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CHAPTER 5 THE STRUCTURE & FUNCTION OF LARGE BIOLOGICAL MOLECULES THE MOLECULE OF LIFE The critically important large molecules of all living things- from bacteria to elephants-fall into just four main classes: Carbohydrates Lipids Proteins and Nucleic acids THE MOLECULE OF LIFE Macromolecules: Carbohydrates Proteins and Nucleic acids Are huge molecules and therefore are known as Macromolecules. A protein main consist of thousands of atoms. With a MASS well over 100,000 daltons. POLYMERES POLYMERS POLYMERS: A polymer is a large molecule (macromolecule) composed of repeating structural units. These subunits are typically connected by covalent chemical bonds. POLYMERS Although the term polymer is sometimes taken to refer to plastics. It actually encompasses a large class of compounds comprising both natural and synthetic materials with a wide variety of properties. POLYMERS Macromolecule: carbohydrates proteins and nucleic acids are long chains-like molecules called polymers MONOMERS MONOMERS is an atom or a small molecule that may bind chemically to other monomers to form a polymer Some of the molecules that serve as monomers also have other functions of their own. MONOMERS & POLYMER SYNTHESIS & BREAKDOWN OF PLOYMERS THE SYNTHESIS AND BREAKDOWN OF POLYMERS The chemical mechanisms by which cells make and break down polymers are basically the same in all cases. Those are called: DEHYDRATION REACTION & HYDROLYSIS In cells, these processes are facilitated by ENZYMES. ENZYMES are protein catalysts. These are specialized macromolecule that speed up chemical reactions. DEHYDRATION REACTION Monomers are connected by a reaction in which two molecules are covalently bonded together to each other, with the loss of water molecule. Each monomer contributes a part of the water molecule that is released during reaction. One monomer provides a HYDROXYL GROUP (-OH). Other provides a HYDROGEN (-H) This reaction is repeated as monomers are added to the chain. DEHYDRATION REACTION HYDROLYSIS HYDROLYSIS This process is the reverse of the DEHYDRATION. Polymers are dissembled to monomers by HYDROLYSIS. The bond between the monomers is broken by the addition of water molecule. HYDROGEN from the water molecule attached to one monomer and HYDROXYL group attached to other HYDROLYSIS THE DIVERSITY OF POLYMERS THE DIVERSITY OF POLYMERS Each cell has thousands of different macromolecules. The collection varies one type of cells to another even with in the same organism The inherent difference between human siblings reflect small variations in polymers, particularly: DNA and Proteins All these molecules are constructed from only 40 to 50 common monomers THE DIVERSITY OF POLYMERS Despite this immense diversity, all macromolecules are grouped into four classes based on their: molecular structure and function CLASS 1: CARBOHYDRATES CARBOHYDRATES Include both sugars and polymers of sugars. MONOSACCHARIDES--are monomers from which more complex carbohydrates are constructed. DISACCHARIDES-consisting of two monosaccharides joined by a covalent bond. POLYSACCHARIDES- polymers composed of many monomer sugars MONOSACCHARIDES General Molecular formula for Monosaccharides is: CH2O GLUCOSE (C6H12O6) the most common monosaccharide Molecule has a carbonyl group (C=O) and Multiple hydroxyl groups (OH) MONOSACCHARIDES Monosaccharides are classified in different ways based on: Location of Carbonyl Group Size of carbon chain Arrangement of atoms around asymmetric carbons. MONOSACCHARIDES Depending on the location of the carbonyl group, a sugar is either an: ALDOSE (Aldehyde sugar) or KETONE (Ketone sugar) Glucose is Aldose Fructose is Ketone MONOSACCHARIDES Another criterion for classifying sugars into size of carbon skeleton. That range from three to seven carbons long known as: Trios Pentose Hexose etc. MONOSACCHARIDES MONOSACCHARIDES Glucose and Galactose differ only in the placement of parts around one asymmetric carbon This small difference is significant enough to give the two sugars distinctive shape and behaviors MONOSACCHARIDES Glucose is the major nutrient for cells. Through cellular respiration, cells extract energy in a series of reaction starting with glucose