Chapter 2 Introduction to Macromolecules PDF

CHAPTER 2 Introduction to Macromolecules Required reading: Karp Chapter 2 2.2-1 2.5 | The Nature of Biological Molecules Macromolecules Macromolecules; Large highly organized molecules that form the structure and carry out the activit...

CHAPTER 2 Introduction to Macromolecules Required reading: Karp Chapter 2 2.2-1 2.5 | The Nature of Biological Molecules Macromolecules Macromolecules; Large highly organized molecules that form the structure and carry out the activities of cells four major categories – the first three are made up of repeating units of monomers making them polymers Proteins (amino acids) Nucleic acids (nucleotides) Polysaccharides (monosaccharides) Lipids (not always considered polymers because some lipids do not Monomers and polymers: have only one repeating monomer polymerization and hydrolysis. and monomers are not bonded to other monomers) Most cell macromolecules are short-lived, except DNA, and are continually broken down and replaced. 2.2-2 Macromolecules 2.2-3  2.7 | Carbohydrates Carbohydrates include: monosaccharides disaccharides polysaccharides Carbohydrates = the most abundant form of organic matter on earth Energy (storage and immediate) Metabolic intermediates can be precursors for other molecules Structural components of RNA and DNA Structural components of cell walls of bacteria and plants Glycoproteins and Glycolipids (inter and intracellular interactions) Most sugars have the general formula (CH2O)n 2.2-4  2.7 | Carbohydrates The Structure of Simple Sugars A sugar molecule has a backbone of carbon atoms linked together in a linear array by single bonds If the carbonyl group is located at an internal position the sugar is a ketose If the carbonyl is located at one end, the molecule is known as an aldose 2.2-5 (C6H12O6) = glucose – but not just glucose Isomers: differ only in the spatial arrangement of atoms 2.2-6  2.7 | Carbohydrates The Structure of Simple Sugars Sugars tend to be highly water soluble due to their hydroxyl groups Sugars more than 5 carbons self-react to produce a ring-containing molecule 2.2-7 Ring structure of D-glucose The anomeric carbon is the carbon derived from the carbonyl carbon (the ketone or aldehyde functional group) of the open-chain form of the carbohydrate molecule Identify the anomeric carbons on these monosaccharides In solution: the anomeric carbon can open and mutarotate 2.2-8 2.2-9 2.7 | Carbohydrates Stereoisomerism The C1 of the pyranose ring has four different groups and becomes a new center of asymmetry within the sugar molecule Because of this extra asymmetric carbon atom, each type of pyranose exists as α and β stereoisomers Formation of an a- and b-pyranose The molecule is an α-pyranose when the OH group of the first carbon projects below the plane of the ring, and a β-pyranose when the hydroxyl projects upward 2.2-10 2.7 | Carbohydrates Linking Sugars Together Monosaccharides can be linked by covalent bonds (Glycosidic Bonds) 2 monosaccarides linked by a glycosidic bond = a disaccharide Glycosidic bonds are formed between OH groups on two separate monosaccharides (or a monosaccharide and another molecule) (Glucose-a(1 4)-glucose) Maltose = glucose + glucose cellubiose = glucose + glucose What is the structural difference betwwen maltose and cellubiose? 2.2-11  2.7 | Carbohydrates Linking Sugars Together Monosaccharides can be linked by covalent bonds (glycosidic bonds) 2 monosaccarides linked by a glycosidic bond = a disaccharide Glycosidic bonds are formed between OH groups on two separate monosaccharides (or a monosaccharide and another molecule) Sucrose = glucose and fructose Lactose = galactose and glucose 2.2-12  2.6 | Carbohydrates Linking Sugars Together When the anomeric carbon of a monosaccharide participates in a glycosidic bond it can no longer mutarotate and the bond is in a fixed position What about the anomeric carbon in the second molecule of glucose – can it still mutarotate? polysaccharide 2.2-13  Glycosidic bonds A glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate When an anomeric carbon reacts with a hydroxyl = O-glycosidic bond When an anomeric carbon reacts with a nitrogen = N-glycosidic bond Glycosidic bonds always involve the hydroxyl of an anomeric carbon If the bond is with another hydroxyl it’s an O-glycosidic bond If the bond is with a nitrogen it’s an N-glycosidic bond The anomeric carbon (whether in an O or N glycosidic bond) will be in an α or β position generating