Scientists Learn the Ropes on Tying Molecular Knots
|
|
- Buck James
- 5 years ago
- Views:
Transcription
1 Scientists Learn the Ropes on Tying Molecular Knots As chemists tie the most complicated molecular knot yet, biophysicists create a periodic table that describes what kinds of knots are possible. By Jordana Cepelewicz Olena Shmahalo/; Source: David Leigh Through directed self-assembly techniques, chemists are making tiny molecular knots in their labs. The illustration portrays the structure of a five-crossing knot synthesized in The world is tied up in knots. They form spontaneously in swirling vortices of smoke, in long strands of yarn or hair, and in the earbud cords that somehow always tangle in one s pocket. Even down at the molecular scale, they appear in the long chains making up some proteins, and when they arise in DNA s twists and coils, enzymes have to help unwind them. Biophysicists study these knots to figure
2 out how they get there and how they contribute to the behavior of those molecules. Chemists, meanwhile, have turned their attention to molecular knots of their own making: smaller synthetic constructions assembled from joined fragments rather than tied in a single continuous biomolecular string. In their labs, they have been painstakingly synthesizing such tiny knots, achieving escalating levels of intricacy, with the hope of eventually exploiting the knots unique topologies in new nanotools, pharmaceuticals and novel materials with desirable properties. The most recent and most complex knot to join these ranks, a composite structure fashioned out of three simpler knots, was reported last month in Nature Chemistry and took years to build. In August, other researchers published a theoretical paper in Nature Communications that tabulated which knots chemists should seek to make next. They hope the work will provide insights into what governs the ability of small artificial knots to assemble themselves spontaneously and help them to get a handle on just how complicated such knots can be. And despite the significant differences between those designs and the knots found in DNA and proteins, some scientists think that analyzing the synthetic systems could eventually inform the understanding of knotting in biological contexts, too. Knot Zoos in the Lab To mathematicians, a knot means something like an ordinary knot tied in string, only the string s ends are then attached so that the tangle can t wiggle loose. More formally, it s a closed curve, embedded in three-dimensional space, that does not intersect itself and cannot be reduced to a simple loop. Knots can be represented as planar projections, two-dimensional drawings with crossings where one part of the thread goes over or under another. Two knots are considered the same if one can be shifted and rotated to form the other without altering its fundamental topology. Lucy Reading-Ikkanda/ Mathematicians classify knots by ordering them according to their minimum number of crossings. After the unknot (a circle) comes the simplest knot, one with three crossings, known as a trefoil. (Knots with one or two crossings are topologically equivalent to the unknot.) Next, there s one with
3 four crossings, two with five crossings, three with six crossings, seven with seven crossings. Those numbers then explode: There are 165 knots with 10 crossings, and for 16 crossings, there are more than a million. Moreover, knots can be connected to one another in specific ways to form composite knots. Chemists want their own creations to attain some of that complexity, but the going has been slow. They manufactured the first molecular knot the trefoil in 1989, and for decades, that was it. That seemed to us an unsatisfactory state of affairs, said David Leigh, a chemist at the University of Manchester in England. Just as in the world of fishermen or climbers, [where] different knots have different functions, the same is true in the molecular world.
4
5 University of Manchester David Leigh, a chemist at the University of Manchester, and his colleagues have synthesized some of the most complex molecular knots to date, including a composite one with nine-crossings. Being able to build more complicated knots will, at the least, help researchers to probe how knots affect the strength, flexibility and other features of materials, and to determine which ones are best suited to which purposes. Some experts foresee a future in which knots might be woven together to form functional materials with heat-resistant or catalyzing properties. Others hope to one day use microscopic knots as nests for the safe transport of drug molecules or other minute cargo. Creating molecular knots is the best way chemists can show they ve really mastered the molecular laws, said Cristian Micheletti, a computational biophysicist at the International School for Advanced Studies in Italy, and the leader of the team that published the Nature Communications paper. It s like an intellectual playground on which researchers can test their mettle. And so Leigh and others have been making more elaborate kinds of knots, using specially designed fragments and an ionically charged molecular scaffold that can position them for joining. In this way, Leigh most recently succeeded in building the two most complex knots to date: an eight-crossing knot, and a composite, nine-crossing one. He s currently applying the same strategy to synthesize new configurations. Ideally, however, scientists would be able to explore such configurations more systematically through an understanding of general knotting patterns and principles of directed self-assembly. That s what Micheletti and his colleagues set out to make possible. A New Knot Table Micheletti s team wanted to investigate which knots could be synthesized most easily. They used simple computational models to stitch three, four or five identical fragments of a helix together into closed chains, then moved the fragments around without breaking their connections. In this way, the researchers generated thousands of potential configurations. They then identified which kinds of knots had appeared, and picked out those that had a certain degree of symmetry something common to the handful of molecular knots that chemists have been able to create so far.
