Disulfide Bonds at the Hair Salon

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "Disulfide Bonds at the Hair Salon"

Transcription

1 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, the linear array can Cross link.using cysteine sidechains. A RedOx Reaction to Make or break Disulfide bonds Peptide Bonds A Special Amide bond in proteins How is it made? Also called a dehydration reaction 1

2 Peptide Bonds( and the neighboring atoms) are planar! Planar Nature of the peptide bonds comes From bonding resonance structures NO FREE ROTATION AROUND THE PEPTIDE BOND (partial double bond character) Bond length implies this double bond character C N = 1.49 Angstroms C=N = 1.27 Angstroms 2

3 Double bonded atoms can be cis or trans Peptide bonds are almost always trans why? Proline is bad in both orientations. Phi and Psi angles can be used to describe A protein s rotational bonds phi psi 3

4 Only certain phi and psi angles are possible in most Proteins other angle combinations are impeded by Steric hinderance. Ramachandran plot reveals the most likely Torsional angle combinations. Linus Pauling.a visionary biochemist In 1948, while in bed recovering from a cold, Pauling playfully constructed a crude paper model of a polypeptide chain using the chemical and stereochemical constraints known at that time such as, that the peptide bond was a flat (planar) shape. He concluded that the polypeptide chain was a single stranded helix, which he named the alphahli helix. He won the Nobel prize in chemistry for this in &hl=en&start=11&tbnid=5rdswDdQTEzyaM:&tbnh=128&tbnw=82&prev=/images%3Fq%3DLinus%2BPauling%26ndsp%3D20%26svnum%3D10%26hl%3Den%26rls%3DADBS,ADBS: ,ADBS:en%26sa%3DN Secondary structure Primary structure of proteins Secondary structure of proteins Alpha helix Beta pleated sheet Random coil Hair pin turns (reverse turn) Beta turn 4

5 Alpha helix Intra strand hydrogen bonding stabilizes Alpha helices Right handed Helix is most Likely.. Supported From the Ramachandran plot 5

6 Ball and stick representation Ribbon Diagram Cylinder representation Some proteins are dominated by alpha helical structure This is ferritin.can you guess what this protein binds? 6

7 Another protein structure made from Alpha helices.its called the Coiled coil.. a strong arrangement (like a braided rope) Used in proteins that need to be strong such as structural Proteins (cytoskeletal, hair, blood clots) Beta sheets They are Pleated, with regards to the R groups attached to the amino acids Alternating R groups above and below The plane of the backbone atoms Different R groups on either side 7

8 Stabilized by Inter strand Hydrogen bonds. Antiparallel beta sheet More stable why? Parallel beta sheet less stable why? Mixed Beta sheet 8

9 Ball and stick of a twisted Beta sheet Ribbon diagrams of the same Beta sheet Perspectives lets you see the shape. A Beta Barrel protein Fatty acid binding Protein Mostly beta strands 9

10 Hair pin turn Stabilized By hydrogen Bonding Usually involves proline Random coil (loops) On proteins can be Important Secondary structural Elements.. Like in antibodies This portion in red Interacts with other molecules. Ball and stick of myoglobin Tertiary Structure A combination Of all of the Secondary Structures in a Protein. MOST WATER SOLUBLE PROTEINS HAVE A COMPACT HYDROPHOBIC CORE! 10

11 The heme prosthetic group. Schematic view Of myoglobin Myoglobin surface charges in space filling models Cross section Porins are inside out. Why? 11

12 A DNA binding Motif a super secondary structure Proteins can have Domains Quaternary Structure = combinations of tertiary structures subunits A dimer 12

13 Hemoglobin is tetramer 13

14 Quaternary Structures form The coats of Most viruses. They self assemble. 4 subunits 60 copies of each = Viral coat! Denaturing agents Destroy Protein 3 D structure RNAse 14

15 Reduction of the disulfide bond using beta mercaptoethanol Proteins can Refold! 15

16 Some amino acid sequences can be Found in different secondary structures Stanley Prusiner, Nobel Laureate 1997 Discovered protein based infectious agents Prions Bovine spongiform encephalopathy (mad cow disease) Cruetzfeld Jakob disease Scrapie 16