α glycosidic linkages or β glycosidic linkages 2.2-14 O-linked and N-linked glycoproteins Glycosidic bonds can form between the anomeric carbon of a polysaccharide and a hydroxyl or a nitrogen of certain amino acids 2.2-15  2.7 | Carbohydrates Nutritional Polysacchararides Polysaccharides are polymers of sugars joined by glycosidic bonds Glycogen is an animal product made of branched glucose polymers Starch is a plant product made of both branched (amylopectic) and unbranched (amylose) glucose polymers Note that a monosaccharide has multiple OH groups that can participate in glycosidic bonds 2.2-16  2.7 | Carbohydrates Nutritional Polysacchararides Amylose = linear polymer, with α(1 4) links between glucose monomers Amylopectin and Glycogen = branched polymer α(1 4) linkages plus α(1 6) linkages amylopectin has a branch about every 25th glucose while glycogen has a branch about every 10th glucose 2.2-17  2.7 | Carbohydrates Structural Polysacchararides Cellulose, chitin, and glycosaminoglycans (GAGs): structural polysaccharides Cellulose: plant product made of unbranched polymers Chitin: component of invertebrate exoskeleton made GAGs: composed of two different sugars and found in extracellular space. 2.2-18 Glycoproteins: one or more oligosaccharides covalently joined to a protein O-linked: oligosaccharide in a glycosidic bond with a serine or threonine hydroxyl (= O-linked glycoprotein) N-linked: oligosaccharide in an N- glycosidic bond to the amide nitrogen of an Asparagine residue ( = N-linked glycoprotein) Glycomics: systematic characterization of all of the carbohydrate components of a cell or tissue (including those attached to proteins or lipids) 2.2-19 2.2-20  2.7 | Lipids Lipids dissolve in organic solvents (Do not dissolve in water) Important cellular lipids include: fats (triacylglycerols -TAGs) steroids phospholipids Fatty acids are long, unbranched hydrocarbon chains with a single carboxyl group at one end Fatty acids are amphipathic: hydrophobic hydrocarbon chain Fats and fatty acids hydrophilic carboxyl group. Fats (Triacylglycerols): glycerol linked by ester bonds to three fatty acids 2.2-21 FYI 2.7 | Lipids Soaps owe their grease-dissolving capability to the fact that the hydrophobic end of each fatty acid can embed itself in the grease, whereas the hydrophilic end can interact with the surrounding water. As a result, greasy materials are converted into complexes (micelles) that can be dispersed by water. Soaps consist of fatty acids 2.2-22  2.7 | Lipids Fatty acids: the simplest lipid molecule Fatty acids differ in their length (usually 14-20 carbons because of the way they are synthesized) and presence of double bonds 2.2-23 each cis double bond inserts a bend into the hydrocarbon chain (~ 30o) which reduces Van der waals interaction, thereby decreasing melting point)  Monomers of fatty acids: are used to build triacylglycerol (fats) and membrane lipids nearly the entire volume of an adipocyte is dedicated to fat storage adipose tissue in animals is made up of adipocytes the number of adipocytes increases most rapidly during late childhood and early adolesence A TAG can contain three identical fatty acids 2.2-24 or it can (and usually does) containing more than one type of fatty acid  2.7 | Lipids Steroids Steroids are built around a four-ringed hydrocarbon skeleton Cholesterol is found in (all) animal cell membranes and is a precursor of the steroid hormones (testosterone, progesterone, and estrogen) Cholesterol is largely absent from plant cells, which is why vegetable oils are “cholesterol-free” The hydroxyl at C-3 makes cholesterol amphipathic 2.2-25  Important cellular lipids include: 2.7 | Lipids fats (triacylglycerols -TAGs) steroids Phospholipids phospholipids A phospholipid molecule has two fatty acid chains (not three) attached to a glycerol backbone = diacylglycerol. The third hydroxyl of glycerol is bonded to a phosphate group, which is bonded to a small polar group like choline. Phospholipids have two ends with different properties: one end contains a phosphate group (hydrophilic); the other end has two fatty acid tails (hydrophobic). 