Proteome Informatics. Brian C. Searle Creative Commons Attribution

Size: px
Start display at page:

Download "Proteome Informatics. Brian C. Searle Creative Commons Attribution"

Transcription

1 Proteome Informatics Brian C. Searle Creative Commons Attribution

2 Section structure Class 1 Class 2 Homework 1 Mass spectrometry and de novo sequencing Database searching and E-value estimation Implementing a simple database search engine Class 3 Mixture model analysis and target/decoy evaluation Class 4 Searching for post-translational modifications Homework 2 Evaluating mixture models

3 de Novo Sequencing Tandem Mass Spectra Taylor JA, Johnson RS. Rapid Commun Mass Spectrom. 1997;11(9): Brian C. Searle Creative Commons Attribution

4 Proteins are digested into peptides with trypsin F V N Q H L C G S K L T I R P T E R C G A E R V L Y L V A E 1. FVNQHLCGSK 2. LVEALYLVCGER 3. AEPTIR 4. TR

5 There are hundreds of thousands of peptides in the human proteome Intensity (10 9 ) M/Z ,000 M/Z Mass/Charge (m/z)

6 Liquid chromatography separates peptides by hydrophobicity intensity intensity intensity intensity m/z m/z m/z m/z

7

8 Sequencing peptides with data dependent acquisition (DDA)

9 DDA relies on dynamic exclusion 400 M/Z 1000 M/Z Retention TIme

10 Sequencing AEPTIR F V N Q H L C G S K L T I R P T E R C G A E R V L Y L V A E 1. FVNQHLCGSK 2. LVEALYLVCGER 3. AEPTIR 4. TR

11 Impart energy in collision cell A E P T I R H 2 O Name AA Mono Glycine G Alanine A Serine S Proline P Valine V Threonine T Cysteine C Isoleucine I Leucine L Asparagine N Name AA Mono Aspartic Acid D Glutamine Q Lysine K Glutamic Acid E Methionine M Histidine H Phenylalanine Y Arginine R Tyrosine Y Tryptophan W

12 Measure mass of daughter ions A E P T A E P Intensity A A 72.0 E M/z

13 B-type Ions A E P T I R H 2 O Intensity M/z

14 B-type Ions A E P T I R H 2 O Intensity A-0 AE-A AEP -AE AEPT -AEP AEPTI -AEPT AEPTIR -AEPTI M/z

15 B-type Ions A E P T I R H 2 O Intensity CO CO CO CO CO CO M/z

16 A-type Ions A E P T I R H 2 O Intensity CO CO CO CO CO CO M/z

17 Y-type Ions H 2 O R I T P E A Intensity M/z

18 Y-type Ions H 2 O R I T P E A Intensity M/z

19 B-type, A-type, Y-type Ions H 2 O R I T P E A Intensity M/z

20 Intensity M/z

21 Intensity M/z

22 Intensity M/z

23 A E P T I R H 2O Intensity M/z

24 Known Ion Types B-type ions A-type ions Y-type ions

25 Known Ion Types B-type ions A-type ions Y-type ions B- or Y-type +2H ions B- or Y-type -NH 3 ions B- or Y-type -H 2 O ions

26 Known Ion Types B-type ions A-type ions Y-type ions 100% 20% 100% B- or Y-type +2H ions B- or Y-type -NH 3 ions B- or Y-type -H 2 O ions 50% 20% 20%

27 Model Spectrum ELVISLIVESK *Courtesy of Dr. Richard Johnson

28 B/Y type ions (100%) B/Y +2H type ions (50%) A type ions B/Y -NH 3 /-H 2 O (20%)

29 Model Spectrum

30 Model Spectrum

31 Model Spectrum

32 How would you sequence this peptide? 132 intensity mass / charge

33 Brute force strategy AAAA AACA NYYY AAAC AACC PYYY AAAD AACD RYYY AAAE AAAF AACE AACF SYYY TYYY AAAG AACG VYYY AAAH AACH WYYY AAAI AACI YYYY

34 Can look for a tag, but how do you know which direction? 132 intensity N 374 A NA or AN? 426 mass / charge

35 Can use ends as context: start at y1/b1 and keep going 132 intensity I/L K/Q mass / charge

36 Shortest path algorithm with a directed acyclic graph (DAG) (B) 1 (Y)

37 Completely interconnected graph (B) 1 (Y)

38 Graph with only amino acid edges (B) 1 N I/L I/L G G A (Y) K/Q [CH] K/Q

39 Convert edges to scores What are good things to score? Amino acid frequency Ion intensities Ion frequencies Likelihood ion produces intense signal

