7.012 Problem Set 1. i) What are two main differences between prokaryotic cells and eukaryotic cells?

Size: px
Start display at page:

Download "7.012 Problem Set 1. i) What are two main differences between prokaryotic cells and eukaryotic cells?"

Transcription

1 ame 7.01 Problem Set 1 Section Question 1 a) What are the four major types of biological molecules discussed in lecture? Give one important function of each type of biological molecule in the cell? b) Briefly answer the following questions. i) What are two main differences between prokaryotic cells and eukaryotic cells? ii) What is the difference between unicellular and multicellular organisms? iii) Are prokaryotes unicellular or multicellular? Are eukaryotes unicellular or multicellular?

2 Question 1, continued c) For the pairs of amino acids given below circle each side chain. Give the strongest type of interaction that occurs between the side chain groups of each pair. Amino Acids Interaction 3 GLYIE 3 GLUTAMIE 3 TYRSIE 3 GLUTAMI AID 3 ASPARAGIE 3 3 LYSIE d) Draw the chemical structure of the following polypeptide at p 7. cysteinealaninetyrosinephenylalanine e) In the structure that you drew above, circle a peptide bond Problem Set 1

3 Question The drug Minoxidil is used orally as an agent against hypertension and topically as a stimulant for hair growth. The structure if Minoxidil is shown. *Minoxidil is uncharged in its active state Minoxidil a) Below is a schematic of a Minoxidil binding site on a hypothetical protein. i) Draw the side chains at amino acid positions 51, 19, 134, and 167. ii) Draw Minoxidil as shown above binding in the site. Be sure to consider the interactions between Minoxidil and the side chains when orienting Minoxidil within the binding site. Glu 51 Asn 167 Val 19 Leu Problem Set 1 3

4 Question, continued b) List all the interactions that would occur between the specified amino acids and Minoxidil in the model you have proposed by filling out the table below. Amino acid Glu 51 Val 19 Leu 134 Asn 167 Interactions with Minoxidil c) To decide if your model is correct, you construct some altered versions of this protein and test whether Minoxidil still binds. Assume all other amino acids remain unchanged. The results are as follows: Protein Position 51 Position 19 Position 134 Position 167 Binds? normal Glu 51 Val 19 Leu 134 Asn 167 yes variant 1 Asp 51 Val 19 Leu 134 Asn 167 yes variant Gly 51 Val 19 Leu 134 Asn 167 yes variant 3 Gly 51 Val 19 Leu 134 Ala 167 no variant 4 Glu 51 Lys 19 Leu 134 Ala 167 no variant 5 Glu 51 Phe 19 Leu 134 Asn 167 yes f the possible orientations for Minoxidil in the binding site, only one orientation is consistent with the results above. Please check your model carefully, revise it if needed and answer the following questions. Explain in terms of your model and the likely interactions why... i) variant will bind Minoxidil but variant 3 will not bind Minoxidil. ii) variant 5 will bind Minoxidil but variant 4 will not bind Minoxidil Problem Set 1 4

5 Question 3 Growth factor receptors (shown below) are transmembrane proteins found on the cell surface. extracellular P P P P P P P P P P P P intracellular growth factor receptors a) The majority of the molecules that constitute the above membrane belong to what class of macromolecules? Explain the important qualities/properties of these molecules that allow them to form membranes Problem Set 1 5

6 Question 3, continued A smaller schematic of the growth factor receptor is shown here. = transmembrane region ] Sequence from this region shown below...phevalglyileleutrpphealalysserargglnasp... 3 b) Which stretch of amino acids in the above sequence is part of the transmembrane region of the receptor? ircle these amino acids and briefly explain your reasoning. When growth factor binds to the extracellular domain of the receptor, a conformational change occurs in the receptor. Growth factor binding causes dimerization of two adjacent receptors in the cell membrane. Upon dimerization, the intracellular domains of the receptors become activated. See schematic below. ligand ligand extracellullar ligandbinding domain Receptor 1 Receptor plasma membrane intracellular domain inactive domains active domains 7.01 Problem Set 1 6