2.2-26  2.7 | Proteins Proteins are macromolecules that carry out a cell’s activities Enzymes catalyze reactions Structural proteins provide mechanical support Signaling proteins determine what a cell reacts to Regulatory proteins determine how that signal is conveyed Filaments and molecular motors provide biological movements Transport proteins allow molecules in and out of cells Proteins have shapes and surfaces that Biological structures composed allow them to interact selectively with predominantly of protein other molecules, so they exhibit a high degree of specificity 2.2-27 Proteins: 4 levels of organization The amino acid sequence determines the three- dimensional structure of a protein The structure of a protein determines the proteins function 2.2-28  2.7 | Building Blocks of Proteins The Structure of Amino Acids Amino acids have asymmetric carbon atoms With the exception of glycine, the α-carbon of amino acids bonds to four different groups so that each amino acid can exist in either a D or an L form Amino acids used in the synthesis of a protein on a ribosome are always Amino acid stereoisomerism. L-amino acids 2.2-29  2.7 | Building Blocks of Proteins The Structure of Amino Acids Proteins are unique polymers made of amino acid monomers Twenty different (standard) amino acids, with different chemical properties, are commonly used in the construction of proteins All amino acids have a carboxyl and an amino group, separated by a single carbon atom, the α-carbon In a neutral solution, the α-carboxyl group loses its proton and is negatively charged, and the α-amino group accepts Amino acid structure. Ball-and- a proton and is positively charged stick model, chemical formula, and peptide bond formation. 2.2-30 Proteins: Primary Structure – amino acids Proteins are built from 20 standard amino acids that differ in Size Shape Charge Hydrogen bonding capacity Hydrophobic character Chemical reactivity 2.2-31 Peptide bond formation Carboxyl group + amino group in a condensation (dehydration) reaction note the C terminus and the N terminus By convention polypeptides are always drawn N terminus on the left and C terminus on the right it’s not a protein until it folds 2.2-32 Proteins: Primary Structure – amino acids (peptides) What color represents the amino group nitrogen? What color represents the carboxyl group carbon? What color represents the α carbon? 2.2-33 Which is the amino terminal? Dipeptide = two amino acids, Which is the carboxyl terminal? Tripeptide = three amino acids, Polypeptide = many amino acids Oxygen is what color? linked together. Hydrogen is what color? Once incorporated into a polypeptide chain, amino acids are termed residues The Properties of the Side Chains Hydropathy index: hydrophobic or hydrophilic properties of side chains Positive = hydrophobic (membranes and protein interiors) Negative = hydrophilic (protein surfaces) 2.2-34 The Properties of the Side Chains Hydropathy index: hydrophobic or hydrophilic properties of side chains Positive = hydrophobic (membranes and protein interiors) Negative = hydrophilic (protein surfaces) 2.2-35  2.7 | Building Blocks of Proteins The Properties of the Side Chains The ionic, polar, or nonpolar character of side chains is very important in protein structure and function Soluble proteins generally have polar residues at their surface to interact with water Non-polar residues are found in the core tightly packed together, where water is excluded Hydrophobic and hydrophilic amino acid Hydrophobic effects are a driving residues in the protein cytochrome c force during protein folding and contribute substantially to the overall stability of the protein 2.2-36 Proteins: Secondary Structure – folded peptides Secondary Structure: folding of the polypeptide backbone Two types of secondary structures are stable and common in proteins α helix b sheet hydrogen bonds among amino acids generate the secondary structure 2.2-37 Proteins: Secondary Structure – folded peptides ( α helix) In the α helix, the carbonyl oxygen of each peptide bond forms a hydrogen bond with the amide hydrogen atom of the amino acid four residues towards the C-terminus What will determine whether the α helix is hydrophobic or hydrophilic? note that with the exception of amino acids at the ends of the peptide, all peptide bonds are participating in hydrogen bonds 2.2-38 Proteins: Secondary Structure – folded peptides ( α helix) space filling model demonstrates that the α helix is not hollow as suggested by the ball and stick model ball and stick model 2.2-39 An α helix can cross a lipid bi-layer Hydrophobic side chains imbed within the hydrophobic portion of the lipid bilayer 2.2-40 Proteins: Secondary Structure – folded peptides ( α helix) four different constraints affect the stability of an a helix: Electrostatic repulsion (or attraction) between