6 Courtesy of Cristian Micheletti Cristian Micheletti in Trieste, Italy, home to the International School for Advanced Studies. There, he does research on the formation of knots in biological and synthetic contexts. Recently, he and his team published work predicting which new knots might be made most easily through directed self-assembly. That left them with only a small repertoire of knots knots that in further simulations did indeed self-assemble more frequently. Among them were most of the knots that had been made experimentally to date, as well as new candidates for synthesis that included a 10-crossing and a 15crossing knot. Most noteworthy, though, was the discovery that simpler knots are not always easier to make. The next knot to appear after five crossings, for instance, did not contain six crossings but rather eight. The researchers realized that adding crossings sometimes lent a knot symmetry that would make it easier to synthesize. That was the case for one of the eight-crossing knots that the work uncovered: It is topologically equivalent to one with four crossings but the four-crossing version is more difficult to make. Working from another way of representing the knots in two dimensions, called braid diagrams (which highlight cyclical aspects of how a thread gets twisted into a knot), Micheletti and his team were able to generalize their findings to larger numbers of building blocks and greater degrees of interwovenness. This in turn allowed the researchers to design a new kind of reference table for knots.
7
8
9
10 Lucy Reading-Ikkanda/; Source: DOI: /s z Micheletti acknowledges that his knot zoo makes certain assumptions that limit its scope for example, that the knots will consist only of identical building blocks. Still, his work can start to guide chemists further synthesis efforts. That goes for other theoretical efforts as well. One group, led by Ivan Coluzza, a computational biophysicist who studies protein folding at the Basque Foundation for Science in Spain, is using Micheletti s work as a reference in tests of how adding new sequences of amino acids to protein-like models affects the fundamental spectrum of knots that arise in them. The work, published earlier this month, has suggested that knotted backbones are so rare in proteins because of the number of amino acid types available for use: With a 20-letter alphabet at their disposal, proteins are less likely to form knots spontaneously than they are when their alphabet consists of only, say, three letters. A Biological Playground By continuing to put together a diverse array of knots in the lab, it may be possible to determine how knots self-assemble, and what the knots do to the properties of synthesized strands. And just maybe, some of those insights could one day help biophysicists learn about what knots are doing in DNA, proteins or other molecules in which they naturally emerge. (Some researchers, for instance, suspect that knots confer greater stability to the small number of proteins in which they re found, but they have yet to prove it.) It s important to emphasize that the self-assembly processes Leigh and Micheletti use are quite different from those that produce biomolecules in nature. Experimentally or computationally, Leigh and Micheletti paste together short pieces of material to attain their knots, and the geometry of those pieces constrains what can form. In contrast, biological knots form when a full-length string of nucleotide bases in DNA, for example, or amino acids in a protein bends and threads through itself to create any of a massive number of structures. Nevertheless, Leigh and his colleagues hope that their synthetic work once it s reached a sufficient level of complexity could improve scientists understanding of knotting in biology. At the very least, by identifying these knots that are more likely to occur it gives us biologists something to look for, said Lynn Zechiedrich, a molecular biologist who studies the structure and function of DNA at the Baylor College of Medicine. With current imaging technology, after all, it s been difficult to confirm the structures of very complicated biological knots. Take uncondensed chromosomes, which look like a tangle of spaghetti: They might harbor these hugely complicated knots [from Micheletti s table], Zechiedrich said. It s just that we don t have the resolution to see it. Micheletti s showing that there are simple ways of creating relatively complex knots. And this might give us a hint that perhaps nature can be using similar ways to create knotted molecules, added Piotr Szymczak, a theoretical physicist at the University of Warsaw. It could also provide information about whether it s possible to get more complex topologies in the natural world. Just how intricately shaped can a knot system be and still self-assemble, and does it appear in biomolecules as well? Leigh, for one, may already be starting to see some hints emerge in his artificial systems (though he
11 cautions that those results have yet to be tested in biological systems). For example, he and his team have observed a correlation between the tightness of knots and how pronounced their chirality, or handedness, is (some knots are chiral, meaning that they can never be rotated or shifted to look exactly like their mirror image). Moreover, in 2016, they constructed a five-crossing knot that could speed up chemical reactions. In its unknotted form, the molecule was unable to act as a catalyst, which demonstrates the powerful effects that knots can have in chemistry and that they may have in biology as well. Some DNA can supercoil, for instance, the way a coiled telephone cord can twist upon itself. Supercoiling has been an object of research for how it might affect the behavior of DNA Zechiedrich thinks that in some cases (at least in bacteria), knots and supercoils that don t get untangled are highly susceptible to mutations yet chemists haven t been able to make knots with that supercoiled property to study it in more detail. But that may change. Leigh s nine-crossing knot shares some key characteristics with supercoiled DNA. So by studying these [composite knots] and understanding them in the simple control systems we make, we may be able to develop some insights into what s happening at the molecular level with supercoiled DNA structures, Leigh said. Not everyone agrees. Micheletti himself is skeptical about extrapolating from the synthetic knots to biological ones. Sophie Jackson, a chemist at the University of Cambridge in England who studies knotted proteins, also thinks that the fact that the synthetic knots are made by such a different process means they can t tell us much about those in DNA and other biomolecules. But it s still early days, Leigh said. We ve made only a few different sorts of knots, and have seen only a few different sorts of properties. I think it s always interesting, Zechiedrich added, to push the boundaries and see what else is out there.
