PROTEINS. Building blocks, structure and function. Aim: You will have a clear picture of protein construction and their general properties

Size: px
Start display at page:

Download "PROTEINS. Building blocks, structure and function. Aim: You will have a clear picture of protein construction and their general properties"

Transcription

1 PROTEINS Building blocks, structure and function Aim: You will have a clear picture of protein construction and their general properties Reading materials: Compendium in Biochemistry, page Microbiology, A1-A12. Variations in GFP result in a rainbow of fluorescent proteins. C&EN

2 Nobel prize in chemistry 2008: Osamu Shimomura, Martin Chalfie and Roger Y Tsien for the discovery and development of the green fluorescent protein, GFP. What are the proteins doing in the cell? Proteins have many functions in the living cell: Catalysis (enzymes) Transport and storage Mechanical support Immune system (antibodies) Movements Nerve signals Control of growth and differentiation This is possible because: LDH Proteins fold into complex three dimensional structures Proteins have chemically functional groups (e.g. -OH, -SH, -COOH, NH 2 ) Proteins can have stiff or flexible parts Proteins can interact with other molecules 2

3 Proteins are built by 20 different L-amino acids (1) α-carbon H N H 2 R COOH H α-amino acid There are 4 groups on the chiral α-carbon: H COOH (COO - ) NH 2 (NH 3+ ) R (= side chain) The character of the R-group will give amino acids with different: size form charge hydrophobicity hydrogen bonding capacity chemical reactivity Proteins are built by 20 L-amino acids (2) Aromatic Phenylalanine Phe F " Tyrosine Tyr Y " Tryptophane Trp W Aliphatic Glycine Gly G " Alanine Ala A " Valine Val V " Leucine Leu L " Isoleucine Iso I " Proline Pro P Side chain structure 3

4 Proteins are built by 20 L-amino acids (3) Acidic Aspartic acid Asp D Side chain structure " Glutaminic acid Glu E Amides Asparagine Asn N " Glutamine Gln Q Basic Lysine Lys K " Histidine His H " Arginine Arg R Sulphurus Cysteine Cys C " Methionine Met M Hydroxylic Serine Ser S " Threonine Thr T Peptides - polypeptides H 3 Amino acid 1 Amino acid 2 Amino acid 3 Amino acid 4 Amino acid 5 Aminoterminal Carboxyterminal The order of amino acids = primary structure 4

5 The peptide bond The peptide bond (CONH) is planar and stiff (double bond character) R 1 -group R 2 -group R 1 -group R 2 -group The peptide bond is almost always in TRANS configuration because of steric hindrance The polypeptide spontaneously folds into regular structures The mixture of STIFF ELEMENTS (the peptide p bond) and ELEMENTS WITH LIMITED MOBILITY in the polypeptide enables the formation of regular structures: ο α-helix ο β-structure ο β-turn o loops These structures are examples of SECONDARY STRUCTURES 5

6 α-helix All NH and CO in the main chain are engaged in hydrogen bonds running PARALLEL to the helix 3,6 Amino acids per turn PILLAR β-structure (β pleated sheet) Antiparallel Parallel Hydrogen bonds BETWEEN the STRETCHED strands WALL 6

7 β-turn and loops The β-turn has a hydrogen bond between CO on aa i and NH on aa i+3 Enables the polypeptide to turn its heel" Loops do not have exact regular structures t but bt are stable tbl and well-defined anyway What keeps the protein together in a complete three-dimensional structure? NH 3 OOC S S Connecting forces: the secondary structures α-helix β-structure, β-turn and loops ionic i bonds between side chains hydrogen bonds between side chains SS-bridges (SH-groups from two adjacent cysteines) the inside of the protein is predominately hydrophobic 7

8 List of terms connected to protein structure Primary structure: chain Secondary structure: Tertiary structure: Quaternary structure: The sequence of the amino acids in the polypeptide The interactions between amino acids close in the sequence (example: α-helix, β-structure, β-turn and loops) Interactions between amino acids distant in the sequence, The structure at large" The arrangement of the subunits in a multimeric protein Subunit: A part (= a complete polypeptide) of a multimeric protein Domain: Some proteins have compact parts with a specific function, e.g. a catalytic domain. Is often coded for by an exon. Random coil: Unfolded polypeptide Native protein: The correctly folded polypeptide structure Denatured protein: The protein has lost its natural folding ( e.g. by extensive heating) In some proteins several polypeptide chains are joined together to multimeric units β α β α β α α β Hemoglobin A tetrameric protein consists of 4 subunits = 4 polypeptide chains 8

9 The structure is determined by the sequence A certain polypeptide sequence always leads to the same structure Why? Random coil Native protein Is not formed is the most stable one = has the lowest energy The folding process is very rapid Random coil 1 s (10 27 år) Native protein = finished, correctly folded protein Local folding and keeping of successful intermediates. Easiest parts first Random coil Amino acids have different propensity to participate in α-helix, β-structure and β-turn Native protein The final adjustment is relatively slow (1 s) Molten globule: Compact structure with most parts in place. Hydrophobic amino acids in the centre. Completed 9