7 Question 3, continued c) Regions of the two receptors that interact upon dimerization are drawn below. In parts (i iv) below, name the strongest type of interaction (choose from; hydrogen bond, ionic, covalent, van der Waals) that occurs between the side chains of the amino acids indicated. Receptor 1 ys36 S S ys8 Receptor Ala45 3 S ys75 Asp68 3 Lys65 Ser53 Gln1 Phe Val98 Interacting Side chains Type of interaction i) Phe50 : Val98 ii) Asp68 : Lys65 iii) ys75 : ys8 iv) Ser53 : Gln1 d) Explain how Gln1 and Val98, which are far apart in the primary sequence of the protein, can be close to each other in the region of the protein diagrammed above Problem Set 1 7

8 7.01 Problem Set 1 8

9 Question 3, continued e) Molecular interactions between the two receptors are important for dimerization. Thus, substitution of certain amino acids in the protein can affect receptor dimerization. Predict whether the receptors will or will not be able to dimerize given the substitutions (i iv) below. EXPLAI your reasoning. i) Asp68 Arg: ii) Ser53 Thr: iii) Phe50 Asn: iv) Val98 Ile: e) Substitution of one amino acid, ys75 Gly, leads to dimerization of the receptors with or without growth factor. Provide a brief explanation for this observation Problem Set 1 9

10 Question 4 The following reaction is the tenth and final step in glycolysis: pyruvate kinase Phosphoenolpyruvate ADP <> pyruvate ATP G o' = 7.5 kcal/mol a) alculate K eq for this reaction under standard conditions at 5 o, and circle the correct statement below. At equilibrium, [phosphoenolpyruvate] > [pyruvate] At equilibrium, [phosphoenolpyruvate] < [pyruvate] b) The following concentrations are found in red blood cells. alculate G for the reaction at 37 o. In which direction will this reaction proceed spontaneously? [ADP] = 10 mm [ATP] = 81 mm [phosphoenolpyruvate] = 10 mm [pyruvate] = 500 mm 7.01 Problem Set 1 10

11 Question 4, continued c) Draw the energy profile for this reaction under physiological conditions. n the diagram be sure to: 1) show relative energy levels of the reactants and the products. ) label the axes 3) label reactants and products 4) indicate the energy of activation 5) indicate G d) ow does pyruvate kinase (the enzyme that catalyzes this reaction) change the energy profile? 7.01 Problem Set 1 11

12 STRUTURES F AMI AIDS at p ALAIE (ala) 3 ARGIIE (arg) 3 ASPARAGIE (asn) 3 ASPARTI AID (asp) S 3 YSTEIE (cys) 3 GLUTAMI AID (glu) 3 GLUTAMIE (gln) 3 GLYIE (gly) 3 ISTIDIE (his) ISLEUIE (ile) 3 LEUIE (leu) LYSIE (lys) S 3 3 METIIE (met) 3 3 TREIE (thr) 3 3 TRYPTPA (trp) PEYLALAIE (phe) 3 PRLIE (pro) TYRSIE (tyr) 3 SERIE (ser) VALIE (val) Problem Set 1 1

13 For the reaction: A B K eq D with G o as its standard free energy at equilibrium: G 0 = RT ln [][D] [A][B] or: ' [][D] G 0 ' [A][B] = e RT where: if T = 5 o then RT = 0.59 kcal mol if T = 37 o then RT = 0.61 kcal mol [][ D] under any conditions: G = G RT ln 0 [A] [ B] Enzyme Kinetics: For the enzyme catalyzed reaction: k 1 S E ES k 3 E P k where: S = substrate E = enzyme P = product the reaction velocity is given by V = V max [S] K M [S] where: K M = k k 3 k 1 and: V max = k 3 [E] total 7.01 Problem Set 1 13

7.014 Quiz I Handout

7.014 Quiz I Handout 7.014 Quiz I andout Quiz I announcements: Quiz I: Friday, February 27 12:05 12:55 Walker Gym, rd floor (room 5040) **This will be a closed book exam** Quiz Review Session: Wednesday, February 25 7:00 9:00

More information

7.012 Problem Set 1 Solutions

7.012 Problem Set 1 Solutions ame TA Section 7.012 Problem Set 1 Solutions Your answers to this problem set must be inserted into the large wooden box on wheels outside 68120 by 4:30 PM, Thursday, September 15. Problem sets will not

More information

Bio 111 Exam #2. Version A 11/13/06. Question Value Score 1 23 TOTAL: 100. Your Name: Solutions can be found in the Biochemistry 5 handout.

