Large Molecule ~ Small Molecule Interactions Project Times Squared Academy Sorys E. Cepeda Jeffrey Doddio Instructor: Kerri Krawczyk.

Slides:

Advertisements

Similar presentations

What phase of water is most common on Earth?

Advertisements

Orientation to last lab of Gel Scramble. Today’s tasks 1) Match protocols to gels. 2) Explain unexpected data.

Gel electrophoresis The gel electrophoresis method was developed in the late 1960's. It is a fundamental tool for DNA sequencing.

Chemical Bonding Chapter 6 Pages (no Section 4)

Cloning Worksheet Winter 2011 Producing a Standard Curve to Determine DNA Fragment Sizes.

Introduction to Sizing DNA on an Agarose Gel HC 70AL Spring 2009 April 2, 2009 By Kristin Gill.

1% Agarose Gel DNA Electrophoresis Running time : 52 minutes Distance measured from the well to the top of the second band: 4,5 cm Running voltage: 100.

Spectrophotometers Nucleic Acids and Proteins. Nucleic Acids and Spectrophotometer The rings of the bases (A, C, G, T, U) are made up of alternating single.

(2-Hydroxyethyl) Triphenylphosphonium Chloride Large Molecule/Small Molecule Interactions Rhode Island College July 14-18, 2008 Bailey Sarber, Samantha.

T ETRAPHENYLPHOSPHONIUM B ROMIDE (TPP) L ARGE M OLECULE ~S MALL M OLECULE I NTERACTIONS Pilgrim High School Mr. Dubois, Mr. Lobdell C.J. Beneduce, Bryan.

By: C.J. Beneduce Maria Guirguis Amanda Rode Mr. Normand Dubois.

Large Molecule ~ Small Molecule Interactions Projects By the Woonsocket Team: Toni DiMarzio Andrea Harnois Alyshia Johnson Claire Laquerre.

SHEA HIGH SCHOOL July 13-17, 2009 Ms. La Roche Cesar Luzon, Janice Miranda, Maldine Santos, Estefania Tabares.

Triphenyl (2-pyridylmethyl) Phosphonium Chloride Large Molecule – Small Molecule Interactions Rhode Island College July 13 – 17, 2009.

South Kingstown High School Kenny Chappell Trevor Hosley Catherine Jones Andrew Sharkey Stephen Vincelette.

bond formed by the giving or Ionic Bond bond formed by the giving or taking of electrons.

EXPERIMENT OBJECTIVE: The objective of this experiment is to develop an understanding of DNA mapping by determining restriction enzyme cleavage sites.

JOINT PROJECT WITH RHODE ISLAND COLLEGE DEPARTMENT OF PHYSICAL SCIENCES JULY , 2009 Interaction of o-Xylylenebis (triphenylphosphonium bromide) and.

Solving Equations with the Variable on Both Sides

Graphing the Set of All Solutions ~adapted from walch education.

Molecular Geometry and Hybrid Orbitals

Restriction Mapping of Plasmid DNA. Restriction Maps Restriction enzymes can be used to construct maps of plasmid DNA Restriction enzymes can be used.

Gel Electrophoresis Biotech I.

Gel Electrophoresis of DNA

Gel Electrophoresis based on motion of charged molecules in an electric field toward the opposite charge. Agarose gels (for larger fragments of DNA) or.

Molecular Biology Technical Skills. Skills  Micropipetting  Preparing solutions  Working with concentrations  Dilutions  Amounts  Agarose gel electrophoresis.

Aim: How do chemists use molecular geometry to predict polarity? Metallic bonding Polarity of water and "hydrogen bonding“ Water.

Gel Electrophoresis.

Lab.8 8RBs0Ghg_48

Proteomics Module Day 1 Tech talk. Experiment: Yeast protein expression changes caused by H 2 O 2 exposure. ► 2 Control groups (A and B): nothing added.

SPECTROPHOTOMETRY IN BIOTECHNOLOGY

Chapter 2 STRUCTURE AND PROPERTIES OF ORGANIC MOLECULES Chapter 2: Structure and Properties of Organic Molecules Helpful web site:

VSEPR Theory: Molecular Shapes Most shapes are based on a __________________. Examples: CH 4 CCl 4 Removing the top of the tetrahedral makes the ________________.

POTASSIUM BROMIDE Name: Yuki Ng Class: 3A Class Number: 30.

Gel Electrophoresis. Definition – COPY ME! Separation of DNA fragments according to size and charge Based on movement through a gel medium when an.

Gel Electrophoresis.

Molecular Shape and Polarity The Importance of Geometry in Determining Physical Properties.

Gel pictures of cloning lab. Section1 Gel1 3 kb 5 kb 1.6 kb M 1 2 Group1Group2Group3 M: DNA 1Kb ladder; 1: Purified cut vector; 2: Purified insert (CAT.

Electrophoresis 7 th Grade,. Learning Objectives Understanding how electrophoresis facilitates the separation of molecules Be familiar with the types.

