Lecture 15: Realities of Genome Assembly Protein Sequencing

Size: px
Start display at page:

Download "Lecture 15: Realities of Genome Assembly Protein Sequencing"

Transcription

1 Lecture 15: Realities of Genome Assembly Protein Sequencing Study Chapter Euler s Theorems A graph is balanced if for every vertex the number of incoming edges equals to the number of outgoing edges: in(v)=out(v) Theorem 1: A connected graph has a Eulerian Cycle if and only if each of its vertices are balanced. In mid-tour for every path onto an island there must be another path off Exceptions are allowed at the start and end of the tour Theorem 2: A connected graph has an Eulerian Path if and only if it contains exactly two semi-balanced vertices and all others are balanced. Semi-balanced vertex: in(v) out(v) =1 One of the semi-balanced vertices, with out(v)=in(v)+1 is the start of the tour The other semi-balanced vertex, with in(v)=out(v)+1 is the end of the tour 2 1

2 Eulerian Cycle Start at any vertex *v*, and follow a trail of edges until you return to *v* As long as there exists any vertex *u* that belongs to the current tour, but has adjacent edges that are not part of the tour Start a new trail from *u* Following unused edges until returning to *u* Join the new trail to the original tour A more complicated Königsberg 3 Example Problem: Eulerian Path Approach S = { ATG, TGG, TGC, GTG, GGC, GCA, GCG, CGT } Vertices correspond to ( l 1 ) mers : { AT, TG, GC, GG, GT, CA, CG } Edges correspond to l mers from S GT CG AT TG GC CA GG Find path that visits every EDGE once 4 2

3 Genome Assembly vs Minimal Superstring Minimal substring problem Every k-mer are known and used as a vertex, (all σ k ) Paths, and there may be multiple, are solutions Read fragments No guarantee that we will see every k-mer Can't disambiguate repeats 5 From DNA to Proteins DNA sequences OS that controls living biological systems Sections of DNA (Genes) encode proteins, like programs Triplets of nucleotides (codons) encode the amino-acid sequences, as well as the stop codes, used to assemble proteins Complications in going from DNA Protein: introns, RNA editing prior to translation, posttranslational modifications 6 3

4 Proteins Proteins are the machinery or hardware Compose the cellular structures Control the biochemical reactions in cells Regulate and trigger the chain reactions (metabolic pathways) that result in the cell s life cycle Determine which parts of the DNA code are activated, executed, and when Like DNA, proteins are long molecular chains Sequences of 20 amino acid residues rather than 4 nucleic acids 7 From Genes to Proteins The central dogma of molecular biology is that information encoded by the bases of DNA are transcribed by RNA and then converted into proteins 8 4

5 Protein Components Proteins are made from 20 amino acids Peptide bonds join amino acids into long chains 100 s to 1000 s of amino acid residues long Amino Acid 3-Letter 1-Letter Molecular Weight Alanine Ala A Cysteine Cys C Aspartate Asp D Glutamate Glu E Phenylalanine Phe F Glycine Gly G Histidine His H Isoleucine Ile I Lysine Lys K Leucine Leu L Amino Acid 3-Letter 1-Letter Molecular Weight Methionine Met M Asparagine Asn N Proline Pro P Glutamine Gln Q Arginine Arg R Serine Ser S Threonine The T Valine Val V Tryptophan Trp W Tyrosine Tyr Y Protein Assembly Amino acids are joined by peptide bonds into long chains These chains fold into proteins Interact with other proteins and large molecules N-terminus C-terminus 10 5

6 Protein Sequencing Purify a sample Break into pieces Proteases cleave proteins into smaller peptide chains Read fragments Edman degradation for short peptide sequences Mass spectrometry measures mass/charge The Hard part Reassemble Relatively easy 11 Peptide Fragmentation Collision Induced Dissociation H...-HN-CH-CO... NH-CH-CO-NH-CH-CO- OH R i-1 R i R i+1 H + Prefix Fragment Suffix Fragment Peptides tend to fragment along the backbone. Fragments can also lose neutral chemical groups like NH 3 and H 2 O. 12 6

7 Breaking Peptides into Fragment Ions Proteases, e.g. trypsin, break proteins into peptides. A Tandem Mass Spectrometer (MS/MS) further breaks the peptides down into fragment ions and measures the mass of each piece. Mass Spectrometer accelerates the fragmented ions; heavier ions accelerate slower than lighter ones. Mass Spectrometer measure mass/charge ratio of an ion. 13 N- and C-terminal Peptides NH 2 - -CO 2 H 14 7

8 Terminal peptides and ion types Peptide Mass (D) = 415 Peptide without Mass (D) = N- and C-terminal Peptides 486 NH 2 - -CO 2 H

9 N- and C-terminal Peptides 486 NH 2 - -CO 2 H N- and C-terminal Peptides

10 N- and C-terminal Peptides Reconstruct peptide from the set of masses of fragment ions (mass-spectrum) Theoretical Mass Spectrum protein = PLAY Amino Acid 3-Letter 1-Letter Molecular Weight Alanine Ala A Cysteine Cys C Aspartate Asp D Glutamate Glu E Phenylalanine Phe F Glycine Gly G Histidine His H Isoleucine Ile I Lysine Lys K Leucine Leu L Amino Acid 3-Letter 1-Letter Molecular Weight Methionine Met M Asparagine Asn N Proline Pro P Glutamine Gln Q Arginine Arg R Serine Ser S Threonine The T Valine Val V Tryptophan Trp W Tyrosine Tyr Y

11 Intensity H 2 O Mass Spectra G V D L K 57 Da = K L G 99 Da = V D V G 0 mass The peaks in the mass spectrum: Prefix and Suffix Fragments. Fragments with neutral losses (-H 2 O, -NH 3 ) Noise and missing peaks. 21 Protein Identification with MS/MS G V D L K MS/MS Peptide Identification: 0 mass 22 11

