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

Size: px
Start display at page:

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

Transcription

1 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 A large variety of shapes and sizes. ecap Proteins are the key functional molecules of life 8 types of protein function 1. Enzymatic 2. Structural 3. Storage 4. Transport 5. ormonal 6. eceptor 7. ontractile and Motor 8. Defensive Proteins 1. Proteins - What are they? And why are they important? 2. The building blocks ( s) and how they are connected 3. The hierarchy of protein structure 4. Three-dimensional protein structure 5. ow are protein structures determined? 1

2 Proteins are polymers of amino acids (polypeptides) 20 groups = 20 s ecap Amino acids divide into 4 subgroups Amino Acid Polymers Amino acids - Are linked by peptide bonds Petide bond is formed by a dehydration reaction- atalytic reaction 2 (a) Peptide bond 2 S 2 2 S Peptide 2 2 bond 2 Side chains Petide bond - covalent bond Backbone (b) Amino end (-terminus) arboxyl end (-terminus) Protein onformation and Function Polypeptides - formed one at a time starting from -terminus - range from a few monomers to 1000 or more Two models of protein conformation Groove Specific polypeptides- unique sequence of s Sequence of the polymer determines the 3D shape of the polypeptide Eg. Lysozyme- an enzyme that Breaks down bacterial cell walls by recognizing and binding to specific molecules on the bacteria (a) A ribbon model Proteins are not just chains of s, they are defined by their shape interactions between backbone residues and -groups A protein s specific conformation - determines how it functions eg. Enzyme binds substrate (b) A space-filling model Groove 2

3 Leu Met Val Lys Val Gly Pro Thr Gly Thr Gly Lys Trp Tyr Leu Ala Gly lle Pro Phe is Glu is Ala Glu Val Ala Thr Phe Val Asn Asp Thr Tyr Thr Ala Val Thr Lys Pro Ala Ala Leu Leu 10/21/10 Protein structure Four Levels of Protein Structure Primary structure Is the unique sequence of amino acids in a polypeptide + 3 Amino end Glu ys Lys Seu Pro Amino acid subunits Leu Asp Ala Val Arg Gly sequence determined by inherited genetic information Glu Lle Asp Gly Pro Thr lle Tyr Ala Arg Arg Tyr Pro o Val Thr Lys Glu c Asn Pro o arboxyl end Secondary structure Is the folding or coiling of the polypeptide into a repeating configuration Includes the α helix and the β pleated sheet esult of ydrogen bonding between the repeating backbone of a polypeptide Alpha-helix Beta pleated sheet Amino acid subunits β pleated sheet α helix -epeated coils or folds in patterns contribute to the overall conformation of a protein 3

4 ydrogen bonds ydrogen bonds are formed by the attraction between a partial positive charge on the atom of the amino group and the partial negative charge on the atom of the peptide bond ydrogen bonds ydrogen bonds are formed by the attraction between a partial positive charge on the atom of the amino group and the partial negative charge on the atom of the peptide bond Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain Beta sheets the bonds are formed between polypeptide chains lying side by side Beta sheets the bonds are formed between polypeptide chains lying side by side ydrogen bonds ydrogen bonds ydrogen bonds are formed by the attraction between a partial positive charge on the atom of the amino group and the partial negative charge on the atom of the peptide bond ydrogen bonds are formed by the attraction between a partial positive charge on the atom of the amino group and the partial negative charge on the atom of the peptide bond Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain Δ + Δ + Alpha helix - the bonds are formed between repeating atoms on the same polypeptide chain eg keratin Δ + Δ + Beta sheets the bonds are formed between polypeptide chains lying side by side Δ + Δ + Beta sheets the bonds are formed between polypeptide chains lying side by side eg. Silk fibrion Individually weak, but strong when repeated Δ + Δ + 4

5 Alpha-helix Beta pleated sheet Up to 60% of a polypeptide chain contains a secondary structure Secondary structure Beta sheet Alpha helix esults from interactions between atoms in the polypeptide backbone α-elix of amino acid 1 binds to the of amino acid residues per helical turn ight-handed coil All bonds have same orientation β-sheet of amino acid on chain 1 binds to the on chain 2 onsists of β-strands - short (5-8 residues) Two types Parallel Anti-parallel Most prevalent structure in polypeptide 5

