Lecture 2 Macromolecules PDF

LECTURE 2 MACROMOLECULES Key concepts Macromolecules are polymers, built from monomers. Carbohydrates serve as fuel and building material. Lipids are a diverse group of hydrophobic molecules. Proteins include a diversity of structures, resulting in a wide range of functions. Nucleic...

LECTURE 2 MACROMOLECULES Key concepts Macromolecules are polymers, built from monomers. Carbohydrates serve as fuel and building material. Lipids are a diverse group of hydrophobic molecules. Proteins include a diversity of structures, resulting in a wide range of functions. Nucleic acids store, transmit, and help express hereditary information. 2.1. Polymers Classes of macromolecules Macromolecules are large and complex molecules that are composed of many covalently connected atoms All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids. Polymers and monomers A polymer is a long molecule consisting of many similar building blocks. The smaller, repeating molecules that serve as building blocks are called monomers. Oligomers: chains containing only few monomers. Three of life’s organic molecules are polymers: carbohydrates, proteins, nucleic acids. Dehydration reaction A dehydration reaction occurs when two monomers bond together through the loss of a water molecule. Enzymes are specialized protein macromolecules that speed up chemical reactions such as those that make or break down polymers. Hydrolysis Polymers are disassembled into monomers by hydrolysis reactions, which are essentially the reverse of dehydration reactions. 2.2. Carbohydrates Carbohydrates introduction Carbohydrates include sugars and polymers of sugars. The simplest carbohydrates are monosaccharides, or single sugars. Carbohydrate macromolecules are polysaccharides, which are polymers composed of many sugar building blocks. Monosaccharides have molecular formulas that are usually multiples of CH2O. Glucose (C6H12O6) is the most common monosaccharide. Monosaccharides Monosaccharides are classified by: Number of carbons in the carbon skeleton. Location of the carbonyl group. Cyclization of sugars Often drawn as linear skeletons; but in aqueous solutions many sugars form rings. The ring structure is more stable in aqueous solutions. Disaccharides A disaccharide forms when a dehydration reaction joins two monosaccharides. This bond is called a glycosidic linkage. Glucose + Glucose = Maltose Glucose + Fructose = Sucrose Glucose + Galactose = Lactose Polysaccharides Polysaccharides are polymers of sugar that have storage and structural roles. The structure and function of a polysaccharide are determined by: its sugar monomers, and the positions of its glycosidic linkages. Starch 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. Amylopectin is somewhat branched. Glycogen Glycogen is a storage polysaccharide in animals. Glycogen is mainly in liver and muscle cells. Hydrolysis of glycogen releases glucose when the demand for energy increases. Cellulose Cellulose is a major component of plant cell walls. Starch is largely helical, whereas cellulose polymers are straight and unbranched. Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ.  and β linkages The glycosidic linkages of cellulose differ from those of starch because the ring forms of glucose in the two polymers are slightly different. Cellulose contains beta (β) glucose instead of alpha ( ) glucose as in starch. Enzymes that hydrolyze (or digest) linkages in starch cannot hydrolyze β linkages in cellulose. Cellulose in human food passes through digestive tract as insoluble fibre. Some microbes have enzymes that digest cellulose. Herbivores, from cows to termites, have symbiotic relationships with these microbes. Chitin Chitin, also a structural polysaccharide, is found in arthropod exoskeletons. Chitin also provides structural support for fungal cell walls. 2.3. Lipids Lipids introduction Lipids are the one class of large biological molecules that does not form polymers. Unifying feature of lipids is little or no affinity for water. Lipids are hydrophobic because they consist mostly of hydrocarbons which are nonpolar. Biologically important lipids include fats, phospholipids, and steroids. Fats Major function of fat is energy storage. Humans and other mammals store their fat in adipose cells. Adipose tissue also cushions vital organs and insulates the body. Fats are constructed from glycerol and fatty acids. Glycerol is a three-carbon alcohol with a hydroxyl attached to each carbon. Fatty acids consist of a carboxyl group linked to a long hydrocarbon chain. In a fat, three fatty acids are joined to glycerol by ester linkages, to form a triacylglycerol (also called triglyceride). The fatty acids can all be the same, or of two or three different kinds Fats separate from water because water molecules hydrogen-bond to each other, but exclude the non-polar fats. Saturated fats Fatty acids vary in length (number of carbons) and in the number and locations of double bonds. Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds. Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature. Most animal fats are saturated. Unsaturated fats Unsaturated fatty acids have one or more double bond. 