12 S#: 1708 RT: AV: 1 NL: 5.27E6 T: + c d Full ms [ ] m/z De Novo vs. Database Search Database Search Relative Abundance De Novo Database of known peptides MDERHILNM, KLQWVCSDL, PTYWASDL, ENQIKRSACVM, TLACHGGEM, NGALPQWRT, HLLERTKMNVV, GGPASSDA, GGLITGMQSD, MQPLMNWE, ALKIIMNVRT, AVGELTK, HEWAILF, GHNLWAMNAC, GVFGSVLRA, EKLNKAATYIN.. Mass, Score W Database of all peptides = 20 n R A V AAAAAAAA,AAAAAAAC,AAAAAAAD,AAAAAAAE, L G T AAAAAAAG,AAAAAAAF,AAAAAAAH,AAAAAAI, E P C L K AVGELTI, AVGELTK W, AVGELTL, AVGELTM, D T YYYYYYYS,YYYYYYYT,YYYYYYYV,YYYYYYYY AVGELTK 23 A Paradox Database of all peptides is huge O(20 n ). Database of all known peptides is much smaller O(10 8 ). However, de novo algorithms can be much faster, even though their search space is much larger! A database search scans all peptides in the database of all known peptides search space to find best one. De novo eliminates the need to scan database of all peptides by modeling the problem as a graph search

Protein Sequencing and Identification by Mass Spectrometry

Protein Sequencing and Identification by Mass Spectrometry Protein Sequencing and Identification by Mass Spectrometry Tandem Mass Spectrometry De Novo Peptide Sequencing Spectrum Graph Protein Identification via Database Search Identifying Post Translationally

More information

Proteins: Characteristics and Properties of Amino Acids

Proteins: Characteristics and Properties of Amino Acids SBI4U:Biochemistry Macromolecules Eachaminoacidhasatleastoneamineandoneacidfunctionalgroupasthe nameimplies.thedifferentpropertiesresultfromvariationsinthestructuresof differentrgroups.thergroupisoftenreferredtoastheaminoacidsidechain.

More information

Using Higher Calculus to Study Biologically Important Molecules Julie C. Mitchell

Using Higher Calculus to Study Biologically Important Molecules Julie C. Mitchell Using Higher Calculus to Study Biologically Important Molecules Julie C. Mitchell Mathematics and Biochemistry University of Wisconsin - Madison 0 There Are Many Kinds Of Proteins The word protein comes

More information

Mass spectrometry in proteomics

Mass spectrometry in proteomics I519 Introduction to Bioinformatics, Fall, 2013 Mass spectrometry in proteomics Haixu Tang School of Informatics and Computing Indiana University, Bloomington Modified from: www.bioalgorithms.info Outline

More information

Translation. A ribosome, mrna, and trna.

Translation. A ribosome, mrna, and trna. Translation The basic processes of translation are conserved among prokaryotes and eukaryotes. Prokaryotic Translation A ribosome, mrna, and trna. In the initiation of translation in prokaryotes, the Shine-Dalgarno

More information

SEQUENCE ALIGNMENT BACKGROUND: BIOINFORMATICS. Prokaryotes and Eukaryotes. DNA and RNA

SEQUENCE ALIGNMENT BACKGROUND: BIOINFORMATICS. Prokaryotes and Eukaryotes. DNA and RNA SEQUENCE ALIGNMENT BACKGROUND: BIOINFORMATICS 1 Prokaryotes and Eukaryotes 2 DNA and RNA 3 4 Double helix structure Codons Codons are triplets of bases from the RNA sequence. Each triplet defines an amino-acid.

More information

Properties of amino acids in proteins

Properties of amino acids in proteins Properties of amino acids in proteins one of the primary roles of DNA (but not the only one!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids repeated

More information

Was T. rex Just a Big Chicken? Computational Proteomics

Was T. rex Just a Big Chicken? Computational Proteomics Was T. rex Just a Big Chicken? Computational Proteomics Phillip Compeau and Pavel Pevzner adjusted by Jovana Kovačević Bioinformatics Algorithms: an Active Learning Approach 215 by Compeau and Pevzner.

More information

Amino Acids and Peptides

Amino Acids and Peptides Amino Acids Amino Acids and Peptides Amino acid a compound that contains both an amino group and a carboxyl group α-amino acid an amino acid in which the amino group is on the carbon adjacent to the carboxyl

More information

Chemistry Chapter 22

Chemistry Chapter 22 hemistry 2100 hapter 22 Proteins Proteins serve many functions, including the following. 1. Structure: ollagen and keratin are the chief constituents of skin, bone, hair, and nails. 2. atalysts: Virtually

More information

Solutions In each case, the chirality center has the R configuration

Solutions In each case, the chirality center has the R configuration CAPTER 25 669 Solutions 25.1. In each case, the chirality center has the R configuration. C C 2 2 C 3 C(C 3 ) 2 D-Alanine D-Valine 25.2. 2 2 S 2 d) 2 25.3. Pro,, Trp, Tyr, and is, Trp, Tyr, and is Arg,

More information

Viewing and Analyzing Proteins, Ligands and their Complexes 2

Viewing and Analyzing Proteins, Ligands and their Complexes 2 2 Viewing and Analyzing Proteins, Ligands and their Complexes 2 Overview Viewing the accessible surface Analyzing the properties of proteins containing thousands of atoms is best accomplished by representing

More information

BENG 183 Trey Ideker. Protein Sequencing

BENG 183 Trey Ideker. Protein Sequencing BENG 183 Trey Ideker Protein Sequencing The following slides borrowed from Hong Li s Biochemistry Course: www.sb.fsu.edu/~hongli/4053notes Introduction to Proteins Proteins are of vital importance to biological