successive amino acid residues with charged R groups Bulkiness of adjacent R groups Interactions between R groups spaced three (or four) residues apart Occurance of Proline and Glycine residues What does it all mean? The tendency of a given segment of a polypeptide chain to fold up as an a helix depends on the identity and sequence of amino acid residues within the segment = primary sequence determines structure 2.2-41  2.7 | Primary and Secondary Structures of Proteins Secondary Structure: beta sheets The beta (b) sheet has several beta strand segments of a polypeptide (strand) lying side by side that form a folded or pleated conformation each strand (β strand) is 5 to 8 residues long and nearly fully extended hydrogen bonding between strands results in a “pleated” structure = β pleated sheet 2.2-42  2.7 | Primary and Secondary Structures of Proteins Secondary Structure hinges, turns, loops, or finger-like extensions are the most flexible portions of a α helix and β polypeptide chain and the sites sheet are the of greatest biological activity major internal supportive Ribbon model elements in a of ribonuclease protein (on average 60% of a protein) α helix and β sheet are the major internal supportive elements in a protein (on average 60% of a protein) 2.2-43  2.7 | Tertiary Structure of Proteins Tertiary structure describes the conformation of the entire polypeptide Secondary structure is stabilized by hydrogen bonds, while tertiary structure is stabilized by noncovalent bonds between the side chains of the protein as well as covalent bonds (in particular disulfide bonds) Secondary structure is limited to a small number of conformations, but tertiary An X-ray diffraction structure is virtually unlimited pattern of myoglobin The detailed tertiary structure of a protein is usually determined using the technique of X-ray crystallography 2.2-44  2.7 | Tertiary Structure of Proteins NMR spectroscopy reveals tertiary structure without crystallization Tertiary structure can also be determined by nuclear magnetic resonance (NMR) spectroscopy, which uses a magnetic field to probe proteins with radio waves to determine distances between atoms X-ray crystallography provides higher resolution structures for larger proteins but is limited by the ability to get any given protein to form pure crystals NMR does not require crystallization, provides information about dynamic changes in structure, and can rapidly reveal drug binding sites, but is difficult to use on larger proteins 2.2-45 Tertiary Structure of Proteins Tertiary structure refers to the overall conformation of ALL its amino acid residues Amino acids that are far apart in the polypeptide sequence and that reside in different secondary structures can interact Tertiary structure is stabilized by noncovalent and covalent interactions The weak nature of these stabilizing forces results in proteins being able to undergo changes in shape – 2.2-46 significant in protein function  Proteins: disulfide bonding Note that covalent disulfide bonding can occur between two cysteines in the same polypeptide or between two cysteines of adjacent polypeptides 2.2-47  2.7 | Tertiary Structure of Proteins Most proteins are categorized by shape as either fibrous proteins - which are elongated globular proteins - which are compact Extracellular materials are fibrous proteins, like collagen and elastin of connective tissues, and keratin of hair and skin, and silk Most proteins within the cell are globular proteins Human serum albumin (64.5 kDa) has 585 residues in a single chain Shown below are the approximate dimensions if this single polypeptide were an extended β sheet or an α helix 2.2-48  2.7 | Tertiary Structure of Proteins Myoglobin: The First Globular Protein Whose Tertiary Structure Was Determined Myoglobin functions in muscle tissue as a storage site for oxygen, bound to an iron atom in the center of a heme group Approximately 75 percent of the 153 amino acids in the polypeptide chain are in the α-helical conformation, and no β sheet was found Myoglobin contains no disulfide bonds; the tertiary structure is held together by noncovalent interactions All of the noncovalent bonds thought to occur between side chains within proteins— hydrogen bonds, ionic bonds, and van der Waals forces—have been found Unlike myoglobin, most globular proteins contain both α helices and β sheets 2.2-49  2.7 | Tertiary Structure of Proteins Tertiary Structure May Reveal Unexpected Similarities in Proteins Similarity