Structure of proteins

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "Structure of proteins"

Transcription

1 Structure of proteins Primary structure: is amino acids sequence or the covalent structure ( ) amino acids M.Wt. of amino acid=110 Dalton (56 110=5610 Dalton). Single chain or more than one polypeptide chain. Gly-Ala-Val Gly-Val-Ala Both the tripeptides shown above contain the same amino acids, but their sequence is altered.when the sequence is changed, the polypeptide is also different. Insulin: Hormone secreted by β- cell of pancreas (facilitate glucose entery to the cell for metabolism) Proinsulin: single polypeptide chain of 86 amino acids. Biologically active insulin consist of (2 chain) A.chain: consist of 21 amino acids. B.chain: consist of 30 amino acids. C peptide: connecting peptide 3-disulfide bonds of cysteine 1

2 Primary structure of insulin Secondary structure: conformation of polypeptide chain is based on rotational angels about covalent bonds. α helix β- plated sheet Collagen helix 1-α-helix: coiled single chain, spiral. 2

3 P = d n P = helix pitch, n = no. of a.a. residues per 360 turn, d= distance between α- carbon of adjacent a.a. characteristic of α- helix: 3.6 a.a. per turn d= 1.5 A, P= 5.4 A Peptide bond β plated sheet: 1-Sheet like 2-The poly peptide chains is almost fully extended. The distance between adjacent amino acids is 3.5 A. 3- Stabilized by H- bonds between N-H and C=O groups of different polypeptide chain 4- Parallel β- sheet or anti parallel 5-Side chain group are projected above and below. 3

4 Collagen helix: Three dimensional structure Tertiary structure: In this structure the protein chain or polypeptide chain form a- 3- dimensional conformation stabilized by non-covalent bonds: hydrogen bonds, hydrophobic bonds, van der walls, electrostatic interaction. Quaternary structure: Is seen only when protein is formed from more than four subunits. Its spatial arrangement of different subunits in the space. Hydrogen bond: is the interaction or bond (non-covalent) formed between the carbonyl oxygen and amide group of polypeptide chain, H- bond could form between not only oxygen and hydrogen, but also between these tow atoms and polar R- groups.the side chain could partisepitate in hydrogen bond formation and according to hydrogen bonds potentiality, we can classify hydrogen bond into 3 groups: 4

5 1-The side chain in amino acid residue could act as hydrogen bond donar. 2-Could act both as H- bond donar and acceptor regardless to PH. 3-Vary with the PH of the medium, they could act at certain PH as hydrogen bond donar and acceptor, if the PH is changed this will make these residue act as donar or acceptor, therefore H-bond varies with the PH of medium. Electrostatic bond: forms between polar side group on the surface of the protein or between two subunits, if protein is formed of more than one subunit, so it will stabilize the quaterally subunit. Could be seen when the electron density of two molecules is high in a close distance, at this distance there will be a conformation between these two atoms. Normally is seen in protein inside it (core of protein not on it surface). Hydrophobic interaction: happens between the non-polar groups of both aliphatic or aromatic amino acid residues. They come in close inside the core of protein and forms this form of interaction. The most abundent conformation is hydrogen and hydrophobic interaction. The energy that partisepitates in the interaction formation is very small to that which forms the covalent bond, but because of the large number of these bonds in protein conformation the stability will be confined the energy difference. 5

6 Collagen Helix: is a triple helix, collagen is abundant in skin, oarta, cartilage.etc. Synthesized by special cells (e.g.: osteoblast, fibrocytes and chondroblast in cartilage). It is rich in amino acids and derived amino acids like proline, glycine, hydroxy proline (OH- proline) and hydroxy glycine (OH-glycine). Hydroxylation is carried out by enzyme hydroxlase in presence of vitamine C and succinate and α- keto glutarate. Addition of carbohydrates (in form of glucose and galactose) prior to the collagen secretion forms its primary structure. When it is formed by 3 polypeptide chains the helix is called tropo- collagen. According to the 3 polypeptides we have five tybes of collagen depending on amino acids sequences. Type II, III and IV have similar amino acids sequence in their 3 polypeptides. Type I and V have only two identical polypeptides chains in the amino acids sequence. Every turn of the helix carry three amino acids and the 3 rd amino acid is always glycine on the same side of the helix. The three helices will be coiled on each other and form the super coiled structure of tropocollagen, the coiling will be always on the 3 rd position (on glycine) to facilitate the conformation. The coiling is stabilized by achieving two bonds: 1-Hydrogen bond 2- Hydrophobic interaction. Deficiency of vitamine C in the body causes scurvey characterized by the break down of RBCs. 6