40 Dijkstra s Shortest Path Algorithm END START

41 Travel the smallest known edge (1) END START Update: Michael was right -- you don t need to multiply by -1

42 Travel the smallest known edge (2) END START

43 Travel the smallest known edge (3) END START

44 Travel the smallest known edge (4) END START

45 Travel the smallest known edge (5) END START

46 Graph with only amino acid edges (B) 1 N I/L I/L G G A (Y) K/Q [CH] K/Q

47 DAG with Topographical Support (1)

48 DAG with Topographical Support (2)

49 DAG with Topographical Support (3)

50 DAG with Topographical Support (4)

51 DAG with Topographical Support (5)

52 DAG with Topographical Support (6)

53 DAG with Topographical Support (7)

54 Trace the path backwards through the DAG

55 Sequencing the peptide (B) 1 N (Y) 19 I/L I/L G G A K/Q [CH] K/Q AN[I/L][K/Q]

56 How would you sequence this peptide? 132 intensity mass / charge

57 How would you sequence this peptide? intensity 132 (y1) 147 (y2) (y3) 374 (y4) 426 K/Q I/L N A

Proteins: Characteristics and Properties of Amino Acids

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

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

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

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

Lecture 15: Realities of Genome Assembly Protein Sequencing

Lecture 15: Realities of Genome Assembly Protein Sequencing Lecture 15: Realities of Genome Assembly Protein Sequencing Study Chapter 8.10-8.15 1 Euler s Theorems A graph is balanced if for every vertex the number of incoming edges equals to the number of outgoing

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

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

Range of Certified Values in Reference Materials. Range of Expanded Uncertainties as Disseminated. NMI Service

Range of Certified Values in Reference Materials. Range of Expanded Uncertainties as Disseminated. NMI Service Calibration and Capabilities Amount of substance,, Russian Federation (Ural Scientific and Research Institiute Metrology, Rosstandart) (D.I. Mendeleyev Institute Metrology, Rosstandart) The uncertainty

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

Protein Secondary Structure Prediction

Protein Secondary Structure Prediction part of Bioinformatik von RNA- und Proteinstrukturen Computational EvoDevo University Leipzig Leipzig, SS 2011 the goal is the prediction of the secondary structure conformation which is local each amino

More information

A rapid and highly selective colorimetric method for direct detection of tryptophan in proteins via DMSO acceleration

A rapid and highly selective colorimetric method for direct detection of tryptophan in proteins via DMSO acceleration A rapid and highly selective colorimetric method for direct detection of tryptophan in proteins via DMSO acceleration Yanyan Huang, Shaoxiang Xiong, Guoquan Liu, Rui Zhao Beijing National Laboratory for

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

C h a p t e r 2 A n a l y s i s o f s o m e S e q u e n c e... methods use different attributes related to mis sense mutations such as

C h a p t e r 2 A n a l y s i s o f s o m e S e q u e n c e... methods use different attributes related to mis sense mutations such as C h a p t e r 2 A n a l y s i s o f s o m e S e q u e n c e... 2.1Introduction smentionedinchapter1,severalmethodsareavailabletoclassifyhuman missensemutationsintoeitherbenignorpathogeniccategoriesandthese

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

ProbSeq a fragmentation model for interpretation of electrospray tandem mass spectrometry data

ProbSeq a fragmentation model for interpretation of electrospray tandem mass spectrometry data Comparative and Functional Genomics Comp Funct Genom 2004; 5: 61 68. Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.370 Conference Paper ProbSeq a fragmentation model

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

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

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

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

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

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

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

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

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

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

Hypergraphs, Metabolic Networks, Bioreaction Systems. G. Bastin

Hypergraphs, Metabolic Networks, Bioreaction Systems. G. Bastin Hypergraphs, Metabolic Networks, Bioreaction Systems. G. Bastin PART 1 : Metabolic flux analysis and minimal bioreaction modelling PART 2 : Dynamic metabolic flux analysis of underdetermined networks 2

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

The Select Command and Boolean Operators

The Select Command and Boolean Operators The Select Command and Boolean Operators Part of the Jmol Training Guide from the MSOE Center for BioMolecular Modeling Interactive version available at http://cbm.msoe.edu/teachingresources/jmol/jmoltraining/boolean.html

