Part A: Amino Acids and Peptides (Is the peptide IAG the same as the peptide GAI?)

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "Part A: Amino Acids and Peptides (Is the peptide IAG the same as the peptide GAI?)"

Transcription

1 ChemActivity 46 Amino Acids, Polypeptides and Proteins 1 ChemActivity 46 Part A: Amino Acids and Peptides (Is the peptide IAG the same as the peptide GAI?) Model 1: The 20 Amino Acids at Biological p See diagram of AA structures at the end of this ChemActivity. Side chains are classified into three general types: those with i) nonpolar sidechains ii) polar sidechains iii) charged sidechains (at biological p) A working definition of nonpolar = the sidechain has more than 2 C's per neutral heteroatom. ("hetero" = "other" and refers to atoms "other" than C or.) 1. Each amino acid has a distinct side chain attached to a carbon referred to as the "alpha carbon." a) Why is this carbon called the "alpha carbon." It is the first carbon next to the carbonyl. This is the same nomenclature used previously. b) Identify a example of an amino acid with a nonpolar sidechain a polar sidechain a charged sidechain. See examples on chart at the end of this activity. 2. All but one amino acid is chiral. a) Which amino acid is not chiral. proline b) What is the absolute configuration ( or S) of alanine? c) Chiral, naturally occurring amino acids are called "L-amino acids." Confirm that, at the alpha carbon, all L-amino acids have the same spatial arrangement of the ammonium, carboxylate, and sidechain groups at the alpha C. ote that because of the rules for assigning and S, cysteine has an assignment even though it is an L amino acid. d) Use wedge and dash bonds to draw a "D-amino acid" (one not found in nature). 3 C 3

2 ChemActivity 46 Amino Acids, Polypeptides and Proteins 2 Model 2: Peptide Bonds/Dipeptides/Polypeptide Chains Specially designed enzyme catalysts can hold two amino acids in the right conformation and covalently link them together, forming a dipeptide. Enzyme catalysts can add more amino acids to the carboxy terminal end, one at a time, building a long unbranched chain of amino acids called a polypeptide. C 2 "Amino Terminus" 3 C 2 S "Carboxy Terminus" (chain extended by adding amino acids to carboxy end) 3. A peptide bond is the bond formed with the help of an enzyme that connects two amino acids. a) Put a slash through the peptide bond in Model 2, as if you were retrosynthesizing this molecule from its constituent amino acids. b) When a peptide bond is made, a carboxylic acid functional group and an amine functional group are combined to form a functional group called an amide. Put a box around the atoms comprising the amide functional group in the dipeptide above. c) n the structure in Model 2, circle together all the atoms that came from an individual amino acid, and identify each of these amino acids by name. Cysteine and serine. 4. The dipeptide shown in Model 2 is named "Cys-Ser" or "CS". a) Explain each of these names. These are the three-letter code and one-letter code names, respectively. b) Draw the tri-peptide IAG. 3 C C 2 C 3 C 3 3 C 5. A polypeptide chain is a long chain of amino acids. a) Write the name (using the three-letter codes) of a 5 amino-acid polypeptide chain that you expect to be very insoluble in water. Such polypeptides are called hydrophobic because they appear to "run away from water." Any polypeptide containing mostly nonpolar (and very few polar) amino acid residues. b) Write the name (using the three-letter codes) of a 5 amino-acid polypeptide chain that you expect to be very soluble in water. Such polypeptides are called hydrophilic because they appear to "love water." IAG

3 ChemActivity 46 Amino Acids, Polypeptides and Proteins 3 Any polypeptide containing mostly polar (and very few nonpolar) amino acid residues. Part B: Proteins (What is the difference between the 1 o, 2 o, 3 o and 4 0 structures of a protein?) Model 3: a-elix and b-pleated Sheet part of a polypeptide chain can coil up into a hollow rod-like structure called an a- helix. This coil can be 10 amino acids long or hundreds of amino acids long. A part of a polypeptide chain can line up with other parts of the chain to form a fabric-like array called a b-pleated sheet. Both α-helices and β-pleated sheets are held together by hydrogen bonding between different amino acids in the polypeptide backbone (backbone shown in bold, below). amino terminus carboxy terminus Schematic of polypeptide backbone (only atoms involved in hydrogen bonding are shown) S S disulfide bond 6. Label the two structures in Model 3 as being either an α-helix or a β-pleated sheet, based on the descriptions at the top of the page. The alpha helix is at the top of the page. 7. What do the dotted lines on these structures represent? ydrogen bonds

4 ChemActivity 46 Amino Acids, Polypeptides and Proteins 4 8. A thiol is like an alcohol, but with S replacing. Two thiols can be oxidized (loss of 2 ) to form a disulfide bond (shown below). S S oxidize S S thiol thiol disulfide 2 a) What amino acid has a thiol sidechain? cysteine b) Modify the drawing of the β-pleated sheet in Model 3 to show how the sidechains shown at the bottom right of the drawing can be oxidized to covalently link two strands of the β-pleated sheet. Model 4: Protein Folding Parts of a large polypeptide chain will spontaneously organize into α-helices, β- pleated sheets and sometimes other less common sub-structures. These "sub-structures" will organize themselves into a specific 3D super-structure, which is mostly held together by non-covalent interactions like hydrogen bonds. A given sequence of amino acids will fold the same way to form the same 3D structure every time. This structure is called a protein. Many proteins are comprised of a single polypeptide chain between 50 and 500 amino acids long. Linear polypeptide chain: ALIVFYWMGPSTGCFPCEGQVIMDTWLAYSKDECGTSPQMWYFVILA...etc. spontaneously forms helices and sheets helix A helix C helix D amino terminus sheet A helix B carboxy terminus sheet B sub-structures spontaneously and repeatably organize into a very specific 3D structure indicates a binding site for another molecule = protein schematic of protein