6 β-sheet Turns -Terminus -Terminus 3-4 residues -Terminus -Terminus Bends Usually contain glycine (small grp=tight U shape) or proline -Terminus -Terminus -Terminus -Terminus Allow proteins to fold into highly compact structures Larger turns are called loops or bends Protein structure Is the overall three-dimensional shape of a polypeptide ; final shape of a polypeptide esults from interactions between the side chains of the amino acids 22 ydrogen bond S S 2 Disulfide bridge Ionic bond ydrophobic interactions and van der Wls interactions Polypeptide backbone 6

7 Bonds involved in 3D structure ydrophobic Van der Wls ydrogen Bonds Ionic bonds/salt bridges Disulphide bridges ydrophobic interactions on-polar groups repelled by water Tend to cluster together Force themselves into the core of a protein Stabilise the overall structure water ydrophobic amino acid Van der Wls interactions: occur between hydrophobic non-polar side chains in close contact Valine ydrophobic interactions and van der Wls interactions Polypeptide backbone Tertiary Structure ydrogen bonds between polar side chains Examples of amino acid side chains that may hydrogen bond to each other: Two alcohols: ser, thr, and tyr. Alcohol () and an acid : asp and tyr Two acids (-): asp and glu Alcohol and amine (3+): ser and lys Alcohol and amide (2): ser and asn 7

8 Ionic bonds /Salt bridges form between positively and negatively charged side groups result from the neutralization of an acid and amine on side chains. The final interaction is ionic between the positive ammonium group and the negative acid group. Any combination of the various acidic or amine amino acid side chains will have this effect. Disulphide bridges form between 2 cysteine residues Disulfide bonds are formed by oxidation of the sulfhydryl groups (-S) on cysteine. Different protein chains or loops within a single chain are held together by the strong covalent disulfide bonds. Eg. Insulin contains important disulphide bridges. Quaternary Structure Is the overall protein structure that results from the aggregation of two or more polypeptide subunits A variety of bonding interactions including hydrogen bonding, salt bridges, and disulfide bonds hold the various chains into a particular geometry. Quaternary structure Fibrous Trimer of alpha-helical Polypeptide chains Globular Globular protein- 4 Polypeptide chains/ subunits Primarily alpha-helical β hains Iron eme There are two major categories of proteins with quaternary structure - fibrous and globular. ollagen Structure allows for great strength igid resistant to stretch Function = connective tissue in skin, bone, tendons, ligaments. 40% of all human protein α hains emoglobin 4 polypeptides bind together to form a round globular shape Functions = carries oxygen 8

9 emoglobin Quaternary structure Fibrous Globular insulin Beta sheet structure of silk fibroin allows for strength and flexibility Globular proteins are usually round in shape and tend to be a mix of alpha-helical and Beta sheet Protein structure summary Protein structure summary The conformation of a protein determines its function Proteins are made of polypeptides which are polymers of amino acids Amino acid polymers are linked by peptide bonds The amino acid sequence determines the 3-D shape of the Protein There are four levels of protein structure Primary Secondary Ter/ary Quaternary 9

From Amino Acids to Proteins - in 4 Easy Steps

From Amino Acids to Proteins - in 4 Easy Steps From Amino Acids to Proteins - in 4 Easy Steps Although protein structure appears to be overwhelmingly complex, you can provide your students with a basic understanding of how proteins fold by focusing

More information

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

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

4. Protein Structure. Forces that maintain 3-D protein conformation. How does a protein hold its 3D shape?

4. Protein Structure. Forces that maintain 3-D protein conformation. How does a protein hold its 3D shape? 4. Protein Structure Dr. Dale ancock D.ancock@mmb.usyd.edu.au ow does a protein hold its 3D shape? Proteins are only biologically active when they have the right shape or 3D conformation. It is no use

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

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

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

More information

Classification of Amino Acids (based on polarity)

Classification of Amino Acids (based on polarity) Amino Acids Amino acids are building blocks for proteins They have a central α-carbon and α-amino and α- carboxyl groups 20 different amino acids Same core structure, but different side group (R) The α-c

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

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

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

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

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

General Structure of Amino Acids

General Structure of Amino Acids General Structure of Amino Acids Three Major Types of Amino Acids Classification based on polarities of side chains 1. Non-polar R groups 2. Uncharged Polar R groups 3. Charged Polar R groups Disulfide

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

Figure 4-1 General structural formula for α-amino acids.