10 The living cell has proteins which promote the folding In the TEST TUBE the protein folding is often easy (Diluted conditions) In the LIVING CELL the situation is chaotic - Different proteins can get mixed during folding - Erroneous SS-bonds can be formed Therefore, the living cell has means, e.g.: - Chaperones (proteins protecting unfolded parts of the polypeptide chain) - Disulphide isomerases (break up SS-bonds allowing them to recombine to the one with lowest energy) Completed proteins can get new properties by modification Proteins are built by 20 amino acids in the ribosome Some amino acids can be modified later e.g.: - Ser and Thr are phosphorylated (often as a way to control protein activity) - Acetylation of the amino terminal (stabilised against degradation) - Carbohydrates can be bound to till Asn (a more hydrophilic protein) - Fatty acids can be bound to e.g. Cys (a more hd hydrophobic hbi protein) i) - Pro in collagen can become hydroxylated (the structure is stabilised) Sometimes a part of the protein is removed (the protein/the enzyme is activated) 10

11 Protein purification Overview Alternative 1 Alternative 2 Bacteria Disintegration (grinding/homogenisation) Beef heart Pure protein e.g. human growth hormone a) coarse conditioning i methods TARGET- MOLECULE Homogenate Centrifugation Raw extract b) high resolution methods How can we separate different proteins? Property Method Size Dialysis, Gel filtration Density Centrifugation Charge Hydrophobicity Specific affinity Solubility Ion exchange chromatography, Electrophoresis Hydrophobic chromatography Affinity chromatography Salt precipitation 11

12 Cells Homogenate Raw extract Salt precipitation More. Pure protein? You must check the result of the purification process! Take samples Run SDS-PAGE Measure protein content Measure enzymatic activity The process should lead to: Fewer number of protein band Higher specific activity (Units/mg protein) SDS PAGE (Sodium Dodecyl Sulphate PolyAcrylamide Gel Electrophoresis) A very common analytic separation method Native protein Denatured protein covered with negatively charged SDS-molecules Heat with SDS-cocktail Polyakrylamide gel between two glass disks - Staining with Coomassie blue + Rawextract Pure protein Standard 12

13 Protein characterization Overview Molecular size Gel filtration SDS PAGE Mass spectrometry Amino acid sequence Edman degradation 3-D structure NMR X-ray crystallography Enzyme activity MALDI: Matrix Assisted Laser Desorption Ionization Sample plate Laser hν AH + 1. Sample (A) is mixed with excess matrix (M) and dried on a MALDI plate. 2. Laser flash ionizes matrix molecules. 3. Sample molecules are ionized by proton transfer from matrix: MH + + A M + AH kv Variable Ground Grid Grid 13

14 Edman degradation works only for the first 50 amino acids! 14

15 X-ray crystallography 15

16 Summary Proteins are biopolymers constructed from 20 α amino acids. The 20 amino acids differ in their side chains: polarity and charge Peptides and proteins are formed by linking amino acids together using amide (peptide) bonds. Protein structure: primary, secondary, tertiary and quaternary Protein sequence analysis: Edman degradation Protein purification: chromatography 16

Proteins. Amino acids, structure and function. The Nobel Prize in Chemistry 2012 Robert J. Lefkowitz Brian K. Kobilka

Proteins. Amino acids, structure and function. The Nobel Prize in Chemistry 2012 Robert J. Lefkowitz Brian K. Kobilka Proteins Amino acids, structure and function The Nobel Prize in Chemistry 2012 Robert J. Lefkowitz Brian K. Kobilka O O HO N N HN OH Ser65-Tyr66-Gly67 The Nobel prize in chemistry 2008 Osamu Shimomura,

More information

CS612 - Algorithms in Bioinformatics

CS612 - Algorithms in Bioinformatics Spring 2016 Protein Structure February 7, 2016 Introduction to Protein Structure A protein is a linear chain of organic molecular building blocks called amino acids. Introduction to Protein Structure Amine

More information

Biomolecules: amino acids

Biomolecules: amino acids Biomolecules: amino acids Amino acids Amino acids are the building blocks of proteins They are also part of hormones, neurotransmitters and metabolic intermediates There are 20 different amino acids in

More information

Objective: You will be able to explain how the subcomponents of

Objective: You will be able to explain how the subcomponents of Objective: You will be able to explain how the subcomponents of nucleic acids determine the properties of that polymer. Do Now: Read the first two paragraphs from enduring understanding 4.A Essential knowledge:

More information

Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 5.4: Proteins have many structures, resulting in a wide range of functions Proteins account for more than 50% of the dry mass of most cells Protein functions include structural support, storage,

More information

Molecular Biology. general transfer: occurs normally in cells. special transfer: occurs only in the laboratory in specific conditions.

Molecular Biology. general transfer: occurs normally in cells. special transfer: occurs only in the laboratory in specific conditions. Chapter 9: Proteins Molecular Biology replication general transfer: occurs normally in cells transcription special transfer: occurs only in the laboratory in specific conditions translation unknown transfer:

More information

Chemical Nature of the Amino Acids. Table of a-amino Acids Found in Proteins

Chemical Nature of the Amino Acids. Table of a-amino Acids Found in Proteins Chemical Nature of the Amino Acids All peptides and polypeptides are polymers of alpha-amino acids. There are 20 a- amino acids that are relevant to the make-up of mammalian proteins (see below). Several

More information

Properties of amino acids in proteins

Properties of amino acids in proteins Properties of amino acids in proteins one of the primary roles of DNA (but far from the only one!!!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids

More information

Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A

Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A Homework Watch the Bozeman video called, Biological Molecules Objective:

More information

Proteins are sometimes only produced in one cell type or cell compartment (brain has 15,000 expressed proteins, gut has 2,000).