More information

Collision Cross Section: Ideal elastic hard sphere collision:

Collision Cross Section: Ideal elastic hard sphere collision: Collision Cross Section: Ideal elastic hard sphere collision: ( r r 1 ) Where is the collision cross-section r 1 r ) ( 1 Where is the collision distance r 1 r These equations negate potential interactions

More information

UNIT TWELVE. a, I _,o "' I I I. I I.P. l'o. H-c-c. I ~o I ~ I / H HI oh H...- I II I II 'oh. HO\HO~ I "-oh

UNIT TWELVE. a, I _,o ' I I I. I I.P. l'o. H-c-c. I ~o I ~ I / H HI oh H...- I II I II 'oh. HO\HO~ I -oh UNT TWELVE PROTENS : PEPTDE BONDNG AND POLYPEPTDES 12 CONCEPTS Many proteins are important in biological structure-for example, the keratin of hair, collagen of skin and leather, and fibroin of silk. Other

More information

Protein structure. Protein structure. Amino acid residue. Cell communication channel. Bioinformatics Methods

Protein structure. Protein structure. Amino acid residue. Cell communication channel. Bioinformatics Methods Cell communication channel Bioinformatics Methods Iosif Vaisman Email: ivaisman@gmu.edu SEQUENCE STRUCTURE DNA Sequence Protein Sequence Protein Structure Protein structure ATGAAATTTGGAAACTTCCTTCTCACTTATCAGCCACCT...

More information

Exam III. Please read through each question carefully, and make sure you provide all of the requested information.

Exam III. Please read through each question carefully, and make sure you provide all of the requested information. 09-107 onors Chemistry ame Exam III Please read through each question carefully, and make sure you provide all of the requested information. 1. A series of octahedral metal compounds are made from 1 mol

More information

Proteomics. November 13, 2007

Proteomics. November 13, 2007 Proteomics November 13, 2007 Acknowledgement Slides presented here have been borrowed from presentations by : Dr. Mark A. Knepper (LKEM, NHLBI, NIH) Dr. Nathan Edwards (Center for Bioinformatics and Computational

More information

Studies Leading to the Development of a Highly Selective. Colorimetric and Fluorescent Chemosensor for Lysine

Studies Leading to the Development of a Highly Selective. Colorimetric and Fluorescent Chemosensor for Lysine Supporting Information for Studies Leading to the Development of a Highly Selective Colorimetric and Fluorescent Chemosensor for Lysine Ying Zhou, a Jiyeon Won, c Jin Yong Lee, c * and Juyoung Yoon a,

More information

Protein Structure Bioinformatics Introduction

Protein Structure Bioinformatics Introduction 1 Swiss Institute of Bioinformatics Protein Structure Bioinformatics Introduction Basel, 27. September 2004 Torsten Schwede Biozentrum - Universität Basel Swiss Institute of Bioinformatics Klingelbergstr

More information

Protein Identification Using Tandem Mass Spectrometry. Nathan Edwards Informatics Research Applied Biosystems

Protein Identification Using Tandem Mass Spectrometry. Nathan Edwards Informatics Research Applied Biosystems Protein Identification Using Tandem Mass Spectrometry Nathan Edwards Informatics Research Applied Biosystems Outline Proteomics context Tandem mass spectrometry Peptide fragmentation Peptide identification

More information

PROTEIN STRUCTURE AMINO ACIDS H R. Zwitterion (dipolar ion) CO 2 H. PEPTIDES Formal reactions showing formation of peptide bond by dehydration:

PROTEIN STRUCTURE AMINO ACIDS H R. Zwitterion (dipolar ion) CO 2 H. PEPTIDES Formal reactions showing formation of peptide bond by dehydration: PTEI STUTUE ydrolysis of proteins with aqueous acid or base yields a mixture of free amino acids. Each type of protein yields a characteristic mixture of the ~ 20 amino acids. AMI AIDS Zwitterion (dipolar

More information

Other Methods for Generating Ions 1. MALDI matrix assisted laser desorption ionization MS 2. Spray ionization techniques 3. Fast atom bombardment 4.

Other Methods for Generating Ions 1. MALDI matrix assisted laser desorption ionization MS 2. Spray ionization techniques 3. Fast atom bombardment 4. Other Methods for Generating Ions 1. MALDI matrix assisted laser desorption ionization MS 2. Spray ionization techniques 3. Fast atom bombardment 4. Field Desorption 5. MS MS techniques Matrix assisted

More information

EXAM 1 Fall 2009 BCHS3304, SECTION # 21734, GENERAL BIOCHEMISTRY I Dr. Glen B Legge

EXAM 1 Fall 2009 BCHS3304, SECTION # 21734, GENERAL BIOCHEMISTRY I Dr. Glen B Legge EXAM 1 Fall 2009 BCHS3304, SECTION # 21734, GENERAL BIOCHEMISTRY I 2009 Dr. Glen B Legge This is a Scantron exam. All answers should be transferred to the Scantron sheet using a #2 pencil. Write and bubble

More information

A Plausible Model Correlates Prebiotic Peptide Synthesis with. Primordial Genetic Code

A Plausible Model Correlates Prebiotic Peptide Synthesis with. Primordial Genetic Code Electronic Supplementary Material (ESI) for ChemComm. This journal is The Royal Society of Chemistry 2018 A Plausible Model Correlates Prebiotic Peptide Synthesis with Primordial Genetic Code Jianxi Ying,

More information

Proteome Informatics. Brian C. Searle Creative Commons Attribution

Proteome Informatics. Brian C. Searle Creative Commons Attribution Proteome Informatics Brian C. Searle searleb@uw.edu Creative Commons Attribution Section structure Class 1 Class 2 Homework 1 Mass spectrometry and de novo sequencing Database searching and E-value estimation

