Biological Macromolecules and Lipids PDF

Lectures by Esraa H. Al-Nsour  Overview: The Molecules of Life All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids Macromolecules are large molecules composed of thousands of covalently connected atoms Molecular s...

Lectures by Esraa H. Al-Nsour  Overview: The Molecules of Life All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids Macromolecules are large molecules composed of thousands of covalently connected atoms Molecular structure and function are inseparable Concept 5.1: Macromolecules are polymers, built from monomers A polymer is a long molecule consisting of many similar building blocks These small building-block molecules are called monomers Three of the four classes of life’s organic molecules are polymers Carbohydrates Proteins Nucleic acids  The Synthesis and Breakdown of Polymers A dehydration reaction two molecules are covalently bonded to each other, with the loss of a water molecule, one monomer provides hydroxyl (OH-), while the other provides (H+): Dehydration synthesis = build by removing H2O. Enzymes are organic catalysts = macromolecules that speed up chemical reactions. Hydrolysis reaction the bond between monomers is broken by the addition of water, where (H+) from water attach to one monomer and the (OH-) to the other one : Hydrolysis = breaking down by adding H2O. Concept 5.2: Carbohydrates serve as fuel and building material Carbohydrates include sugars and the polymers of sugars The simplest carbohydrates are monosaccharides, or single sugars Disaccharides are double sugars, consisting of two monosaccharides joined by a covalent bond. Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks  Sugars Monosaccharides have molecular formulas that are usually multiples of CH2O Glucose (C6H12O6) is the most common monosaccharide Monosaccharides are classified by : 1. The location of the carbonyl group (as aldose or ketose) 2. The number of carbons in the carbon skeleton  Though often drawn as linear skeletons, in aqueous solutions many sugars form rings, because they are the most stable form of these sugars under physiological conditions. Monosaccharides serve as a major fuel for cells and as raw material for building molecules (A) Linear and ring forms (B) Abbreviated ring structure  A disaccharide is formed when a dehydration reaction joins two monosaccharides by removing H2O to form a covalent bond. This covalent bond is called a glycosidic linkage. The dehydration synthesis reaction: C6H12O6 + C6H12O6 = C12H22O11 Examples of disaccharides: a. Maltose (glucose + glucose). b. Sucrose (glucose + fructose). c. Lactose (glucose + galactose). Polysaccharides Polysaccharides are macromolecules, the 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.  Storage Polysaccharides Starch is a plant storage polysaccharide. Starch is made of glucose monomers. Plants store surplus starch as granules within chloroplasts and other plastids. Glycogen is an animal storage polysaccharide. Glycogen is found in the liver and muscles. Storage polysaccharides of plants and animals Chloroplast Starch Mitochondria Glycogen granules 0.5 µm 1 µm Amylose Amylopectin Glycogen (a) Starch: a plant polysaccharide (b) Glycogen: an animal polysaccharide Structural Polysaccharides The polysaccharide cellulose is a major component of the tough wall of plant cells Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ The difference is based on two ring forms for glucose: alpha () and beta () (a)  and  glucose ring structures 4 1 4 1  Glucose  Glucose 1 4 1 4 (b) Starch: 1–4 linkage of  glucose monomers (c) Cellulose: 1–4 linkage of  glucose monomers - Polymers with  glucose are helical - Polymers with  glucose are straight - In straight structures, H atoms on one strand can bond with OH groups on other strands - Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants  Enzymes that digest starch by hydrolyzing  linkages can’t hydrolyze  linkages in cellulose. Cellulose in human food passes through the digestive tract as insoluble fiber. Some microbes use enzymes to digest cellulose. Many herbivores, from cows to termites, have symbiotic relationships with these microbes.  Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods. Chitin also provides structural support for the cell walls of fungi. Unlike starch and glycogen, chitin is a polysaccharide with nitrogen ( N ) in each sugar monomer. Concept 5.3: Lipids are a diverse group of hydrophobic molecules Lipids are the one 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 form nonpolar covalent bonds. The most biologically important lipids are fats, phospholipids, and steroids. 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 hydrocarbon chain. This fatty acid hydrocarbon can be either saturated or unsaturated.  Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride  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 , All C - C bonds are single Unsaturated fatty acids have one or more double bonds, double bonds C = C  Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature Most animal fats are saturated 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. Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen. Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds = trans fats. These trans fats may contribute more than saturated fats to cardiovascular disease.  The major function of fats is energy storage Humans and other mammals store their fat in adipose cells Adipose tissue also cushions vital organs and insulates the body Phospholipids In a phospholipid, two fatty acids and a phosphate group are attached to glycerol The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head A phospholipid is an amphipathic molecule: hydrophilic head and hydrophobic tails.  