positive and negative charge. Therefore they arrange themselvesto minimize their contact with water. A hydrogen bond is the name given to the interaction between a hydrogen atom with a slight positive charge and an electronegativeatom of another molecule.Hydrogen bonds are much weaker than covalent bonds. When water freezes, water molecules becomehydrogen bonded to four other water molecules. Hydrogen bonds give water molecules the property of cohesion, meaning that they stick to one another. pH is a measure of concentration of protons in solution + pH=-log[H ] The pH can range from 0-14 and a difference of one unit corresponds to a tenfold difference (*10). When the concentration of protons is higher than hydroxide ions, the pH is lower than 7 and is acidic. When the concentration of protons is lower than hydroxide ions, the pH is higher than 7 and is basic. 2.4 Carbon: Life's Chemical Backbone Carbon moleculesplay such an important role in living organisms that carbon-containing molecules have a special name-- organic molecules. In forming molecularorbitals, a carbon atom behaves as if it had four unpaired electrons. Carbon has other properties that contribute to its ability to form a diversity of molecules.For example, carbon atoms can link with each other by covalent bonds to form long chains. These chains can be branched or two carbons at the ends of the chain or within the chain can link to form a ring. Moleculesthat have the same chemical formula but different structures are known as isomers. 2.5 Organic Molecules Proteins provide structural support and act as catalysts for chemical reactions. Nucleic acids encode and transmit genetic information. Bio 281 Lecture Page 3 Nucleic acids encode and transmit genetic information. Carbohydrates provide a source of energy and make up the cell wall. Lipids make up the cell membrane,store energy and act as signaling molecules. These moleculesare all large, consisting of hundreds or thousands of atoms and many are polymers. Proteins are polymersof amino acids. Nucleic acids are polymersof nucleotides. Carbohydrates such as starch are polymers of simple sugars. Lipids membranes that define cell boundaries consist of fatty acids bonded to other organic molecules. The simple repeating units of polymersare often based on a nonpolar core of carbon atoms. But attached to these carbon atoms are functional groups. Among the functional groups frequently encountered in biological molecules are amine (=NH), amino (–NH ),2carboxyl (–COOH), hydroxyl (–OH), ketone (=O), phosphate(–O–PO H ), sulfhydr3l2(– SH), and methyl (–CH ). 3he nitrogen, oxygen, phosphorus, and sulfur atoms in these functional groups are more electronegative than the carbon atoms, and functional groups containing these atoms are polar. The methyl group (–CH ), on3the other hand, is nonpolar. -Macmillan Higher Education Proteins are composedof amino acids. Some work as catalysts that acceleratethe rates of chemical reactions (enzymes) The general structure of an amino acid contains a central carbon atom, the α (alpha) carbon, carboxyl group, a hydrogen atom,and an R group or side chain. Amino acids are linked in a chain to form a protein (Fig 2.17c). The carbon atom in the carboxyl group of one amino acid is joined to the nitrogen atom in the amino group of the next by a covalent linkage called a peptide bond. Nucleic acids encode genetic information in their nucleotide sequence The nucleic acid deoxyribonucleic acid (DNA) is the genetic material in all organisms. Ribonucleic acid (RNA) has multiple functions; it is a key player in protein synthesis and the regulation of gene expression Nucleotides, in turn are composedof three components:a 5-carbon sugar, a nitrogen-containing compound called a base and one or morephosphate groups. The bases are built from nitrogen-containing rings and are of two types. The pyrimidine bases have a single ring and contain cytosine,thymine and uracil. The purine bases have a double-ring structure and contain guanine and adenine. In DNA and RNA, each adjacent pair of nucleotide is connected by a phosphodiester bond, when a phosphate group is covalentlybonded to the sugar in another nucleotide. This results in a lost water molecule. DNA consists of two strands of nucleotides forming a double helix. The bases from specific purine-pyrimidine pairs that are complementary Complex carbohydrates are made up of simple sugars. Sugars (saccharides) belong to a class of moleculescalled carbohydrates. A simple sugar is also called a monosaccharide and two sugars linked covalentlyare called a disaccharide. Simple sugars combine to form polymerscalled polysaccharides. Long, branched chains of monosaccharidesare called complex carbohydrates. Bio 281 Lecture Page 4 Simple sugars combine to form polymerscalled polysaccharides. Long, branched chains of monosaccharidesare called complex carbohydrates. Monosaccharidesare attached to each other by covalentbonds called glycosidicbonds. Lipids are hydrophobic molecules Triacylglycerol is an example of a lipid that is used for energy storage. It is