Bio 111 Exam #2. Version A 11/13/06. Question Value Score 1 23 TOTAL: 100. Your Name: Solutions can be found in the Biochemistry 5 handout. Bio 111 Exam #2 Version A 11/13/06 Your ame: TA's ame: Lab Section Write your initials on every page in the space provided. This exam has 11 pages including this coversheet. heck that you have pages 111.

More information

L L. Figure by MIT OCW.

L L. Figure by MIT OCW. MIT Biology Department 7.012: Introductory Biology Fall 20 Instructors: Professor Eric ander, Professor Robert A. Weinberg, Dr. laudette Gardel ame: Question 1 7.012 Problem Set 2 Please print out this

More information

7.014 Problem Set 2. [substrate] mm Initial reaction velocity* mmol/min

7.014 Problem Set 2. [substrate] mm Initial reaction velocity* mmol/min ame ection 7.014 Problem et 2 Answers to this problem set are to be turned in at the box outside 68120 by 4:00 pm Wednesday, February 20. Problem sets will not be accepted late. olutions will be posted

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

Proteins: Characteristics and Properties of Amino Acids

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

More information

Any protein that can be labelled by both procedures must be a transmembrane protein.

Any protein that can be labelled by both procedures must be a transmembrane protein. 1. What kind of experimental evidence would indicate that a protein crosses from one side of the membrane to the other? Regions of polypeptide part exposed on the outside of the membrane can be probed

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

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

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

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

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

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

Amino Acid Side Chain Induced Selectivity in the Hydrolysis of Peptides Catalyzed by a Zr(IV)-Substituted Wells-Dawson Type Polyoxometalate

Amino Acid Side Chain Induced Selectivity in the Hydrolysis of Peptides Catalyzed by a Zr(IV)-Substituted Wells-Dawson Type Polyoxometalate Amino Acid Side Chain Induced Selectivity in the Hydrolysis of Peptides Catalyzed by a Zr(IV)-Substituted Wells-Dawson Type Polyoxometalate Stef Vanhaecht, Gregory Absillis, Tatjana N. Parac-Vogt* Department

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

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

Biological Macromolecules

Biological Macromolecules Introduction for Chem 493 Chemistry of Biological Macromolecules Dr. L. Luyt January 2008 Dr. L. Luyt Chem 493-2008 1 Biological macromolecules are the molecules of life allow for organization serve a

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

C H E M I S T R Y N A T I O N A L Q U A L I F Y I N G E X A M I N A T I O N SOLUTIONS GUIDE

C H E M I S T R Y N A T I O N A L Q U A L I F Y I N G E X A M I N A T I O N SOLUTIONS GUIDE C H E M I S T R Y 2 0 0 0 A T I A L Q U A L I F Y I G E X A M I A T I SLUTIS GUIDE Answers are a guide only and do not represent a preferred method of solving problems. Section A 1B, 2A, 3C, 4C, 5D, 6D,

More information

Ramachandran Plot. 4ysz Phi (degrees) Plot statistics

Ramachandran Plot. 4ysz Phi (degrees) Plot statistics B Ramachandran Plot ~b b 135 b ~b ~l l Psi (degrees) 5-5 a A ~a L - -135 SER HIS (F) 59 (G) SER (B) ~b b LYS ASP ASP 315 13 13 (A) (F) (B) LYS ALA ALA 315 173 (E) 173 (E)(A) ~p p ~b - -135 - -5 5 135 (degrees)

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

NAME. EXAM I I. / 36 September 25, 2000 Biochemistry I II. / 26 BICH421/621 III. / 38 TOTAL /100

NAME. EXAM I I. / 36 September 25, 2000 Biochemistry I II. / 26 BICH421/621 III. / 38 TOTAL /100 EXAM I I. / 6 September 25, 2000 Biochemistry I II. / 26 BIH421/621 III. / 8 TOTAL /100 I. MULTIPLE HOIE (6 points) hoose the BEST answer to the question by circling the appropriate letter. 1. An amino