When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior The structure of phospholipids results in a bilayer arrangement found in cell membranes Phospholipids are the major component of all cell membranes 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 Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease Concept 5.4: 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 functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances Proteins are polymers called polypeptides. Amino acids are the monomers used to build proteins. Examples of proteins functions:  Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life  Polypeptides Polypeptides are unbranched polymers built from the same set of 20 amino acids A protein is a biologically functional molecule that consists of one or more polypeptides Amino Acid Monomers Amino acids are organic molecules with carboxyl and amino groups attached to a central carbon. Amino acids differ in their properties due to variable side chains, called R groups There are 20 different amino acids because there are 20 different side chains.  Amino Acid Polymers Amino acids are linked by covalent bonds called peptide bonds C - N 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 (C-terminus) and an amino end (N-terminus). Protein Structure and Function A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape A protein folds into a specific Shape / Structure so it can perform its Function Groove Groove (a) A ribbon model of lysozyme (b) A space-filling model of lysozyme  The sequence of amino acids determines a protein’s three-dimensional structure A protein’s structure determines its function An antibody binding to a protein from a flu virus Antibody protein Protein from flu virus Four Levels of Protein Structure The primary structure of a protein is its unique sequence of amino acids Secondary structure consists of regular coils and folds in the polypeptide backbone made by hydrogen bonds. Tertiary structure is determined by interactions among various side chains (R groups) Quaternary structure results when a protein consists of multiple polypeptide chains 4 Levels of protein structure Primary Secondary Tertiary Quaternary Structure Structure Structure Structure  pleated sheet +H N 3 Amino end Examples of amino acid subunits  helix  Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word Primary structure is determined by inherited genetic information (DNA).  The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures are a coil called an  helix and a folded structure called a  pleated sheet  Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents These R group interactions fold the polypeptide into a globular shape 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 Figure 5.20f Hydrogen bond Hydrophobic interactions and van der Waals interactions Disulfide bridge Ionic bond Polypeptide backbone  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 each with an iron heme group. Sickle-Cell Disease: A 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 What Determines Protein Structure? 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 Protein Folding in the Cell It is hard to predict a protein’s structure from its primary structure Most proteins probably go through several stages on their way to a stable structure Chaperonins are protein molecules that assist the proper folding of other proteins Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfolded proteins  Scientists use X-ray crystallography to determine a protein’s structure Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization Bioinformatics uses computer programs to predict protein structure from amino acid sequences Concept 5.5: Nucleic acids store, transmit, and help express hereditary information The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid made of monomers called nucleotides The Roles of Nucleic Acids There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA provides directions for its own replication DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis Protein synthesis occurs on ribosomes Figure 5.25-3 DNA 1 Synthesis of mRNA mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into Ribosome cytoplasm 3 Synthesis of protein Amino Polypeptide acids The Components of Nucleic Acids 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 Figure 5.26 Sugar-phosphate backbone 5 end Nitrogenous bases Pyrimidines 5C 3C Nucleoside Nitrogenous base Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) 5C Purines 1C Phosphate 3C group Sugar 5C (pentose) Adenine (A) Guanine (G) 3C (b) Nucleotide Sugars 3 end (a) Polynucleotide, or nucleic acid Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components  Nucleoside = nitrogenous base + sugar There are two families of nitrogenous bases Pyrimidines (cytosine, thymine, and uracil) have a single six- membered ring Purines (adenine and guanine) have a six-membered ring fused to a five-membered ring In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose Nucleotide = nucleoside + phosphate group Nucleotide Polymers Nucleotide polymers are linked together to build a polynucleotide 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 The sequence of bases along a DNA or mRNA polymer is unique for each gene  The Structures of DNA and RNA Molecules RNA molecules usually exist as single polypeptide chains 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 from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes  The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C) 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 (U) so A and U pair