Proteins are sometimes only produced in one cell type or cell compartment (brain has 15,000 expressed proteins, gut has 2,000). Lecture 2: Principles of Protein Structure: Amino Acids Why study proteins? Proteins underpin every aspect of biological activity and therefore are targets for drug design and medicinal therapy, and in

More information

9/6/2011. Amino Acids. C α. Nonpolar, aliphatic R groups

9/6/2011. Amino Acids. C α. Nonpolar, aliphatic R groups Amino Acids Side chains (R groups) vary in: size shape charge hydrogen-bonding capacity hydrophobic character chemical reactivity C α Nonpolar, aliphatic R groups Glycine (Gly, G) Alanine (Ala, A) Valine

More information

Chemistry 121 Winter 17

Chemistry 121 Winter 17 Chemistry 121 Winter 17 Introduction to Organic Chemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. Ohio State) E-mail: upali@latech.edu Office: 311 Carson Taylor Hall ; Phone: 318-257-4941;

More information

Gentilucci, Amino Acids, Peptides, and Proteins. Peptides and proteins are polymers of amino acids linked together by amide bonds CH 3

Gentilucci, Amino Acids, Peptides, and Proteins. Peptides and proteins are polymers of amino acids linked together by amide bonds CH 3 Amino Acids Peptides and proteins are polymers of amino acids linked together by amide bonds Aliphatic Side-Chain Amino Acids - - H CH glycine alanine 3 proline valine CH CH 3 - leucine - isoleucine CH

More information

The Structure and Function of Large Biological Molecules Part 4: Proteins Chapter 5

The Structure and Function of Large Biological Molecules Part 4: Proteins Chapter 5 Key Concepts: The Structure and Function of Large Biological Molecules Part 4: Proteins Chapter 5 Proteins include a diversity of structures, resulting in a wide range of functions Proteins Enzymatic s

More information

Page 8/6: The cell. Where to start: Proteins (control a cell) (start/end products)

Page 8/6: The cell. Where to start: Proteins (control a cell) (start/end products) Page 8/6: The cell Where to start: Proteins (control a cell) (start/end products) Page 11/10: Structural hierarchy Proteins Phenotype of organism 3 Dimensional structure Function by interaction THE PROTEIN

More information

Introduction to proteins and protein structure

Introduction to proteins and protein structure Introduction to proteins and protein structure The questions and answers below constitute an introduction to the fundamental principles of protein structure. They are all available at [link]. What are

More information

Amino Acids. Review I: Protein Structure. Amino Acids: Structures. Amino Acids (contd.) Rajan Munshi

Amino Acids. Review I: Protein Structure. Amino Acids: Structures. Amino Acids (contd.) Rajan Munshi Review I: Protein Structure Rajan Munshi BBSI @ Pitt 2005 Department of Computational Biology University of Pittsburgh School of Medicine May 24, 2005 Amino Acids Building blocks of proteins 20 amino acids

More information

AP Bio. Protiens Chapter 5 1

AP Bio. Protiens Chapter 5 1 Concept.4: Proteins have many structures, resulting in a wide range of functions Proteins account for more than 0% of the dry mass of most cells Protein functions include structural support, storage, transport,

More information

Reactions and amino acids structure & properties

Reactions and amino acids structure & properties Lecture 2: Reactions and amino acids structure & properties Dr. Sameh Sarray Hlaoui Common Functional Groups Common Biochemical Reactions AH + B A + BH Oxidation-Reduction A-H + B-OH + energy ª A-B + H

More information

The Structure and Function of Macromolecules

The Structure and Function of Macromolecules The Structure and Function of Macromolecules Macromolecules are polymers Polymer long molecule consisting of many similar building blocks. Monomer the small building block molecules. Carbohydrates, proteins

More information

Macromolecules of Life -3 Amino Acids & Proteins

Macromolecules of Life -3 Amino Acids & Proteins Macromolecules of Life -3 Amino Acids & Proteins Shu-Ping Lin, Ph.D. Institute of Biomedical Engineering E-mail: splin@dragon.nchu.edu.tw Website: http://web.nchu.edu.tw/pweb/users/splin/ Amino Acids Proteins

More information

Methionine (Met or M)

Methionine (Met or M) Fig. 5-17 Nonpolar Fig. 5-17a Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Polar Trypotphan (Trp

More information

Review II: The Molecules of Life

Review II: The Molecules of Life Review II: The Molecules of Life Judy Wieber BBSI @ Pitt 2007 Department of Computational Biology University of Pittsburgh School of Medicine May 24, 2007 Outline Introduction Proteins Carbohydrates Lipids

More information

Short polymer. Dehydration removes a water molecule, forming a new bond. Longer polymer (a) Dehydration reaction in the synthesis of a polymer

Short polymer. Dehydration removes a water molecule, forming a new bond. Longer polymer (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3 H HO H Short polymer Dehydration removes a water molecule, forming a new bond Unlinked monomer H 2 O HO 1 2 3 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3

More information

Human Biochemistry Option B

Human Biochemistry Option B Human Biochemistry Option B A look ahead... Your body has many functions to perform every day: Structural support, genetic information, communication, energy supply, metabolism Right now, thousands of