7 Cross linking: the amino acids will be first oxidized into aldehydes by an enzyme called lysyl oxidase and then will be pass into chain of reactions in covalent bond cross linkage between these helices, this is important in the stability of collagen fiber. The protein is classified according to the quaternary structure into: Fibrous and globular proteins. Fibrous proteins: Have a rode shape structure for example: collagen, they have low solubility in water, vary in molecular weight, have a high tensile structure important in matrices for certain tissues, have high amount of regular secondary structure. Globular proteins: Spherical in shape, water soluble, have secondary and tertiary and quaternary structures, for example: haemoglobin and myoglobin Haemoglobin: Formed by four polypeptide chain, each two of identical primary structure. Binds with O 2 and CO 2 from lungs and tissues. Types: 1-Adult haemoglobin (HbA). 2-Infant haemoglobin (HbF) 3-HbA 2. 7

8 Myoglobin: Oxygen binding protein in muscles, made of a single polypeptide chain, has only on oxygen binding site. 8

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

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

Proteins the primary biological macromolecules of living organisms

Proteins the primary biological macromolecules of living organisms Proteins the primary biological macromolecules of living organisms Protein structure and folding Primary Secondary Tertiary Quaternary structure of proteins Structure of Proteins Protein molecules adopt

More information

AP BIOLOGY 2008 SCORING GUIDELINES

AP BIOLOGY 2008 SCORING GUIDELINES AP BIOLOGY 2008 SCORING GUIDELINES Question 1 1. The physical structure of a protein often reflects and affects its function. (a) Describe THREE types of chemical bonds/interactions found in proteins.

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

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

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

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

(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

Lecture Overview. Hydrogen Bonds. Special Properties of Water Molecules. Universal Solvent. ph Scale Illustrated. special properties of water

Lecture Overview. Hydrogen Bonds. Special Properties of Water Molecules. Universal Solvent. ph Scale Illustrated. special properties of water Lecture Overview special properties of water > water as a solvent > ph molecules of the cell > properties of carbon > carbohydrates > lipids > proteins > nucleic acids Hydrogen Bonds polarity of water

More information

Proteins and Nucleic Acids

Proteins and Nucleic Acids Proteins and Nucleic Acids Chapter 5 Macromolecules: Proteins Proteins Most structurally & functionally diverse group of biomolecules. : o Involved in almost everything o Enzymes o Structure (keratin,

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

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

Peptide Bond Amino acids are linked together by peptide bonds to form polypepetide chain.

Peptide Bond Amino acids are linked together by peptide bonds to form polypepetide chain. Peptide Bond Peptide Bond Amino acids are linked together by peptide bonds to form polypepetide chain. + H 2 O 2 Peptide bonds are strong and not broken by conditions that denature proteins, such as heating.

More information

Worksheet 13.1. Chapter 13: Human biochemistry glossary

Worksheet 13.1. Chapter 13: Human biochemistry glossary Worksheet 13.1 Chapter 13: Human biochemistry glossary α-helix Refers to a secondary structure of a protein where the chain is twisted to form a regular helix, held by hydrogen bonds between peptide bonds

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

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

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

Introduction to Protein Folding

Introduction to Protein Folding Introduction to Protein Folding Chapter 4 Proteins: Three Dimensional Structure and Function Conformation - three dimensional shape Native conformation - each protein folds into a single stable shape (physiological

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

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

8/20/2012 H C OH H R. Proteins

8/20/2012 H C OH H R. Proteins Proteins Rubisco monomer = amino acids 20 different amino acids polymer = polypeptide protein can be one or more polypeptide chains folded & bonded together large & complex 3-D shape hemoglobin Amino acids

More information

Non-Covalent Bonds (Weak Bond)

Non-Covalent Bonds (Weak Bond) Non-Covalent Bonds (Weak Bond) Weak bonds are those forces of attraction that, in biological situations, do not take a large amount of energy to break. For example, hydrogen bonds are broken by energies

More information

Role of Hydrogen Bonding on Protein Secondary Structure Introduction

Role of Hydrogen Bonding on Protein Secondary Structure Introduction Role of Hydrogen Bonding on Protein Secondary Structure Introduction The function and chemical properties of proteins are determined by its three-dimensional structure. The final architecture of the protein