Figure 4-1 General structural formula for α-amino acids. Figure 4-1 General structural formula for α-amino acids. Voet Biochemistry 3e Page 65 Figure 4-2 Zwitterionic form of the α-amino acids that occur at physiological ph values. Voet Biochemistry 3e Page

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

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

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

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

Chapter 23. Organic Chemistry. The Organic Chemistry of Amino Acids, Peptides, and Proteins. 6 th Edition. Paula Yurkanis Bruice

Chapter 23. Organic Chemistry. The Organic Chemistry of Amino Acids, Peptides, and Proteins. 6 th Edition. Paula Yurkanis Bruice Organic Chemistry 6 th Edition Chapter 23 Paula Yurkanis Bruice The Organic Chemistry of Amino Acids, Peptides, and Proteins 1 Peptides and proteins are polymers of amino acids linked together by amide

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

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

Protein Structure. Amino acid 1 Amino acid R H O. Dipeptide

Protein Structure. Amino acid 1 Amino acid R H O. Dipeptide Why? Protein Structure What are the levels of protein structure and what role do functional groups play? Proteins accomplish many cellular tasks such as facilitating chemical reactions, providing structure,

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

AMINO ACIDS, POLYPEPTIDES, AND PROTEINS

AMINO ACIDS, POLYPEPTIDES, AND PROTEINS 29 09/28/2013 8:30:17 Page 427 APTER 29 AMIN AIDS, PLYPEPTIDES, AND PRTEINS SLUTINS T REVIEW QUESTINS 1. The designation a (alpha) means that the amine group in common amino acids is connected to the carbon

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

Contact: Raymond Hovey Genomics Center - SFS

Contact: Raymond Hovey Genomics Center - SFS Bioinformatics Lunch Seminar (Summer 2014) Every other Friday at 1 pm. 20-30 minutes plus discussion Informal, ask questions anytime, start discussions Content will be based on feedback Targeted at broad

More information

Proteins: Workshop II

Proteins: Workshop II ame hem 306 Proteins: Workshop II In our previous workshop we investigated the nature of the building blocks of proteins amino acids. In this workshop you will investigate the structure, chemistry, and

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

2) Here is tyrosine with its pka values noted:

2) Here is tyrosine with its pka values noted: 1. a) At ph 1.0, the following amino acid side chains have (+) charge: Lys, Arg, His b) At ph 12.0, only the side chain of Arg has (+1) charge. 2) Here is tyrosine with its pka values noted: remember that

More information

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

Introduction to Proteins; Amino Acids, the Building Blocks of Proteins Lecture 3 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)

More information

Chapter 10. Proteins Workers of the. Cell Pearson Education, Inc.

Chapter 10. Proteins Workers of the. Cell Pearson Education, Inc. Chapter 10 Proteins Workers of the Cell Outline 10.1 Amino Acids A Second Look 10.2 Protein Formation 10.3 The Three-Dimensional Structure of Proteins 10.4 Denaturation of Proteins 10.5 Protein Functions

More information

2. Molecular Genetics: Proteins 2.1. Amino Acids. Proteins are long molecules composed of a string of amino acids. There are 20 commonly seen amino

2. Molecular Genetics: Proteins 2.1. Amino Acids. Proteins are long molecules composed of a string of amino acids. There are 20 commonly seen amino 2. Molecular Genetics: Proteins 2.1. Amino Acids. Proteins are long molecules composed of a string of amino acids. There are 20 commonly seen amino acids. These are given in table 1 with their full names

More information

Amino Acids and Proteins

Amino Acids and Proteins Amino Acids and Proteins Biology 12 A. Allen 1 Where do we find proteins? What do gelatin desserts, hair, antibodies, spider webs, blood clots, egg whites, tofu, and fingernails all have in common? They