More information

CHAPTER 21: Amino Acids, Proteins, & Enzymes. General, Organic, & Biological Chemistry Janice Gorzynski Smith

CHAPTER 21: Amino Acids, Proteins, & Enzymes. General, Organic, & Biological Chemistry Janice Gorzynski Smith CHAPTER 21: Amino Acids, Proteins, & Enzymes General, Organic, & Biological Chemistry Janice Gorzynski Smith CHAPTER 21: Amino Acids, Proteins, Enzymes Learning Objectives: q The 20 common, naturally occurring

More information

Amino Acids. Amino Acids. Fundamentals. While their name implies that amino acids are compounds that contain an NH. 3 and CO NH 3

Amino Acids. Amino Acids. Fundamentals. While their name implies that amino acids are compounds that contain an NH. 3 and CO NH 3 Fundamentals While their name implies that amino acids are compounds that contain an 2 group and a 2 group, these groups are actually present as 3 and 2 respectively. They are classified as α, β, γ, etc..

More information

Biomolecules Amino Acids & Protein Chemistry

Biomolecules Amino Acids & Protein Chemistry Biochemistry Department Date: 17/9/ 2017 Biomolecules Amino Acids & Protein Chemistry Prof.Dr./ FAYDA Elazazy Professor of Biochemistry and Molecular Biology Intended Learning Outcomes ILOs By the end

More information

PROTEINS. Amino acids are the building blocks of proteins. Acid L-form * * Lecture 6 Macromolecules #2 O = N -C -C-O.

PROTEINS. Amino acids are the building blocks of proteins. Acid L-form * * Lecture 6 Macromolecules #2 O = N -C -C-O. Proteins: Linear polymers of amino acids workhorses of the cell tools, machines & scaffolds Lecture 6 Macromolecules #2 PRTEINS 1 Enzymes catalysts that mediate reactions, increase reaction rate Structural

More information

Judy Wieber. Department of Computational Biology. May 27, 2008

Judy Wieber. Department of Computational Biology. May 27, 2008 Review II: The Molecules of Life Judy Wieber BBSI @ Pitt 2008 Department of Computational Biology University it of Pittsburgh School of Medicine i May 27, 2008 Outline Introduction Proteins Carbohydrates

More information

Macromolecules Structure and Function

Macromolecules Structure and Function Macromolecules Structure and Function Within cells, small organic molecules (monomers) are joined together to form larger molecules (polymers). Macromolecules are large molecules composed of thousands

More information

CHM333 LECTURE 6: 1/25/12 SPRING 2012 Professor Christine Hrycyna AMINO ACIDS II: CLASSIFICATION AND CHEMICAL CHARACTERISTICS OF EACH AMINO ACID:

CHM333 LECTURE 6: 1/25/12 SPRING 2012 Professor Christine Hrycyna AMINO ACIDS II: CLASSIFICATION AND CHEMICAL CHARACTERISTICS OF EACH AMINO ACID: AMINO ACIDS II: CLASSIFICATION AND CHEMICAL CHARACTERISTICS OF EACH AMINO ACID: - The R group side chains on amino acids are VERY important. o Determine the properties of the amino acid itself o Determine

More information

1. Describe the relationship of dietary protein and the health of major body systems.

1. Describe the relationship of dietary protein and the health of major body systems. Food Explorations Lab I: The Building Blocks STUDENT LAB INVESTIGATIONS Name: Lab Overview In this investigation, you will be constructing animal and plant proteins using beads to represent the amino acids.

More information

Introduction to Protein Structure Collection

Introduction to Protein Structure Collection Introduction to Protein Structure Collection Teaching Points This collection is designed to introduce students to the concepts of protein structure and biochemistry. Different activities guide students

More information

Moorpark College Chemistry 11 Fall Instructor: Professor Gopal. Examination # 5: Section Five May 7, Name: (print)

Moorpark College Chemistry 11 Fall Instructor: Professor Gopal. Examination # 5: Section Five May 7, Name: (print) Moorpark College Chemistry 11 Fall 2013 Instructor: Professor Gopal Examination # 5: Section Five May 7, 2013 Name: (print) Directions: Make sure your examination contains TEN total pages (including this

More information

Bio Factsheet. Proteins and Proteomics. Number 340

Bio Factsheet. Proteins and Proteomics.   Number 340 Number 340 Proteins and Proteomics Every living thing on the planet is composed of cells, and cells in turn are made of many types of molecules, including the biological molecules carbohydrates, lipids,

More information

(30 pts.) 16. (24 pts.) 17. (20 pts.) 18. (16 pts.) 19. (5 pts.) 20. (5 pts.) TOTAL (100 points)

(30 pts.) 16. (24 pts.) 17. (20 pts.) 18. (16 pts.) 19. (5 pts.) 20. (5 pts.) TOTAL (100 points) Moorpark College Chemistry 11 Spring 2009 Instructor: Professor Torres Examination # 5: Section Five April 30, 2009 ame: (print) ame: (sign) Directions: Make sure your examination contains TWELVE total

More information

Chapter 20 and GHW#10 Questions. Proteins

Chapter 20 and GHW#10 Questions. Proteins Chapter 20 and GHW#10 Questions Proteins Proteins Naturally occurring bioorganic polyamide polymers containing a sequence of various combinations of 20 amino acids. Amino acids contain the elements carbon,

More information

LAB#23: Biochemical Evidence of Evolution Name: Period Date :