More information

Principles of Biochemistry

Principles of Biochemistry Principles of Biochemistry Fourth Edition Donald Voet Judith G. Voet Charlotte W. Pratt Chapter 4 Amino Acids: The Building Blocks of proteins (Page 76-90) Chapter Contents 1- Amino acids Structure: 2-

More information

Read more about Pauling and more scientists at: Profiles in Science, The National Library of Medicine, profiles.nlm.nih.gov

Read more about Pauling and more scientists at: Profiles in Science, The National Library of Medicine, profiles.nlm.nih.gov 2018 Biochemistry 110 California Institute of Technology Lecture 2: Principles of Protein Structure Linus Pauling (1901-1994) began his studies at Caltech in 1922 and was directed by Arthur Amos oyes to

More information

Potentiometric Titration of an Amino Acid. Introduction

Potentiometric Titration of an Amino Acid. Introduction NAME: Course: DATE Sign-Off: Performed: Potentiometric Titration of an Amino Acid Introduction In previous course-work, you explored the potentiometric titration of a weak acid (HOAc). In this experiment,

More information

Lecture 14 - Cells. Astronomy Winter Lecture 14 Cells: The Building Blocks of Life

Lecture 14 - Cells. Astronomy Winter Lecture 14 Cells: The Building Blocks of Life Lecture 14 Cells: The Building Blocks of Life Astronomy 141 Winter 2012 This lecture describes Cells, the basic structural units of all life on Earth. Basic components of cells: carbohydrates, lipids,

More information

1. Amino Acids and Peptides Structures and Properties

1. Amino Acids and Peptides Structures and Properties 1. Amino Acids and Peptides Structures and Properties Chemical nature of amino acids The!-amino acids in peptides and proteins (excluding proline) consist of a carboxylic acid ( COOH) and an amino ( NH

More information

Protein Struktur (optional, flexible)

Protein Struktur (optional, flexible) Protein Struktur (optional, flexible) 22/10/2009 [ 1 ] Andrew Torda, Wintersemester 2009 / 2010, AST nur für Informatiker, Mathematiker,.. 26 kt, 3 ov 2009 Proteins - who cares? 22/10/2009 [ 2 ] Most important

More information

Biochemistry Quiz Review 1I. 1. Of the 20 standard amino acids, only is not optically active. The reason is that its side chain.

Biochemistry Quiz Review 1I. 1. Of the 20 standard amino acids, only is not optically active. The reason is that its side chain. Biochemistry Quiz Review 1I A general note: Short answer questions are just that, short. Writing a paragraph filled with every term you can remember from class won t improve your answer just answer clearly,

More information

12/6/12. Dr. Sanjeeva Srivastava IIT Bombay. Primary Structure. Secondary Structure. Tertiary Structure. Quaternary Structure.

12/6/12. Dr. Sanjeeva Srivastava IIT Bombay. Primary Structure. Secondary Structure. Tertiary Structure. Quaternary Structure. Dr. anjeeva rivastava Primary tructure econdary tructure Tertiary tructure Quaternary tructure Amino acid residues α Helix Polypeptide chain Assembled subunits 2 1 Amino acid sequence determines 3-D structure

More information

PROTEIN SECONDARY STRUCTURE PREDICTION: AN APPLICATION OF CHOU-FASMAN ALGORITHM IN A HYPOTHETICAL PROTEIN OF SARS VIRUS

PROTEIN SECONDARY STRUCTURE PREDICTION: AN APPLICATION OF CHOU-FASMAN ALGORITHM IN A HYPOTHETICAL PROTEIN OF SARS VIRUS Int. J. LifeSc. Bt & Pharm. Res. 2012 Kaladhar, 2012 Research Paper ISSN 2250-3137 www.ijlbpr.com Vol.1, Issue. 1, January 2012 2012 IJLBPR. All Rights Reserved PROTEIN SECONDARY STRUCTURE PREDICTION:

More information

Problem Set 1

Problem Set 1 2006 7.012 Problem Set 1 Due before 5 PM on FRIDAY, September 15, 2006. Turn answers in to the box outside of 68-120. PLEASE WRITE YOUR ANSWERS ON THIS PRINTOUT. 1. For each of the following parts, pick

More information

CHMI 2227 EL. Biochemistry I. Test January Prof : Eric R. Gauthier, Ph.D.

CHMI 2227 EL. Biochemistry I. Test January Prof : Eric R. Gauthier, Ph.D. CHMI 2227 EL Biochemistry I Test 1 26 January 2007 Prof : Eric R. Gauthier, Ph.D. Guidelines: 1) Duration: 55 min 2) 14 questions, on 7 pages. For 70 marks (5 marks per question). Worth 15 % of the final

More information

BCH 4053 Exam I Review Spring 2017

BCH 4053 Exam I Review Spring 2017 BCH 4053 SI - Spring 2017 Reed BCH 4053 Exam I Review Spring 2017 Chapter 1 1. Calculate G for the reaction A + A P + Q. Assume the following equilibrium concentrations: [A] = 20mM, [Q] = [P] = 40fM. Assume

More information

Exam I Answer Key: Summer 2006, Semester C

Exam I Answer Key: Summer 2006, Semester C 1. Which of the following tripeptides would migrate most rapidly towards the negative electrode if electrophoresis is carried out at ph 3.0? a. gly-gly-gly b. glu-glu-asp c. lys-glu-lys d. val-asn-lys

More information

Towards Understanding the Origin of Genetic Languages

Towards Understanding the Origin of Genetic Languages Towards Understanding the Origin of Genetic Languages Why do living organisms use 4 nucleotide bases and 20 amino acids? Apoorva Patel Centre for High Energy Physics and Supercomputer Education and Research