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

Chapter 19 Aminoacids and Proteins

Chapter 19 Aminoacids and Proteins Chapter 19 Aminoacids and Proteins Amino acids are the building blocks of proteins; they contain a carboxylic acid group and an amino group on the alpha (α) carbon, the carbon adjacent to the C=O; because

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

What amino acids really look like

What amino acids really look like What amino acids really look like Tetrahedral carbon Cα Page 13 (12) Molecular Asymmetry Page 18 (16) Chiral Carbon with 4 different substituent groups (hand) Achiral Amino acid Structure The central carbon

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

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

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

Figure 1. Figure from Introduction to Protein Architecture, by Arthur Lesk showing a hydrophobicity scale for amino acids

Figure 1. Figure from Introduction to Protein Architecture, by Arthur Lesk showing a hydrophobicity scale for amino acids 2. Molecular Genetics: Proteins 2.1. Amino Acids. Proteins are long molecules composed of a string of amino acids. There are 20 commonly seen amino acids. These are given in table 1 with their full names

More information

Review Questions Proteins

Review Questions Proteins Review Questions Proteins 1. Why are proteins so important to living organisms? Every cell in every organism is built of thousands of different proteins. There are an estimated 1 billion different proteins

More information

Proteins. α-helix. Primary Protein Structure The linear sequence of amino acids in a protein chain. Determines secondary and tertiary structures.

Proteins. α-helix. Primary Protein Structure The linear sequence of amino acids in a protein chain. Determines secondary and tertiary structures. Proteins Proteins are naturally occuring peptides with 40 or more amino acid The function and the shape of a protein is described by their structure 4 levels of protein structure: Primary Secondary Tertiary

More information

CHAPTER 29 AMINO ACIDS, POLYPEPTIDES, AND PROTEINS SOLUTIONS TO REVIEW QUESTIONS. alpha carbon atom

CHAPTER 29 AMINO ACIDS, POLYPEPTIDES, AND PROTEINS SOLUTIONS TO REVIEW QUESTIONS. alpha carbon atom EIS29-451-462.v2.qxd 12/9/07 10:50 PM Page 451 APTER 29 AMIO AIDS, POLYPEPTIDES, AD PROTEIS SOLUTIOS TO REVIEW QUESTIOS 1. The amino acids of proteins are called alpha amino acids because the amine group

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

CH 2. Chem 226 Problem Set #13 Fundamentals of Organic Chemistry, 4 th edition, John McMurry. Chapter 15

CH 2. Chem 226 Problem Set #13 Fundamentals of Organic Chemistry, 4 th edition, John McMurry. Chapter 15 hem 226 Problem et #13 Fundamentals of rganic hemistry, 4 th edition, John McMurry. hapter 15 2. Eighteen of the 19 L-amino acids have the configuration at the α-carbon. ysteine is the only L- amino acid

More information

Amino acids & Protein Structure Chemwiki: Chapter , with most emphasis on 16.3, 16.4 and 16.6

Amino acids & Protein Structure Chemwiki: Chapter , with most emphasis on 16.3, 16.4 and 16.6 Amino acids & Protein Structure Chemwiki: Chapter 16. 16.1, 16.3-16.9 with most emphasis on 16.3, 16.4 and 16.6 1 1. Most jobs (except information storage) in cells are performed by proteins. 2. Proteins

More information

Using molecular marker technology in studies on plant genetic diversity Protein-based technologies Protein basics

Using molecular marker technology in studies on plant genetic diversity Protein-based technologies Protein basics Using molecular marker technology in studies on plant genetic diversity Protein-based technologies Protein basics Copyright: IPGRI and Cornell University, 2003 Protein basics 1 Contents! Protein basics!

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

Understanding Protein Structure Atoms to Ecosystems

Understanding Protein Structure Atoms to Ecosystems Name: Understanding Protein Structure Atoms to Ecosystems Part 1: Primary Protein Structure 1. Examine the structures of glycine and arginine, two of the 20 amino acids biological organisms use to build

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

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

The Peptide Bond A peptide bond is an amide bond. forms between the carboxyl group of one amino acid and the amino group of the next amino acid.