LAB#23: Biochemical Evidence of Evolution Name: Period Date : LAB#23: Biochemical Evidence of Name: Period Date : Laboratory Experience #23 Bridge Worth 80 Lab Minutes If two organisms have similar portions of DNA (genes), these organisms will probably make similar

More information

2. Which of the following amino acids is most likely to be found on the outer surface of a properly folded protein?

2. Which of the following amino acids is most likely to be found on the outer surface of a properly folded protein? Name: WHITE Student Number: Answer the following questions on the computer scoring sheet. 1 mark each 1. Which of the following amino acids would have the highest relative mobility R f in normal thin layer

More information

Chapter 5: Structure and Function of Macromolecules AP Biology 2011

Chapter 5: Structure and Function of Macromolecules AP Biology 2011 Chapter 5: Structure and Function of Macromolecules AP Biology 2011 1 Macromolecules Fig. 5.1 Carbohydrates Lipids Proteins Nucleic Acids Polymer - large molecule consisting of many similar building blocks

More information

Lipids: diverse group of hydrophobic molecules

Lipids: diverse group of hydrophobic molecules Lipids: diverse group of hydrophobic molecules Lipids only macromolecules that do not form polymers li3le or no affinity for water hydrophobic consist mostly of hydrocarbons nonpolar covalent bonds fats

More information

Introduction to Proteomics Dr. Sanjeeva Srivastava Department of Biosciences and Bioengineering Indian Institute of Technology - Bombay

Introduction to Proteomics Dr. Sanjeeva Srivastava Department of Biosciences and Bioengineering Indian Institute of Technology - Bombay Introduction to Proteomics Dr. Sanjeeva Srivastava Department of Biosciences and Bioengineering Indian Institute of Technology - Bombay Lecture 01 Introduction to Amino Acids Welcome to the proteomic course.

More information

1-To know what is protein 2-To identify Types of protein 3- To Know amino acids 4- To be differentiate between essential and nonessential amino acids

1-To know what is protein 2-To identify Types of protein 3- To Know amino acids 4- To be differentiate between essential and nonessential amino acids Amino acids 1-To know what is protein 2-To identify Types of protein 3- To Know amino acids 4- To be differentiate between essential and nonessential amino acids 5-To understand amino acids synthesis Amino

More information

Four Classes of Biological Macromolecules. Biological Macromolecules. Lipids

Four Classes of Biological Macromolecules. Biological Macromolecules. Lipids Biological Macromolecules Much larger than other par4cles found in cells Made up of smaller subunits Found in all cells Great diversity of func4ons Four Classes of Biological Macromolecules Lipids Polysaccharides

More information

For questions 1-4, match the carbohydrate with its size/functional group name:

For questions 1-4, match the carbohydrate with its size/functional group name: Chemistry 11 Fall 2013 Examination #5 PRACTICE 1 For the first portion of this exam, select the best answer choice for the questions below and mark the answers on your scantron. Then answer the free response

More information

A Chemical Look at Proteins: Workhorses of the Cell

A Chemical Look at Proteins: Workhorses of the Cell A Chemical Look at Proteins: Workhorses of the Cell A A Life ciences 1a Lecture otes et 4 pring 2006 Prof. Daniel Kahne Life requires chemistry 2 amino acid monomer and it is proteins that make the chemistry

More information

Multiple-Choice Questions Answer ALL 20 multiple-choice questions on the Scantron Card in PENCIL

Multiple-Choice Questions Answer ALL 20 multiple-choice questions on the Scantron Card in PENCIL Multiple-Choice Questions Answer ALL 20 multiple-choice questions on the Scantron Card in PENCIL For Questions 1-10 choose ONE INCORRECT answer. 1. Which ONE of the following statements concerning the

More information

For questions 1-4, match the carbohydrate with its size/functional group name:

For questions 1-4, match the carbohydrate with its size/functional group name: Chemistry 11 Fall 2013 Examination #5 PRACTICE 1 ANSWERS For the first portion of this exam, select the best answer choice for the questions below and mark the answers on your scantron. Then answer the

More information

(65 pts.) 27. (10 pts.) 28. (15 pts.) 29. (10 pts.) TOTAL (100 points) Moorpark College Chemistry 11 Spring Instructor: Professor Gopal

(65 pts.) 27. (10 pts.) 28. (15 pts.) 29. (10 pts.) TOTAL (100 points) Moorpark College Chemistry 11 Spring Instructor: Professor Gopal Moorpark College Chemistry 11 Spring 2012 Instructor: Professor Gopal Examination # 5: Section Five May 1, 2012 Name: (print) GOOD LUCK! Directions: Make sure your examination contains TWELVE total pages

More information

Fundamentals of Organic Chemistry CHEM 109 For Students of Health Colleges

Fundamentals of Organic Chemistry CHEM 109 For Students of Health Colleges Fundamentals of Organic Chemistry CHEM 109 For Students of Health Colleges Credit hrs.: (2+1) King Saud University College of Science, Chemistry Department CHEM 109 CHAPTER 9. AMINO ACIDS, PEPTIDES AND

More information

Practice Problems 3. a. What is the name of the bond formed between two amino acids? Are these bonds free to rotate?

