RPI-BIOL-2120 Lecture 4: Macromolecules PDF

BIOL-2120 INTRODUCTION TO CELL & MOLECULAR BIOLOGY Dr. Michael T. Klein ([email protected]) LECTURE 4 MACROMOLECULES Reference text: Essential Cell Biology, 5th ed., Alberts et al. 2019. Chapters 2, 3, & 4 Images pr...

BIOL-2120 INTRODUCTION TO CELL & MOLECULAR BIOLOGY Dr. Michael T. Klein ([email protected]) LECTURE 4 MACROMOLECULES Reference text: Essential Cell Biology, 5th ed., Alberts et al. 2019. Chapters 2, 3, & 4 Images provided by M. T. Klein or W. W. Norton & Company unless stated otherwise MTK, 2025-01-06 (1)  OVERVIEW  Macromolecules are large molecules composed of covalently connected atoms numbering in the thousands or more  Each cell has many thousands of different macromolecules  Macromolecules vary among cells of an organism, vary more between members of a species, and vary even more between different species  All living things are made up of four classes of macromolecules: carbohydrate, proteins, nucleic acids, and lipids Which of these is not like the others? MTK, 2025-01-06 (2)  POLYMERS ARE BUILT FROM MONOMERS  A polymer is a long molecule consisting of many similar building blocks called monomers When part of a polymer, the subunits are usually referred to differently; e.g., when amino acids are linked together into polypeptides they are referred to as amino acid residues  An immense variety of polymers can be built from a small set of monomers  A dehydration reaction occurs when two monomers bond together through the loss of a water molecule  Polymers are broken down to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction  3 of the 4 classes biological machromolecules are polymers: carbohydrates, proteins, and nucleic acids MTK, 2025-01-06 (3)  CARBOHYDRATES  Carbohydrates serve mainly as fuel and building material  Carbohydrates include simple sugars and polymers of sugars The simplest carbohydrates are monosaccharides, single sugars Two linked sugar molecules are called disaccharides Short chains of sugars are called oligosaccharides The most complex carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks MTK, 2025-01-06 (4)  CARBOHYDRATES MONOSACCHARIDES  Monosaccharides have molecular formulas that are usually multiples of CH2O  Glucose (C6H12O6) is the most common monosaccharide  Monosaccharides are classified by the location of the carbonyl group (as aldose or ketose) and the number of carbons in the carbon skeleton  Monosaccharides serve as a major fuel for cells and as raw material for building molecules  Consider: In relation to ribose, what kind of isomer is ribulose? Are glucose and galactose actually different molecules? MTK, 2025-01-06 (5)  CARBOHYDRATES MONOSACCHARIDES  Though often drawn as linear skeletons, many sugars form rings in aqueous solutions Spontaneous isomerization occurs; equilibrium favors the ring structure in aqueous solutions You should be able to recognize sugars in both linear and cyclic forms MTK, 2025-01-06 (6)  CARBOHYDRATES DISACCHARIDES  A disaccharide is formed when a dehydration reaction joins two monosaccharides  This covalent bond is called a glycosidic linkage MTK, 2025-01-06 (7)  CARBOHYDRATES OLIGOSACCHARIDES  Oligosaccharides are short polymers of sugars and have many roles in nature, including: Building blocks for more complex carbohydrates Signaling molecules Cell-cell recognition as part of glycoproteins and glycolipids  Why do you think oligosaccharides are so useful in cell-cell recognition? https://www.researchgate.net/profile/Ari_Helenius/publication/12064398/figure/fig2/AS:282257899180036@1444306936021/Biosynthesis-of-the-N-linked-core-oligosaccharide-Synthesis- starts-on-the-cytosolic.png MTK, 2025-01-06 (8)  CARBOHYDRATES POLYSACCHARIDES  Polysaccharides, the long polymers of sugars, have storage and structural roles  The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages E.g., starch and cellulose are both polymers of glucose but have very different structures and functions MTK, 2025-01-06 (9)  CARBOHYDRATES STRUCTURAL POLYSACCHARIDES  The difference in these glycosidic linkages is based on two ring forms for glucose: alpha () and beta () Polymers with α glucose are helical Polymers with β glucose are straight MTK, 2025-01-06 (10)  CARBOHYDRATES STORAGE POLYSACCHARIDES  Starch, a storage polysaccharide of plants, consists entirely