More information

Part 4 The Select Command and Boolean Operators

Part 4 The Select Command and Boolean Operators Part 4 The Select Command and Boolean Operators http://cbm.msoe.edu/newwebsite/learntomodel Introduction By default, every command you enter into the Console affects the entire molecular structure. However,

More information

Periodic Table. 8/3/2006 MEDC 501 Fall

Periodic Table. 8/3/2006 MEDC 501 Fall Periodic Table 8/3/2006 MEDC 501 Fall 2006 1 rbitals Shapes of rbitals s - orbital p -orbital 8/3/2006 MEDC 501 Fall 2006 2 Ionic Bond - acl Electronic Structure 11 a :: 1s 2 2s 2 2p x2 2p y2 2p z2 3s

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

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

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

Patrick: An Introduction to Medicinal Chemistry 5e Chapter 03

Patrick: An Introduction to Medicinal Chemistry 5e Chapter 03 01) Which of the following statements is not true regarding the active site of an enzyme? a. An active site is normally on the surface of an enzyme. b. An active site is normally hydrophobic in nature.

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

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

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

(Bio)chemical Proteomics. Alex Kentsis October, 2013

(Bio)chemical Proteomics. Alex Kentsis October, 2013 (Bio)chemical Proteomics Alex Kentsis October, 2013 http://alexkentsis.net A brief history of chemical proteomics 1907: Eduard Buchner, demonstration of cell-free alcohol fermentation (i.e. enzymes) 1946:

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

How did they form? Exploring Meteorite Mysteries

How did they form? Exploring Meteorite Mysteries Exploring Meteorite Mysteries Objectives Students will: recognize that carbonaceous chondrite meteorites contain amino acids, the first step towards living plants and animals. conduct experiments that

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

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

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

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

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

Structures in equilibrium at point A: Structures in equilibrium at point B: (ii) Structure at the isoelectric point:

Structures in equilibrium at point A: Structures in equilibrium at point B: (ii) Structure at the isoelectric point: ame 21 F10-Final Exam Page 2 I. (42 points) (1) (16 points) The titration curve for L-lysine is shown below. Provide (i) the main structures in equilibrium at each of points A and B indicated below and

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

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

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

BioSystems 109 (2012) Contents lists available at SciVerse ScienceDirect. BioSystems

BioSystems 109 (2012) Contents lists available at SciVerse ScienceDirect. BioSystems BioSystems 9 (22) 79 85 Contents lists available at SciVerse ScienceDirect BioSystems journa l h o me pa g e: www.elsevier.com/locate/biosystems Periodic patterns in distributions of peptide masses Shane

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

Scoring Matrices. Shifra Ben-Dor Irit Orr

Scoring Matrices. Shifra Ben-Dor Irit Orr Scoring Matrices Shifra Ben-Dor Irit Orr Scoring matrices Sequence alignment and database searching programs compare sequences to each other as a series of characters. All algorithms (programs) for comparison

More information

Discussion Section (Day, Time):

Discussion Section (Day, Time): Chemistry 27 Spring 2005 Exam 3 Chemistry 27 Professor Gavin MacBeath arvard University Spring 2005 our Exam 3 Friday April 29 th, 2005 11:07 AM 12:00 PM Discussion Section (Day, Time): TF: Directions:

More information

National Nutrient Database for Standard Reference Release 28 slightly revised May, 2016

National Nutrient Database for Standard Reference Release 28 slightly revised May, 2016 National base for Standard Reference Release 28 slightly revised May, 206 Full Report (All s) 005, Cheese, cottage, lowfat, 2% milkfat Report Date: February 23, 208 02:7 EST values and weights are for

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

Systematic approaches to study cancer cell metabolism

Systematic approaches to study cancer cell metabolism Systematic approaches to study cancer cell metabolism Kivanc Birsoy Laboratory of Metabolic Regulation and Genetics The Rockefeller University, NY Cellular metabolism is complex ~3,000 metabolic genes

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

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

Electrospray Ionization High-Resolution Ion Mobility Spectrometry for the Detection of Organic Compounds, 1. Amino Acids

Electrospray Ionization High-Resolution Ion Mobility Spectrometry for the Detection of Organic Compounds, 1. Amino Acids Anal. Chem. 2001, 73, 3028-3034 Electrospray Ionization High-Resolution Ion Mobility Spectrometry for the Detection of Organic Compounds, 1. Amino Acids Luther W. Beegle and Isik Kanik* Jet Propulsion