Practice Problems 3. a. What is the name of the bond formed between two amino acids? Are these bonds free to rotate? Life Sciences 1a Practice Problems 3 1. Draw the oligopeptide for Ala-Phe-Gly-Thr-Asp. You do not need to indicate the stereochemistry of the sidechains. Denote with arrows the bonds formed between the

More information

Biology. Lectures winter term st year of Pharmacy study

Biology. Lectures winter term st year of Pharmacy study Biology Lectures winter term 2008 1 st year of Pharmacy study 3 rd Lecture Chemical composition of living matter chemical basis of life. Atoms, molecules, organic compounds carbohydrates, lipids, proteins,

More information

BIO 311C Spring Lecture 15 Friday 26 Feb. 1

BIO 311C Spring Lecture 15 Friday 26 Feb. 1 BIO 311C Spring 2010 Lecture 15 Friday 26 Feb. 1 Illustration of a Polypeptide amino acids peptide bonds Review Polypeptide (chain) See textbook, Fig 5.21, p. 82 for a more clear illustration Folding and

More information

This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is worth 2 points.

This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is worth 2 points. MBB 407/511 Molecular Biology and Biochemistry First Examination - October 1, 2002 Name Social Security Number This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is

More information

9/16/15. Properties of Water. Benefits of Water. More properties of water

9/16/15. Properties of Water. Benefits of Water. More properties of water Properties of Water Solid/Liquid Density Water is densest at 4⁰C Ice floats Allows life under the ice Hydrogen bond Ice Hydrogen bonds are stable Liquid water Hydrogen bonds break and re-form Benefits

More information

CHY2026: General Biochemistry. Unit 4:Amino Acid Chemistry

CHY2026: General Biochemistry. Unit 4:Amino Acid Chemistry CHY2026: General Biochemistry Unit 4:Amino Acid Chemistry http://www.hcc.mnscu.edu/programs/dept/chem/v.27/amino_acid_structure_2.jpg Hydrogen Amino group Carboxyl Group Unique side chain (R-group) R Central

More information

Midterm 1 Last, First

Midterm 1 Last, First Midterm 1 BIS 105 Prof. T. Murphy April 23, 2014 There should be 6 pages in this exam. Exam instructions (1) Please write your name on the top of every page of the exam (2) Show all work for full credit

More information

Chapter 3: Amino Acids and Peptides

Chapter 3: Amino Acids and Peptides Chapter 3: Amino Acids and Peptides BINF 6101/8101, Spring 2018 Outline 1. Overall amino acid structure 2. Amino acid stereochemistry 3. Amino acid sidechain structure & classification 4. Non-standard

More information

AMINO ACIDS STRUCTURE, CLASSIFICATION, PROPERTIES. PRIMARY STRUCTURE OF PROTEINS

AMINO ACIDS STRUCTURE, CLASSIFICATION, PROPERTIES. PRIMARY STRUCTURE OF PROTEINS AMINO ACIDS STRUCTURE, CLASSIFICATION, PROPERTIES. PRIMARY STRUCTURE OF PROTEINS Elena Rivneac PhD, Associate Professor Department of Biochemistry and Clinical Biochemistry State University of Medicine

More information

Lecture 3: 8/24. CHAPTER 3 Amino Acids

Lecture 3: 8/24. CHAPTER 3 Amino Acids Lecture 3: 8/24 CHAPTER 3 Amino Acids 1 Chapter 3 Outline 2 Amino Acid Are Biomolecules and their Atoms Can Be Visualized by Two Different Ways 1) Fischer projections: Two dimensional representation of

More information

Maha AbuAjamieh. Tamara Wahbeh. Mamoon Ahram

Maha AbuAjamieh. Tamara Wahbeh. Mamoon Ahram 12 Maha AbuAjamieh Tamara Wahbeh Mamoon Ahram - - Go to this sheet s last page for definitions of the words with an asterisk above them (*) - You should memorise the 3-letter abbreviations, of all the

More information

Biochemistry - I. Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology, Kharagpur Lecture 1 Amino Acids I

Biochemistry - I. Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology, Kharagpur Lecture 1 Amino Acids I Biochemistry - I Prof. S. Dasgupta Department of Chemistry Indian Institute of Technology, Kharagpur Lecture 1 Amino Acids I Hello, welcome to the course Biochemistry 1 conducted by me Dr. S Dasgupta,

More information

PHAR3316 Pharmacy biochemistry Exam #2 Fall 2010 KEY

PHAR3316 Pharmacy biochemistry Exam #2 Fall 2010 KEY 1. How many protons is(are) lost when the amino acid Asparagine is titrated from its fully protonated state to a fully deprotonated state? A. 0 B. 1 * C. 2 D. 3 E. none Correct Answer: C (this question

More information

Chapter 21 Lecture Outline

Chapter 21 Lecture Outline Chapter 21 Lecture Outline Amino Acids, Proteins, and Enzymes! Introduction! Proteins are biomolecules that contain many amide bonds, formed by joining amino acids. Prepared by Andrea D. Leonard University

More information

Structure of proteins

Structure of proteins Structure of proteins Presented by Dr. Mohammad Saadeh The requirements for the Pharmaceutical Biochemistry I Philadelphia University Faculty of pharmacy Structure of proteins The 20 a.a commonly found

More information

Lecture 4. Grouping Amino Acid 7/1/10. Proteins. Amino Acids. Where Are Proteins Located. Nonpolar Amino Acids

Lecture 4. Grouping Amino Acid 7/1/10. Proteins. Amino Acids. Where Are Proteins Located. Nonpolar Amino Acids Proteins Lecture 4 Proteins - Composition of Proteins (Amino Acids) Chapter 21 ection 1-6! Proteins are compounds of high molar mass consisting almost entirely of amino acid chain(s)! Molar masses range

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

Q1: Circle the best correct answer: (15 marks)

Q1: Circle the best correct answer: (15 marks) Q1: Circle the best correct answer: (15 marks) 1. Which one of the following incorrectly pairs an amino acid with a valid chemical characteristic a. Glycine, is chiral b. Tyrosine and tryptophan; at neutral

More information

If you like us, please share us on social media. The latest UCD Hyperlibrary newsletter is now complete, check it out.