molecules. Carbon skeleton of monosaccharides also serve as raw material for the synthesis of many other molecules such as: amino acids fatty acids etc DISACCHARIDES Consists of two monosaccharides. Joined by a GLYCOSIDIC LINKAGE, a covalent bond. The most common example is SUCROSE POLYSACCHARIDES POLYSACCHARIDES Are MACROMOLECULES, polymers with a few hundred to a few thousands monosaccharides joined by glycosidic linkage Some polysaccharides serve as storage material such as: Starch Glycogen Other polysaccharides serve as building materials such as Cellulose Chitin STORAGE POLYSACCHARIDES STARCH: A polymer of glucose, stored by plants as granules within cellular structure known as PLASTIDS. Human and most animals can hydrolyze starch, making glucose available as a nutrient for cells. Most of the glucose molecules are joined by alpha 1-4linkage The simplest form of starch is unbranched AMYLOSE. AMYLOPECTIN is branched polymer with 1-6 linkage at the branch point STORAGE POLYSACCHARIDES GLYCOGEN: Animals store carbohydrate as glycogen in their liver and muscles. It is like amylopectin but much highly branched. This storage can last less than a day. STRUCTURAL POLYSACCHARIDES The polysaccharide call CELLULOSE is the major component of the tough wall that enclose plant cells. On planet plants produce almost 100 billion tons of cellulose in a year. It is also a polymer of glucose but glycosidic linkage is different STRUCTURAL POLYSACCHARIDES Different glycosidic linkages in starch and cellulose give them distinct threedimensional shapes. Starch molecules are largely helical Cellulose molecule is straight. Enzyme that digest starch by hydrolyzing it alphalinkage cannot hydrolyze the beta-linkage of cellulose. STRUCTURAL POLYSACCHARIDES Cellulose is many “insoluble fiber” in our diet. CHITIN is another structural polysaccharide. Used by arthropods to built their exoskeleton. Pure CHATIN is leathery and flexible It become hardened when encrusted with calcium carbonate. STRUCTURAL POLYSACCHARIDES CHITIN is similar to cellulose, with Beta-linkage The glucose monomer in chitin has a nitrogencontaining appendage. LIPIDS Lipids are the one class of large biological molecules that does not include true polymer. They are generally not big enough to be considered macromolecules. Lipids are a group of nonpolar compounds which mix poorly, if at all, with water. The hydrophobic behavior of lipid is due to its hydrocarbon regions LIPIDS Types of lipids: Waxes Fats Phospholipids Steroids Fats are not polymers. It is construct from two kinds of smaller molecules: glycerol and fatty acids Major function of fat in body is energy storage FATTY ACIDS Glycerol is an alcohol, each of its three carbon bears a hydroxyl group FATTY ACIDS: has a long carbons skeleton, usually 16 to 18 carbon atoms in length. The carbon at one end of the skeleton is part of a carboxyl group. FATTY ACIDS The carboxyl is a functional group that gives these molecules the name FATTY ACIDS. The rest of the skeleton consist of a hydrocarbon chain. The relatively nonpolar C-H bonds in the chains are the reason fats are hydrophobic. TRIACYLGLYCEROL &FATTY ACIDS TRIACYLGLYCEROL (triglyceride): Consists of three fatty acids linked to one glycerol molecules. Fatty acids in a TG can be the same. Or they can be of two of three different kinds TYPES OF FATTY ACIDS TYPES OF FATTY ACIDS SATURATED FATTY ACIDS: solid at room temperature Contribute to heart disease UNSATURATED FATTY ACIDS: liquid at room temperature Omega 3 and Omega 6 FATTY ACIDS are essential fatty acids Trans-FATTY ACIDS Produce during Hydrogenation of unsaturated fatty acids May contribute more than saturated fatty acids to heart diseases cis-trans FATTY ACIDS PHOSPHOLIPIDS PHOSPHOLIPIDS Is similar to a fat molecule but has only two fatty acids attached to glycerol rather than three. The third hydroxyl group of glycerol is joined to a phosphate group Phosphate has negative charge PHOSPHOLIPIDS At the surface of the cell, phospholipids are arranged in a similar bilayer. The hydrophobic heads of the molecules are on the outside of the bilayer. The hydrophobic tails pointed towards the interior of the bilayer STEROLS STEROIDS Are lipids characterized by a carbon skeleton consisting