Tiny Knots, Untold Possibilities
FILED UNDER: CHEMICAL STRUCTURE AND PROPERTIES OF MATTER DNA/RNA MATERIALS SCIENCE (CHEMISTRY) MATERIALS SCIENCE (TECHNOLOGY) MICRO AND NANOTECHNOLOGY Tiny Knots, Untold Possibilities by Timothy Erick
More informationKnots, Coloring and Applications
Knots, Coloring and Applications Ben Webster University of Virginia March 10, 2015 Ben Webster (UVA) Knots, Coloring and Applications March 10, 2015 1 / 14 This talk is online at http://people.virginia.edu/~btw4e/knots.pdf
More informationQuiz 07a. Integers Modulo 12
MA 3260 Lecture 07 - Binary Operations Friday, September 28, 2018. Objectives: Continue with binary operations. Quiz 07a We have a machine that is set to run for x hours, turn itself off for 3 hours, and
More informationKnot Just Another Math Article
Knot Just Another Math Article An Introduction to the Mathematics of Knots and Links BY ROBIN KOYTCHEFF Take a string, such as a loose shoelace, tie it up in some manner and then tape the two ends together
More informationBis2A: 2.3 Interpreting Chemical Reactions
OpenStax-CNX module: m59229 1 Bis2A: 2.3 Interpreting Chemical Reactions The BIS2A Team This work is produced by OpenStax-CNX and licensed under the Creative Commons Attribution License 4.0 Abstract This
More informationBackground: Comment [1]: Comment [2]: Comment [3]: Comment [4]: mass spectrometry
Background: Imagine it is time for your lunch break, you take your sandwich outside and you sit down to enjoy your lunch with a beautiful view of Montana s Rocky Mountains. As you look up, you see what
More informationResilient Knots and Links as Form-Finding Structures
Bridges 2011: Mathematics, Music, Art, Architecture, Culture Resilient Knots and Links as Form-Finding Structures Dmitri Kozlov Research Institute of Theory and History of Architecture and Town-planning
More informationLesson Overview The Structure of DNA
12.2 THINK ABOUT IT The DNA molecule must somehow specify how to assemble proteins, which are needed to regulate the various functions of each cell. What kind of structure could serve this purpose without
More informationBackground: Imagine it is time for your lunch break, you take your sandwich outside and you sit down to enjoy your lunch with a beautiful view of
Background: Imagine it is time for your lunch break, you take your sandwich outside and you sit down to enjoy your lunch with a beautiful view of Montana s Rocky Mountains. As you look up, you see what
More informationCombinatorial approaches to RNA folding Part I: Basics
Combinatorial approaches to RNA folding Part I: Basics Matthew Macauley Department of Mathematical Sciences Clemson University http://www.math.clemson.edu/~macaule/ Math 4500, Spring 2015 M. Macauley (Clemson)
More informationfile:///biology Exploring Life/BiologyExploringLife04/
Objectives Identify carbon skeletons and functional groups in organic molecules. Relate monomers and polymers. Describe the processes of building and breaking polymers. Key Terms organic molecule inorganic
More informationAmount of Substance and Its Unit Mole- Connecting the Invisible Micro World to the Observable Macro World Part 2 (English, mp4)
Amount of Substance and Its Unit Mole- Connecting the Invisible Micro World to the Observable Macro World Part 2 (English, mp4) [MUSIC PLAYING] Instructor: Hi, everyone. Welcome back. I hope you had some
More informationNotes Chapter 4 Cell Reproduction. That cell divided and becomes two, two become four, four become eight, and so on.