If you like us, please share us on social media. The latest UCD Hyperlibrary newsletter is now complete, check it out. Sign In Forgot Password Register username username password password Sign In If you like us, please share us on social media. The latest UCD Hyperlibrary newsletter is now complete, check it out. ChemWiki

More information

Protein Structure Klemens Wild, BZH,

Protein Structure Klemens Wild, BZH, Protein Structure recommended books Proteins protein definition From gr. proteios (superior, erstrangig) 1836 JJ Berzelius Functions: structural, enzymes, muscle, transport immune system, Linear polymer

More information

The Basics: A general review of molecular biology:

The Basics: A general review of molecular biology: The Basics: A general review of molecular biology: DNA Transcription RNA Translation Proteins DNA (deoxy-ribonucleic acid) is the genetic material It is an informational super polymer -think of it as the

More information

استاذ الكيمياءالحيوية

استاذ الكيمياءالحيوية قسم الكيمياء الحيوية د.دولت على سالمه استاذ الكيمياءالحيوية ٢٠١٥-٢٠١٤ الرمز الكودي : ٥١٢ المحاضرة األولى ١ Content : Definition of proteins Definition of amino acids Definition of peptide bond General

More information

Amino Acids. Lecture 4: Margaret A. Daugherty. Fall Swiss-prot database: How many proteins? From where?

Amino Acids. Lecture 4: Margaret A. Daugherty. Fall Swiss-prot database: How many proteins? From where? Lecture 4: Amino Acids Margaret A. Daugherty Fall 2004 Swiss-prot database: How many proteins? From where? 1986 Use http://us.expasy.org to get to swiss-prot database Proteins are the workhorses of the

More information

The Structure and Func.on of Macromolecules Proteins GRU1L6

The Structure and Func.on of Macromolecules Proteins GRU1L6 The Structure and Func.on of Macromolecules Proteins GRU1L6 Proteins Proteins Most structurally & functionally diverse group Function: involved in almost everything enzymes (pepsin, DNA polymerase) structure

More information

Classification of amino acids: -

Classification of amino acids: - Page 1 of 8 P roteinogenic amino acids, also known as standard, normal or primary amino acids are 20 amino acids that are incorporated in proteins and that are coded in the standard genetic code (subunit

More information

Moorpark College Chemistry 11 Fall Instructor: Professor Gopal. Examination #5: Section Five December 7, Name: (print) Section:

Moorpark College Chemistry 11 Fall Instructor: Professor Gopal. Examination #5: Section Five December 7, Name: (print) Section: Moorpark College Chemistry 11 Fall 2011 Instructor: Professor Gopal Examination #5: Section Five December 7, 2011 Name: (print) Section: alkene < alkyne < amine < alcohol < ketone < aldehyde < amide

More information

I) Choose the best answer: 1- All of the following amino acids are neutral except: a) glycine. b) threonine. c) lysine. d) proline. e) leucine.

I) Choose the best answer: 1- All of the following amino acids are neutral except: a) glycine. b) threonine. c) lysine. d) proline. e) leucine. 1- All of the following amino acids are neutral except: a) glycine. b) threonine. c) lysine. d) proline. e) leucine. 2- The egg white protein, ovalbumin, is denatured in a hard-boiled egg. Which of the

More information

So where were we? But what does the order mean? OK, so what's a protein? 4/1/11

So where were we? But what does the order mean? OK, so what's a protein? 4/1/11 So where were we? We know that DNA is responsible for heredity Chromosomes are long pieces of DNA DNA turned out to be the transforming principle We know that DNA is shaped like a long double helix, with

More information

Raghad Abu Jebbeh. Amani Nofal. Mamoon Ahram

Raghad Abu Jebbeh. Amani Nofal. Mamoon Ahram ... 14 Raghad Abu Jebbeh Amani Nofal Mamoon Ahram This sheet includes part of lec.13 + lec.14. Amino acid peptide protein Terminology: 1- Residue: a subunit that is a part of a large molecule. 2- Dipeptide:

More information

Amino acids. (Foundation Block) Dr. Essa Sabi

Amino acids. (Foundation Block) Dr. Essa Sabi Amino acids (Foundation Block) Dr. Essa Sabi Learning outcomes What are the amino acids? General structure. Classification of amino acids. Optical properties. Amino acid configuration. Non-standard amino

More information

AA s are the building blocks of proteins

AA s are the building blocks of proteins Chamras Chemistry 106 Lecture otes Chapter 24: Amino Acids, Peptides, and Proteins General Formula: () n (') α-amino Acids: (n = 1) Example: Amino Acids and Proteins: Glycine Alanine Valine AA s are the