More information

Secondary Structure. Bioch/BIMS 503 Lecture 2. Structure and Function of Proteins. Further Reading. Φ, Ψ angles alone determine protein structure

Secondary Structure. Bioch/BIMS 503 Lecture 2. Structure and Function of Proteins. Further Reading. Φ, Ψ angles alone determine protein structure Bioch/BIMS 503 Lecture 2 Structure and Function of Proteins August 28, 2008 Robert Nakamoto rkn3c@virginia.edu 2-0279 Secondary Structure Φ Ψ angles determine protein structure Φ Ψ angles are restricted

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

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

Advanced Certificate in Principles in Protein Structure. You will be given a start time with your exam instructions

Advanced Certificate in Principles in Protein Structure. You will be given a start time with your exam instructions BIRKBECK COLLEGE (University of London) Advanced Certificate in Principles in Protein Structure MSc Structural Molecular Biology Date: Thursday, 1st September 2011 Time: 3 hours You will be given a start

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

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

NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease

NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease University of Wollongong Research Online Faculty of Science - Papers (Archive) Faculty of Science, Medicine and Health 2009 NMR study of complexes between low molecular mass inhibitors and the West Nile

More information

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces: Electronic Supplementary

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces: Electronic Supplementary Electronic Supplementary Material (ESI) for Journal of Materials Chemistry B. This journal is The Royal Society of Chemistry 21 What makes a good graphene-binding peptide? Adsorption of amino acids and

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

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

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

Chemical Models, Properties and Structures Learning Goals:

Chemical Models, Properties and Structures Learning Goals: hemical Models, Properties and Structures Learning Goals: 1. To practice with the different atoms used in Bio 111: to know the number of bonds made by each kind of atom, the structures that they form,

More information

7.014 Problem Set 1. A nswers to this problem set are to be turned in. Problem sets will not be accepted late. Solutions will be posted on the web.

7.014 Problem Set 1. A nswers to this problem set are to be turned in. Problem sets will not be accepted late. Solutions will be posted on the web. MIT Department of Biology 7.014 Introductory Biology, Spring 2005 Name: Section : 7.014 Problem Set 1 A nswers to this problem set are to be turned in. Problem sets will not be accepted late. Solutions

More information

Prof. Jason Kahn Your Signature: Exams written in pencil or erasable ink will not be re-graded under any circumstances.

Prof. Jason Kahn Your Signature: Exams written in pencil or erasable ink will not be re-graded under any circumstances. 1 Biochemistry 461 February 16, 1995 Exam #1 Prof. Jason Kahn Your Printed Name: Your SS#: Your Signature: You have 75 minutes for this exam. Exams written in pencil or erasable ink will not be re-graded

More information

Final Chem 4511/6501 Spring 2011 May 5, 2011 b Name

Final Chem 4511/6501 Spring 2011 May 5, 2011 b Name Key 1) [10 points] In RNA, G commonly forms a wobble pair with U. a) Draw a G-U wobble base pair, include riboses and 5 phosphates. b) Label the major groove and the minor groove. c) Label the atoms of

More information

Central Dogma. modifications genome transcriptome proteome

Central Dogma. modifications genome transcriptome proteome entral Dogma DA ma protein post-translational modifications genome transcriptome proteome 83 ierarchy of Protein Structure 20 Amino Acids There are 20 n possible sequences for a protein of n residues!

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

B O C 4 H 2 O O. NOTE: The reaction proceeds with a carbonium ion stabilized on the C 1 of sugar A.

B O C 4 H 2 O O. NOTE: The reaction proceeds with a carbonium ion stabilized on the C 1 of sugar A. hbcse 33 rd International Page 101 hemistry lympiad Preparatory 05/02/01 Problems d. In the hydrolysis of the glycosidic bond, the glycosidic bridge oxygen goes with 4 of the sugar B. n cleavage, 18 from

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

Signal Transduction Phosphorylation Protein kinases. Misfolding diseases. Protein Engineering Lysozyme variants

Signal Transduction Phosphorylation Protein kinases. Misfolding diseases. Protein Engineering Lysozyme variants Signal Transduction Phosphorylation Protein kinases Misfolding diseases Protein Engineering Lysozyme variants Cells and Signals Regulation The cell must be able to respond to stimuli Cellular activities

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

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

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

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

What binds to Hb in addition to O 2?

