BIOL 1305 Week 3 Notes
BIOL 1305 Week 3 Notes 1305
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This 10 page Class Notes was uploaded by Taylor Ann Coit on Sunday September 18, 2016. The Class Notes belongs to 1305 at University of Texas at El Paso taught by Dr. Schuyler Pike in Fall 2016. Since its upload, it has received 5 views. For similar materials see General Biology in Science at University of Texas at El Paso.
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Date Created: 09/18/16
Chapter 3: Nucleic Acids, Proteins, and Enzymes Genome- complete set of DNA in a living organism Genes- DNA sequence that encodes specific proteins and are transcribed into RNA. -Not all genes are transcribed in all cells of an organism. Nucleic Acids- polymers specialized for storage, transmission, and use of genetic information. DNA= Deoxyribonucleic Acid RNA= Ribonucleic Acid Nucleotide: Pentose sugar + N-containing base + phosphate group Nucleosides: Pentose sugar + N-containing base Pyrimidines: Cytosine (C), Thymine (T), Uracil (U) Purines: Adenine (A) and Guanine (G) Oligonucleotides- about 20 monomers, and include small RNA molecules important for DNA replication and gene expression. -DNA and RNA are polynucleotides, the longest polymers in the living world. Complementary base pairing: Adenosine=Thymine (Thymine=Uracil in RNA) Cytosine=Guanine (applies to both DNA & RNA) -DNA is an informational molecule: genetic information is in the sequence of base pairs. -DNA undergoes two functions: 1.Replication 2.Gene expression- base sequences are copied to RNA, and specify amino acids sequences in proteins. -DNA replication and transcription depend on the base pairing: 5’-TCAGCA- 3’ 3’-AGTCGT-5’ -3’-AGTCGT-5’ transcribes to RNA with the sequence 5’- UCAGCA-3’. -DNA base sequences reveal evolutionary relationships. -Closely relate living species should have more similar base sequences than species that are more distantly related. -Scientists are now able to determine and compare entire genomes of organisms to study evolutionary relationships. Major Functions of proteins: Enzymes- catalytic proteins Defensive proteins (e.g., antibodies) Hormonal and regulatory proteins- control physiological processes Receptors proteins- receive and respond to molecular signals Storage proteins store amino acids Structural proteins- physical stability and movement Transport proteins carry substances (e.g., hemoglobin) Genetic regulatory proteins- regulate when, how, and to what extent a gene is expressed Protein monomers are amino acids. Amino and carboxylic acid functional groups give amino acids both acidic and basic properties. The R group differs for each amino acid and gives the amino acid its individual properties. Cysteine side chains can form covalent bonds- a disulfide bridge, or disulfide bond. Oligopeptides or peptides- short polymers of 20 or fewer amino acids (some hormones and signaling molecules) Polypeptide or proteins range in size form insulin, which had 51 amino acids, to huge molecules such as the muscle protein titin, with 34,350 amino acids. Primary Structure of a protein- the sequence of amino acids Tertiary Structure- polypeptide chain is bent and folded; results in the definitive 3-D shape. The outer surfaces present functional groups that can interact with other molecules. Interactions between R groups determine tertiary structure. Disulfide bridges hold a folded polypeptide together Hydrogen bonds stabilize folds Hydrophobic side chains can aggregate Van Der Waals interactions between hydrophobic side chains Ionic interactions form salt bridges Secondary and Tertiary Protein Structure derive from primary structure. Denaturing- heat or chemicals are used to disrupt weaker interactions in a protein, destroying secondary and tertiary structure. In many cases, the protein can return to normal when cooled because all the information needed to specify the unique shape is contained in the primary structure. Factors that can disrupt the interactions that determine protein structure (denaturing): Temperature + Concentration of H High Concentrations of polar substances Nonpolar substances Living systems depend on reactions that occur spontaneously, but at very slow rates. Catalysts- substances that speed up reactions without being permanently altered. No catalyst makes a reaction occur that cannot otherwise occur. Most biological catalysts are proteins (enzymes); a few are RNA molecules (ribozymes). Enzymes lower the activation energy- they allow reactants to come together and react more easily. Example: a molecule of sucrose in solution may hydrolyze in about 15 days; with sucrose present, the same reaction occurs in 1 second. Enzymes are highly specific—each one catalyzes only one chemical reaction. Reactants are substrates: they bind to a specific site on the enzyme—the active site. Specificity results from the exact 3D shape and chemical properties of the active site. Enzyme-Substrate Complex (ES)- held together by hydrogen bonding, electrical attraction, or temporary covalent bonding. E + S = ES= E+P The enzyme is not changes at the end of the reaction Enzymes may use one or more mechanisms to catalyze a reaction: Inducing Strain- bonds in the substrate are stretched., putting it in an unstable transition state. Substrate Orientation- substrates are brought together so that bonds can form. Adding chemical groups- R groups may be directly involved in the reaction Some Enzymes require ions or other molecules in order to function: Cofactors- inorganic ions Coenzymes add or remove chemical groups from the substrate. They can participate in many different reactions. Prosthetic groups (non-amino acid groups)- permanently bound to their enzymes. Rates if catalyzed reactions: -There is usually less enzyme than substrate present, so reaction rate levels off when the enzyme becomes saturated. Saturated- all enzyme molecules are bound to substrate molecules. WILL NEED TO KNOW FOR TEST Maximum rate is used to calculate enzyme efficiency-molecules of substrate converted to product per unit of time (turnover). *It ranges from 1 to 40 million molecules per second! * Homeostasis- the maintenance of stable internal conditions. Cells can regulate metabolism by controlling the amount of an enzyme. Cells often have the ability to turn synthesis of enzymes off or on and in many cases turn the enzyme on or off. Protein kinases are enzymes that regulate responses to the environment by organisms. They are subject to allosteric regulation The active form regulates the activity of other enzymes, by phosphorylating allosteric or active sites on other enzymes. Allosteric Regulation- non substrate molecules binds a site other than the active site (the allosteric state) The enzyme changes shape, which alters the chemical attraction (affinity) off the active site for the substrate. Allosteric regulation can activate or inactivate enzymes. Enzyme-catalyzed reactions are part of metabolic pathways- the products of one reaction is a substrate for the next Metabolic pathways: The first reaction is in the commitment step- other reactions then happen in sequence. Feedback inhibition (end-product inhibition)- the final product acts as a noncompetitive inhibitor of the first enzyme, which shuts down the pathway. pH affects enzyme activity: + Acidic side chains generate H and become anions. + Basic side chains attract H and become cations. Example: Glutamic acid---COOH Glutamic acid---COO + H + The law of mass action—the higher the H + concentration, the more reaction is driven to the left to the less hydrophilic form. This can affect enzyme shape and function. Protein tertiary structure (and thus function) is very sensitive to the concentration of H (pH) in the environment, All enzymes have an optimal pH for activity. Temperature affects enzyme activity: Warming increases rates of chemical reactions, but if temperature is too high, non-covalent bonds break and inactivate enzymes. All enzymes have an optimal temperature for activity. Isozymes- catalyze the same reaction but have different composition and physical properties. Isozymes may have different optimal temperatures or pH, allowing an organism to adapt to changes in its environment. Aspirin binds to and inhibits the enzyme cyclooxygenase. Cyclooxygenase--catalyzes the commitment step for metabolic pathways that produce: Prostaglandins--involved in inflammation and pain Thromboxanes—stimulate blood clotting and constriction of blood vessels. Aspirin binds at the active site of cyclooxygenase and transfers an acetyl group to a serine residue. Serine becomes more hydrophobic, which changes the shape of the active site and makes it inaccessible to the substrate.