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. Phospholipids In phospholipids, two fatty acids and a phosphate group are attached to glycerol. The two fatty acid tails are hydrophobic. The phosphate head group is hydrophilic. Phospholipids in biological membranes Phospholipids are the major component of cell membranes. When phospholipids are added to water, they spontaneously self-assemble into a bilayer. The hydrophobic tails point towards the interior of bilayer, and the hydrophillic head groups on the surface associate with water. The structure of phospholipids results in the bilayer arrangement of membranes. Steroids Steroids are lipids with a carbon skeleton consisting of four fused rings called sterol. Cholesterol is a component in animal cell membranes. Although cholesterol is an essential component of animal cell membranes, high levels in blood may contribute to cardiovascular disease. 2.4. Proteins Proteins introduction Proteins account for more than 50% of the dry mass of most cells. Protein functions overview Protein functions overview Amino acid and peptides All proteins are polymers constructed from the same set of 20 amino acids. Amino acids are linked together into unbranched polymers called polypeptides. A protein is a biologically functional molecule that consists of one or more polypeptide. Amino acids are organic molecules with carboxyl and amino groups. 20 amino acids Amino acids differ in their properties due to differing side chains, called R groups. Peptide bond Amino acids are linked by peptide bonds. Polypeptides range in length from a few to more than a thousand amino acids Each polypeptide has unique linear sequence of amino acids, with an amino end (N-terminus) and a carboxyl end (C-terminus). The sequence of amino acids determines a protein’s three-dimensional structure. Protein structure determines its function. We can study protein structure at four different levels: primary, secondary, tertiary, and quaternary. Primary protein structure Primary structure, the sequence of amino acids, is like the order of letters in a long word. Primary structure is determined by inherited genetic information. Secondary protein structure Secondary structure results from hydrogen bonds between repeating constituents. Typical secondary structures include coils called an -helix, and folded structures called β-pleated sheets. Tertiary protein structure Tertiary structure is the overall shape of a polypeptide. It is determined by interactions between R groups, not by interactions between backbone constituents. These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions. Strong covalent bonds called disulfide bridges may reinforce the protein’s structure. Quaternary protein structure Quaternary structure results when two or more polypeptide chains form one macromolecule. Collagen is a fibrous protein consisting of three polypeptides coiled like a rope. Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains. Change in primary structure A slight change in primary structure can affect a protein’s structure and ability to function. Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin. Change in higher levels In addition to primary structure, physical and chemical conditions can affect structure. Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel. This loss of a protein’s native structure is called denaturation. A denatured protein is biologically inactive. Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfolded proteins. X-ray crystallography X-ray crystallography can be used to determine a protein’s 3-D structure. In 2006, Roger Kornberg received Nobel Prize for solving 3-D conformation of RNA Polymerase II. 2.5. Nucleic acids Nucleic acids introduction There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Synthesis of nucleic acids DNA provides directions for its own replication. DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis. This process referred to as gene expression: Transcription Translation Nucleotides Nucleic acids are polymers called polynucleotides. Each polynucleotide is made of monomers called nucleotides. Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups. The portion of a nucleotide without the phosphate group is called a nucleoside. Nucleoside = nitrogenous base + sugar Nucleotide = nucleoside + phosphate group Nucleoside components There are two types of nitrogenous bases: Pyrimidines (cytosine, thymine, uracil) have a single six-membered ring. Purines (adenine, guanine) have a six-membered ring fused to a five-membered ring. In DNA, the sugar is deoxyribose. In RNA, the sugar is ribose. Polynucleotide Nucleotides are linked together to build a polynucleotide via phosphodiester linkage. Adjacent nucleotides are joined by covalent bonds that form between the —OH group on the 3’ carbon of one nucleotide and the phosphate on the 5’ carbon on the next. These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages. DNA double helix DNA molecules have two polynucleotides spiralling around an imaginary axis, forming a double helix. In DNA double helix, two backbones run in opposite 5’→ 3’ directions from each other, an arrangement referred to as antiparallel. Complementary base pairing: DNA bases in opposite strands pair by hydrogen bonding: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C). RNA is single-stranded RNA molecules are usually single-stranded. Complementary pairing can occur between two RNA molecules or within same molecule. In RNA, thymine is replaced by uracil (U) so A and U pair.