5 ChemActivity 46 Amino Acids, Polypeptides and Proteins 5 9. Model 4 describes three levels of protein structure, usually called primary (1 o ), secondary (2 o ), and tertiary (3 o ) structure. a) If you know the primary structure of a protein, what do you know? You know the linear sequence of amino acids in the protein. b) If you know the secondary structure of a protein, what do you know? You know what sections of the protein fold into alpha helices, beta pleated sheets (and other substructures). c) If you know the tertiary structure of a protein, what do you know? You know the three dimensional shape of the folded protein. Model 5: Protein Function Proteins (on average) make up 50% of the dry weight of a cell. They serve a myriad of chemical and structural functions including structure (hair, skin, connective tissue, muscle etc.) enzymes (very specific and efficient catalysts such as those in Model 2) antibodies hormones transport for smaller molecules (e.g. 2 /C 2 to and from the lungs and mitochondria = the tiny combustion engine that provides power to each of our cells). 10. The chicken and the egg paradox speaks to the problem of how the first chicken got here. Explain how this parable relates to proteins. (int: see Model 2). Since proteins are needed to make other proteins, this creates a paradox how was the first protein synthesized? Exercises for Part A 1. There is a difference between the tripeptides IAG and GAI. Explain.

6 ChemActivity 46 Amino Acids, Polypeptides and Proteins 6 2. Simply mixing the three amino acids shown below results in an extremely low yield of the tripeptide IAG. 3 C 3 3 C C 2 C 3 C 3 3 This is partly because a carboxylate ion is a terrible electrophile and an ammonium ion is a terrible nucleophile. The enzymes involved in peptide synthesis overcomes these problems by activating the amino and carboxy ends of each amino acid. 3 withdraws e- EnzymeA donates e- withdraws e- EnzymeB donates e- ' a) EnzymeA and EnzymeB, above, either donate or withdraw electron density. For each enzyme, circle the correct function and cross out the wrong one. b) What other function must the enzyme perform to ensure a 100% yield of the tripeptide IAG? c) ame one possible peptide sideproduct that would form if the protein simply activated both ends of the three amino acids shown above. Exercises for Part B 3. In the 1960's Linus Pauling and E.J. Corey discovered that certain sequences of amino acids tend to organize themselves into rod-like structures (α-helix) while other sequences organize into sheet-like structures (β-pleated sheet). Still other sequences form neither. For example, a sequence that has many proline amino acids will double back on itself too often to be able to form either an α-helix or a β- pleated sheet. Among all amino acids, what is unique about proline? 4. Some very large proteins are actually made up of smaller protein sub-units. For example, the transport protein, hemoglobin is comprised of four nearly identical polypeptide chains. Each chain undergoes folding to produce a specific secondary (2 o ) then tertiary (3 o ) structure. Finally, the four 3 o structures come together to form the quaternary (4 o ) structure of the protein hemoglobin. What is the difference between tertiary structure and quaternary structure of a protein?

7 ChemActivity 46 Amino Acids, Polypeptides and Proteins 7 5. Explain the following statement: "At this point in time, we are very bad at predicting the tertiary structure of a protein based on its linear amino acid sequence. evertheless, the amino acid sequence of a protein determines the tertiary structure of the protein." 6. The following pathway is an example of the trouble a chemist has to go through to create a single peptide bond in the laboratory. Describe at least two things this cumbersome synthesis accomplishes that simply adding two amino acids together cannot accomplish. 2 ' Cl neutralize STEP 1 STEP 2 ' ' 2 ' STEP 5 ' " 3 " dipeptide 2 " nucleophile STEP 4 This is an amino acid with the carboxy end protected to make it a poor nucleophile. 2 " unprotected amino acid STEP 3 SCl 2 ' electrophile Cl

8 ChemActivity 46 Amino Acids, Polypeptides and Proteins 8 The 20 Amino Acids at Biological p (with three-letter and one-letter abbreviations) non-polar sidechains Alanine (Ala) A Leucine (Leu) L Isoleucine (Ile) I Valine (Val) V Phenylalanine (Phe) F S Tyrosine (Tyr) Y Tryptophan (Trp) W Glycine (Gly) G Proline (Pro) P Methionine (Met) M polar sidechains 2 2 S Serine (Ser) S Threonine (Thr) T Asparagine (Asn) Glutamine (Gln) Q Cysteine (Cys) C charged sidechains Lysine (Lys) K Arginine (Arg) Aspartic Acid (Asp) D Glutamic Acid (Glu) E istidine (is)

9 ChemActivity 46 Amino Acids, Polypeptides and Proteins 9

Pipe Cleaner Proteins. Essential question: How does the structure of proteins relate to their function in the cell?

Pipe Cleaner Proteins. Essential question: How does the structure of proteins relate to their function in the cell? Pipe Cleaner Proteins GPS: SB1 Students will analyze the nature of the relationships between structures and functions in living cells. Essential question: How does the structure of proteins relate to their

More information

Advanced Medicinal & Pharmaceutical Chemistry CHEM 5412 Dept. of Chemistry, TAMUK

Advanced Medicinal & Pharmaceutical Chemistry CHEM 5412 Dept. of Chemistry, TAMUK Advanced Medicinal & Pharmaceutical Chemistry CHEM 5412 Dept. of Chemistry, TAMUK Dai Lu, Ph.D. dlu@tamhsc.edu Tel: 361-221-0745 Office: RCOP, Room 307 Drug Discovery and Development Drug Molecules Medicinal

More information

IV. -Amino Acids: carboxyl and amino groups bonded to -Carbon. V. Polypeptides and Proteins

IV. -Amino Acids: carboxyl and amino groups bonded to -Carbon. V. Polypeptides and Proteins IV. -Amino Acids: carboxyl and amino groups bonded to -Carbon A. Acid/Base properties 1. carboxyl group is proton donor! weak acid 2. amino group is proton acceptor! weak base 3. At physiological ph: H