in primary sequence is often used to decide whether two proteins may have similar structure and function Sometimes proteins unrelated at the primary sequence level have similar tertiary structures Interactions and enzymatic activity of a protein are deduced from the tertiary structure Different sequences, similar structure Actin (eukaryotic) and MreB (an actin homolog (prokaryotic) show no similarity at the primary level but do at the tertiary level 2.2-50  2.7 | Tertiary Structure of Proteins Protein Domains Domain: a substructure produced by any part of a polypeptide chain that can fold independently into a stable structure that generally has a specific function The different domains often represent parts that function semi-independently Protein domains are often identified with a specific function, and the functions of a newly identified protein can usually be predicted by its domains Shuffling of domains during evolution creates proteins with unique combinations of activities. Proteins are made up of 2.2-51 domains that can be conserved.  2.7 | Tertiary Structure of Proteins Protein Domains: Src homology domains Every cell in your body contains Src protein kinase (coded by the SRC gene) The Src protein is one peptide It’s an enzyme (a tyrosine kinase) Specifically a non-receptor tyrosine kinase (cytosolic kinase) Src protein is composed of four domains 2 of the domains form the protein kinase (catalytic domains) 2 of the domains are involved in binding (regulatory domains) MANY proteins – particulary those involved in signal transduction also have SH2 and SH3 domains which are used for anchoring to other molecules 2.2-52  2.7 | Tertiary Structure of Proteins Dynamic Changes Within Proteins Proteins are not static and inflexible, but capable of internal movements The X-ray crystallographic structure of a protein can be considered an average structure, or “ground state” NMR can monitor shifts in hydrogen bonds, waving movements of external side chains, and the full rotation of the aromatic rings of tyrosine and phenylalanine residues Non-random movements within a protein Dynamic movements within the triggered by binding of a specific enzyme acetylcholinesterase. molecule are called conformational changes 2.2-53 2.7 | Quaternary Structure of Proteins Most proteins have more than one chain, or subunit, linked by covalent disulfide bonds or held together by noncovalent bonds Proteins composed of subunits are said to have quaternary structure Homodimer = protein composed of two identical subunits Heterodimer = a protein 2.2-54 composed of two nonidentical Hemoglobin (heterotetramer) two α-globin and two β-globin polypeptides, subunits each of which binds a single molecule of oxygen  2.7 | Quaternary Structure of Proteins Protein-Protein Interactions Different proteins can become physically associated to form a much larger multiprotein complex The pyruvate dehydrogenase complex consists of 60 polypeptide chains constituting three different enzymes The product of one enzyme can be channeled directly to the Pyruvate dehydrogenase: next enzyme in the sequence a multiprotein complex without becoming diluted in the cell 2.2-55  2.17 | Quaternary Structure of Proteins Protein-Protein Interactions Which of these proteins have a quaternary structure? Which of these is the biggest protein? 2.2-56  2.7 | Protein Folding denaturation = unfolding of a protein detergents organic solvents radiation heat, compounds such as urea Ribonuclease molecules that had re-formed from the unfolded protein were indistinguishable both structurally and functionally from the correctly folded molecules present at the beginning of the experiment. The linear (primary) sequence of amino acids contained all of the information required for the Denaturation and formation of the polypeptide’s 3D refolding of ribonuclease conformation 2.2-57  2.7 | Protein Folding The Role of Molecular Chaperones Proteins undergoing folding have to be prevented from interacting non- selectively with other molecules in the crowded compartments of the cell Remember: some proteins do undergo assisted folding in vivo Chaperones: the class of proteins that helps other intracellular proteins fold 1. Molecular chaperones - proteins that bind and stabilize unfolded or partially folded polypeptides thereby preventing these proteins from aggregating and being degraded (Hsp70) 2. Chaperonins -directly facilitate the folding of proteins (elaborate protein complexes) 2.2-58  2.7 | Protein Folding