More information

7.05 Spring 2004 February 27, Recitation #2

7.05 Spring 2004 February 27, Recitation #2 Recitation #2 Contact Information TA: Victor Sai Recitation: Friday, 3-4pm, 2-132 E-mail: sai@mit.edu ffice ours: Friday, 4-5pm, 2-132 Unit 1 Schedule Recitation/Exam Date Lectures covered Recitation #2

More information

BIS Office Hours

BIS Office Hours BIS103-001 001 ffice ours TUE (2-3 pm) Rebecca Shipman WED (9:30-10:30 am) TUE (12-1 pm) Stephen Abreu TUR (12-1 pm) FRI (9-11 am) Steffen Abel Lecture 2 Topics Finish discussion of thermodynamics (ΔG,

More information

CHEMISTRY ATAR COURSE DATA BOOKLET

CHEMISTRY ATAR COURSE DATA BOOKLET CHEMISTRY ATAR COURSE DATA BOOKLET 2018 2018/2457 Chemistry ATAR Course Data Booklet 2018 Table of contents Periodic table of the elements...3 Formulae...4 Units...4 Constants...4 Solubility rules for

More information

Chemical Properties of Amino Acids

Chemical Properties of Amino Acids hemical Properties of Amino Acids Protein Function Make up about 15% of the cell and have many functions in the cell 1. atalysis: enzymes 2. Structure: muscle proteins 3. Movement: myosin, actin 4. Defense:

More information

Using an Artificial Regulatory Network to Investigate Neural Computation

Using an Artificial Regulatory Network to Investigate Neural Computation Using an Artificial Regulatory Network to Investigate Neural Computation W. Garrett Mitchener College of Charleston January 6, 25 W. Garrett Mitchener (C of C) UM January 6, 25 / 4 Evolution and Computing

More information

Computational Methods For Identification Of Cyclic Peptides Using Mass Spectrometry. Julio Ng Bioinformatics Program, UCSD March, 26 th 2010

Computational Methods For Identification Of Cyclic Peptides Using Mass Spectrometry. Julio Ng Bioinformatics Program, UCSD March, 26 th 2010 Computational Methods or Identification Of Cyclic Peptides Using Mass Spectrometry Julio Ng Bioinformatics Program, UCSD March, 26 th 2010 Outline Importance of natural products Mass spectrometry on cyclic

More information

Separation of Large and Small Peptides by Supercritical Fluid Chromatography and Detection by Mass Spectrometry

Separation of Large and Small Peptides by Supercritical Fluid Chromatography and Detection by Mass Spectrometry Separation of Large and Small Peptides by Supercritical Fluid Chromatography and Detection by Mass Spectrometry Application Note Biologics and Biosimilars Author Edgar Naegele Agilent Technologies, Inc.

More information

A Logic-Based Approach to Polymer Sequence Analysis

A Logic-Based Approach to Polymer Sequence Analysis A Logic-Based Approach to Polymer Sequence Analysis Renato Bruni Dep. of Electronic and Information Engineering, University of Perugia, Via G. Duranti, 93-06125 Perugia - Italy. E-mail: renato.bruni@diei.unipg.it

More information

Lecture'18:'April'2,'2013

Lecture'18:'April'2,'2013 CM'224' 'rganic'chemistry'ii Spring'2013,'Des'Plaines' 'Prof.'Chad'Landrie 2 3 N cysteine (Cys) S oxidation S S 3 N cystine N 3 Lecture'18:'April'2,'2013 Disaccharides+&+Polysaccharides Amino+acids++(26.1926.3)

More information

(Lys), resulting in translation of a polypeptide without the Lys amino acid. resulting in translation of a polypeptide without the Lys amino acid.

(Lys), resulting in translation of a polypeptide without the Lys amino acid. resulting in translation of a polypeptide without the Lys amino acid. 1. A change that makes a polypeptide defective has been discovered in its amino acid sequence. The normal and defective amino acid sequences are shown below. Researchers are attempting to reproduce the

More information

Protein Struktur. Biologen und Chemiker dürfen mit Handys spielen (leise) go home, go to sleep. wake up at slide 39

Protein Struktur. Biologen und Chemiker dürfen mit Handys spielen (leise) go home, go to sleep. wake up at slide 39 Protein Struktur Biologen und Chemiker dürfen mit Handys spielen (leise) go home, go to sleep wake up at slide 39 Andrew Torda, Wintersemester 2016/ 2017 Andrew Torda 17.10.2016 [ 1 ] Proteins - who cares?

More information

Basic Principles of Protein Structures

Basic Principles of Protein Structures Basic Principles of Protein Structures Proteins Proteins: The Molecule of Life Proteins: Building Blocks Proteins: Secondary Structures Proteins: Tertiary and Quartenary Structure Proteins: Geometry Proteins

More information

THE UNIVERSITY OF MANITOBA. PAPER NO: _1_ LOCATION: 173 Robert Schultz Theatre PAGE NO: 1 of 5 DEPARTMENT & COURSE NO: CHEM / MBIO 2770 TIME: 1 HOUR

THE UNIVERSITY OF MANITOBA. PAPER NO: _1_ LOCATION: 173 Robert Schultz Theatre PAGE NO: 1 of 5 DEPARTMENT & COURSE NO: CHEM / MBIO 2770 TIME: 1 HOUR THE UNIVERSITY OF MANITOBA 1 November 1, 2016 Mid-Term EXAMINATION PAPER NO: _1_ LOCATION: 173 Robert Schultz Theatre PAGE NO: 1 of 5 DEPARTMENT & COURSE NO: CHEM / MBIO 2770 TIME: 1 HOUR EXAMINATION:

More information

Section Week 3. Junaid Malek, M.D.