More information

1. 1. Amino acids and proteins. 1: Biochemistry of macromolecules and metabolic pathways. Key terms

1. 1. Amino acids and proteins. 1: Biochemistry of macromolecules and metabolic pathways. Key terms 1. 1 Amino acids and proteins Key terms Polymer: A large molecule made from repeating units called monomers. Monomer: A molecule that is a basic unit; many monomers join together to make a polymer. Amino

More information

Shu-Ping Lin, Ph.D. E-mail: splin@dragon.nchu.edu.tw

Shu-Ping Lin, Ph.D. E-mail: splin@dragon.nchu.edu.tw Amino Acids & Proteins Shu-Ping Lin, Ph.D. Institute te of Biomedical Engineering ing E-mail: splin@dragon.nchu.edu.tw Website: http://web.nchu.edu.tw/pweb/users/splin/ edu tw/pweb/users/splin/ Date: 10.13.2010

More information

Amino Acids, Peptides, Proteins

Amino Acids, Peptides, Proteins Amino Acids, Peptides, Proteins Functions of proteins: Enzymes Transport and Storage Motion, muscle contraction Hormones Mechanical support Immune protection (Antibodies) Generate and transmit nerve impulses

More information

The amino acids differ in the properties of their side chains. Hydrophobic, non acidic (the H+ ion won t associate with water)

The amino acids differ in the properties of their side chains. Hydrophobic, non acidic (the H+ ion won t associate with water) Amino Acids 101 What is an amino acid? Amino acids, or alpha- amino acids, are the building blocks of peptides and proteins They are composed of amine and carboxylic acid groups, separated by the alpha-carbon

More information

The Organic Chemistry of Amino Acids, Peptides, and Proteins

The Organic Chemistry of Amino Acids, Peptides, and Proteins Essential rganic Chemistry Chapter 16 The rganic Chemistry of Amino Acids, Peptides, and Proteins Amino Acids a-amino carboxylic acids. The building blocks from which proteins are made. H 2 N C 2 H Note:

More information

Recap. Lecture 2. Protein conformation. Proteins. 8 types of protein function 10/21/10. Proteins.. > 50% dry weight of a cell

Recap. Lecture 2. Protein conformation. Proteins. 8 types of protein function 10/21/10. Proteins.. > 50% dry weight of a cell Lecture 2 Protein conformation ecap Proteins.. > 50% dry weight of a cell ell s building blocks and molecular tools. More important than genes A large variety of functions http://www.tcd.ie/biochemistry/courses/jf_lectures.php

More information

Concept 5.4: Proteins include a diversity of structures, resulting in a wide range of functions

Concept 5.4: Proteins include a diversity of structures, resulting in a wide range of functions Concept 5.4: Proteins include a diversity of structures, resulting in a wide range of functions Proteins account for more than 50% of the dry mass of most cells Some proteins speed up chemical reactions

More information

A. A peptide with 12 amino acids has the following amino acid composition: 2 Met, 1 Tyr, 1 Trp, 2 Glu, 1 Lys, 1 Arg, 1 Thr, 1 Asn, 1 Ile, 1 Cys

A. A peptide with 12 amino acids has the following amino acid composition: 2 Met, 1 Tyr, 1 Trp, 2 Glu, 1 Lys, 1 Arg, 1 Thr, 1 Asn, 1 Ile, 1 Cys Questions- Proteins & Enzymes A. A peptide with 12 amino acids has the following amino acid composition: 2 Met, 1 Tyr, 1 Trp, 2 Glu, 1 Lys, 1 Arg, 1 Thr, 1 Asn, 1 Ile, 1 Cys Reaction of the intact peptide

More information

Introduction to Proteins; Amino Acids, the Building Blocks of Proteins

Introduction to Proteins; Amino Acids, the Building Blocks of Proteins Introduction to Proteins; Amino Acids, the Building Blocks of Proteins Reading: Berg, Tymoczko & Stryer: Chapter 2, pp. 25-34 Appendix to Chapter 2, pp. 60-61 (visualizing protein structures) Review General

More information

Chapter 19 Amino Acids and Proteins

Chapter 19 Amino Acids and Proteins Chapter 19 Amino Acids and Proteins 19.1 Proteins and Amino Acids 19.2 Amino Acids as Acids and Bases Copyright 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings 1 Functions of Proteins Proteins

More information

BOC334 (Proteomics) Practical 1. Calculating the charge of proteins

BOC334 (Proteomics) Practical 1. Calculating the charge of proteins BC334 (Proteomics) Practical 1 Calculating the charge of proteins Aliphatic amino acids (VAGLIP) N H 2 H Glycine, Gly, G no charge Hydrophobicity = 0.67 MW 57Da pk a CH = 2.35 pk a NH 2 = 9.6 pi=5.97 CH

More information

Chemistry 110. Bettelheim, Brown, Campbell & Farrell. Introduction to General, Organic and Biochemistry Chapter 22 Proteins

Chemistry 110. Bettelheim, Brown, Campbell & Farrell. Introduction to General, Organic and Biochemistry Chapter 22 Proteins hemistry 110 Bettelheim, Brown, ampbell & Farrell Ninth Edition Introduction to General, rganic and Biochemistry hapter 22 Proteins Step-growth polyamide (polypeptide) polymers or oligomers of L-α-aminoacids.