The Peptide Bond A peptide bond is an amide bond. forms between the carboxyl group of one amino acid and the amino group of the next amino acid. Chapter: Amino Acids, Proteins, and Enzymes Cellular functions of protein Enzymes Biological catalysts Defense proteins antibodies Transport proteins Hemoglobin or myoglobin Regulatory proteins Insulin

More information

Biological Science, 5e (Freeman) Chapter 3 Protein Structure and Function

Biological Science, 5e (Freeman) Chapter 3 Protein Structure and Function Biological Science, 5e (Freeman) Chapter 3 Protein Structure and Function 1) Side chains of amino acids. A) are all nonpolar B) are nonpolar if they contain N or S C) are all polar D) may be polar or nonpolar

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

1. Which of the following amino acids does not have a cyclic (ring) structure in its R-group?

1. Which of the following amino acids does not have a cyclic (ring) structure in its R-group? 1. Which of the following amino acids does not have a cyclic (ring) structure in its Rgroup? A) arginine B) proline C) tyrosine D) tryptophan E) phenylalanine 2. Which of the following amino acids does

More information

C Cys Cysteine Cysteine is a small till intermediately large hydrophobic residue. It doesn t like the alpha helix, but doesn t mind strand and turn. I

C Cys Cysteine Cysteine is a small till intermediately large hydrophobic residue. It doesn t like the alpha helix, but doesn t mind strand and turn. I A Ala Alanine Alanine is a small, hydrophobic residue. Its side chain, R, is just a methyl group. Alanine likes to sit in an alpha helix,it doesn t like beta strand very much, but it hates beta-turns.

More information

Biochemistry 2000 Midterm 1 1 of 6. Student Name : Student ID :

Biochemistry 2000 Midterm 1 1 of 6. Student Name : Student ID : Biochemistry 2000 Midterm 1 1 of 6 Student Name : 2007-10-11 Student ID : Instructions: Write neatly and clearly. Cross out with a single line any material you do not wish to have marked. Marks will be

More information

POLYMERIC MACROMOLECULES: CARBOHYDRATES, PROTEINS

POLYMERIC MACROMOLECULES: CARBOHYDRATES, PROTEINS POLYMERIC MACROMOLECULES: CARBOHYDRATES, PROTEINS CARBOHYDRATES Sugars, starches, glycogens, celluloses Cn(H2O)n "carbo-hydrate" Glucose (representative monomer) (C6H12O6) Different sugars have different

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

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

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

CHEM 121. Chapter 20 Name: Date:

CHEM 121. Chapter 20 Name: Date: CHEM 121. Chapter 20 Name: Date: 1. Proteins are polymers in which A) unbranched chains of amino acids are present. B) branched chains of amino acids are present. C) both unbranched and branched chains

More information

PROTEINS. Proteins play key roles in living systems. An Introduction to Structure and Functions of Proteins. Function of a Protein Depends mainly on:

PROTEINS. Proteins play key roles in living systems. An Introduction to Structure and Functions of Proteins. Function of a Protein Depends mainly on: PROTEINS An Introduction to Structure and Functions of Proteins Proteins play key roles in living systems Examples of protein functions Catalysis: Almost all chemical reactions in a living cell are catalyzed

More information

Protein Structure and Function. Amino acid structure

Protein Structure and Function. Amino acid structure Protein Structure and Function Lecture 2b: Amino acid structure and properties Amino acid structure Un-ionized form Dipolar form (zwitterion) 2 Amine (α-amino) Carboxylic acid C 3 C Side chain 1 Ionization

More information

Amino Acids and Proteins

Amino Acids and Proteins Amino Acids and Proteins Chapter 27 1 C 2-2 Amino Acids 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

More information

1.5: Proteins and Nucleic Acids pg

1.5: Proteins and Nucleic Acids pg UNIT 1: Biochemistry 1.5: Proteins and Nucleic Acids pg. 39 47 Amino Acids Amino acid - is a molecule that contains a carboxyl group and an amino group: serves as the monomer subunit of proteins. All proteins