More information

1. (38 pts.) 2. (25 pts.) 3. (15 pts.) 4. (12 pts.) 5. (10 pts.) Bonus (12 pts.) TOTAL (100 points)

1. (38 pts.) 2. (25 pts.) 3. (15 pts.) 4. (12 pts.) 5. (10 pts.) Bonus (12 pts.) TOTAL (100 points) Moorpark College Chemistry 11 Spring 2010 Instructor: Professor Torres Examination #5: Section Five May 4, 2010 ame: (print) ame: (sign) Directions: Make sure your examination contains TWELVE total pages

More information

Bioinformatics for molecular biology

Bioinformatics for molecular biology Bioinformatics for molecular biology Structural bioinformatics tools, predictors, and 3D modeling Structural Biology Review Dr Research Scientist Department of Microbiology, Oslo University Hospital -

More information

Protein Investigator. Protein Investigator - 3

Protein Investigator. Protein Investigator - 3 Protein Investigator Objectives To learn more about the interactions that govern protein structure. To test hypotheses regarding protein structure and function. To design proteins with specific shapes.

More information

Date: EXERCISE 4. Figure 1. Amino acid structure.

Date: EXERCISE 4. Figure 1. Amino acid structure. Student s name: Date: Points: Assistant s signature: Index numer: /6 EXERISE 4 AMIN AIDS AND PRTEINS. Amino acids are structural units (monomers) of proteins. There are 20 different amino acids coded for

More information

Levels of Protein Structure:

Levels of Protein Structure: Levels of Protein Structure: PRIMARY STRUCTURE (1 ) - Defined, non-random sequence of amino acids along the peptide backbone o Described in two ways: Amino acid composition Amino acid sequence M-L-D-G-C-G

More information

UNIT 2 Amino acids and Proteins

UNIT 2 Amino acids and Proteins UNIT 2 Amino acids and Proteins Significance of Proteins 1. Keep the cells and tissues growing, renewing and mending 2. Take part in some kinds of important physiological activities 3. Oxidation and supply

More information

Organic Molecules: Proteins

Organic Molecules: Proteins Organic Molecules: Proteins Proteins Most structurally & functionally diverse group Function: involved in almost everything enzymes (pepsin, DNA polymerase) structure (keratin, collagen) carriers & transport

More information

2. Ionization Sources 3. Mass Analyzers 4. Tandem Mass Spectrometry

2. Ionization Sources 3. Mass Analyzers 4. Tandem Mass Spectrometry Dr. Sanjeeva Srivastava 1. Fundamental of Mass Spectrometry Role of MS and basic concepts 2. Ionization Sources 3. Mass Analyzers 4. Tandem Mass Spectrometry 2 1 MS basic concepts Mass spectrometry - technique

More information

Introduction. Basic Structural Principles PDB

Introduction. Basic Structural Principles PDB BCHS 6229 Protein Structure and Function Lecture 1 (October 11, 2011) Introduction Basic Structural Principles PDB 1 Overview Main Goals: Carry out a rapid review of the essentials of protein structure

More information

Protein structure. Dr. Mamoun Ahram Summer semester,

Protein structure. Dr. Mamoun Ahram Summer semester, Protein structure Dr. Mamoun Ahram Summer semester, 2017-2018 Overview of proteins Proteins have different structures and some have repeating inner structures, other do not. A protein may have gazillion

More information

paper and beads don t fall off. Then, place the beads in the following order on the pipe cleaner:

paper and beads don t fall off. Then, place the beads in the following order on the pipe cleaner: Beady Pipe Cleaner Proteins Background: Proteins are the molecules that carry out most of the cell s dayto-day functions. While the DNA in the nucleus is "the boss" and controls the activities of the cell,

More information

BIOB111 - Tutorial activity for Session 14

BIOB111 - Tutorial activity for Session 14 BIOB111 - Tutorial activity for Session 14 General topics for week 7 Session 14 Amino acids and proteins Students review the concepts learnt and answer the selected questions from the textbook. General

More information

Chapter 3. Structure of Enzymes. Enzyme Engineering

Chapter 3. Structure of Enzymes. Enzyme Engineering Chapter 3. Structure of Enzymes Enzyme Engineering 3.1 Introduction With purified protein, Determining M r of the protein Determining composition of amino acids and the primary structure Determining the

More information

Green Segment Contents

Green Segment Contents Green Segment Contents Parts Reference Guide Green Segment 1 8 2 6 3 4 5 7 1. Amino Acid Side Chain Chart shows the properties and atomic structure of side chains. 2. Amino Acid Side Chains affect protein

More information

Head. Tail. Carboxyl group. group. group. air water. Hydrocarbon chain. lecture 5-sa Seth Copen Goldstein 2.

Head. Tail. Carboxyl group. group. group. air water. Hydrocarbon chain. lecture 5-sa Seth Copen Goldstein 2. Lipids Some lipid structures Organic compounds Amphipathic Polar head group (hydrophilic) Non-polar tails (hydrophobic) Lots of uses Energy storage Membranes Hormones Vitamins HO O C H 2 C CH 2 H 2 C CH

More information

Proteins: Structure and Function 2/8/2017 1

Proteins: Structure and Function 2/8/2017 1 Proteins: Structure and Function 2/8/2017 1 outline Protein functions hemistry of amino acids Protein Structure; Primary structure Secondary structure Tertiary structure Quaternary structure 2/8/2017 2

More information