More information

Molecular Biology Basic Concepts

Molecular Biology Basic Concepts Molecular Biology Basic Concepts Prof. Dr. Antônio Augusto Fröhlich Charles Ivan Wust LISHA - UFSC {guto charles}@lisha.ufsc.br http://www.lisha.ufsc.br/~{guto charles} September 2003 September 2003 http://www.lisha.ufsc.br/~guto

More information

Peptide bonds: resonance structure. Properties of proteins: Peptide bonds and side chains. Dihedral angles. Peptide bond. Protein physics, Lecture 5

Peptide bonds: resonance structure. Properties of proteins: Peptide bonds and side chains. Dihedral angles. Peptide bond. Protein physics, Lecture 5 Protein physics, Lecture 5 Peptide bonds: resonance structure Properties of proteins: Peptide bonds and side chains Proteins are linear polymers However, the peptide binds and side chains restrict conformational

More information

DNA Lecture II Protein Synthesis Notes. Using the Code of Life DNA & RNA. Page #1 (Stratton 2010) Name: 2. : production of proteins

DNA Lecture II Protein Synthesis Notes. Using the Code of Life DNA & RNA. Page #1 (Stratton 2010) Name: 2. : production of proteins Page #1 Using the Code of Life DNA & RNA Slide #2 Two process involve DNA : making an copy of DNA a. purpose: b. occurs: c. uses: DNA : production of proteins a. purpose: & b. occurs: between nucleus &

More information

Chapter 26 Biomolecules: Amino Acids, Peptides, and Proteins

Chapter 26 Biomolecules: Amino Acids, Peptides, and Proteins John E. McMurry www.cengage.com/chemistry/mcmurry Chapter 26 Biomolecules: Amino Acids, Peptides, and Proteins Proteins Amides from Amino Acids Amino acids contain a basic amino group and an acidic carboxyl

More information

Built from 20 kinds of amino acids

Built from 20 kinds of amino acids Built from 20 kinds of amino acids Each Protein has a three dimensional structure. Majority of proteins are compact. Highly convoluted molecules. Proteins are folded polypeptides. There are four levels

More information

Structure and properties of proteins. Vladimíra Kvasnicová

Structure and properties of proteins. Vladimíra Kvasnicová Structure and properties of proteins Vladimíra Kvasnicová Chemical nature of proteins biopolymers of amino acids macromolecules (M r > 10 000) Classification of proteins 1) by localization in an organism

More information

18.2 Protein Structure and Function: An Overview

18.2 Protein Structure and Function: An Overview 18.2 Protein Structure and Function: An Overview Protein: A large biological molecule made of many amino acids linked together through peptide bonds. Alpha-amino acid: Compound with an amino group bonded

More information

Amino Acids and Proteins

Amino Acids and Proteins Amino Acids and Proteins Proteins are composed of amino acids. There are 20 amino acids commonly found in proteins. All have: N2 C α R COO Amino acids at neutral p are dipolar ions (zwitterions) because

More information

Amino Acids, Proteins, and Enzymes. Primary and Secondary Structure Tertiary and Quaternary Structure Protein Hydrolysis and Denaturation

Amino Acids, Proteins, and Enzymes. Primary and Secondary Structure Tertiary and Quaternary Structure Protein Hydrolysis and Denaturation Amino Acids, Proteins, and Enzymes Primary and Secondary Structure Tertiary and Quaternary Structure Protein Hydrolysis and Denaturation 1 Primary Structure of Proteins H 3 N The particular sequence of

More information

Structure of proteins

Structure of proteins Structure of proteins Primary structure: is amino acids sequence or the covalent structure (50-2500) amino acids M.Wt. of amino acid=110 Dalton (56 110=5610 Dalton). Single chain or more than one polypeptide

More information

Ch18_PT MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

Ch18_PT MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. Ch18_PT MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. 1) All of the following can be classified as biomolecules except A) lipids. B) proteins. C)

More information

Proteins are polymers of amino acids. Protein-over 50 amino acids, peptide-under 50 amino acids.

Proteins are polymers of amino acids. Protein-over 50 amino acids, peptide-under 50 amino acids. Amino Acids and Proteins: Protein Functions: enzymes, transport (hemoglobin-o 2, tranferrin-fe), protection (MHC molecules, immunoglobulins), hormones (insulin, glucagons), gene transcription regulation

More information

The peptide bond is rigid and planar

The peptide bond is rigid and planar Level Description Bonds Primary Sequence of amino acids in proteins Covalent (peptide bonds) Secondary Structural motifs in proteins: α- helix and β-sheet Hydrogen bonds (between NH and CO groups in backbone)

More information

Amino Acids. Amino acids are the building blocks of proteins. All AA s have the same basic structure: Side Chain. Alpha Carbon. Carboxyl. Group.

Amino Acids. Amino acids are the building blocks of proteins. All AA s have the same basic structure: Side Chain. Alpha Carbon. Carboxyl. Group. Protein Structure Amino Acids Amino acids are the building blocks of proteins. All AA s have the same basic structure: Side Chain Alpha Carbon Amino Group Carboxyl Group Amino Acid Properties There are

More information

MCAT Organic Chemistry - Problem Drill 23: Amino Acids, Peptides and Proteins

MCAT Organic Chemistry - Problem Drill 23: Amino Acids, Peptides and Proteins MCAT rganic Chemistry - Problem Drill 23: Amino Acids, Peptides and Proteins Question No. 1 of 10 Question 1. Which amino acid does not contain a chiral center? Question #01 (A) Serine (B) Proline (C)

More information

INTRODUCTION TO PROTEIN STRUCTURE

INTRODUCTION TO PROTEIN STRUCTURE Name Class: Partner, if any: INTRODUCTION TO PROTEIN STRUCTURE PRIMARY STRUCTURE: 1. Write the complete structural formula of the tripeptide shown (frame 10). Circle and label the three sidechains which

More information

H H N - C - C 2 R. Three possible forms (not counting R group) depending on ph

H H N - C - C 2 R. Three possible forms (not counting R group) depending on ph Amino acids - 0 common amino acids there are others found naturally but much less frequently - Common structure for amino acid - C, -N, and functional groups all attached to the alpha carbon N - C - C

More information

CHAPTER 29 AMINO ACIDS, POLYPEPTIDES, AND PROTEINS SOLUTIONS TO REVIEW QUESTIONS

CHAPTER 29 AMINO ACIDS, POLYPEPTIDES, AND PROTEINS SOLUTIONS TO REVIEW QUESTIONS APTER 29 AMI AIDS, PLYPEPTIDES, AD PRTEIS SLUTIS T REVIEW QUESTIS 1. The designation, α, means that the amine group in common amino acids is connected to the carbon immediately adjacent to the carboxylic

More information

Chemical Structures. Part I: Structures on paper and in 3-d

Chemical Structures. Part I: Structures on paper and in 3-d hemical Structures bjectives 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, and the charges they have. 2.