What binds to Hb in addition to O 2? Reading: Ch5; 158-169, 162-166, 169-174 Problems: Ch5 (text); 3,7,8,10 Ch5 (study guide-facts); 1,2,3,4,5,8 Ch5 (study guide-apply); 2,3 Remember Today at 5:30 in CAS-522 is the second chance for the MB

More information

Supplementary figure 1. Comparison of unbound ogm-csf and ogm-csf as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine

Supplementary figure 1. Comparison of unbound ogm-csf and ogm-csf as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine Supplementary figure 1. Comparison of unbound and as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine GM-CSF (slate) with bound GM-CSF in the GIF:GM-CSF complex (GIF: green,

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

Major Types of Association of Proteins with Cell Membranes. From Alberts et al

Major Types of Association of Proteins with Cell Membranes. From Alberts et al Major Types of Association of Proteins with Cell Membranes From Alberts et al Proteins Are Polymers of Amino Acids Peptide Bond Formation Amino Acid central carbon atom to which are attached amino group

More information

1. What is an ångstrom unit, and why is it used to describe molecular structures?

1. What is an ångstrom unit, and why is it used to describe molecular structures? 1. What is an ångstrom unit, and why is it used to describe molecular structures? The ångstrom unit is a unit of distance suitable for measuring atomic scale objects. 1 ångstrom (Å) = 1 10-10 m. The diameter

More information

Proton Acidity. (b) For the following reaction, draw the arrowhead properly to indicate the position of the equilibrium: HA + K + B -

Proton Acidity. (b) For the following reaction, draw the arrowhead properly to indicate the position of the equilibrium: HA + K + B - Proton Acidity A01 Given that acid A has a pk a of 15 and acid B has a pk a of 10, then: (a) Which of the two acids is stronger? (b) For the following reaction, draw the arrowhead properly to indicate

More information

Unraveling the degradation of artificial amide bonds in Nylon oligomer hydrolase: From induced-fit to acylation processes

Unraveling the degradation of artificial amide bonds in Nylon oligomer hydrolase: From induced-fit to acylation processes Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2015 Supporting Information for Unraveling the degradation of artificial amide bonds

More information

Protein Fragment Search Program ver Overview: Contents:

Protein Fragment Search Program ver Overview: Contents: Protein Fragment Search Program ver 1.1.1 Developed by: BioPhysics Laboratory, Faculty of Life and Environmental Science, Shimane University 1060 Nishikawatsu-cho, Matsue-shi, Shimane, 690-8504, Japan

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

Chem 250 Evening Exam 2

Chem 250 Evening Exam 2 Page 1 of 10 Evening Exam 2 ame:: Chem 250 Evening Exam 2 This exam is composed of 40 questions. As discussed in the course syllabus, honesty and integrity are absolute essentials for this class. In fairness

More information

Desorption/Ionization Efficiency of Common Amino Acids in. Surface-assisted Laser Desorption/ionization Mass Spectrometry

Desorption/Ionization Efficiency of Common Amino Acids in. Surface-assisted Laser Desorption/ionization Mass Spectrometry SUPPORTING INFORMATION Desorption/Ionization Efficiency of Common Amino Acids in Surface-assisted Laser Desorption/ionization Mass Spectrometry (SALDI-MS) with Nanostructured Platinum Syuhei Nitta, Hideya

More information

Supporting information

Supporting information Electronic Supplementary Material (ESI) for New Journal of Chemistry. This journal is The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2015 Supporting information Influence

More information

Sequential resonance assignments in (small) proteins: homonuclear method 2º structure determination

Sequential resonance assignments in (small) proteins: homonuclear method 2º structure determination Lecture 9 M230 Feigon Sequential resonance assignments in (small) proteins: homonuclear method 2º structure determination Reading resources v Roberts NMR of Macromolecules, Chap 4 by Christina Redfield