Lewis Dot Structure.  Predicts Molecular Structure (Shape)  Looks at Central Atom of the Compound  # Electron pairs,  Bonded  Non-Bonded  Electrons.

Immunodiffusion techniques

Page Gel Electrophoresis gel electrophoresis – moving DNA through a gel medium using an electric current Why can we move DNA with electricity?

Gel Electrophoresis Biotechnology Unit. Principles of Electrophoresis Definition – Process in which particle, DNA, RNA and proteins- or their fragments.

UNI Plant Physiology Measuring Light Absorbance UNI Plant Physiology Spring 2005.

Biochemist’s View of the DNA Double Helix Major groove Minor groove.

Branches of Chemistry & Research. 1)I work in a crime scene investigation lab and determine the composition of an unknown sample. Which branch of chemistry.

SOLUBILITY BASICS. Why do things dissolve?  To understand solubility, it is important to understand why things dissolve. Why some things dissolve and.

Spectrophotometry & Chromatography

Gel electrophoresis.

Agarose Gel Electrophoresis

Restriction Enzyme Digestion of Phage DNA

ExTRacting DNA from C. elegans

Uses of Restriction Enzymes

Small Molecule Large Molecule Interactions

Does TPEOB Interact with DNA?

α-Triphenylphosphonium-p-toluic acid bromide

Polarity within a Molecule

“CTP” cinnamyltriphenylphosphonium chloride

Molecular Biology Working with DNA.

Ch 6 Covalent Compounds What determines whether two atoms will form a bond? How can a hydrogen atom, which has one valence electron, bond with chlorine,

Restriction Digestion and Analysis of Lambda DNA Kit

Electrophoresis Timothy G. Standish, Ph. D..

Agarose gel Electrophoresis

MATTER Definition States/Phases Takes up space Has mass

Chemistry 11 Matter.

Molecular Biology Working with DNA.

Gel Electrophoresis Ms. Cuthrell.

Gel Electrophoresis Analysis

Presentation transcript:

Large Molecule ~ Small Molecule Interactions Project Times Squared Academy Sorys E. Cepeda Jeffrey Doddio Instructor: Kerri Krawczyk

p-Xylylene bis (triphenyl phosphonium bromide) “PTPB” C 44 H 38 Br 2 P 2 Structure: – Size u – Non Planar, Aromatic. – Hazards: Irritant- Irritable to eyes, skin, and respiratory system. Physical Properties: – mp->300°C – Water Soluble Uses: This compound was created because it could be the possible solution to problems that chemists find.

Salmon DNA Melting using Cary Spectrophotometer Melting Point: Native DNA- 57°C DNA + PTPB-65°C

Salmon DNA Melting using Cary Spectrophotometer Melting Point: Native DNA- 57°C DNA + PTPB- 63°C

Salmon DNA Melting using Bio-Rad Smart Spec Plus Melting Point: Native DNA-49°C DNA + PTPB- 57°C

Salmon DNA Melting using Bio-Rad Smart Spec Plus Melting Point: Native DNA- 51°C DNA + PTPB- 64°C

Electrophoresis WELL # 7-XB28 6-XB20 5-X 4-Ladder 3-EB28 2-EB20 1. E Band # Distance Traveled (cm) Est. Size (Base Pairs) Est. Mass (ng) Linearized DNA Uncut Plasmid DNA

Electrophoresis Distance(cm)# of Base PairsMass (ng)

HyperChem This is our compound, “PTPB”, via HyperChem

HyperChem Predictions HyperChem Energy Minimizations TestProgramAlgorithmOrientationRandomG/C RichA/T Rich PTPB in Major Groove AmberPolak-RibiereX PTPB in Major Groove AmberPolak-RibiereY PTPB in Major Groove AmberPolak-RibiereZ PTPB in Minor Groove AmberPolak-RibiereX PTPB in Minor Groove AmberPolak-RibiereY PTPB in Minor Groove AmberPolak-RibiereZ

HyperChem Predictions We have discovered that our compound prefers Y-Orientation because the energy once in the DNA was the least.

HyperChem Predictions We have also discovered that our compound dislikes X-Orientation, because the energy once in the DNA was the greatest.

Discussion After having tried four different concentrations in two different Gel Electrophoresis experiments, there were no changes seen in the migration of the DNA through the gels. The DNA in the HyperChem showed possible binding with PTPB in the Y- Orientation in the minor groove with random DNA. The Cary Spectrophotometer and the Smart Spec Plus did show a shift in the melting curve when the Salmon Testes DNA was combined with PTPB. In the future, we would like to duplicate the experiments to confirm/ compare results. If the experiment was repeated with the Smart Spec Plus, a different cuvette holder should be used to eliminate the possibilities of spills and the cuvette tilting over.

Special Thanks.. We would just like to say thanks to Dr. Tiskus, Dr. Williams, all those who helped plan this program, and Rhode Island College for giving us this opportunity. We know we will use the skills gained here in the future, and this program has benefited us tremendously. THANK YOU!!!!