More information

Atomic masses. Atomic masses of elements. Atomic masses of isotopes. Nominal and exact atomic masses. Example: CO, N 2 ja C 2 H 4

Atomic masses. Atomic masses of elements. Atomic masses of isotopes. Nominal and exact atomic masses. Example: CO, N 2 ja C 2 H 4 High-Resolution Mass spectrometry (HR-MS, HRAM-MS) (FT mass spectrometry) MS that enables identifying elemental compositions (empirical formulas) from accurate m/z data 9.05.2017 1 Atomic masses (atomic

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

Evidence from Evolution Activity 75 Points. Fossils Use your textbook and the diagrams on the next page to answer the following questions.

Evidence from Evolution Activity 75 Points. Fossils Use your textbook and the diagrams on the next page to answer the following questions. Name(s): Biology Evidence from Evolution Activity 75 Points Fossils Use your textbook and the diagrams on the next page to answer the following questions. 1. What are fossils? How are most fossils formed?

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

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

Introduction to Proteomics: Fragmentation of protonated peptides and manual sequencing

Introduction to Proteomics: Fragmentation of protonated peptides and manual sequencing Introduction to Proteomics: ragmentation of protonated peptides and manual sequencing Árpád Somogyi CCIC SP SU Summer Workshop S/S hod using ESI Ion rap (Bottom up) 1 An alternative strategy for complex

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

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

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

A study of matrix energy during peptide formation through chemical graphs

A study of matrix energy during peptide formation through chemical graphs International Journal of Mathematics and Soft Computing Vol.3, No.2 (2013), 11-15. ISSN Print : 2249-3328 ISSN Online: 2319-5215 A study of matrix energy during peptide formation through chemical graphs

More information

1 large 50g. 1 extra large 56g

1 large 50g. 1 extra large 56g National base for Standard Reference Release 28 slightly revised May, 206 Full Report (All s) 023, Egg, whole, raw, fresh Report Date: February 08, 208 06:8 EST values and weights are for edible portion.

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

Module No. 31: Peptide Synthesis: Definition, Methodology & applications

Module No. 31: Peptide Synthesis: Definition, Methodology & applications PAPER 9: TECHNIQUES USED IN MOLECULAR BIOPHYSICS I Module No. 31: Peptide Synthesis: Definition, Methodology & applications Objectives: 1. Introduction 2. Synthesis of peptide 2.1. N-terminal protected

More information

A Theoretical Inference of Protein Schemes from Amino Acid Sequences

A Theoretical Inference of Protein Schemes from Amino Acid Sequences A Theoretical Inference of Protein Schemes from Amino Acid Sequences Angel Villahoz-Baleta angel_villahozbaleta@student.uml.edu ABSTRACT Proteins are based on tri-dimensional dispositions generated from

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

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

Figure S1. Interaction of PcTS with αsyn. (a) 1 H- 15 N HSQC NMR spectra of 100 µm αsyn in the absence (0:1, black) and increasing equivalent

Figure S1. Interaction of PcTS with αsyn. (a) 1 H- 15 N HSQC NMR spectra of 100 µm αsyn in the absence (0:1, black) and increasing equivalent Figure S1. Interaction of PcTS with αsyn. (a) 1 H- 15 N HSQC NMR spectra of 100 µm αsyn in the absence (0:1, black) and increasing equivalent concentrations of PcTS (100 µm, blue; 500 µm, green; 1.5 mm,

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

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

1. Wings 5.. Jumping legs 2. 6 Legs 6. Crushing mouthparts 3. Segmented Body 7. Legs 4. Double set of wings 8. Curly antennae

1. Wings 5.. Jumping legs 2. 6 Legs 6. Crushing mouthparts 3. Segmented Body 7. Legs 4. Double set of wings 8. Curly antennae Biology Cladogram practice Name Per Date What is a cladogram? It is a diagram that depicts evolutionary relationships among groups. It is based on PHYLOGENY, which is the study of evolutionary relationships.

More information

2 Answer all the questions. CH(NH 2. )COOH, R is CH [1] (ii) Draw the structures of the ions formed by alanine at ph 6.0 and at ph 1.5.