a major component of animal fat and vegetable oil. Glycerol is a 3-carbon molecule with OH groups attached to each carbon. Fatty acids that do not contain double bonds are described as saturated. These acids that contain carbon-carbon double bonds are unsaturated. The constant motion of electrons in fatty acids lead to regions of slight positive and slight negative charges which attract neighboring moleculeswhich are temporarily polarized. These moleculesweakly bind to one another because of the attraction of opposite charges. These interactions are known as van der Waals forces. These are weaker than hydrogen bonds and due to these forces the melting points of fatty acids depend on their length and level of saturation. Steroids such as cholesterolare a second type of lipid. They are composedof 20 carbon atomsbonded to form four fused rings and it is hydrophobic. Phospholipids are a third type of lipid. Chapter 3: 3.1 Major Biological Functions of DNA Experimentsto discover what molecule was responsible for the genetic transfer of information were carried out most notably by Frederick Griffith in 1928when he used the pneumonia virus to show whether or not it would affect mice. After experimentation,by adding substances such as Rnase, Proteaseand Dnase, it was discovered that DNA was responsible for this transfer. DNA is copied via replication. An unrepaired error in DNA replication results in a mutation which is a change in the genetic information in DNA. Genetic information flows from DNA to RNA to protein In specifying the amino acid sequence of proteins, DNA acts through an intermediarymolecule known as ribonucleic acid (RNA). The flow of informationfrom DNA to RNA to protein is known as the central dogma of molecular biology. The first step in this process is transcription,in which the genetic information in a molecule of DNA is used as a template. The second step in the readout of genetic information is translation, where RNA is used as a code for the sequence of amino acids in a protein. Genes can be expressed only at certain times and places and not expressed at other times and places. In prokaryotes,transcription and translation occur in the cytoplasm,but in eukaryotes,transcription occurs in the nucleus and translation in the cytoplasm. In 1953,James D. Watson and Francis H. C. Crick announced a description of the three-dimensional structure of DNA. DNA strands consists of subunits called nucleotides The elegant shape of the twisting strands relies on the structure of DNA's subunits, called nucleotides. Nucleotides are made up of three components:a 5-carbon sugar, a base, and one or more phosphate groups. The characteristic covalent bond that connects one nucleotide to the next is indicated by the vertical red lines that connect the 3' carbon of one nucleotide to the 5' carbon of the next nucleotide in line through the 5'-phosphate group. This C-O-P-O-C linkage is known as the phosphodiester bond which in DNA is a relativelystable bond. The phosphodiester linkages in a DNA strand give it polarity. The nucleotide at the top has a free 5' phosphate, known as the 5' end. The DNA strand in Fig. 3.7 has a sequence of bases AGCT from top to bottom,but because of strand polarity we need to specify which end is which. This strand of the base sequence is 5'-AGCT-3' or equivalently 3'-TCGA-5' Bio 281 Lecture Page 5 The phosphodiester linkages in a DNA strand give it polarity. The nucleotide at the top has a free 5' phosphate, known as the 5' end. The DNA strand in Fig. 3.7 has a sequence of bases AGCT from top to bottom,but because of strand polarity we need to specify which end is which. This strand of the base sequence is 5'-AGCT-3' or equivalently 3'-TCGA-5' When a base sequence is stated without specifying the 5' end by conventionthe end at the left is the 5' end. Watson and Crick aimed to make the first DNA model. The watson-crick structure, now often called the double helix is a space-filling model. The outside contours of the twisted strands form an uneven pair of grooves, called the major groove and the minor groove. Individual DNA strands in the double helix are antiparallel, which means they run in opposite directions. The ribbon model of the structure closelyresembles a spiral staircase with the backbones forming the banisters and the base pairs the steps. Because the base pairs form specific pairs, they are complementary. Two big factors contributing to the stability of the double helix are the hydrogen bonding between the bases in opposite strands and base stacking of bases within a strand. The three dimensional structure of DNA gave important clues about its functions. DNA in prokaryotesare circular and form supercoils in which the moleculecoils upon itself. This is caused by enzymescalled topoisomerasesthat cleave, partially unwind and reattach a DNA strand. Supercoils then relieve the strain and help perserve the 10 base pairs per turn. In eukaryotes,most DNA moleculesare linear and each molecule forms one chromosome. Bio 281 Lecture Page 6
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