4.1 Cell Division and Mitosis Many organisms start as one cell. Notes Chapter 4 Cell Reproduction That cell divided and becomes two, two become four, four become eight, and so on. Many-celled organisms,
More informationMODULE 2: BIOLOGICAL MOLECULES
PEER-LED TEAM LEARNING INTRDUCTRY BILGY MDULE 2: BILGICAL MLECULES JSEP GRISWLD, + DEAN STETLER,* AND MICAEL GAINES, ( + City College of New York, *University of Kansas, Univ. of Miami;) I. Introduction
More informationMr. Carpenter s Biology Biochemistry. Name Pd
Mr. Carpenter s Biology Biochemistry Name Pd Chapter 2 Vocabulary Atom Element Compound Molecule Ion Cohesion Adhesion Solution Acid Base Carbohydrate Monosaccharide Lipid Protein Amino acid Nucleic acid
More informationTopic 6 Cell Cycle and Mitosis. Day 1
Topic 6 Cell Cycle and Mitosis Day 1 Bell Ringer (5 minutes) *pick up worksheet by the door* Get out your homework and answer these questions on the back page: What do I need to do to pass my real EOC?
More informationReceptor Based Drug Design (1)
Induced Fit Model For more than 100 years, the behaviour of enzymes had been explained by the "lock-and-key" mechanism developed by pioneering German chemist Emil Fischer. Fischer thought that the chemicals
More informationQuantum Groups and Link Invariants
Quantum Groups and Link Invariants Jenny August April 22, 2016 1 Introduction These notes are part of a seminar on topological field theories at the University of Edinburgh. In particular, this lecture
More informationENZYME KINETICS AND INHIBITION
ENZYME KINETICS AND INHIBITION The kinetics of reactions involving enzymes are a little bit different from other reactions. First of all, there are sometimes lots of steps involved. Also, the reaction
More informationAn Introduction to Metabolism
An Introduction to Metabolism PREFACE The living cell is a chemical factory with thousands of reactions taking place, many of them simultaneously This chapter is about matter and energy flow during life
More informationNotes Chapter 4 Cell Reproduction. That cell divided and becomes two, two become, four become eight, and so on.
Notes Chapter 4 Cell Reproduction 4.1 Cell Division and Mitosis Many organisms start as. That cell divided and becomes two, two become, four become eight, and so on. Many-celled organisms, including you,
More informationVaughan Jones and Knot Theory A New Zealand Mathematician Unravels a New Invariant which links Diverse Sciences in an Unforeseen Thread
NZMS Newsletter 37 August 1986 CENTREFOLD Vaughan Jones and Knot Theory A New Zealand Mathematician Unravels a New Invariant which links Diverse Sciencen an Unforeseen Thread What is so fascinating about
More informationHonors Biology Reading Guide Chapter 11
Honors Biology Reading Guide Chapter 11 v Promoter a specific nucleotide sequence in DNA located near the start of a gene that is the binding site for RNA polymerase and the place where transcription begins
More information4 HOW DID THE EARTH FORM?
4 HOW DID THE EARTH FORM? New stars and space debris spinning like pizza dough are a couple of the things that explain the formation of solar systems like ours. In this three-part lecture, David Christian
More informationIntroductory Quantum Chemistry Prof. K. L. Sebastian Department of Inorganic and Physical Chemistry Indian Institute of Science, Bangalore
Introductory Quantum Chemistry Prof. K. L. Sebastian Department of Inorganic and Physical Chemistry Indian Institute of Science, Bangalore Lecture - 4 Postulates Part 1 (Refer Slide Time: 00:59) So, I
More informationLIFE SCIENCE CHAPTER 5 & 6 FLASHCARDS
LIFE SCIENCE CHAPTER 5 & 6 FLASHCARDS Why were ratios important in Mendel s work? A. They showed that heredity does not follow a set pattern. B. They showed that some traits are never passed on. C. They
More informationPolynomials in knot theory. Rama Mishra. January 10, 2012
January 10, 2012 Knots in the real world The fact that you can tie your shoelaces in several ways has inspired mathematicians to develop a deep subject known as knot theory. mathematicians treat knots
More informationA Simple Protein Synthesis Model
A Simple Protein Synthesis Model James K. Peterson Department of Biological Sciences and Department of Mathematical Sciences Clemson University September 3, 213 Outline A Simple Protein Synthesis Model
More informationUNIT 5. Protein Synthesis 11/22/16
UNIT 5 Protein Synthesis IV. Transcription (8.4) A. RNA carries DNA s instruction 1. Francis Crick defined the central dogma of molecular biology a. Replication copies DNA b. Transcription converts DNA
More informationMIT BLOSSOMS INITIATIVE
MIT BLOSSOMS INITIATIVE The Broken Stick Problem Taught by Professor Richard C. Larson Mitsui Professor of Engineering Systems and of Civil and Environmental Engineering Segment 1 Hi! My name is Dick Larson