More information

Structure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase Cwc27

Structure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase Cwc27 Acta Cryst. (2014). D70, doi:10.1107/s1399004714021695 Supporting information Volume 70 (2014) Supporting information for article: Structure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase

More information

Peptide Syntheses. Illustrative Protection: BOC/ t Bu. A. Introduction. do not acid

Peptide Syntheses. Illustrative Protection: BOC/ t Bu. A. Introduction. do not acid Kevin Burgess, May 3, 2017 1 Peptide yntheses from chapter(s) in the recommended text A. Introduction do not acid -Met-e- -Met-Met- -e-e- -e-met- dipeptide dipeptide dipeptide dipeptide diketopiperazine

More information

The Structure of Enzymes!

The Structure of Enzymes! The Structure of Enzymes Levels of Protein Structure 0 order amino acid composition Primary Secondary Motifs Tertiary Domains Quaternary ther sequence repeating structural patterns defined by torsion angles

More information

The Structure of Enzymes!

The Structure of Enzymes! The Structure of Enzymes Levels of Protein Structure 0 order amino acid composition Primary Secondary Motifs Tertiary Domains Quaternary ther sequence repeating structural patterns defined by torsion angles

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

2. In regards to the fluid mosaic model, which of the following is TRUE?

2. In regards to the fluid mosaic model, which of the following is TRUE? General Biology: Exam I Sample Questions 1. How many electrons are required to fill the valence shell of a neutral atom with an atomic number of 24? a. 0 the atom is inert b. 1 c. 2 d. 4 e. 6 2. In regards

More information

Objective: Students will be able identify peptide bonds in proteins and describe the overall reaction between amino acids that create peptide bonds.

Objective: Students will be able identify peptide bonds in proteins and describe the overall reaction between amino acids that create peptide bonds. Scott Seiple AP Biology Lesson Plan Lesson: Primary and Secondary Structure of Proteins Purpose:. To understand how amino acids can react to form peptides through peptide bonds.. Students will be able

More information

Clustering and Model Integration under the Wasserstein Metric. Jia Li Department of Statistics Penn State University

Clustering and Model Integration under the Wasserstein Metric. Jia Li Department of Statistics Penn State University Clustering and Model Integration under the Wasserstein Metric Jia Li Department of Statistics Penn State University Clustering Data represented by vectors or pairwise distances. Methods Top- down approaches

More information

Biochemical Pathways

Biochemical Pathways Biochemical Pathways Living organisms can be divided into two large groups according to the chemical form in which they obtain carbon from the environment. Autotrophs can use carbon dioxide from the atmosphere

More information

An Introduction to Metabolism

An 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 information

Supplementary Information. Broad Spectrum Anti-Influenza Agents by Inhibiting Self- Association of Matrix Protein 1

Supplementary Information. Broad Spectrum Anti-Influenza Agents by Inhibiting Self- Association of Matrix Protein 1 Supplementary Information Broad Spectrum Anti-Influenza Agents by Inhibiting Self- Association of Matrix Protein 1 Philip D. Mosier 1, Meng-Jung Chiang 2, Zhengshi Lin 2, Yamei Gao 2, Bashayer Althufairi

More information

Chemistry Problem Set #9 Due on Thursday 11/15/18 in class.

Chemistry Problem Set #9 Due on Thursday 11/15/18 in class. Chemistry 391 - Problem Set #9 Due on Thursday 11/15/18 in class. Name 1. There is a real enzyme called cocaine esterase that is produced in bacteria that live at the base of the coca plant. The enzyme

More information

BSc and MSc Degree Examinations

BSc and MSc Degree Examinations Examination Candidate Number: Desk Number: BSc and MSc Degree Examinations 2018-9 Department : BIOLOGY Title of Exam: Molecular Biology and Biochemistry Part I Time Allowed: 1 hour and 30 minutes Marking

More information

Overview of Kinetics

Overview of Kinetics Overview of Kinetics [P] t = ν = k[s] Velocity of reaction Conc. of reactant(s) Rate of reaction M/sec Rate constant sec -1, M -1 sec -1 1 st order reaction-rate depends on concentration of one reactant

