Biomolecules Study Documents

What is an enantiomer? Non-superimposable mirror image What is a Epimer Sugar which differs by a single carbon atom What are Diasteriosmers? Molecules with multiple chiral centres Sugar with an aldehyde group + 6 carbons = Aldohexose Sugar with a ketone group + 6 carbons = ketohexose Reference to the direction the hydroxyl group attached to the chiral carbon furthest away from the aldehyde/ketone Difference between L and D Carbohy- group faces drates? D = OH right L = OH left Alpha Glucose If C1 and C6 on the same side of the sugar ring then OH pointing down Beta Glucose If C1 and C6 are on the same side of the sugar ring then OH pointing across Which bonds hold together individual monosaccharides in polysaccharides? Glycodisic Bonds What is Agar made of? Agarose and Agaropectin Disaccharide 2 monosaccharides Oligosaccharides 3 - 20 monosaccharides Polysaccharide 21 - 1000 monosaccharides Phosphate comes from ATP hydrolysis How are phosphodiester bonds in DNA formed? Water also produced Main enzymes involved in DNA Replication 1/7 DNA Polymerase I DNA Polymerase II Short single stranded nucleic acid with a free 3' OH What is a primer? Made of RNA Generated by an enzyme called Primase Relationship between pH and pI pH has to be higher than pI for the protein to become negatively charged What is Affinity Chromatography? Beads have region which binds to specific protein Tiny charged beads Anion Exchange Resin - Positive beads bind to them What is ion exchange chromatography? Cation Exchange Resin - Negative beads bind to them Seperates based on charge Gel ranges in pH from top to bottom Isoelectric focussing This means that the proteins flow through it until the pH = pI which makes the net charge 0 seperates proteins based on pI What is Reverse Phase Chromatography? Hydrophobic molecules adsorb to the hydrophobic beads Polar molecules dont stick to the beads and quickly move down the column Distance moved by sample / Distance moved by solvent How to calculate Rf value 2/7 Start with SDS PAge Put into a Western Transfer Sandwich Stack gel with Nitrocellulose of PVDV Membrane Either side are filter paper or sponges What is Western Blotting? Activate electric field All protein are negative because of SDS Protein goes towards positive electrode based on molecular mass For identification What is ELISA Use of antibodies to detect and quantify a protein in solution What is Beers Law Light absorbtion proportional to the number of absorbing molecules (concentration) What is Lamberts Law? Light absorption proportional to path legend What is spectrometry measured using Spectrophotometer A = Absorbance C = Concentration A=CxExL E = Extinction Coefficient L = Pathlength (normally 1cm) What is the Matrix? Material packed into the column What is the Eluant What comes out of the column relies on porous beads; larger molecules What is size exclusion chromatography? elute first because they are not trapped in small pores 3/7 What is Electrophoresis the movement of charged particles in a fluid or gel under the influence of an electric field. Speed = V E = Strength of the Electric Field V = Ez/f Z = Net Charge of the molecule F = Frictional Coefficient (drag) Agarose and Polyacrylamide Which gels are electrophoresis carried out in? form a mesh Why are primers needed for DNA repli- DNA polymerase can only add nucation? cleotides to an existing chain with an OHWhat is the Okazaki fragment? Fragments of DNA on lagging strand during DNA replication by polymerase 3 What do telomeres do? Protect ends of chromosomes from nucleases and maintain the integrity of linear chromosomes What does Amphipathic mean? both hydrophobic and hydrophilic What is pKa pH at which a molecule can become protonated What is a Sphingolipids Backbone is sphingosine Alpha Glucose Beta Glucose 4/7 Which bonds hold Amino Acids together peptide bonds Which bond holds ATP together How to calculate Vmax from a graph Y intercept = 1/Vmax What units used for Vmax Same units as the y intercept How to calculate Km from a graph X intercept = -1/Km Gradient = Km / Vmax Spontaneous 3 ways to damage DNA Endogenous Factors (inside cell) Exogenous Factors (environment) Hydrolytic Depurination Examples of Spontaneous DNA Damage Hydrolytic Deamination of Bases Use of water to lose a purine base from DNA What is Hydrolytic Depurination? Leaving just the sugar phosphate backbone What is Hydrolytic Deamination of bases Use of water to remove the amine group (NH3) Cytosine -> Uracil Deaminated version of Adenine Hypoxanthine Deaminated version of Guanine Xanthine Deaminated version of Cytosine Uracil Deaminated version of Thymine no deamination 5/7 Excision and Elimination of the damaged nucleotide DNA polymerase fills the gap using the other strand as template Mechanisms to correct DNA damage Nick in the DNA strand is healed by a DNA ligase If concentration is doubled the Vmax ,,,, Vmax doubles If concentration doubles the Km .... Km remains constant Plasmid is linearised or cut Piece of foreign DNA is ligated to cut ends of the plasmid Process of Gene Cloning Recombinant plasmid is inserted into bacteria = transformaton Bacterial colonies screened for presence of recombinant plasmid What is a vector containing a foreign DNA called recombinant DNA What is Allostery The binding of a ligand to one site on the protein which affects the binding properties of another site on the same protein What is Cooperativity can occur in multimeric assemblies. The binding of one ligand affects the affinities of any remaining unfilled ligand binding sites. Give sigmoidal binding curve What is Degeneracy more than one codon for each amino acid Only one start codon What is Methionine AUG 6/7 UAA Stop Codons include UAG UGA 7/7