More information

Introduction to Chemical Biology

Introduction to Chemical Biology Professor Stuart Conway Introduction to Chemical Biology University of xford Introduction to Chemical Biology ecommended books: Professor Stuart Conway Department of Chemistry, Chemistry esearch Laboratory,

More information

Student Handout 1 A dual coloring scheme allows students to first 3dmoleculardesigns.com Introduction - Page 1

Student Handout 1 A dual coloring scheme allows students to first 3dmoleculardesigns.com Introduction - Page 1 Proteins are large, linear polymers of amino acids that spontaneously fold into complex 3D shapes. Although protein structure appears to be very complex, the chemical properties that determine protein

More information

Molecules of Life. Chapter 3 Part 2

Molecules of Life. Chapter 3 Part 2 Molecules of Life Chapter 3 Part 2 3.5 Proteins Diversity in Structure and Function Proteins are the most diverse biological molecule (structural, nutritious, enzyme, transport, communication, and defense

More information

Part I: 2-d simulation with the Protein Investigator

Part I: 2-d simulation with the Protein Investigator Protein Structure verview In this lab session, you will explore protein structure using two different approaches: 2-dimensional simulation: you will use the Protein Investigator to construct proteins and

More information

CSC 2427: Algorithms for Molecular Biology Spring 2006. Lecture 16 March 10

CSC 2427: Algorithms for Molecular Biology Spring 2006. Lecture 16 March 10 CSC 2427: Algorithms for Molecular Biology Spring 2006 Lecture 16 March 10 Lecturer: Michael Brudno Scribe: Jim Huang 16.1 Overview of proteins Proteins are long chains of amino acids (AA) which are produced

More information

Protein Physics. A. V. Finkelstein & O. B. Ptitsyn LECTURE 1

Protein Physics. A. V. Finkelstein & O. B. Ptitsyn LECTURE 1 Protein Physics A. V. Finkelstein & O. B. Ptitsyn LECTURE 1 PROTEINS Functions in a Cell MOLECULAR MACHINES BUILDING BLOCKS of a CELL ARMS of a CELL ENZYMES - enzymatic catalysis of biochemical reactions

More information

Ionization of amino acids

Ionization of amino acids Amino Acids 20 common amino acids there are others found naturally but much less frequently Common structure for amino acid COOH, -NH 2, H and R functional groups all attached to the a carbon Ionization

More information

AMINO ACIDS & PEPTIDE BONDS STRUCTURE, CLASSIFICATION & METABOLISM

AMINO ACIDS & PEPTIDE BONDS STRUCTURE, CLASSIFICATION & METABOLISM AMINO ACIDS & PEPTIDE BONDS STRUCTURE, CLASSIFICATION & METABOLISM OBJECTIVES At the end of this session the student should be able to, recognize the structures of the protein amino acid and state their

More information

2007 7.013 Problem Set 1 KEY

2007 7.013 Problem Set 1 KEY 2007 7.013 Problem Set 1 KEY Due before 5 PM on FRIDAY, February 16, 2007. Turn answers in to the box outside of 68-120. PLEASE WRITE YOUR ANSWERS ON THIS PRINTOUT. 1. Where in a eukaryotic cell do you

More information

Solution key Problem Set 1

Solution key Problem Set 1 Solution key-7.016 Problem Set 1 Question 1 The following line-angle drawings represent three chemical structures. On each drawing, the hydrogen atoms that should be bonded to the NON-carbon atoms are

More information

Proteins. Amino Acids. Chapter 3. Molecular Diagnostics Fundamentals, Methods and Clinical Applications Second Edition 2/5/2013

Proteins. Amino Acids. Chapter 3. Molecular Diagnostics Fundamentals, Methods and Clinical Applications Second Edition 2/5/2013 Proteins Chapter 3 Amino Acids Nonpolar Alanine, Ala, A Isoleucine, Ile, I Leucine, Leu, L Methionine, Met, M Phenylalanine, Phe, F Tryptophan,Trp, W Valine, Val, V Negatively Charged (Acidic) Aspartic

More information

THE CHEMICAL SYNTHESIS OF PEPTIDES

THE CHEMICAL SYNTHESIS OF PEPTIDES TE EMIAL SYTESIS F PEPTIDES Peptides are the long molecular chains that make up proteins. Synthetic peptides are used either as drugs (as they are biologically active) or in the diagnosis of disease. Peptides

More information

Chapter 16 Amino Acids, Proteins, and Enzymes. Functions of Proteins. Examples of Amino Acids. Amino Acids. Nonpolar Amino Acids. Types of Amino Acids

Chapter 16 Amino Acids, Proteins, and Enzymes. Functions of Proteins. Examples of Amino Acids. Amino Acids. Nonpolar Amino Acids. Types of Amino Acids Chapter 16 Amino Acids, Proteins, and Enzymes 16.1 Functions of Proteins 16.2 Amino Acids 16.3 Amino Acids as Acids and Bases Functions of Proteins Proteins perform many different functions in the body.

More information

Paper: 6 Chemistry 2.130 University I Chemistry: Models Page: 2 of 7. 4. Which of the following weak acids would make the best buffer at ph = 5.0?