More informationThe Intersection of Chemistry and Biology: An Interview with Professor W. E. Moerner
The Intersection of Chemistry and Biology: An Interview with Professor W. E. Moerner Joseph Nicolls Stanford University Professor W.E Moerner earned two B.S. degrees, in Physics and Electrical Engineering,
More informationCounting Out πr 2. Teacher Lab Discussion. Overview. Picture, Data Table, and Graph. Part I Middle Counting Length/Area Out πrinvestigation
5 6 7 Middle Counting Length/rea Out πrinvestigation, page 1 of 7 Counting Out πr Teacher Lab Discussion Figure 1 Overview In this experiment we study the relationship between the radius of a circle and
More informationCell Division. Genetic info must be copied. Each cell gets a complete copy of that info. It occurs in two main stages:
10-2 Cell Division Key Questions: 1)What is the role of chromosomes in cell division? 2) What are the main events of the cell cycle? 3) What events occur during each of the four phases of mitosis? 4) How
More informationMITOCW enzyme_kinetics
MITOCW enzyme_kinetics In beer and wine production, enzymes in yeast aid the conversion of sugar into ethanol. Enzymes are used in cheese-making to degrade proteins in milk, changing their solubility,
More informationNanobiotechnology. Place: IOP 1 st Meeting Room Time: 9:30-12:00. Reference: Review Papers. Grade: 40% midterm, 60% final report (oral + written)
Nanobiotechnology Place: IOP 1 st Meeting Room Time: 9:30-12:00 Reference: Review Papers Grade: 40% midterm, 60% final report (oral + written) Midterm: 5/18 Oral Presentation 1. 20 minutes each person
More informationHi, my name is Dr. Ann Weaver of Argosy University. This WebEx is about something in statistics called z-
Hi, my name is Dr. Ann Weaver of Argosy University. This WebEx is about something in statistics called z- Scores. I have two purposes for this WebEx, one, I just want to show you how to use z-scores in
More informationWhat Do You Think? Investigate GOALS
Activity 3 Atoms and Their Masses GOALS In this activity you will: Explore the idea of atoms by trying to isolate a single atom. Measure how many times greater the mass of a copper atom is than a magnesium
More information4.2 The Mysterious Electron
2 Chapter 4 Modern Atomic Theory 4.2 The Mysterious Electron Where there is an open mind, there will always be a frontier. Charles F. Kettering (876-958) American engineer and inventor Scientists have
More informationCHEM 181: Chemical Biology
Instructor Prof. Jane M. Liu (SN-216) jane.liu@pomona.edu CHEM 181: Chemical Biology Office Hours Anytime my office door is open or by appointment COURSE OVERVIEW Class TR 8:10-9:25 am Prerequisite: CHEM115
More informationTranslation. Genetic code
Translation Genetic code If genes are segments of DNA and if DNA is just a string of nucleotide pairs, then how does the sequence of nucleotide pairs dictate the sequence of amino acids in proteins? Simple
More informationQuantitative Stability/Flexibility Relationships; Donald J. Jacobs, University of North Carolina at Charlotte Page 1 of 12
Quantitative Stability/Flexibility Relationships; Donald J. Jacobs, University of North Carolina at Charlotte Page 1 of 12 The figure shows that the DCM when applied to the helix-coil transition, and solved
More informationChemical Reactions Chapter 2 L book pages L44 - L73. examples?
Name: Period: Chemical Reactions Chapter 2 L book pages L44 - L73 Vocabulary Word What is this? (definition) What are some examples? What does it look like? (draw a picture or diagram) Physical property
More informationAn Introduction to Mathematical Knots
An Introduction to Mathematical Knots Nick Brettell Postgrad talk, 2011 Nick Brettell (UC) An Introduction to Mathematical Knots Postgrad talk 1 / 18 Outline 1 Introduction to knots Knots and Links History
More informationARTSCIENCE MUSEUM PRESENTS. RICHARD FEYNMAN S CURIOUS LIFE 20 October March 2019 ACTIVITY SHEET
ARTSCIENCE MUSEUM PRESENTS RICHARD FEYNMAN S CURIOUS LIFE 20 October 2018 3 March 2019 ACTIVITY SHEET INTRODUCTION ArtScience Museum is dedicated to the exploration of the interconnection between art,
More informationReaction Rates and Equilibrium
CHAPTER 7 14 SECTION Chemical Reactions Reaction Rates and Equilibrium KEY IDEAS As you read this section, keep these questions in mind: How can you increase the rate of a reaction? What does a catalyst
More informationCIS 2033 Lecture 5, Fall
CIS 2033 Lecture 5, Fall 2016 1 Instructor: David Dobor September 13, 2016 1 Supplemental reading from Dekking s textbook: Chapter2, 3. We mentioned at the beginning of this class that calculus was a prerequisite
More information1. Re-teach Notes Compare Structures of Biomolecules. Compare Dehydration Synthesis and Hydrolysis.