More information

Conformational Properties of Polypeptide Chains

Conformational Properties of Polypeptide Chains Conformational Properties of Polypeptide Chains Levels of Organization Primary structure Amino acid sequence of the protein Secondary structure H bonds in the peptide chain backbone α helix and β sheets

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

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

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

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

Chemistry: Introduction to General, Organic & Biological Chemistry (Timberlake) Chapter 16: Amino Acids, Proteins, and Enzymes

Chemistry: Introduction to General, Organic & Biological Chemistry (Timberlake) Chapter 16: Amino Acids, Proteins, and Enzymes Chemistry: Introduction to General, Organic & Biological Chemistry (Timberlake) Chapter 16: Amino Acids, Proteins, and Enzymes MULTIPLE CHOICE 1) Which of the following is NOT a function of proteins? A)

More information

1. The diagram below represents a biological process

1. The diagram below represents a biological process 1. The diagram below represents a biological process 5. The chart below indicates the elements contained in four different molecules and the number of atoms of each element in those molecules. Which set

More information

Hydrogen Bonds The electrostatic nature of hydrogen bonds

Hydrogen Bonds The electrostatic nature of hydrogen bonds Hydrogen Bonds Hydrogen bonds have played an incredibly important role in the history of structural biology. Both the structure of DNA and of protein a-helices and b-sheets were predicted based largely

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

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

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

Carbon-organic Compounds

Carbon-organic Compounds Elements in Cells The living substance of cells is made up of cytoplasm and the structures within it. About 96% of cytoplasm and its included structures are composed of the elements carbon, hydrogen, oxygen,

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

Chemical Bonds and Groups - Part 1

Chemical Bonds and Groups - Part 1 hemical Bonds and Groups - Part 1 ARB SKELETS arbon has a unique role in the cell because of its ability to form strong covalent bonds with other carbon atoms. Thus carbon atoms can join to form chains.

More information

Lecture 4: Peptides and Protein Primary Structure [PDF] Key Concepts. Objectives See also posted Peptide/pH/Ionization practice problems.

Lecture 4: Peptides and Protein Primary Structure [PDF] Key Concepts. Objectives See also posted Peptide/pH/Ionization practice problems. Lecture 4: Peptides and Protein Primary Structure [PDF] Reading: Berg, Tymoczko & Stryer, Chapter 2, pp. 34-37 Practice problems (peptide ionization) [PDF]; problems in textbook: chapter 2, pp. 63-64,

More information

LECTURE-2. Basics of Amino acids and Proteins HANDOUT. Proteins are the most complex and versatile macromolecules comprised of amino acids

LECTURE-2. Basics of Amino acids and Proteins HANDOUT. Proteins are the most complex and versatile macromolecules comprised of amino acids LECTURE-2 Basics of Amino acids and Proteins HANDOUT PREAMBLE Proteins are the most complex and versatile macromolecules comprised of amino acids as the building blocks. There are 20 standard amino acids

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

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

Previously published in Biophysical Society On-line Textbook PROTEINS CHAPTER 1. PROTEIN STRUCTURE. Section 1. Primary structure, secondary motifs,

Previously published in Biophysical Society On-line Textbook PROTEINS CHAPTER 1. PROTEIN STRUCTURE. Section 1. Primary structure, secondary motifs, Previously published in Biophysical Society On-line Textbook PROTEINS CHAPTER 1. PROTEIN STRUCTURE Section 1. Primary structure, secondary motifs, tertiary architecture, and quaternary organization Jannette

More information

INTERMOLECULAR FORCES

INTERMOLECULAR FORCES INTERMOLECULAR FORCES Intermolecular forces- forces of attraction and repulsion between molecules that hold molecules, ions, and atoms together. Intramolecular - forces of chemical bonds within a molecule

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

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

Papers listed: Cell2. This weeks papers. Chapt 4. Protein structure and function

Papers listed: Cell2. This weeks papers. Chapt 4. Protein structure and function Papers listed: Cell2 During the semester I will speak of information from several papers. For many of them you will not be required to read these papers, however, you can do so for the fun of it (and it

More information

Introduction to the Protein Folding Problem

Introduction to the Protein Folding Problem Lecture Notes - 1 7.24/7.88J/5.48J The Protein Folding Problem Student Review: Side chains of the L amino acids and their pk's L/D difference Planarity of the peptide Bond Lecture Overview: Introduction

More information

Computational Systems Biology. Lecture 2: Enzymes

Computational Systems Biology. Lecture 2: Enzymes Computational Systems Biology Lecture 2: Enzymes 1 Images from: David L. Nelson, Lehninger Principles of Biochemistry, IV Edition, Freeman ed. or under creative commons license (search for images at http://search.creativecommons.org/)