Section Week 3. Junaid Malek, M.D. Section Week 3 Junaid Malek, M.D. Biological Polymers DA 4 monomers (building blocks), limited structure (double-helix) RA 4 monomers, greater flexibility, multiple structures Proteins 20 Amino Acids,

More information

Protein Sequencing and Identification by Mass Spectrometry

Protein Sequencing and Identification by Mass Spectrometry Protein Sequencing and Identification by Mass Spectrometry Outline Tandem Mass Spectrometry De Novo Peptide Sequencing Spectrum Graph Protein Identification via Database Search Identifying Post Translationally

More information

Rotamers in the CHARMM19 Force Field

Rotamers in the CHARMM19 Force Field Appendix A Rotamers in the CHARMM19 Force Field The people may be made to follow a path of action, but they may not be made to understand it. Confucius (551 BC - 479 BC) ( ) V r 1 (j),r 2 (j),r 3 (j),...,r

More information

Lecture 15. Saad Mneimneh

Lecture 15. Saad Mneimneh Computat onal Biology Lecture 15 DNA sequencing Shortest common superstring SCS An elegant theoretical abstraction, but fundamentally flawed R. Karp Given a set of fragments F, Find the shortest string

More information

DNA sequencing. Bad example (repeats) Lecture 15. Shortest common superstring SCS. Given a set of fragments F,

DNA sequencing. Bad example (repeats) Lecture 15. Shortest common superstring SCS. Given a set of fragments F, Computat onal Biology Lecture 15 DNA sequencing Shortest common superstring SCS An elegant theoretical abstraction, but fundamentally flawed R. Karp Given a set of fragments F, Find the shortest string

More information

Sequence comparison: Score matrices

Sequence comparison: Score matrices Sequence comparison: Score matrices http://facultywashingtonedu/jht/gs559_2013/ Genome 559: Introduction to Statistical and omputational Genomics Prof James H Thomas FYI - informal inductive proof of best

More information

Protein Structure Marianne Øksnes Dalheim, PhD candidate Biopolymers, TBT4135, Autumn 2013

Protein Structure Marianne Øksnes Dalheim, PhD candidate Biopolymers, TBT4135, Autumn 2013 Protein Structure Marianne Øksnes Dalheim, PhD candidate Biopolymers, TBT4135, Autumn 2013 The presentation is based on the presentation by Professor Alexander Dikiy, which is given in the course compedium:

More information

Dental Biochemistry Exam The total number of unique tripeptides that can be produced using all of the common 20 amino acids is

Dental Biochemistry Exam The total number of unique tripeptides that can be produced using all of the common 20 amino acids is Exam Questions for Dental Biochemistry Monday August 27, 2007 E.J. Miller 1. The compound shown below is CH 3 -CH 2 OH A. acetoacetate B. acetic acid C. acetaldehyde D. produced by reduction of acetaldehyde

More information

Sequence comparison: Score matrices. Genome 559: Introduction to Statistical and Computational Genomics Prof. James H. Thomas

Sequence comparison: Score matrices. Genome 559: Introduction to Statistical and Computational Genomics Prof. James H. Thomas Sequence comparison: Score matrices Genome 559: Introduction to Statistical and omputational Genomics Prof James H Thomas Informal inductive proof of best alignment path onsider the last step in the best

More information

C CH 3 N C COOH. Write the structural formulas of all of the dipeptides that they could form with each other.

C CH 3 N C COOH. Write the structural formulas of all of the dipeptides that they could form with each other. hapter 25 Biochemistry oncept heck 25.1 Two common amino acids are 3 2 N alanine 3 2 N threonine Write the structural formulas of all of the dipeptides that they could form with each other. The carboxyl

More information

INTRODUCTION. Amino acids occurring in nature have the general structure shown below:

INTRODUCTION. Amino acids occurring in nature have the general structure shown below: Biochemistry I Laboratory Amino Acid Thin Layer Chromatography INTRODUCTION The primary importance of amino acids in cell structure and metabolism lies in the fact that they serve as building blocks for

More information

Discussion Section (Day, Time): TF:

Discussion Section (Day, Time): TF: ame: Chemistry 27 Professor Gavin MacBeath arvard University Spring 2004 Final Exam Thursday, May 28, 2004 2:15 PM - 5:15 PM Discussion Section (Day, Time): Directions: TF: 1. Do not write in red ink.

More information

A. Two of the common amino acids are analyzed. Amino acid X and amino acid Y both have an isoionic point in the range of

A. Two of the common amino acids are analyzed. Amino acid X and amino acid Y both have an isoionic point in the range of Questions with Answers- Amino Acids & Peptides A. Two of the common amino acids are analyzed. Amino acid X and amino acid Y both have an isoionic point in the range of 5.0-6.5 (Questions 1-4) 1. Which

More information

Molecular Selective Binding of Basic Amino Acids by a Water-soluble Pillar[5]arene

Molecular Selective Binding of Basic Amino Acids by a Water-soluble Pillar[5]arene Electronic supplementary information Molecular Selective Binding of Basic Amino Acids y a Water-solule Pillar[5]arene Chunju Li,* a, Junwei Ma, a Liu Zhao, a Yanyan Zhang, c Yihua Yu, c Xiaoyan Shu, a

More information

Peptides And Proteins

Peptides And Proteins Kevin Burgess, May 3, 2017 1 Peptides And Proteins from chapter(s) in the recommended text A. Introduction B. omenclature And Conventions by amide bonds. on the left, right. 2 -terminal C-terminal triglycine

More information

Conformational Analysis

Conformational Analysis Conformational Analysis C01 3 C C 3 is the most stable by 0.9 kcal/mole C02 K eq = K 1-1 * K 2 = 0.45-1 * 0.048 = 0.11 C04 The intermediate in the reaction of 2 has an unfavorable syn-pentane interaction,