17 Similarites Transmissible agent is aggregates of proteins of different molecular weight Protein aggregates are resistant to denaturation Protein is derived from a normal protein found in the brain Protein only Model for Prion diseases. Prions in Action Prion protein Misfolded form Oligomer aggregates protofibrils 17

18 Amyloid Plaques Protein folding is HIGHLY Cooperative! Half folded Proteins don t seem to exist at least they can be measured 18

19 Monkey typing Shakespeare s Hamlet If random correct keystrokes Are retained, then it can be done! This is how folding of proteins is Believed to take place so quickly! Local regions form first, then quickly condense Modifications found in some proteins 19

20 20

21 21

22 22

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

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

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

Peptide Bonds: Structure

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

More information

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

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

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

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

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

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

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

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

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

Introduction to Proteins and Enzymes

Introduction to Proteins and Enzymes Introduction to Proteins and Enzymes Basics of protein structure and composition The life of a protein Enzymes Theory of enzyme function Not all enzymes are proteins / not all proteins are enzymes Enzyme

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

GSAK YLDR WGSM. (b) (5 pts) Explain why neither of these steps alone is sufficient to unambiguously determine the sequence of your peptide.

GSAK YLDR WGSM. (b) (5 pts) Explain why neither of these steps alone is sufficient to unambiguously determine the sequence of your peptide. Problem 1. (total 30 points) You have to determine the amino acid sequence of a peptide. You performed the following steps using enzyme cleavage of your peptide (see table on the front page) combined with

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

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

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

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

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

More information

(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

Ramachandran Plots. Amino Acid Configuration in Proteins

Ramachandran Plots. Amino Acid Configuration in Proteins . Amino Acid onfiguration in Proteins Introduction The secondary structures that polypeptides can adopt in proteins are governed by hydrogen bonding interactions between the electronegative carbonyl oxygen

More information

WEEK ONE VOCABULARY. Adhesion- the attraction between water molecules and other molecules

WEEK ONE VOCABULARY. Adhesion- the attraction between water molecules and other molecules WEEK ONE VOCABULARY Acid- hydrogen donors; acids increase the hydrogen ion concentration in solution Adhesion- the attraction between water molecules and other molecules Alpha (α) helix- secondary protein

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

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

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

More information

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

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

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

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

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

Structure and Function of DNA

Structure and Function of DNA Structure and Function of DNA DNA and RNA Structure DNA and RNA are nucleic acids. They consist of chemical units called nucleotides. The nucleotides are joined by a sugar-phosphate backbone. The four

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

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

Structures of Proteins. Primary structure - amino acid sequence

Structures of Proteins. Primary structure - amino acid sequence Structures of Proteins Primary structure - amino acid sequence Secondary structure chain of covalently linked amino acids folds into regularly repeating structures. Secondary structure is the result of

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

Bonds and Structural Supports

Bonds and Structural Supports Bonds and Structural Supports Part of the Jmol Training Guide from the MSOE Center for BioMolecular Modeling Interactive version available at http://cbm.msoe.edu/teachingresources/jmol/jmoltraining/struts.html

More information

Oxygen-Binding Proteins

Oxygen-Binding Proteins Oxygen-Binding Proteins Myoglobin, Hemoglobin, Cytochromes bind O 2. Oxygen is transported from lungs to various tissues via blood in association with hemoglobin In muscle, hemoglobin gives up O 2 to myoglobin

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

Chapter 3 Molecules of Cells

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

More information

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

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

Solution key Problem Set 1

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

More information

Quaternary structure

Quaternary structure Quaternary structure Assembly of multiple polypeptide chains in one integral structure The arrangement of the subunits gives rise to a stable structure Subunits may be identical or different A common shorthand

More information

The Structure and Function of Large Biological Molecules by Dr. Ty C.M. Hoffman

The Structure and Function of Large Biological Molecules by Dr. Ty C.M. Hoffman The Structure and Function of Large Biological Molecules by Dr. Ty C.M. Hoffman Slide 1 All of the biological macromolecules are built from smaller subunits. Each subunit features - H and - OH substituents

More information

The Molecules of Cells

The Molecules of Cells The Molecules of Cells I. Introduction A. Most of the world s population cannot digest milk-based foods. 1. These people are lactose intolerant because they lack the enzyme lactase. 2. This illustrates