1. Re-teach Notes Compare Structures of Biomolecules. Compare Dehydration Synthesis and Hydrolysis. Carbohydrates 1. Made of sugar units called 2. Classified based on the number of sugar units in total
More informationExhaustive search. CS 466 Saurabh Sinha
Exhaustive search CS 466 Saurabh Sinha Agenda Two different problems Restriction mapping Motif finding Common theme: exhaustive search of solution space Reading: Chapter 4. Restriction Mapping Restriction
More informationGene Switches Teacher Information
STO-143 Gene Switches Teacher Information Summary Kit contains How do bacteria turn on and turn off genes? Students model the action of the lac operon that regulates the expression of genes essential for
More informationCarbon and the Molecular Diversity of Life
Chapter 4 Carbon and the Molecular Diversity of Life PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions
More informationQuantum Socks and Photon Polarization Revision: July 29, 2005 Authors: Appropriate Level: Abstract:
Title: Quantum Socks and Photon Polarization Revision: July 29, 2005 Authors: Appropriate Level: Abstract: Time Required: Equipment: Acknowledgement: Lisa Larrimore, Saikat Ghosh, and George Wolf AP or
More informationMU TRANSPOSOSOME ISABEL DARCY, JOHN LUECKE, AND MARIEL VAZQUEZ
MU TRANSPOSOSOME ISABEL DARCY, JOHN LUECKE, AND MARIEL VAZQUEZ Abstract. xxxx In [PJH], Pathania et al determined the shape of DNA bound within the Mu transposase protein complex using an experimental
More informationLesson Overview. Ribosomes and Protein Synthesis 13.2
13.2 The Genetic Code The first step in decoding genetic messages is to transcribe a nucleotide base sequence from DNA to mrna. This transcribed information contains a code for making proteins. The Genetic
More informationTeaching & Learning Company 1204 Buchanan St., P.O. Box 10 Carthage, IL
Matter and Motion Written by Edward Shevick Illustrated by Marguerite Jones Teaching & Learning Company 1204 Buchanan St., P.O. Box 10 Carthage, IL 62321-0010 Table of Contents Science Action Labs 1: Fun
More informationOctet Rule Mix-and-Match: An Inquiry Activity. by Emily O Loughlin, MAT student, University of Portland
Octet Rule Mix-and-Match: An Inquiry Activity by Emily O Loughlin, MAT student, University of Portland In chemistry classrooms when we begin teaching students about atomic theory and the parts that make
More informationCHEM 121: Chemical Biology
Instructors Prof. Jane M. Liu (HS-212) jliu3@drew.edu x3303 Office Hours Anytime my office door is open CHEM 121: Chemical Biology Class MF 2:30-3:45 pm PRE-REQUISITES: CHEM 117 COURSE OVERVIEW This upper-level
More information4) Chapter 1 includes heredity (i.e. DNA and genes) as well as evolution. Discuss the connection between heredity and evolution?
Name- Chapters 1-5 Questions 1) Life is easy to recognize but difficult to define. The dictionary defines life as the state or quality that distinguishes living beings or organisms from dead ones and from
More informationBerg Tymoczko Stryer Biochemistry Sixth Edition Chapter 1:
Berg Tymoczko Stryer Biochemistry Sixth Edition Chapter 1: Biochemistry: An Evolving Science Tips on note taking... Remember copies of my lectures are available on my webpage If you forget to print them
More informationSecret Link Uncovered Between Pure Math and Physics
Secret Link Uncovered Between Pure Math and Physics An eminent mathematician reveals that his advances in the study of millennia-old mathematical questions owe to concepts derived from physics. By Kevin
More informationClassification of Four-Component Rotationally Symmetric Rose Links
Rose-Hulman Undergraduate Mathematics Journal Volume 18 Issue 1 Article 8 Classification of Four-Component Rotationally Symmetric Rose Links Julia Creager Birmingham-Southern College Nirja Patel Birmingham-Southern
More informationSelf Assembly of Polystyrene Hexagons
Self Assembly of Polystyrene Hexagons Purpose Introduce students to the concept of self assembly Demonstrate effect of different variables applied to a self assembling system in the macro scale and their
More informationModifying natural products: a fresh look at traditional medicine
R&D Solutions for Pharma & Life Sciences INTERVIEW Modifying natural products: a fresh look at traditional medicine In 2014, Professor Dawen Niu was one of three young chemists to win the prestigious Reaxys
More informationNIH Public Access Author Manuscript J Math Chem. Author manuscript; available in PMC 2013 January 01.