of glucose monomers  Plants store surplus starch as granules within chloroplasts and other plastids  The simplest form of starch is amylose; a branched form of plant starch is amylopectin MTK, 2025-01-06 (11)  CARBOHYDRATES STORAGE POLYSACCHARIDES  Glycogen is a storage polysaccharide in animals  The carbohydrate component of glycogen is α glucose  Humans and other vertebrates store glycogen mainly in liver and muscle cells MTK, 2025-01-06 (12)  CARBOHYDRATES STRUCTURAL POLYSACCHARIDES  Cellulose is a major component of the cell walls of plant cells Cellulose differs from starch by the glycosidic linkages  In the straight structure of cellulose, H atoms on one strand can for hydrogen bonds with OH groups on other cellulose strands  Parallel cellulose molecules held together this way are grouped into microfibrils, strong building materials for plants MTK, 2025-01-06 (13)  CARBOHYDRATES STRUCTURAL POLYSACCHARIDES  Enzymes like amylase that digest starch by hydrolyzing  linkages cannot hydrolyze  linkages in cellulose  To break  linkages, an organism would need to express a cellulase like cellobiase Various fungi, bacteria, protistans, and all plants express cellulases Animals do not express cellulases  Many animals, like ruminates and termites, have symbiotic relationships with microbes that aid in cellulose digestion  Most cellulose eaten by humans passes through the digestive tract as insoluble fiber MTK, 2025-01-06 (14)  CARBOHYDRATES STRUCTURAL POLYSACCHARIDES  Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods  Chitin also provides structural support for the cell walls of many fungi  Unlike cellulose, animals can digest chitin, though very slowly MTK, 2025-01-06 (15)  PROTEINS  Proteins include a diversity of structures, resulting in a wide range of functions  Proteins account for more than 50% of the dry mass of most cells  Protein’s functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances What kinds of proteins do you think are most prevalent in muscle tissue? Proteins will be covered in more detail in Lecture 5 MTK, 2025-01-06 (16)  PROTEINS HUGE DIVERSITY OF STRUCTURES AND FUNCTIONS Enzymatic proteins Defensive proteins Function: Selective acceleration of chemical reactions Function: Protection against disease Example: Digestive enzymes catalyze the hydrolysis Example: Antibodies inactivate and help destroy of bonds in food molecules. viruses and bacteria. Antibodies Enzyme Virus Bacterium Storage proteins Transport proteins Function: Storage of amino acids Function: Transport of substances Examples: Casein, the protein of milk, is the major Examples: Hemoglobin, the iron-containing protein of source of amino acids for baby mammals. Plants have vertebrate blood, transports oxygen from the lungs to storage proteins in their seeds. Ovalbumin is the other parts of the body. Other proteins transport protein of egg white, used as an amino acid source molecules across cell membranes. for the developing embryo. Transport protein Ovalbumin Amino acids for embryo Cell membrane MTK, 2025-01-06 (17)  PROTEINS HUGE DIVERSITY OF STRUCTURES AND FUNCTIONS Hormonal proteins Receptor proteins Function: Coordination of an organism’s activities Function: Response of cell to chemical stimuli Example: Insulin, a hormone secreted by the Example: Receptors built into the membrane of a pancreas, causes other tissues to take up glucose, nerve cell detect signaling molecules released by thus regulating blood sugar concentration other nerve cells. Receptor Insulin Signaling protein High secreted Normal molecules blood sugar blood sugar Contractile and motor proteins Structural proteins Function: Movement Function: Support Examples: Motor proteins are responsible for the Examples: Keratin is the protein of hair, horns, undulations of cilia and flagella. Actin and myosin feathers, and other skin appendages. Insects and proteins are responsible for the contraction of spiders use silk fibers to make their cocoons and webs, muscles. respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Actin Myosin Collagen Muscle tissue Connective 100 m tissue 60 m MTK, 2025-01-06 (18)  PROTEINS AMINO ACID MONOMERS  A protein is a biologically functional molecule that consists of one or more polypeptides  Polypeptides are unbranched polymers built from the same set of 20 amino acids  Amino acids are organic molecules with carboxyl and amino groups  Amino acids differ in their properties due to differing side chains, called R groups  19 of the 20 amino acids have chiral centers at their α carbon (glycine being the exception) Polypeptides are only built from L-isomers (left-handed isomers) D-isomers are rarely use in nature overall MTK, 2025-01-06 (19)  PROTEINS AMINO ACID MONOMERS  In most of nature, polypeptides are built from these 20 amino acids This isn’t to say that these are the only animo acids that occur in proteins – why might this be?  