More information

Chapter 3. Protein Structure and Function

Chapter 3. Protein Structure and Function Chapter 3 Protein Structure and Function Broad functional classes So Proteins have structure and function... Fine! -Why do we care to know more???? Understanding functional architechture gives us POWER

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

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

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

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

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

More information

Chapter 5: The Structure and Function of Large Biological Molecules

Chapter 5: The Structure and Function of Large Biological Molecules Name Period Concept 5.1 Macromolecules are polymers, built from monomers 1. The large molecules of all living things fall into just four main classes. Name them. 2. Circle the three classes that are called

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

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

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

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

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

More information

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

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

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

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

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

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

More information

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

Chemistry Honors Lesson 3 Molecular Biology/Biochemistry

Chemistry Honors Lesson 3 Molecular Biology/Biochemistry Chemistry Honors Lesson 3 Molecular Biology/Biochemistry Noncovalent Interactions In Biology, the way molecules interact are determined by weak interactions that result in unique 3D structures and function.

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

R H important because the backbone atoms of each residue

R H important because the backbone atoms of each residue Protein Folding Proteins are not extended polypeptide chains. Instead, most proteins form compact folded three-dimensional arrangements, with well-defined, specific structures. Several types of non-covalent

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

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

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

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

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

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

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

More information

FROM 2D TO 3D: PROTEIN FOLDING AND. Week 5 HEMOGLOBIN FUNCTION

FROM 2D TO 3D: PROTEIN FOLDING AND. Week 5 HEMOGLOBIN FUNCTION FROM 2D TO 3D: PROTEIN FOLDING AND Week 5 HEMOGLOBIN FUNCTION QUIZ QUESTION ANNOUNCEMENTS Recently Updated Grades Week 4 Quiz Basepairer Write Up Remember to follow the rubric. Not following the rubric

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

Biological molecules:

Biological molecules: Biological molecules: All are organic (based on carbon). Monomers vs. polymers: Monomers refer to the subunits that, when polymerized, make up a larger polymer. Monomers may function on their own in some

More information

Genetic information (DNA) determines structure of proteins DNA RNA proteins cell structure 3.11 3.15 enzymes control cell chemistry ( metabolism )

Genetic information (DNA) determines structure of proteins DNA RNA proteins cell structure 3.11 3.15 enzymes control cell chemistry ( metabolism ) Biology 1406 Exam 3 Notes Structure of DNA Ch. 10 Genetic information (DNA) determines structure of proteins DNA RNA proteins cell structure 3.11 3.15 enzymes control cell chemistry ( metabolism ) Proteins

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

Section I Using Jmol as a Computer Visualization Tool

Section I Using Jmol as a Computer Visualization Tool Section I Using Jmol as a Computer Visualization Tool Jmol is a free open source molecular visualization program used by students, teachers, professors, and scientists to explore protein structures. Section

More information

Basic Concepts of DNA, Proteins, Genes and Genomes

Basic Concepts of DNA, Proteins, Genes and Genomes Basic Concepts of DNA, Proteins, Genes and Genomes Kun-Mao Chao 1,2,3 1 Graduate Institute of Biomedical Electronics and Bioinformatics 2 Department of Computer Science and Information Engineering 3 Graduate

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

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

DNA Glycosylase Exercise - Levels 1 & 2: Answer Key

DNA Glycosylase Exercise - Levels 1 & 2: Answer Key Name StarBiochem DNA Glycosylase Exercise - Levels 1 & 2: Answer Key Background In this exercise, you will explore the structure of a DNA repair protein found in most species, including bacteria. DNA repair

More information

Replication Study Guide

Replication Study Guide Replication Study Guide This study guide is a written version of the material you have seen presented in the replication unit. Self-reproduction is a function of life that human-engineered systems have

More information

Laboratorio di Bioinformatica Lezione #6

Laboratorio di Bioinformatica Lezione #6 Laboratorio di Bioinformatica Lezione #6 Dr. Marco Fondi Contact: marco.fondi@unifi.it www.unifi.it/dblemm/ tel. 0552288248 Dip.to di Biologia Evoluzionistica Laboratorio di Evoluzione Microbica e Molecolare,

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

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