2 Answer all the questions. CH(NH 2. )COOH, R is CH [1] (ii) Draw the structures of the ions formed by alanine at ph 6.0 and at ph 1.5. 2 Answer all the questions. 1 This question looks at the properties and chemistry of some α-amino acids. The general formula of an α-amino acid is R(N 2 ). (a) In the α-amino acid alanine, 3 (N 2 ), R

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

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

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

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

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

Discussion Section (Day, Time):

Discussion Section (Day, Time): Chemistry 27 pring 2005 Exam 3 Chemistry 27 Professor Gavin MacBeath arvard University pring 2005 our Exam 3 Friday April 29 th, 2005 11:07 AM 12:00 PM Discussion ection (Day, Time): TF: Directions: 1.

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

Performing pka Calculations in Proteins Using Free Energy Perturbation Adiabatic Charging (FEP/AC)

Performing pka Calculations in Proteins Using Free Energy Perturbation Adiabatic Charging (FEP/AC) Performing pka Calculations in Proteins Using Free Energy Perturbation Adiabatic Charging (FEP/AC) Lynn Kamerlin Uppsala University Purpose of the workshop: The aim of this workshop will be to provide

More information

Proteins and Amino Acids in Fine Particulate Matter in Rural. Guangzhou, Southern China: Seasonal Cycles, Sources, and. Atmospheric Processes

Proteins and Amino Acids in Fine Particulate Matter in Rural. Guangzhou, Southern China: Seasonal Cycles, Sources, and. Atmospheric Processes Proteins and Amino Acids in Fine Particulate Matter in Rural Guangzhou, Southern China: Seasonal Cycles, Sources, and Atmospheric Processes Tianli Song, Shan Wang, Yingyi Zhang, *, Junwei Song, Fobang

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

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

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

Edward Susko Department of Mathematics and Statistics, Dalhousie University. Introduction. Installation

Edward Susko Department of Mathematics and Statistics, Dalhousie University. Introduction. Installation 1 dist est: Estimation of Rates-Across-Sites Distributions in Phylogenetic Subsititution Models Version 1.0 Edward Susko Department of Mathematics and Statistics, Dalhousie University Introduction The

More information

Content : Properties of amino acids.. Separation and Analysis of Amino Acids

Content : Properties of amino acids.. Separation and Analysis of Amino Acids قسم الكيمياء الحيوية.دولت على سالمه د. استاذ الكيمياء الحيوية ٢٠١٥-٢٠١٤ المحاضرة الثانية 1 Content : Properties of amino acids.. Separation and Analysis of Amino Acids 2 3 Physical Properties of Amino

More information

Near UV-Visible Electronic Absorption Originating from Charged

Near UV-Visible Electronic Absorption Originating from Charged Electronic Supplementary Material (ESI) for Chemical Science. This journal is The Royal Society of Chemistry 2017 Supporting Information Near UV-Visible Electronic Absorption Originating from Charged Amino

More information

Novel 2D Graphic Representation of Protein Sequence and Its Application

Novel 2D Graphic Representation of Protein Sequence and Its Application Journal of Fiber Bioengineering and Informatics 7:1 (2014) 23 33 doi:10.3993/jfbi03201403 Novel 2D Graphic Representation of Protein Sequence and Its Application Yongbin Zhao, Xiaohong Li, Zhaohui Qi College

More information

4. The Michaelis-Menten combined rate constant Km, is defined for the following kinetic mechanism as k 1 k 2 E + S ES E + P k -1

4. The Michaelis-Menten combined rate constant Km, is defined for the following kinetic mechanism as k 1 k 2 E + S ES E + P k -1 Fall 2000 CH 595C Exam 1 Answer Key Multiple Choice 1. One of the reasons that enzymes are such efficient catalysts is that a) the energy level of the enzyme-transition state complex is much higher than

More information

SPECTRA LIBRARY ASSISTED DE NOVO PEPTIDE SEQUENCING FOR HCD AND ETD SPECTRA PAIRS

SPECTRA LIBRARY ASSISTED DE NOVO PEPTIDE SEQUENCING FOR HCD AND ETD SPECTRA PAIRS SPECTRA LIBRARY ASSISTED DE NOVO PEPTIDE SEQUENCING FOR HCD AND ETD SPECTRA PAIRS 1 Yan Yan Department of Computer Science University of Western Ontario, Canada OUTLINE Background Tandem mass spectrometry

More information

BI/CH421 Biochemistry I Exam 1 09/29/2014

BI/CH421 Biochemistry I Exam 1 09/29/2014 Part I: Multiple choice for each question, circle the choice that best answers the question. Do not write the letter in the margin to indicate your answer, circle it. 3 points each. 1. For a reaction with

More information