More information

Biochemistry 2000 Sample Questions 1 Amino Acids & Proteins 1. (1) Give brief definitions or unique descriptions of the following terms:

Biochemistry 2000 Sample Questions 1 Amino Acids & Proteins 1. (1) Give brief definitions or unique descriptions of the following terms: (1) Give brief definitions or unique descriptions of the following terms: (a) oligopeptide (b) quaternary structure (c) zwitterion (d) salting out (2) Consider the 20 amino acids that commonly occur in

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

Protein Structure. C483 Spring 2013

Protein Structure. C483 Spring 2013 Protein Structure C483 Spring 2013 1. Which statement is false about a globular protein that performs its biological function as a single independent polypeptide chain? A) Its tertiary structure is likely

More information

Protein: Polymers made up of difference sequences of 20 standard amino acids.

Protein: Polymers made up of difference sequences of 20 standard amino acids. Protein: Polymers made up of difference sequences of 20 standard amino acids. Functions: Enzymes, defensive proteins, hormonal and regulatory proteins Function is dependent on structure of the protein!

More information

Biochemistry 2000 Sample Question 2 Proteins

Biochemistry 2000 Sample Question 2 Proteins (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

Review I: Protein Structure

Review I: Protein Structure Review I: Protein Structure Rajan Munshi BBSI @ Pitt 2006 Department of Computational Biology University of Pittsburgh School of Medicine May 23, 2006 Amino Acids Building blocks of proteins 20 amino acids

More information

Protein structure. CS/CME/BioE/Biophys/BMI 279 Sept. 29 and Oct. 4, 2016 Ron Dror

Protein structure. CS/CME/BioE/Biophys/BMI 279 Sept. 29 and Oct. 4, 2016 Ron Dror Protein structure CS/CME/BioE/Biophys/BMI 279 Sept. 29 and Oct. 4, 2016 Ron Dror A reminder Please interrupt if you have questions, and especially if you re confused! Outline Visualizing proteins The Protein

More information

Chem Lecture 2 Protein Structure Part 3

Chem Lecture 2 Protein Structure Part 3 Chem 452 - Lecture 2 Protein Structure Part 3 Question of the Day: Most proteins are made from a repertoire of 20 different amino acids. A small protein contains around 100 amino acids strung together

More information

Part 4. Chapter 19 Proteins: Structure: primary Secondary Tertiary Quaternary Loss of protein structure Tests for proteins (lab) Sections:

Part 4. Chapter 19 Proteins: Structure: primary Secondary Tertiary Quaternary Loss of protein structure Tests for proteins (lab) Sections: Part 4 Chapter 19 Proteins: Structure: primary Secondary Tertiary Quaternary Loss of protein structure Tests for proteins (lab) Sections: 19.4-19.5 Proteins Structures: Primary Proteins are polypeptides

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

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

Chapter 5. The Structure and Function of Large Biological Molecules

Chapter 5. The Structure and Function of Large Biological Molecules Chapter 5 The Structure and Function of Large Biological Molecules Lecture Outline Concept 5.1 Most macromolecules are polymers, built from monomers Three of the four classes of macromolecules carbohydrates,

More information

Lecture 6: Protein Primary, Secondary and Tertiary Structure Assigned reading in Campbell: Chapter , Chapter 5.4

Lecture 6: Protein Primary, Secondary and Tertiary Structure Assigned reading in Campbell: Chapter , Chapter 5.4 Biochemistry I, Fall Term Sept 12, 2005 Lecture 6: Protein Primary, Secondary and Tertiary Structure Assigned reading in ampbell: hapter 4.1-4.3, hapter 5.4 Key Terms: ative conformation Subunit Domain

More information

BCH 4053 Summer 2001 Chapter 6 Lecture Notes

BCH 4053 Summer 2001 Chapter 6 Lecture Notes BCH 4053 Summer 2001 Chapter 6 Lecture Notes 1 CHAPTER 6 Proteins: Secondary, Tertiary, and Quaternary Structure 2 Levels of Protein Structure Primary (sequence) Secondary (ordered structure along peptide