We will be revisiting individual amino acids in Lecture 5, but it’s wise to start studying the structures, names, and properties of these amino acids MTK, 2025-01-06 (20)  PROTEINS POLYPEPTIDES  Amino acids are linked by peptide bonds  A polypeptide is a polymer of amino acids  Polypeptides range in length from a few to more than a thousand monomers  Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (the C-terminus) and an amino end (the N-terminus) MTK, 2025-01-06 (21)  PROTEINS STRUCTURE AND FUNCTION  A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape  The sequence of amino acids determines a protein’s three-dimensional structure  A protein’s structure determines its function MTK, 2025-01-06 (22)  PROTEINS PROPER FOLDING  In addition to primary structure, physical and chemical conditions can affect structure  Changes in pH, salt concentration, temperature, or the presence of detergents can cause a protein to unravel  Loss of a protein’s native structure is called denaturation  A denatured protein is biologically inactive MTK, 2025-01-06 (23)  NUCLEIC ACIDS  Nucleic acids are polymers that store, transmit, and help express hereditary information  The amino acid sequence of a polypeptide is coded by a unit of inheritance called a gene  Genes are made of DNA, a nucleic acid made of monomers called nucleotides  There are two types of nucleic acids: Deoxyribonucleic acid (DNA) ‒ DNA provides directions for its own replication Ribonucleic acid (RNA) ‒ DNA directs synthesis of mRNA and, through mRNA, controls protein synthesis; other types of RNA’s also exist within the cell and have very important functions Nucleic acids will be covered in more detail in Lecture 6 MTK, 2025-01-06 (24)  NUCLEIC ACIDS NUCLEOTIDES  Nucleic acids are made of monomers called nucleotides Polynucleotide is the generic name for single strands of DNA and RNA  A nucleotide consists of a nitrogenous base, pentose sugar, and one or more phosphates  The adjacent nucleotides are joined by covalent bonds between the OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next nucleotide  These links create a backbone of sugar- phosphate units with nitrogenous bases as appendages MTK, 2025-01-06 (25)  NUCLEIC ACIDS NUCLEOTIDES  Nucleoside = nitrogenous base + sugar  Nucleotide = nucleoside + phosphate group  In DNA, the sugar is deoxyribose; in RNA, it’s ribose  There are two families of nitrogenous bases: Pyrimidines have a single six-membered ring: cytosine, thymine (DNA only), uracil (RNA only) Purines have a six-membered ring fused to a five-membered ring: adenine, guanine MTK, 2025-01-06 (26)  NUCLEIC ACIDS BASE-PAIRING  The nitrogenous bases in DNA pair up, forming hydrogen bonds: Adenine (A) with thymine (T), 2 hydrogen bonds Guanine (G) with cytosine (C), 3 hydrogen bonds  This is called complementary base pairing  Complementary pairing can also occur between two RNA molecules or between parts of the same molecule  In RNA, thymine is replaced by uracil, so: Adenine (A) with uracil (U), 2 hydrogen bonds Guanine (G) with cytosine (C), 3 hydrogen bonds  Note that adenine is equally capable of base pairing with either thymine or uracil MTK, 2025-01-06 (27)  NUCLEIC ACIDS STRUCTURES OF DNA  DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix  In the DNA double helix, the two backbones run in opposite 5→ 3 directions, an arrangement referred to as antiparallel MTK, 2025-01-06 (28)  NUCLEIC ACIDS STRUCTURES OF RNA  RNA molecules usually exist as single polynucleotide chains  These chains can fold back on themselves, with base-pairs associating with each other to stabilize the three dimensional structure  Shown is a transfer RNA (tRNA) MTK, 2025-01-06 (29)  LIPIDS  Lipids are a diverse group of hydrophobic molecules  Lipids are the only class