More information

Introduction, Noncovalent Bonds, and Properties of Water

Introduction, Noncovalent Bonds, and Properties of Water Lecture 1 Introduction, Noncovalent Bonds, and Properties of Water Reading: Berg, Tymoczko & Stryer: Chapter 1 problems in textbook: chapter 1, pp. 23-24, #1,2,3,6,7,8,9, 10,11; practice problems at end

More information

Unit Vocabulary: o Organic Acid o Alcohol. o Ester o Ether. o Amine o Aldehyde

Unit Vocabulary: o Organic Acid o Alcohol. o Ester o Ether. o Amine o Aldehyde Unit Vocabulary: Addition rxn Esterification Polymer Alcohol Ether Polymerization Aldehyde Fermentation Primary Alkane Functional group Saponification Alkene Halide (halocarbon) Saturated hydrocarbon Alkyne

More information

Amino Acids as Acids, Bases and Buffers:

Amino Acids as Acids, Bases and Buffers: Amino Acids as Acids, Bases and Buffers: - Amino acids are weak acids - All have at least 2 titratable protons (shown below as fully protonated species) and therefore have 2 pka s o α-carboxyl (-COOH)

More information

Chemical Bonds. Chemical Bonds. The Nature of Molecules. Energy and Metabolism < < Covalent bonds form when atoms share 2 or more valence electrons.

Chemical Bonds. Chemical Bonds. The Nature of Molecules. Energy and Metabolism < < Covalent bonds form when atoms share 2 or more valence electrons. The Nature of Molecules Chapter 2 Energy and Metabolism Chapter 6 Chemical Bonds Molecules are groups of atoms held together in a stable association. Compounds are molecules containing more than one type

More information

INTRODUCTION TO HORMONES

INTRODUCTION TO HORMONES INTRODUCTION TO HORMONES UNIVERSITY OF PNG SCHOOL OF MEDICINE AND HEALTH SCIENCES DISCIPLINE OF BIOCHEMISTRY & MOLECULAR BIOLOGY PBL MBBS II SEMINAR VJ Temple What are hormones? Cells in multi-cellular

More information

Chapter 05 The Three-Dimensional Structure of Proteins

Chapter 05 The Three-Dimensional Structure of Proteins Chapter 05 The Three-Dimensional Structure of Proteins The covalent backbone of a typical protein contains hundreds of individual bonds. Because free rotation is possible around many of these bonds, the

More information

--not necessarily a protein! (all proteins are polypeptides, but the converse is not true)

--not necessarily a protein! (all proteins are polypeptides, but the converse is not true) 00Note Set 5b 1 PEPTIDE BONDS AND POLYPEPTIDES OLIGOPEPTIDE: --chain containing only a few amino acids (see tetrapaptide, Fig 5.9) POLYPEPTIDE CHAINS: --many amino acids joined together --not necessarily

More information

Food Proteins. Prof. Dr. Mohamed Fawzy Ramadan Hassanien Zagazig University, Egypt

Food Proteins. Prof. Dr. Mohamed Fawzy Ramadan Hassanien Zagazig University, Egypt Food Proteins Prof. Dr. Mohamed Fawzy Ramadan Hassanien Zagazig University, Egypt -Amino Acid Sequence -Protein Conformation -Levels of Protein Structure -Primary structure -Secondary structure -Tertiary

More information

Lecture 19: Proteins, Primary Struture

Lecture 19: Proteins, Primary Struture CPS260/BGT204.1 Algorithms in Computational Biology November 04, 2003 Lecture 19: Proteins, Primary Struture Lecturer: Pankaj K. Agarwal Scribe: Qiuhua Liu 19.1 The Building Blocks of Protein [1] Proteins

More information

The Chemical Basis of Life. Chemical Bonds

The Chemical Basis of Life. Chemical Bonds The Chemical Basis of Life white=hydrogen red=oxygen gray=carbon yellow=phosphorus blue=nitrogen green=sulfur All organisms are made up of water, inorganic ions, small molecules (77% by weight) and macromolecules

More information

PRACTICE TEST QUESTIONS

PRACTICE TEST QUESTIONS PART A: MULTIPLE CHOICE QUESTIONS PRACTICE TEST QUESTIONS DNA & PROTEIN SYNTHESIS B 1. One of the functions of DNA is to A. secrete vacuoles. B. make copies of itself. C. join amino acids to each other.