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

Answer Key Evening Exam 2v1

Answer Key Evening Exam 2v1 Page 1 of 11 Evening Exam 2 ame: Chem 250 Answer Key Evening Exam 2v1 This exam is composed of 40 questions. As discussed in the course syllabus, honesty and integrity are absolute essentials for this

More information

Supporting information to: Time-resolved observation of protein allosteric communication. Sebastian Buchenberg, Florian Sittel and Gerhard Stock 1

Supporting information to: Time-resolved observation of protein allosteric communication. Sebastian Buchenberg, Florian Sittel and Gerhard Stock 1 Supporting information to: Time-resolved observation of protein allosteric communication Sebastian Buchenberg, Florian Sittel and Gerhard Stock Biomolecular Dynamics, Institute of Physics, Albert Ludwigs

More information

Chapter 6- An Introduction to Metabolism*

Chapter 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 information

Biochemistry 3100 Sample Problems Binding proteins, Kinetics & Catalysis

Biochemistry 3100 Sample Problems Binding proteins, Kinetics & Catalysis (1) Draw an approximate denaturation curve for a typical blood protein (eg myoglobin) as a function of ph. (2) Myoglobin is a simple, single subunit binding protein that has an oxygen storage function

More information

BIRKBECK COLLEGE (University of London)

BIRKBECK COLLEGE (University of London) BIRKBECK COLLEGE (University of London) SCHOOL OF BIOLOGICAL SCIENCES M.Sc. EXAMINATION FOR INTERNAL STUDENTS ON: Postgraduate Certificate in Principles of Protein Structure MSc Structural Molecular Biology

More information

A) at equilibrium B) endergonic C) endothermic D) exergonic E) exothermic.

A) at equilibrium B) endergonic C) endothermic D) exergonic E) exothermic. CHEM 2770: Elements of Biochemistry Mid Term EXAMINATION VERSION A Date: October 29, 2014 Instructor: H. Perreault Location: 172 Schultz Time: 4 or 6 pm. Duration: 1 hour Instructions Please mark the Answer

More information

Beaming in your answers

Beaming in your answers Bio 111 andout for Biochemistry 1 This handout contains: 1. Today s iclicker Questions 2. The handout for today s lecture. iclicker Question #13A - before lecture Your lunch consists primarily of polymers.

More information

TRANSLATION: How to make proteins?

TRANSLATION: How to make proteins? TRANSLATION: How to make proteins? EUKARYOTIC mrna CBP80 NUCLEUS SPLICEOSOME 5 UTR INTRON 3 UTR m 7 GpppG AUG UAA 5 ss 3 ss CBP20 PABP2 AAAAAAAAAAAAA 50-200 nts CYTOPLASM eif3 EJC PABP1 5 UTR 3 UTR m 7

More information

Physiochemical Properties of Residues

Physiochemical Properties of Residues Physiochemical Properties of Residues Various Sources C N Cα R Slide 1 Conformational Propensities Conformational Propensity is the frequency in which a residue adopts a given conformation (in a polypeptide)

More information

MOLECULAR DRUG TARGETS

MOLECULAR DRUG TARGETS MOLECULAR DRUG TARGETS LEARNING OUTCOMES At the end of this session student shall be able to: List different types of druggable targets Describe forces involved in drug-receptor interactions Describe theories

More information

X-ray crystallography NMR Cryoelectron microscopy

X-ray crystallography NMR Cryoelectron microscopy Molecular Graphics with PyMOL Overview of: Protein Data Bank Coordinates Jean-Yves Sgro PyMOL interface Hands-on! Experimental Methods 3 Main: X-ray crystallography NMR Cryoelectron microscopy X-ray source

More information

f) Adding an enzyme does not change the Gibbs free energy. It only increases the rate of the reaction by lowering the activation energy.

f) Adding an enzyme does not change the Gibbs free energy. It only increases the rate of the reaction by lowering the activation energy. Problem Set 2-Answer Key BILD1 SP16 1) How does an enzyme catalyze a chemical reaction? Define the terms and substrate and active site. An enzyme lowers the energy of activation so the reaction proceeds

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

First Problem Set, Due 30 Sep. (1st midterm is 7 Oct.) If you want it graded by 6 Oct, turn in on or before 30 Sep. at 5 pm.