Paper: 6 Chemistry 2.130 University I Chemistry: Models Page: 2 of 7. 4. Which of the following weak acids would make the best buffer at ph = 5.0? Paper: 6 Chemistry 2.130 University I Chemistry: Models Page: 2 of 7 4. Which of the following weak acids would make the best buffer at ph = 5.0? A) Acetic acid (Ka = 1.74 x 10-5 ) B) H 2 PO - 4 (Ka =

More information

Chapter 16 Amino Acids, Proteins, and Enzymes

Chapter 16 Amino Acids, Proteins, and Enzymes Chapter 16 Amino Acids, Proteins, and Enzymes 1 Functions of Proteins Proteins in the body are polymers made from 20 different amino acids differ in characteristics and functions that depend on the order

More information

Chapter 3: Biological Molecules. 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acids

Chapter 3: Biological Molecules. 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acids Chapter 3: Biological Molecules 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acids Elements in Biological Molecules Biological macromolecules are made almost entirely of just 6 elements: Carbon (C)

More information

MBLG1001_lecture 4 Page 1. University of Sydney Library Electronic Item COURSE: MBLG1001. Lecturer: Dale Hancock Forming the Protein

MBLG1001_lecture 4 Page 1. University of Sydney Library Electronic Item COURSE: MBLG1001. Lecturer: Dale Hancock Forming the Protein MBLG1001_lecture 4 Page 1 University of Sydney Library Electronic Item URSE: MBLG1001 Lecturer: Dale ancock Forming the Protein MMWEALT F AUSTRALIA opyright Regulation WARIG This material has been reproduced

More information

Solutions for Biochemistry Unit Exam

Solutions for Biochemistry Unit Exam Solutions for Biochemistry Unit Exam Question 1 a) An example of a structural representation is shown in the adjacent box. Draw a structural representation of the amino acid, Aspartic acid, which has the

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

Chapter 2: Biochemistry Problems

Chapter 2: Biochemistry Problems hapter 2: Biochemistry Problems Biochemistry Problems If you were a biochemist, you would study chemical substances and vital processes that occur in living organisms. You might study macromolecules such

More information

Exam 4 Outline CH 105 Spring 2012

Exam 4 Outline CH 105 Spring 2012 Exam 4 Outline CH 105 Spring 2012 You need to bring a pencil and your ACT card. Chapter 24: Lipids 1. Describe the properties and types of lipids a. All are hydrophobic b. Fatty acid-based typically contain

More information

Ruth Sundeen. Lesson 9 Part 1. Help Your Students Learn. Greetings and felicitations from Mrs. Ruth!

Ruth Sundeen. Lesson 9 Part 1. Help Your Students Learn. Greetings and felicitations from Mrs. Ruth! Ruth Sundeen Lesson 9 Part 1 Help Your Students Learn Ages: Eighth grade to high school senior Topics: Protein Synthesis Enzymes Experiment to demonstrate fragility of enzymes Greetings and felicitations

More information

Carbohydrates, proteins and lipids

Carbohydrates, proteins and lipids Carbohydrates, proteins and lipids Chapter 3 MACROMOLECULES Macromolecules: polymers with molecular weights >1,000 Functional groups THE FOUR MACROMOLECULES IN LIFE Molecules in living organisms: proteins,

More information

UNIT (11) MOLECULES OF LIFE: LIPIDS AND PROTEINS

UNIT (11) MOLECULES OF LIFE: LIPIDS AND PROTEINS UNIT (11) MOLECULES OF LIFE: LIPIDS AND PROTEINS 11.1 Types of Lipids Lipids are also biochemical compounds that contain carbon, hydrogen, and oxygen. But lipids, unlike carbohydrates, share no common

More information

Proteins. Proteins. Amino Acids. Most diverse and most important molecule in. Functions: Functions (cont d)

Proteins. Proteins. Amino Acids. Most diverse and most important molecule in. Functions: Functions (cont d) Proteins Proteins Most diverse and most important molecule in living i organisms Functions: 1. Structural (keratin in hair, collagen in ligaments) 2. Storage (casein in mother s milk) 3. Transport (HAEMOGLOBIN!)

More information

Chapter 12 - Proteins

Chapter 12 - Proteins Roles of Biomolecules Carbohydrates Lipids Proteins 1) Catalytic 2) Transport 3) Regulatory 4) Structural 5) Contractile 6) Protective 7) Storage Nucleic Acids 12.1 -Amino Acids Chapter 12 - Proteins Amino

More information

Disulfide Bonds at the Hair Salon

Disulfide Bonds at the Hair Salon Disulfide Bonds at the Hair Salon Three Alpha Helices Stabilized By Disulfide Bonds! In order for hair to grow 6 inches in one year, 9 1/2 turns of α helix must be produced every second!!! In some proteins,

More information

Package acide-amine.sty

Package acide-amine.sty Package acide-amine.sty This package provide commands who draw an amino acid. You will nd below the list of amino acids available. Molecules were initialy drawn by Florian Hollandt, see : http://www.texample.net/tikz/examples/author/florian-hollandt/

More information

Nafith Abu Tarboush DDS, MSc, PhD natarboush@ju.edu.jo www.facebook.com/natarboush

Nafith Abu Tarboush DDS, MSc, PhD natarboush@ju.edu.jo www.facebook.com/natarboush Nafith Abu Tarboush DDS, MSc, PhD natarboush@ju.edu.jo www.facebook.com/natarboush α-keratins, bundles of α- helices Contain polypeptide chains organized approximately parallel along a single axis: Consist

More information

http://faculty.sau.edu.sa/h.alshehri

http://faculty.sau.edu.sa/h.alshehri http://faculty.sau.edu.sa/h.alshehri Definition: Proteins are macromolecules with a backbone formed by polymerization of amino acids. Proteins carry out a number of functions in living organisms: - They

More information

Biological Molecules

Biological Molecules Biological Molecules I won t lie. This is probably the most boring topic you have ever done in any science. It s pretty much as simple as this: learn the material deal with it. Enjoy don t say I didn t