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

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

Protein structures Primary structure (linear polymer of amino acids) (backbone held together with peptide bonds) Secondary structure (standard 3-D

Protein structures Primary structure (linear polymer of amino acids) (backbone held together with peptide bonds) Secondary structure (standard 3-D Protein Structures Protein structures Primary structure (linear polymer of amino acids) (backbone held together with peptide bonds) Secondary structure (standard 3-D patterns) ( -helix, ß-sheet, held together

More information

Proteins: Primary Structure Lecture 6 Chapters 4 & 5. Structural Hierarchy in proteins. There are four levels of protein structure

Proteins: Primary Structure Lecture 6 Chapters 4 & 5. Structural Hierarchy in proteins. There are four levels of protein structure Proteins are the Body s Worker Molecules Proteins: Primary Structure Lecture 6 Chapters 4 & 5 9/10/09 Figure from The Structures of Life (NIH) Protein function as: 1. Enzymes:biological catalysts 2. Regulators

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

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

Summary of protein structure/function

Summary of protein structure/function Summary of protein structure/function 1. The 20 common aa s have different R groups. 2. Amino acids are linked by peptide bonds to form polypeptides & proteins. 3. Proteins are often large & have complex

More information

Tertiary Structure. Lecture 7 & 8: PROTEIN ARCHITECTURE IV: Tertiary and Quaternary Structure. Margaret Daugherty Fall 2003

Tertiary Structure. Lecture 7 & 8: PROTEIN ARCHITECTURE IV: Tertiary and Quaternary Structure. Margaret Daugherty Fall 2003 How to tell a left- vs. right-handed a-helix Lecture 7 & 8: PROTEIN ARCHITECTURE IV: Tertiary and Quaternary Structure Margaret Daugherty Fall 2003 Point your thumb up in the direction of the α-helix (N-->C).

More information

10.3 The Three-Dimensional Structure of Proteins Pearson Education, Inc.

10.3 The Three-Dimensional Structure of Proteins Pearson Education, Inc. 10.3 The Three-Dimensional Structure of Proteins 10.4 Denaturation of Proteins Denaturation is a process that disrupts the stabilizing attractive forces in the secondary, tertiary, or quaternary structure.

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

Conformational Structure How does the polypeptide chain fold?

Conformational Structure How does the polypeptide chain fold? Protein Structure Conformational Structure How does the polypeptide chain fold? 4 levels of protein structure In order to understand these levels of structure, you need to understand the nature of the

More information

THIS NOW DON T PUT IT OFF.

THIS NOW DON T PUT IT OFF. Lecture 3: Introduction to Proteins; Amino Acids, the Building Blocks of Proteins [PDF] Reading: Berg, Tymoczko & Stryer: Chapter 2, pp. 25-34; Appendix to chapter 2, pp. 61-62 (visualizing protein structures)

More information

A disaccharide is formed when a dehydration reaction joins two monosaccharides. This covalent bond is called a glycosidic linkage.

A disaccharide is formed when a dehydration reaction joins two monosaccharides. This covalent bond is called a glycosidic linkage. CH 5 Structure & Function of Large Molecules: Macromolecules Molecules of Life All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic

More information

Chapter 5. The Structure and Function of Large Biological Molecules

Chapter 5. The Structure and Function of Large Biological Molecules Chapter 5 The Structure and Function of Large Biological Molecules Focus on: Elements in each large biological molecule. How these molecules are linked and unlinked. Examples and functions of each type

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

6. Appendix: Protein structure

6. Appendix: Protein structure 6. Appendix: Protein structure The following section contains a very brief introduction to some aspects of protein and peptide structure. It is basically a summary of the description given by Mathews and

More information

CELLULAR CHEMISTRY 1 O H E N C C H C OH OH OH OH H C C C. 1. Which of these molecules would be used when making a protein?

CELLULAR CHEMISTRY 1 O H E N C C H C OH OH OH OH H C C C. 1. Which of these molecules would be used when making a protein? CELLULAR CHEMISTRY 1 Functional groups to macromolecules 1. Biologically important macromolecules are assembled by polymerizing small subunit molecules using condensation reactions. (T/F) 2. Chemical reactions

More information