The Role of Molecular Chaperones The role of molecular chaperones in encouraging protein folding Chaperones of the Hsp70 family bind to polypeptides as they emerge from the ribosome and prevent them from binding to other proteins in the cytosol Proteins can be released by the chaperones to spontaneously fold into their native state, or repeatedly bound and released until they are fully folded Larger polypeptides are transferred to a different type of chaperone called a chaperonin, a cylindrical protein complex that provides a folding environment TRiC is a chaperonin thought to assist in the folding of up to 15 percent of the polypeptides synthesized in mammalian cells 2.2-59  FYI 2.7 | The Human Perspective Protein Misfolding Can Have Deadly Consequences The prion protein is encoded by a gene within the cell’s own chromosomes In normal brain tissue PrpC (prion protein cellular) is made, while in affected patients PrpSc (prion protein scrapie) is present PrpC is soluble and is destroyed by protein-digesting enzymes, while PrpSc forms insoluble fibrils and is resistant to digestion Structures are different: PrpC is mainly α-helical and PrpSc is largely β sheet. PrpSc can bind to PrpC) and cause it to fold into the abnormal form Creutzfeld-Jakob disease (CJD), is a rare, fatal disorder that can be inherited or acquired by transfer of abnormally folded proteins that attacks the brain, causing a loss of motor coordination and dementia A contrast in structure between normal and infectious prion protein Eating contaminated beef from cows suffering from 2.2-60 “mad cow disease” caused people to acquire CJD  FYI 2.7 | The Human Perspective Protein Misfolding Can Have Deadly Consequences Alzheimer’s disease (AD) is a common disorder that strikes as many as 10 percent of individuals who are at least 65 years old AD patients exhibit memory loss, confusion, and loss of reasoning ability The brain of a person with AD contains fibrillar deposits of an insoluble material referred to as amyloid The fibrillar deposits result from the self-association of a polypeptide composed predominantly of β sheet Alzheimer’s disease 2.2-61  FYI 2.7 | Proteomics and Interactomics Proteomics The entire inventory of proteins that is produced by an organism is known as that organism’s proteome, and is also applied to the inventory of all proteins that are present in a particular tissue, cell, or cellular organelle Traditionally, protein biochemists have sought to answer questions about protein structure, function, and location, one protein at a time Proteomics researchers attempt to answer questions on a more comprehensive scale using large-scale (or high-throughput) techniques to catalog the vast array of proteins produced by a particular cell Many efforts have been made to compare the proteins present in the blood of healthy individuals with those present in the blood of persons suffering from various diseases, especially cancer 2.2-62  2.7 | Nucleic Acids nucleotides = polymers of nucleic acids that store and transmit genetic information Deoxyribonucleic acid (DNA) holds the genetic information in all cellular organisms and some viruses Ribonucleic acid (RNA) is the genetic material in some viruses Nucleotides and nucleotide strands of RNA Nucleotides are connected by 3’-5’ phosphodiester bonds between the phosphate of one nucleotide and the 3’ carbon of the next 2.2-63  2.7 | Nucleic Acids Each nucleotide consists of three parts: a five-carbon sugar a phosphate group a nitrogenous base Bases are either purines or pyrimidines The purines adenine and guanine in both DNA and RNA The pyrimidines cytosine and uracil in RNA Nitrogenous bases in nucleic acids uracil is replaced by thymine in DNA 2.2-64  Learning objectives for chapter 2 macromolecules Understand what macromolecules and what a functional groups are Know the characteristics of glucose Be very, very clear on glycosidic bonds and glycoproteins and glycolipids What defines a nutritional polysaccharide (with examples) Know the three common types of cellular lipids and their characteristics Understand the characteristics of a fatty acid Be clear on the basic characteristics of cholesterol and phospholipids Understand the role of proteins in a cell Understand what a hydropathy index is and the consequences for amino acids Understand the levels of organization of proteins Be clear on peptide bonds, alpha helices and beta sheets Understand what a domain is Understand the basic role of chaperones 2.2-65