More information

Biochemistry 2000 Sample Question Proteins. (1) Identify the secondary structure described in each of the following statements:

Biochemistry 2000 Sample Question Proteins. (1) Identify the secondary structure described in each of the following statements: (1) Identify the secondary structure described in each of the following statements: a. A coiled peptide chain held in place by hydrogen bonding between peptide bonds in the same chain b. A structure that

More information

Protein Structure and Function

Protein Structure and Function Jones & Bartlett Learning, LL. T F SALE DISTIBUTI Protein Structure and Function SETI I APTE 2 APTE 3 Protein Structure Protein Function 27 Jones & Bartlett Learning, LL. T F SALE DISTIBUTI 2 Protein Structure

More information

Combinatorial Biochemistry and Phage Display

Combinatorial Biochemistry and Phage Display Combinatorial Biochemistry and Phage Display Prof. Valery A. Petrenko Director - Valery Petrenko Instructors Galina Kouzmitcheva and I-Hsuan Chen Auburn 2006, Spring semester COMBINATORIAL BIOCHEMISTRY

More information

The peptide bond Peptides and proteins are linear polymers of amino acids. The amino acids are

The peptide bond Peptides and proteins are linear polymers of amino acids. The amino acids are Introduction to Protein Structure Proteins are large heteropolymers usually comprised of 50 2500 monomer units, although larger proteins are observed 7. The monomer units of proteins are amino acids. The

More information

Biochemistry - I. Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology, Kharagpur Lecture-11 Enzyme Mechanisms II

Biochemistry - I. Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology, Kharagpur Lecture-11 Enzyme Mechanisms II Biochemistry - I Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology, Kharagpur Lecture-11 Enzyme Mechanisms II In the last class we studied the enzyme mechanisms of ribonuclease A

More information

Chapter 3 Molecules of Cells

Chapter 3 Molecules of Cells Bio 100 Molecules of cells 1 Chapter 3 Molecules of Cells Compounds containing carbon are called organic compounds Molecules such as methane that are only composed of carbon and hydrogen are called hydrocarbons

More information

Activity 4/5.1 How Can You Identify Organic Macromolecules?

Activity 4/5.1 How Can You Identify Organic Macromolecules? Answers? Activity 4/5.1 ow an You Identify rganic Macromolecules? efer to the figure (Some Simple hemistry) on the next page when doing this activity. Part A. Answer the questions. Then use your answers

More information

Polypeptides and Proteins

Polypeptides and Proteins Polypeptides and Proteins These molecules are composed, at least in part, of chains of amino acids. Each amino acid is joined to the next one through an amide or peptide bond from the carbonyl carbon of

More information

This class deals with the fundamental structural features of proteins, which one can understand from the structure of amino acids, and how they are

This class deals with the fundamental structural features of proteins, which one can understand from the structure of amino acids, and how they are This class deals with the fundamental structural features of proteins, which one can understand from the structure of amino acids, and how they are put together. 1 A more detailed view of a single protein

More information

I N V E S T I C E D O R O Z V O J E V Z D Ě L Á V Á N Í

I N V E S T I C E D O R O Z V O J E V Z D Ě L Á V Á N Í I V E S T I E D Z V J E V Z D Ě L Á V Á Í AMIAIDS PEPTIDES AMIAIDS = substitutional/functional derivatives of carboxylic acids = basic units of proteins (2-aminoacids) General formula of 2-aminoacids (α-aminoacids):

More information

In addition to being shorter than a single bond, the double bonds in ethylene don t twist the way single bonds do. In other words, the other atoms

In addition to being shorter than a single bond, the double bonds in ethylene don t twist the way single bonds do. In other words, the other atoms In addition to being shorter than a single bond, the double bonds in ethylene don t twist the way single bonds do. In other words, the other atoms attached to the carbons (hydrogens in this case) can no

More information

PROTEINS STRUCTURE AND FUNCTION (DR. TRAISH)

PROTEINS STRUCTURE AND FUNCTION (DR. TRAISH) Introduction to Proteins - Proteins are abundant and functionally diverse molecules - They participate in cell regulation at all levels - They share a common structural feature: all are linear polymers

More information

(c) How would your answers to problem (a) change if the molecular weight of the protein was 100,000 Dalton?

(c) How would your answers to problem (a) change if the molecular weight of the protein was 100,000 Dalton? Problem 1. (12 points total, 4 points each) The molecular weight of an unspecified protein, at physiological conditions, is 70,000 Dalton, as determined by sedimentation equilibrium measurements and by

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 B 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

Invariant residue-a residue that is always conserved. It is assumed that these residues are essential to the structure or function of the protein.

Invariant residue-a residue that is always conserved. It is assumed that these residues are essential to the structure or function of the protein. Chapter 6 The amino acid side chains have polar and nonpolar properties, and the relative hydrophobicity of the amino acid side chains is critical for the folding and stability of a protein. The more hydrophobic

More information

Peptide Bonds: Structure

Peptide Bonds: Structure Peptide Bonds: Structure Peptide primary structure The amino acid sequence, from - to C-terminus, determines the primary structure of a peptide or protein. The amino acids are linked through amide or peptide

More information

PROTEINS THE PEPTIDE BOND. The peptide bond, shown above enclosed in the blue curves, generates the basic structural unit for proteins.