More information

Enzyme Catalysis & Biotechnology

Enzyme Catalysis & Biotechnology L28-1 Enzyme Catalysis & Biotechnology Bovine Pancreatic RNase A Biochemistry, Life, and all that L28-2 A brief word about biochemistry traditionally, chemical engineers used organic and inorganic chemistry

More information

Discussion Section (Day, Time):

Discussion Section (Day, Time): Chemistry 27 Spring 2005 Exam 1 Chemistry 27 Professor Gavin MacBeath arvard University Spring 2005 our Exam 1 Friday, February 25, 2005 11:07 AM 12:00 PM Discussion Section (Day, Time): TF: Directions:

More information

NH 2. Biochemistry I, Fall Term Sept 9, Lecture 5: Amino Acids & Peptides Assigned reading in Campbell: Chapter

NH 2. Biochemistry I, Fall Term Sept 9, Lecture 5: Amino Acids & Peptides Assigned reading in Campbell: Chapter Biochemistry I, Fall Term Sept 9, 2005 Lecture 5: Amino Acids & Peptides Assigned reading in Campbell: Chapter 3.1-3.4. Key Terms: ptical Activity, Chirality Peptide bond Condensation reaction ydrolysis

More information

Sequence comparison: Score matrices. Genome 559: Introduction to Statistical and Computational Genomics Prof. James H. Thomas

Sequence comparison: Score matrices. Genome 559: Introduction to Statistical and Computational Genomics Prof. James H. Thomas Sequence comparison: Score matrices Genome 559: Introduction to Statistical and omputational Genomics Prof James H Thomas FYI - informal inductive proof of best alignment path onsider the last step in

More information

Resonance assignments in proteins. Christina Redfield

Resonance assignments in proteins. Christina Redfield Resonance assignments in proteins Christina Redfield 1. Introduction The assignment of resonances in the complex NMR spectrum of a protein is the first step in any study of protein structure, function

More information

Introduction to Comparative Protein Modeling. Chapter 4 Part I

Introduction to Comparative Protein Modeling. Chapter 4 Part I Introduction to Comparative Protein Modeling Chapter 4 Part I 1 Information on Proteins Each modeling study depends on the quality of the known experimental data. Basis of the model Search in the literature

More information

LS1a Fall 2014 Problem Set #2 Due Monday 10/6 at 6 pm in the drop boxes on the Science Center 2 nd Floor

LS1a Fall 2014 Problem Set #2 Due Monday 10/6 at 6 pm in the drop boxes on the Science Center 2 nd Floor LS1a Fall 2014 Problem Set #2 Due Monday 10/6 at 6 pm in the drop boxes on the Science Center 2 nd Floor Note: Adequate space is given for each answer. Questions that require a brief explanation should

More information

Protein Sequencing and Identification by Mass Spectrometry

Protein Sequencing and Identification by Mass Spectrometry Protein Sequencing and Identification by Mass Spectrometry Tandem Mass Spectrometry De Novo Peptide Sequencing Spectrum Graph Protein Identification via Database Search Identifying Post Translationally

More information

CHEM 3653 Exam # 1 (03/07/13)

CHEM 3653 Exam # 1 (03/07/13) 1. Using phylogeny all living organisms can be divided into the following domains: A. Bacteria, Eukarya, and Vertebrate B. Archaea and Eukarya C. Bacteria, Eukarya, and Archaea D. Eukarya and Bacteria

More information

Practice Midterm Exam 200 points total 75 minutes Multiple Choice (3 pts each 30 pts total) Mark your answers in the space to the left:

Practice Midterm Exam 200 points total 75 minutes Multiple Choice (3 pts each 30 pts total) Mark your answers in the space to the left: MITES ame Practice Midterm Exam 200 points total 75 minutes Multiple hoice (3 pts each 30 pts total) Mark your answers in the space to the left: 1. Amphipathic molecules have regions that are: a) polar

More information

NSCI Basic Properties of Life and The Biochemistry of Life on Earth

NSCI Basic Properties of Life and The Biochemistry of Life on Earth NSCI 314 LIFE IN THE COSMOS 4 Basic Properties of Life and The Biochemistry of Life on Earth Dr. Karen Kolehmainen Department of Physics CSUSB http://physics.csusb.edu/~karen/ WHAT IS LIFE? HARD TO DEFINE,

More information

Protein Structure. Role of (bio)informatics in drug discovery. Bioinformatics

Protein Structure. Role of (bio)informatics in drug discovery. Bioinformatics Bioinformatics Protein Structure Principles & Architecture Marjolein Thunnissen Dep. of Biochemistry & Structural Biology Lund University September 2011 Homology, pattern and 3D structure searches need

More information

8 Grundlagen der Bioinformatik, SS 09, D. Huson, April 28, 2009

8 Grundlagen der Bioinformatik, SS 09, D. Huson, April 28, 2009 8 Grundlagen der Bioinformatik, SS 09, D. Huson, April 28, 2009 2 Pairwise alignment We will discuss: 1. Strings 2. Dot matrix method for comparing sequences 3. Edit distance and alignment 4. The number

More information

Energy and Cellular Metabolism

Energy and Cellular Metabolism 1 Chapter 4 About This Chapter Energy and Cellular Metabolism 2 Energy in biological systems Chemical reactions Enzymes Metabolism Figure 4.1 Energy transfer in the environment Table 4.1 Properties of

More information

8 Grundlagen der Bioinformatik, SoSe 11, D. Huson, April 18, 2011

8 Grundlagen der Bioinformatik, SoSe 11, D. Huson, April 18, 2011 8 Grundlagen der Bioinformatik, SoSe 11, D. Huson, April 18, 2011 2 Pairwise alignment We will discuss: 1. Strings 2. Dot matrix method for comparing sequences 3. Edit distance and alignment 4. The number