of large biological molecules that do not form polymers  The unifying feature of lipids is having little or no affinity for water  Lipids are hydrophobic because they consist mostly of hydrocarbons, which have mostly nonpolar covalent bonds  The most biologically important lipids are: Fats Phospholipids Steroids MTK, 2025-01-06 (30)  LIPIDS FATS  Fats are constructed from two types of smaller molecules: glycerol and fatty acids Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon A fatty acid consists of a carboxyl group attached to a long carbon skeleton MTK, 2025-01-06 (31)  LIPIDS FATS  Fats separate from water because water molecules form hydrogen bonds with each other and exclude hydrophobic molecules like fats  In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride MTK, 2025-01-06 (32)  LIPIDS FATS  Fatty acids vary in length (number of carbons) and in the number and locations of double bonds  Saturated fatty acids These have the maximum number of hydrogen atoms possible, thus they have no double bonds Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature Most mammal fats are saturated MTK, 2025-01-06 (33)  LIPIDS FATS  Unsaturated fatty acids These have one or more double bonds Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at room temperature Plant fats and fish fats are usually unsaturated  A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits MTK, 2025-01-06 (34)  LIPIDS CIS-FATS AND TRANS-FATS  Hydrogenation is the process of breaking carbon- carbon double bonds in unsaturated fats, adding hydrogens to these carbons  When hydrogenating vegetable oils, the process often creates fats with trans double bonds called trans-fats and behave like saturated fats  Human metabolism has difficulty digesting trans- fats, leading them to accumulate in the body MTK, 2025-01-06 (35)  LIPIDS FATS IN THE BODY  The major function of fats is energy storage Why are fats so energy dense?  Humans and other mammals store their fat in adipose cells  Adipose tissue also cushions vital organs and insulates the body MTK, 2025-01-06 (36)  LIPIDS PHOSPHOLIPIDS  In a phospholipid, two fatty acids and a phosphate group are attached to glycerol The phosphate group can be further modified to have different attachments, giving the phospholipid different properties  The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head This is an example of an amphipathic molecule MTK, 2025-01-06 (37)  LIPIDS PHOSPHOLIPIDS  When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior Why do they do this? What forces are involved?  The structure of phospholipids results in a bilayer arrangement found in cell membranes  Phospholipids are the major component of all cell membranes  This will be covered in more detail in Lecture 11 MTK, 2025-01-06 (38)  LIPIDS STEROIDS  Steroids are lipids characterized by a carbon skeleton consisting of four fused rings  Cholesterol, an important steroid, is a component in animal cell membranes – increases fluidity in cold environments and increases viscosity in hot environments  Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease Cholesterol MTK, 2025-01-06 (39)  EXTRA CREDIT DISCUSSION: DIET USE BLACKBOARD DISCUSSION BOARD TO POST ANSWERS  As best you can, break down what you eat tomorrow into amounts  Then, use this table to (in grams) of these categories: determine what percent of the recommended daily Protein (including amino acids) value* of each nutrient you consumed Lipids: Food Component Grams ꟷ Saturated fat Protein 50 ꟷ Unsaturated fat Saturated fat 20 Unsaturated fat 58 ꟷ Cholesterol Colesterol 0.3 Carbohydrates: Simple sugars and disaccharides 50 ꟷ Simple sugars and disaccharides (e.g., sucrose) Complex ꟷ Digestible polysaccharides carbohydrates 225 ꟷ Insoluble fiber Dietary/insoluable fiber 28  Use this resource to estimate that amount of these nutrients *These values are the current present in your food: https://hnrca.tufts.edu/resources/nutrition- FDA recommendations for a resources/calculating-calories-and-nutrients-meals 2000 calorie diet MTK, 2025-01-06 (40)  QUICK REFERENCE SOME OF THE TYPES OF SUGARS MTK, 2025-01-06 (41)  QUICK REFERENCE FATTY ACIDS AND OTHER LIPIDS MTK, 2025-01-06 (42)  QUICK REFERENCE THE 20 AMINO ACIDS FOUND IN MTK, 2025-01-06 PROTEINS (43)  QUICK REFERENCE NUCLEOTIDES AND THEIR DERIVATIVES MTK, 2025-01-06 (44)