NIH Public Access Author Manuscript Published in final edited form as: J Math Chem. 2012 January 1; 50(1): 220 232. doi:10.1007/s10910-011-9907-3. ON THE CHEMICAL SYNTHESIS OF NEW TOPOLOGICAL STRUCTURES
More informationThe Rayleigh Pulse Forming Network
The Rayleigh Pulse Forming Network The ideal power supply for many high current applications is one which supplies a square voltage wave over a short, but predetermined, time. Since these applications
More informationAn Introduction to Metabolism
An Introduction to Metabolism PREFACE The living cell is a chemical factory with thousands of reactions taking place, many of them simultaneously This chapter is about matter and energy flow during life
More informationChapter 17: Chemical Reactions
Chapter 17: Chemical Reactions Section 1: Chemical Formulas and Equations Chemical Equations Balancing Chemical Equations Law of Conservation of Mass Evidences of Chemical Reactions Symbols to represent
More informationBacterial Genetics & Operons
Bacterial Genetics & Operons The Bacterial Genome Because bacteria have simple genomes, they are used most often in molecular genetics studies Most of what we know about bacterial genetics comes from the
More information1. (5) Draw a diagram of an isomeric molecule to demonstrate a structural, geometric, and an enantiomer organization.
Organic Chemistry Assignment Score. Name Sec.. Date. Working by yourself or in a group, answer the following questions about the Organic Chemistry material. This assignment is worth 35 points with the
More informationBME 5742 Biosystems Modeling and Control
BME 5742 Biosystems Modeling and Control Lecture 24 Unregulated Gene Expression Model Dr. Zvi Roth (FAU) 1 The genetic material inside a cell, encoded in its DNA, governs the response of a cell to various
More informationAN OVERVIEW OF KNOT INVARIANTS
AN OVERVIEW OF KNOT INVARIANTS WILL ADKISSON ABSTRACT. The central question of knot theory is whether two knots are isotopic. This question has a simple answer in the Reidemeister moves, a set of three
More informationStrategies for Organic Synthesis
Strategies for rganic Synthesis ne of the things that makes chemistry unique among the sciences is synthesis. Chemists make things. New pharmaceuticals, food additives, materials, agricultural chemicals,
More informationStandards Alignment... 5 Safe Science... 9 Scienti c Inquiry Assembling Rubber Band Books...15
Standards Alignment... 5 Safe Science... 9 Scienti c Inquiry... 11 Assembling Rubber Band Books...15 Earth in Space and Time The Scoop on Stars...17 Telescopes...19 Magnify the Sky...21 Star Samples...27
More informationSection Objectives: Recognize some possible benefits from studying biology. Summarize the characteristics of living things.
Section Objectives: Recognize some possible benefits from studying biology. Summarize the characteristics of living things. The Science of Biology The concepts, principles, and theories that allow people
More informationEVOLUTION ALGEBRA Hartl-Clark and Ayala-Kiger
EVOLUTION ALGEBRA Hartl-Clark and Ayala-Kiger Freshman Seminar University of California, Irvine Bernard Russo University of California, Irvine Winter 2015 Bernard Russo (UCI) EVOLUTION ALGEBRA 1 / 10 Hartl
More informationAP Biology. Proteins. AP Biology. Proteins. Multipurpose molecules
Proteins Proteins Multipurpose molecules 2008-2009 1 Proteins Most structurally & functionally diverse group Function: involved in almost everything u enzymes (pepsin, DNA polymerase) u structure (keratin,
More informationLiving Matter a theoretical physics perspective
Living Matter a theoretical physics perspective Ramin Golestanian Rudolf Peierls Centre for Theoretical Physics A Noy & R Golestanian, Phys Rev Lett (2012) Flexing your genes. DNA flexibility depends on
More informationChapter 4 and Chapter 5. Chapter 5
Chapter 4 and Chapter 5 Summary Chapter 4 The nucleus controls the functions of life. Chromosomes found within the nucleus contain the genes that store the information to make proteins. (4.1) Genetic information
More informationScience 9 Biology. Cell Division and Reproduction Booklet 1 M. Roberts RC Palmer
Science 9 Biology Cell Division and Reproduction Booklet 1 M. Roberts RC Palmer How do all living organisms reproduce and grow? Goal 1: Cell Review Recall and become reacquainted with the structures found
More informationare essentially different? Imagine them as made out of string. No fidgeting with them (without cutting) can make them look identical!
The first Abel Prize has been awarded to Jean-Pierre Serre, one of the great mathematicians of our time. Serre is an Emeritus Professor at the Collège de France in Paris. He has made profound contributions
More informationTable of Contents. Science Action Labs. iii
Table of Contents Science Action Labs 1: Fun with Physical Science..............................5 2: What s the Matter?...................................8 3: The Characteristics of Matter..........................12
More informationAn Introduction to Metabolism
An Introduction to Metabolism I. All of an organism=s chemical reactions taken together is called metabolism. A. Metabolic pathways begin with a specific molecule, which is then altered in a series of
More informationCOMPOSITE KNOT DETERMINANTS
COMPOSITE KNOT DETERMINANTS SAMANTHA DIXON Abstract. In this paper, we will introduce the basics of knot theory, with special focus on tricolorability, Fox r-colorings of knots, and knot determinants.
