bio 151 exam 2 Questions And Answers

Operon - ANS the promotor and the repressor binding site. An operon is a group of genes that are transcribed together that are in the same pathway. Almost exclusively in prokaryotes transcription factor - ANS activators Activators - ANS a type of transcription factor, Activators can work synergistically, Activators bind to the enhancers and turn on genes, Activator is a protein, enhancer is DNA, Activator comes to bind to the enhancer and helps to unwind the DNA from the histone making it more available to the TF. repressor - ANS Equivalent to a road block. Chromatin - ANS The complex of DNA and proteins mainly histones, that compose eukaryotic chromosomes. Highly compact: heterochromatin. Loosely coiled: Euchromatin. Regulon - ANS a large set of genes in a bacteria that are controlled by a single type of reulatory molecule. Regulon genes are transcribed in response to environmental cues and allow cells to respond to changing environments. Constitutive - ANS Always occurring; always present. Commonly used to describe enzymes and other proteins that are synthesized continuously. Histone - ANS one of several positively charged proteins associated with DNA in the chromatin of eukaryotic cells. DNA wraps around histones positive - ANS turns on transcription; the ligand comes to the activator and lands on the which turns on RNA polymerase which then starts transcribing; Activator and ligand are specific to each other. ; Activator is a protein; Ligand is for example maltose, etc, a sugar; Expressed only when an activator is present regulatory protein binds to activator and turns it on - activator turns on; When system just turns a gene on; Activator binds to enhancer site telling the polymerase to go bind there Negative inducible - ANS Both make the protein in response to the ligand; Repressor is like a road block and the ligand removes the blockade; Inducible: turned off unless some metabolite present regulatory- activator derepresses expression; Normally off but gets turned on in response to some ligand; example: The lactose gene is turned on when there is no glucose present Negative Repressible - ANS Turned off by product of transcription or metabolite: constitutive expression; Binds to repressor and shuts it off. ; Normally on; Example: when theres e coli is always producing tryp but when there is so much tryp around it doesn't have to so it is turned off. Positive has an activator negative has a repressor How is replica plating used to understand biosynthetic pathways? - ANS You can see exactly where there is a problem in producing the protein. Why? A repressor protein can't bind the ligand. The repressor protein is not expressed An enzyme in the synthesis pathway is not expressed. Where do RNA polymerase and sigma fit into transcriptional control? - ANS Promotor is where the sigma factor bind They both regulate transcription, something must keep them from transcribing Barr Body - ANS In women one of the x's in every cell is turned into heterochromatin and not transcribed. Barr Body, (tightly wound. As tightly wound as possible) basal transcription factors - ANS Like sigma or a ligand. Enhancer - ANS activator binds to the enhancer. Enhancer is DNA What is the difference between an activator and an enhancer? - ANS Activators bind to the enhancers and turn on genes Activator is a protein, enhancer is DNA Activator comes to bind to the enhancer and helps to unwind the DNA from the histone making it more available to the TF Catabolic pathways - ANS Catabolic pathways are inducible. (because you don't need to be running it all the time) breaking things down. Catabolism refers to chemical reactions that result in the breakdown of more complex organic molecules into simpler substances. Catabolic reactions usually release energy that is used to drive chemical reactions. Anabolic pathways - ANS Anabolic pathways tend to be repressible. Always making it unless theres lots around. Like if theres lots of triptiphan around then e coli stop making it, therefore it is repressible. Anabolism refers to chemical reactions in which simpler substances are combined to form more complex molecules. Anabolic reactions usually require energy. Anabolic reactions build new molecules and/or store energy. polymer - ANS Any long molecule composed of small repeating units (monomers) bonded together. The main biological polymers are proteins, nucleic acids, and polysaccharides. Monomer - ANS a small molecule that can covalently bind to other similar molecules to form a larger macromolecule. Macromolecule - ANS any very large organic molecule, usually made up of smaller molecules (monomers) joined together into a polymer. The main biological macromolecules are proteins, nucleic acids, and polysaccharides. peptide bond - ANS The covalent bond formed by a condensation reaction between two amino acids; links the residues in peptides and proteins. Condensation Reaction - ANS A chemical reaction in which two molecules are joined covalently with the removal of an -OH from one and an -H from another to form water. Also called a dehydration reaction. Hydrolysis - ANS A chemical reaction in which a molecule is split into smaller molecules by reacting with water. In biology, most hydrolysis reactions involve the splitting of polymers into monomers. Dimer - ANS An association of two molecules that may be identical (homodimer) or different (heterodimer) Trimer - ANS a polymer comprised of 3 monomer units Amphiphillic - ANS having both hydrophilic and hydrophobic parts (polar and nonpolar) How is the amino carboxyl directionality similar to the 5'-3' directionality of DNA and how is it different? Is there always a match between 5' -3' and N-C. - ANS Yes it is similar to the directionality of DNA. There is a start end, which is N-terminus and a finish end which is C-terminus. There is always a match between 5'-3' and N-C Polar - ANS Polar, charged, side chains interact readily with water, hydrophilic, meaning they dissolve in water easily nonpolar - ANS Nonpolar side change lack charged or highly electronegative atoms capable of forming hydrogen bonds with water, hydrophobic, meaning they coalesce in water. acidic or basic - ANS If the side chain has a negative charge it is acidic, if it has a positive charge it is basic. If it is uncharged and has an oxygen the electronegative oxygen with result in a polar covalent bond and thus is uncharged polar. How is protein hydrophobicity affected by the amino acids in the protein? - ANS If the amino acid is polar it interacts readily with water and dissolves, it is hydrophilic. If the amino acid is nonpolar it coalesces in water, hydrophobic. What does protein hydrophobicity tell you about the protein's function? Does it matter where it is hydrophobic? - ANS It tells you where the protein might be located. What determines the shape of the protein - ANS The amino acids, how many and in what order. The hydrophobicity and it's hydrogen and sulfur bonds. How many B-sheets and a-helixes. Also how many different strands of amino acids come together. Can we predict the shape of a protein? - ANS We cannot predict how a protein is going to fold, but all of the same proteins are going to fold the same way. What type of bond forms between which molecules to allow for a helix or beta sheet. - ANS Whether it is a helix or a beta sheet depends on the amino acids but the bonds that form between them are hydrogen bonds. What is meant by protein folding and how can it go wrong? - ANS The 4 levels of protein folding. There are different bonds that connect the proteins in different places for each of the levels of bonds. Proteins can misfold.