More information

Biochemistry by Mary K. Campbell & Shawn O. Farrell 8th. Ed. 2016

Biochemistry by Mary K. Campbell & Shawn O. Farrell 8th. Ed. 2016 3 Biochemistry by Mary K. Campbell & Shawn. Farrell 8th. Ed. 2016 3-1 3 Amino Acids & Peptides 3-2 3 Learning bjectives 1. What are amino acids, and what is their threedimensional structure? 2. What are

More information

CHEM J-9 June 2014

CHEM J-9 June 2014 CEM1611 2014-J-9 June 2014 Alanine (ala) and lysine (lys) are two amino acids with the structures given below as Fischer projections. The pk a values of the conjugate acid forms of the different functional

More information

Chapter 3 - Amino Acids

Chapter 3 - Amino Acids hapter 3 Amino Acids αamino Acids are the main constituents of proteins. But they also can function as neurotransmitters (glutamate, γaminobutyric acid), hormones (thyroxine; see right), as bacterial cell

More information

Packing of Secondary Structures

Packing of Secondary Structures 7.88 Lecture Notes - 4 7.24/7.88J/5.48J The Protein Folding and Human Disease Professor Gossard Retrieving, Viewing Protein Structures from the Protein Data Base Helix helix packing Packing of Secondary

More information

Introduction to graph theory and molecular networks

Introduction to graph theory and molecular networks Introduction to graph theory and molecular networks Sushmita Roy sroy@biostat.wisc.edu Computational Network Biology Biostatistics & Medical Informatics 826 https://compnetbiocourse.discovery.wisc.edu

More information

Chapter 4: Amino Acids

Chapter 4: Amino Acids Chapter 4: Amino Acids All peptides and polypeptides are polymers of alpha-amino acids. lipid polysaccharide enzyme 1940s 1980s. Lipids membrane 1960s. Polysaccharide Are energy metabolites and many of

More information

All Proteins Have a Basic Molecular Formula

All Proteins Have a Basic Molecular Formula All Proteins Have a Basic Molecular Formula Homa Torabizadeh Abstract This study proposes a basic molecular formula for all proteins. A total of 10,739 proteins belonging to 9 different protein groups

More information

Advanced Topics in RNA and DNA. DNA Microarrays Aptamers

Advanced Topics in RNA and DNA. DNA Microarrays Aptamers Quiz 1 Advanced Topics in RNA and DNA DNA Microarrays Aptamers 2 Quantifying mrna levels to asses protein expression 3 The DNA Microarray Experiment 4 Application of DNA Microarrays 5 Some applications

More information

Videos. Bozeman, transcription and translation: https://youtu.be/h3b9arupxzg Crashcourse: Transcription and Translation - https://youtu.

Videos. Bozeman, transcription and translation: https://youtu.be/h3b9arupxzg Crashcourse: Transcription and Translation - https://youtu. Translation Translation Videos Bozeman, transcription and translation: https://youtu.be/h3b9arupxzg Crashcourse: Transcription and Translation - https://youtu.be/itsb2sqr-r0 Translation Translation The

More information

On the Structure Differences of Short Fragments and Amino Acids in Proteins with and without Disulfide Bonds

On the Structure Differences of Short Fragments and Amino Acids in Proteins with and without Disulfide Bonds On the Structure Differences of Short Fragments and Amino Acids in Proteins with and without Disulfide Bonds A thesis submitted for the degree of Doctor of Philosophy Saravanan Dayalan B.E., M.App.Sc(IT),

More information

MS/MS of Peptides Manual Sequencing of Protonated Peptides

MS/MS of Peptides Manual Sequencing of Protonated Peptides S/S of Peptides anual Sequencing of Protonated Peptides Árpád Somogyi Associate irector CCIC, ass Spectrometry and Proteomics Laboratory SU July 11, 2018 Peptides Product Ion Scan Product ion spectra contain

More information

CHAPTER 29 HW: AMINO ACIDS + PROTEINS

CHAPTER 29 HW: AMINO ACIDS + PROTEINS CAPTER 29 W: AMI ACIDS + PRTEIS For all problems, consult the table of 20 Amino Acids provided in lecture if an amino acid structure is needed; these will be given on exams. Use natural amino acids (L)

More information

Dental Biochemistry EXAM I

Dental Biochemistry EXAM I Dental Biochemistry EXAM I August 29, 2005 In the reaction below: CH 3 -CH 2 OH -~ ethanol CH 3 -CHO acetaldehyde A. acetoacetate is being produced B. ethanol is being oxidized to acetaldehyde C. acetaldehyde

More information

Supplementary Figure 3 a. Structural comparison between the two determined structures for the IL 23:MA12 complex. The overall RMSD between the two

Supplementary Figure 3 a. Structural comparison between the two determined structures for the IL 23:MA12 complex. The overall RMSD between the two Supplementary Figure 1. Biopanningg and clone enrichment of Alphabody binders against human IL 23. Positive clones in i phage ELISA with optical density (OD) 3 times higher than background are shown for

More information

Mass Spectrometry Based De Novo Peptide Sequencing Error Correction

Mass Spectrometry Based De Novo Peptide Sequencing Error Correction Mass Spectrometry Based De Novo Peptide Sequencing Error Correction by Chenyu Yao A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Master of Mathematics

More information

Housekeeping. Housekeeping. Molecules of Life: Biopolymers

Housekeeping. Housekeeping. Molecules of Life: Biopolymers Molecules of Life: Biopolymers Dr. Dale Hancock D.Hancock@mmb.usyd.edu.au Room 377 Biochemistry building Housekeeping Answers to the practise calculations and a narration are on WebT. Access these through

More information