More informationSuggested solutions for Chapter 14
s for Chapter 14 14 PRBLEM 1 Are these molecules chiral? Draw diagrams to justify your answer. 2 C 2 C Reinforcement of the very important criterion for chirality. Make sure you understand the answer.
More informationAnnouncements. CS 188: Artificial Intelligence Fall Causality? Example: Traffic. Topology Limits Distributions. Example: Reverse Traffic
CS 188: Artificial Intelligence Fall 2008 Lecture 16: Bayes Nets III 10/23/2008 Announcements Midterms graded, up on glookup, back Tuesday W4 also graded, back in sections / box Past homeworks in return
More informationFeynman Says: Newton implies Kepler, No Calculus Needed!
The Journal of Symbolic Geometry Volume 1 (2006) Feynman Says: Newton implies Kepler, No Calculus Needed! Brian Beckman http://weblogs.asp.net/brianbec Abstract: We recapitulate Feynman's demonstration
More informationAP Biology. Metabolism & Enzymes
Metabolism & Enzymes From food webs to the life of a cell energy energy energy Flow of energy through life: Life is built on chemical reactions transforming energy from one form to another organic molecules
More informationAnswer Key. Cell Growth and Division
Cell Growth and Division Answer Key SECTION 1. THE CELL CYCLE Cell Cycle: (1) Gap1 (G 1): cells grow, carry out normal functions, and copy their organelles. (2) Synthesis (S): cells replicate DNA. (3)
More informationWhat Can Physics Say About Life Itself?
What Can Physics Say About Life Itself? Science at the Interface of Physics and Biology Michael Manhart Department of Physics and Astronomy BioMaPS Institute for Quantitative Biology Source: UIUC, Wikimedia
More informationDIFFERENTIAL EQUATIONS
DIFFERENTIAL EQUATIONS Basic Concepts Paul Dawkins Table of Contents Preface... Basic Concepts... 1 Introduction... 1 Definitions... Direction Fields... 8 Final Thoughts...19 007 Paul Dawkins i http://tutorial.math.lamar.edu/terms.aspx
More information1 The fundamental group Topology I
Fundamental group 1 1 The fundamental group Topology I Exercise: Put the picture on the wall using two nails in such a way that removing either of the nails will make the picture fall down to the floor.
More informationHow to use this book. How the book is organised. Answering questions. Learning and using the terminology. Developing skills
How to use this book Welcome to the beginning of your Human and Social Biology course! We hope that you really enjoy your course, and that this book will help you to understand your work, and to do well
More informationThe Origin of Life on Earth
Study Guide The Origin of Life on Earth Checking Your Knowledge You should be able to write out the definitions to each of the following terms in your own words: abiotic Miller-Urey experiment ribozyme
More informationProteins. Division Ave. High School Ms. Foglia AP Biology. Proteins. Proteins. Multipurpose molecules
Proteins Proteins Multipurpose molecules 2008-2009 Proteins Most structurally & functionally diverse group Function: involved in almost everything u enzymes (pepsin, DNA polymerase) u structure (keratin,
More informationChapter 6- An Introduction to Metabolism*
Chapter 6- An Introduction to Metabolism* *Lecture notes are to be used as a study guide only and do not represent the comprehensive information you will need to know for the exams. The Energy of Life
More informationREVISION WORKSHEET (1) Diversity of life Syllabus coverage pgs
United Arab Emirates Abu Dhabi Educational Council Int'l Jubilee Private School American Syllabus Student Name: Grade: 8 a,b Date: / / 2013 Subject: Science Revision REVISION WORKSHEET (1) Diversity of
More informationSlide 1 / Describe the setup of Stanley Miller s experiment and the results. What was the significance of his results?
Slide 1 / 57 1 Describe the setup of Stanley Miller s experiment and the results. What was the significance of his results? Slide 2 / 57 2 Explain how dehydration synthesis and hydrolysis are related.
More informationDescribe how proteins and nucleic acids (DNA and RNA) are related to each other.
Name Date Molecular Biology Review Part 1 IB Papers Topic 2.1 Molecules to Metabolism Living organisms control their composition by a complex web of chemical interactions. Be able to: Explain how molecular
More informationBayes Nets III: Inference
1 Hal Daumé III (me@hal3.name) Bayes Nets III: Inference Hal Daumé III Computer Science University of Maryland me@hal3.name CS 421: Introduction to Artificial Intelligence 10 Apr 2012 Many slides courtesy
More information10.1 Growth and Cell Reproduction
10.1 Growth and Cell Reproduction Growth is a characteristic of all living things. You started out as a single cell. That cell quickly divided into two cells. Two cells became four and four became eight.
More informationFigure 1: Doing work on a block by pushing it across the floor.
Work Let s imagine I have a block which I m pushing across the floor, shown in Figure 1. If I m moving the block at constant velocity, then I know that I have to apply a force to compensate the effects
More information