More information

Sickle cell anemia: Altered beta chain Single AA change (#6 Glu to Val) Consequence: Protein polymerizes Change in RBC shape ---> phenotypes

Sickle cell anemia: Altered beta chain Single AA change (#6 Glu to Val) Consequence: Protein polymerizes Change in RBC shape ---> phenotypes Protein Structure Polypeptide: Protein: Therefore: Example: Single chain of amino acids 1 or more polypeptide chains All polypeptides are proteins Some proteins contain >1 polypeptide Hemoglobin (O 2 binding

More information

Types, production of antibodies and Antibody/antigen interaction

Types, production of antibodies and Antibody/antigen interaction Types, production of antibodies and Antibody/antigen interaction Antibodies Secreted by B lymphocytes Great diversity and specificity: >109 different antibodies; can distinguish between very similar molecules

More information

Isomers Have same molecular formula, but different structures

Isomers Have same molecular formula, but different structures Isomers ave same molecular formula, but different structures Constitutional Isomers Differ in the order of attachment of atoms (different bond connectivity) Stereoisomers Atoms are connected in the same

More information

Overview'of'Solid-Phase'Peptide'Synthesis'(SPPS)'and'Secondary'Structure'Determination'by'FTIR'

Overview'of'Solid-Phase'Peptide'Synthesis'(SPPS)'and'Secondary'Structure'Determination'by'FTIR' verviewofsolid-phasepeptidesynthesis(spps)andsecondarystructuredeterminationbyftir Introduction Proteinsareubiquitousinlivingorganismsandcells,andcanserveavarietyoffunctions.Proteinscanactas enzymes,hormones,antibiotics,receptors,orserveasstructuralsupportsintissuessuchasmuscle,hair,and

More information

1 Peptide bond rotation

1 Peptide bond rotation 1 Peptide bond rotation We now consider an application of data mining that has yielded a result that links the quantum scale with the continnum level electrostatic field. In other cases, we have considered

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

1 The water molecule and hydrogen bonds in water

1 The water molecule and hydrogen bonds in water The Physics and Chemistry of Water 1 The water molecule and hydrogen bonds in water Stoichiometric composition H 2 O the average lifetime of a molecule is 1 ms due to proton exchange (catalysed by acids

More information

Peptides & Proteins. (thanks to Hans Börner)

Peptides & Proteins. (thanks to Hans Börner) Peptides & Proteins (thanks to Hans Börner) 1 Proteins & Peptides Proteuos: Proteus (Gr. mythological figure who could change form) proteuo: "first, ref. the basic constituents of all living cells peptos:

More information

The correct answer is d C. Answer c is incorrect. Reliance on the energy produced by others is a characteristic of heterotrophs.

The correct answer is d C. Answer c is incorrect. Reliance on the energy produced by others is a characteristic of heterotrophs. 1. An autotroph is an organism that a. extracts energy from organic sources b. converts energy from sunlight into chemical energy c. relies on the energy produced by other organisms as an energy source

More information

Water. Definition: A mole (or mol ) Water can IONIZE transiently. NONpolar covalent molecules do not dissolve in water + + + + + + + + + + + + + + + +

Water. Definition: A mole (or mol ) Water can IONIZE transiently. NONpolar covalent molecules do not dissolve in water + + + + + + + + + + + + + + + + Today s Topics Polar Covalent Bonds ydrogen bonding Properties of water p Water C bonds are Nonpolar Will these molecules dissolve in water? Start Macromolecules Carbohydrates & Lipids Sept 4, 05 Why are

More information

Protein Folding. The resulting three-dimensional structure is determined by the amino acid sequence (Anfinsen's dogma).

Protein Folding. The resulting three-dimensional structure is determined by the amino acid sequence (Anfinsen's dogma). Protein Folding Protein folding is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil. Each protein exists as an unfolded

More information

Chapter 12 Organic Compounds with Oxygen and Sulfur

Chapter 12 Organic Compounds with Oxygen and Sulfur Chapter 12 Organic Compounds with Oxygen and Sulfur 1 Alcohols An alcohol contains a hydroxyl group ( OH) that replaces a hydrogen atom in a hydrocarbon. A phenol contains a hydroxyl group ( OH) attached

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

7 Answers to end-of-chapter questions

7 Answers to end-of-chapter questions 7 Answers to end-of-chapter questions Multiple choice questions 1 B 2 B 3 A 4 B 5 A 6 D 7 C 8 C 9 B 10 B Structured questions 11 a i Maintenance of a constant internal environment within set limits i Concentration

More information