First Problem Set, Due 30 Sep. (1st midterm is 7 Oct.) If you want it graded by 6 Oct, turn in on or before 30 Sep. at 5 pm. First Problem Set, Due 30 Sep. (1st midterm is 7 ct.) If you want it graded by 6 ct, turn in on or before 30 Sep. at 5 pm. Show your work calculations / steps!! Problems from Chapter 1 1 EM of a eukaryotic

More information

Amino Acids and Proteins at ZnO-water Interfaces in Molecular Dynamics Simulations: Electronic Supplementary Information

Amino Acids and Proteins at ZnO-water Interfaces in Molecular Dynamics Simulations: Electronic Supplementary Information Amino Acids and Proteins at ZnO-water Interfaces in Molecular Dynamics Simulations: Electronic Supplementary Information Grzegorz Nawrocki and Marek Cieplak Institute of Physics, Polish Academy of Sciences,

More information

NAME IV. /22. I. MULTIPLE CHOICE. (48 points; 2 pts each) Choose the BEST answer to the question by circling the appropriate letter.

NAME IV. /22. I. MULTIPLE CHOICE. (48 points; 2 pts each) Choose the BEST answer to the question by circling the appropriate letter. NAME Exam I I. /48 September 25, 2017 Biochemistry I II. / 4 BI/CH 421/621 III. /26 IV. /22 TOTAL /100 I. MULTIPLE CHOICE. (48 points; 2 pts each) Choose the BEST answer to the question by circling the

More information

Patrick: An Introduction to Medicinal Chemistry 5e Chapter 04

Patrick: An Introduction to Medicinal Chemistry 5e Chapter 04 01) Which of the following statements is not true about receptors? a. Most receptors are proteins situated inside the cell. b. Receptors contain a hollow or cleft on their surface which is known as a binding

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

Sample Questions for the Chemistry of Life Topic Test

Sample Questions for the Chemistry of Life Topic Test Sample Questions for the Chemistry of Life Topic Test 1. Enzymes play a crucial role in biology by serving as biological catalysts, increasing the rates of biochemical reactions by decreasing their activation

More information

2017 DECEMBER BIOLOGY SEMESTER EXAM DISTRICT REVIEW

2017 DECEMBER BIOLOGY SEMESTER EXAM DISTRICT REVIEW Name: Period: 2017 DECEMBER BIOLOGY SEMESTER EXAM DISTRICT REVIEW 1. List the characteristics of living things. (p 7) 2. Use the Aquatic Food Web above to answer the following questions (Ch. 2) a. Which

More information

Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013

Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013 Hydration of protein-rna recognition sites Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India 1 st November, 2013 Central Dogma of life DNA

More information

Midterm Review Guide. Unit 1 : Biochemistry: 1. Give the ph values for an acid and a base. 2. What do buffers do? 3. Define monomer and polymer.

Midterm Review Guide. Unit 1 : Biochemistry: 1. Give the ph values for an acid and a base. 2. What do buffers do? 3. Define monomer and polymer. Midterm Review Guide Name: Unit 1 : Biochemistry: 1. Give the ph values for an acid and a base. 2. What do buffers do? 3. Define monomer and polymer. 4. Fill in the Organic Compounds chart : Elements Monomer

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

Prof. Jason D. Kahn Your Signature: Exams written in pencil or erasable ink will not be re-graded under any circumstances.

Prof. Jason D. Kahn Your Signature: Exams written in pencil or erasable ink will not be re-graded under any circumstances. 1 Biochemistry 461, Section I February 27, 1997 Exam #1 Prof. Jason D. Kahn Your Printed ame: Your SS#: Your Signature: You have 80 minutes for this exam. Exams written in pencil or erasable ink will not

More information

Supplement information

Supplement information Electronic Supplementary Material (ESI) for Physil Chemistry Chemil Physics. This journal is the Owner Societies 216 Supplement information Fullerenol C 6 (OH) 16 prevents amyloid fibrillization of Aβ

More information