PROTEINS THE PEPTIDE BOND. The peptide bond, shown above enclosed in the blue curves, generates the basic structural unit for proteins. Ca 2+ The contents of this module were developed under grant award # P116B-001338 from the Fund for the Improvement of Postsecondary Education (FIPSE), United States Department of Education. However, those

More information

CHAPTER 3 THE CHEMISTRY OF ORGANIC MOLECULES

CHAPTER 3 THE CHEMISTRY OF ORGANIC MOLECULES CHAPTER 3 THE CHEMISTRY OF ORGANIC MOLECULES 3.1 Organic Molecules The chemistry of carbon accounts for the diversity of organic molecules found in living things. Carbon has six electrons, four of which

More information

4 Titration Curve of an Amino Acid

4 Titration Curve of an Amino Acid p H 4 Titration Curve of an Amino Acid Simple amino acid Acidic amino acid Basic amino acid 7 OH - equivalents Objectives: A) To determine the titration curve for an amino acid and B) to use this curve

More information

4. Which carbohydrate would you find as part of a molecule of RNA? a. Galactose b. Deoxyribose c. Ribose d. Glucose

4. Which carbohydrate would you find as part of a molecule of RNA? a. Galactose b. Deoxyribose c. Ribose d. Glucose 1. How is a polymer formed from multiple monomers? a. From the growth of the chain of carbon atoms b. By the removal of an OH group and a hydrogen atom c. By the addition of an OH group and a hydrogen

More information

the nature and importance of biomacromolecules in the chemistry of the cell: synthesis of biomacromolecules through the condensation reaction lipids

the nature and importance of biomacromolecules in the chemistry of the cell: synthesis of biomacromolecules through the condensation reaction lipids the nature and importance of biomacromolecules in the chemistry of the cell: synthesis of biomacromolecules through the condensation reaction lipids and their sub-units; the role of lipids in the plasma

More information

Reading Assignment: pp , ,

Reading Assignment: pp , , Chapter 6 "Mechanisms of Enzymes" Reading Assignment: pp. 158-167, 171-176, 182-187. Problem Assignment: 1, 3, and 4. I. Introduction The first objective of this chapter is to obtain a conceptual understanding

More information

Chapter 5. The Structure and Function of Macromolecule s

Chapter 5. The Structure and Function of Macromolecule s Chapter 5 The Structure and Function of Macromolecule s Most Macromolecules are polymers: Polymer: (poly: many; mer: part) Large molecules consisting of many identical or similar subunits connected together.

More information

Guidelines for Writing a Scientific Paper

Guidelines for Writing a Scientific Paper Guidelines for Writing a Scientific Paper Writing an effective scientific paper is not easy. A good rule of thumb is to write as if your paper will be read by a person who knows about the field in general

More information

Helices From Readily in Biological Structures

Helices From Readily in Biological Structures The α Helix and the β Sheet Are Common Folding Patterns Although the overall conformation each protein is unique, there are only two different folding patterns are present in all proteins, which are α

More information

Myoglobin and Hemoglobin

Myoglobin and Hemoglobin Myoglobin and Hemoglobin Myoglobin and hemoglobin are hemeproteins whose physiological importance is principally related to their ability to bind molecular oxygen. Myoglobin (Mb) The oxygen storage protein

More information

Molecular Facts and Figures

Molecular Facts and Figures Nucleic Acids Molecular Facts and Figures DNA/RNA bases: DNA and RNA are composed of four bases each. In DNA the four are Adenine (A), Thymidine (T), Cytosine (C), and Guanine (G). In RNA the four are

More information

NO CALCULATORS OR CELL PHONES ALLOWED

NO CALCULATORS OR CELL PHONES ALLOWED Biol 205 Exam 1 TEST FORM A Spring 2008 NAME Fill out both sides of the Scantron Sheet. On Side 2 be sure to indicate that you have TEST FORM A The answers to Part I should be placed on the SCANTRON SHEET.

More information

Lecture 13-14 Conformation of proteins Conformation of a protein three-dimensional structure native state. native condition

Lecture 13-14 Conformation of proteins Conformation of a protein  three-dimensional structure native state. native condition Lecture 13-14 Conformation of proteins Conformation of a protein refers to the three-dimensional structure in its native state. There are many different possible conformations for a molecule as large as

More information

Gene Translation:RNA -> Protein

Gene Translation:RNA -> Protein Gene Translation:RN -> Protein How does a particular sequence of nucleotides specify a particular sequence of amino acids? The answer: by means of transfer RN molecules, each specific for one amino acid

More information

Covalent bonds are the strongest chemical bonds contributing to the protein structure A peptide bond is formed between with of the following?

Covalent bonds are the strongest chemical bonds contributing to the protein structure A peptide bond is formed between with of the following? MCAT Question Covalent bonds are the strongest chemical bonds contributing to the protein structure A peptide bond is formed between with of the following? A. Carboxylic group and amino group B. Two carboxylic

More information

Acidic amino acids: Those whose side chains can carry a negative charge at certain ph values. Typically aspartic acid, glutamic acid.

Acidic amino acids: Those whose side chains can carry a negative charge at certain ph values. Typically aspartic acid, glutamic acid. A Acidic amino acids: Those whose side chains can carry a negative charge at certain ph values. Typically aspartic acid, glutamic acid. Active site: Usually applied to catalytic site of an enzyme or where

More information

Smaller coiled-coil structures are also found at the interaction interface between. Copyright Mark Brandt, Ph.D. 42

Smaller coiled-coil structures are also found at the interaction interface between. Copyright Mark Brandt, Ph.D. 42 Examples of tein Structures tein types teins fall into three general classes, based on their overall three-dimensional structure and on their functional role: fibrous, membrane, and globular. Fibrous proteins

More information

Disaccharides consist of two monosaccharide monomers covalently linked by a glycosidic bond. They function in sugar transport.

Disaccharides consist of two monosaccharide monomers covalently linked by a glycosidic bond. They function in sugar transport. 1. The fundamental life processes of plants and animals depend on a variety of chemical reactions that occur in specialized areas of the organism s cells. As a basis for understanding this concept: 1.

More information

Lecture 1. Introduction

Lecture 1. Introduction Lecture 1 Introduction Before coming to class consider the analogy of the cell as being the city. Where in a city are the plans and all of the directions to run and maintain the city come from? What would

More information