of four fused rings. Important steroids: CHOLESTEROL SEX HORMONES ETC. They are distinguished by the particular chemical groups attached to rings. CHOLESTEROL Cholesterol is synthesized in the liver and obtained from the diet. It is integral part of every animal tissue. Precursor of Vitamin D and Bile. A high level of cholesterol in blood may contribute to atherosclerosis PROTEIN PROTEIN Nearly every dynamic function of a living being depends on proteins. Greek word “proteios” meaning “primany”. Proteins account for more than 50% of the dry mass of most cells. PROTEINS ARE GROUPED INTO TWO SECTIONS WORKING PROTEINS STRUCTURAL PROTEINS PROTEIN WORKING PROTEINS Enzymes Hormones Antibodies Transport proteins STRUCTURAL PROTEINS Tendon ligaments Hair and Nails etc. PROTEIN A human has tens of thousands of different proteins Each with a specific structure and function Proteins are the most structurally sophisticated molecules known Each type of protein have a unique three dimensional shape POLYPEPTIDES Protein are all unbranched polymers of same set of 20 amino acids Two amino acids are joined with each other by a peptide bond Polymers of amino acids are called POLYPEPTIDES Proteins are consists of one or more polypeptides, each fold and coiled into a specific three dimensional structure AMINO ACID MONOMERS All amino acids share a common structure. Possess both an AMINO group and a CARBOXYL group. At the center of the amino acid is an ASYMMETRIC carbon atom exists. That is called ALPHACARBON . AMINO ACID MONOMERS The physical and chemical properties of the side chain determine the unique characteristics of a particular amino acid. Amino acids with non-polar side chain are hydrophobic. Some are acidic Some are basic in nature In a polypeptide of a significant size, the side chains far out number the terminal groups. So the chemical nature of the molecule as a whole is determined by the kind and sequence of the side chain. PROTEIN STRUCTURE & FUNCTION A functional protein is not just a polypeptide chain, but one or more polypeptide precisely: twisted folded and coiled Into molecule of unique shape. PROTEIN STRUCTURE & FUNCTION When a cell synthesizes a polypeptide, the chain generally folds spontaneously This folding is driven and reinforced by the formation of variety of bonds between parts of the chain. Which in turn depends on the sequence of amino acids Protein’s specific structure determines how it works. In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecules. Natural signaling molecules Example: A signaling molecule called ENDORPHINS bind to specific receptor proteins on the surface of brain cells in humans, producing euphoria and relieving pain. Morphine, heroin and other opiate drugs are able to mimic endorphins because they all share a similar shape with endorphins and can thus fit into and bind to endorphin receptors in the brain. FOUR LEVELS OF PRTEIN STRUCTURE FOUR LEVELS OF PRTEIN STRUCTURE All proteins share three superimposed levels of structure, known as: PRIMARY SECONDARY & TERTIARY A fourth level, quaternary structure, arise when a protein consists of two or more polypeptide chains. PRIMARY STRUCTURE The primary structure is a long chain of amino acids. Its precise structure is determined by the genetic information. The primary structure in turn dictates SECONDARY & TERTIARY structure. SECONDARY STRUCTURE Most proteins have segments of their polypeptide chains repeatedly coiled or folded in patterns that contribute to the protein’s overall shape. These structures can be: Alpha-Helix or Beta-pleated sheet They are called SECONDARY STRUCTURE TERTIARY STRUCTURE Is the overall shape of a polypeptide resulting from interactions between the side chains of various amino acids. Those interactions can be due to: Hydrophobic amino acids negative and positive charges disulfide bridges QUATERNARY STRUCTURE This structure is results from the aggregation of two or more polypeptides subunits. Example: Hemoglobin Collagen SIKLE-CELL DISEASE Is an intertied blood disorder. Caused by the substitution of one amino acid (VALINE) for the normal one (GLUTAMIC ACID) at the particular position in the primary structure of hemoglobin. WHAT DETERMINS PROTEIN STRUCTURE WHAT DETERMINES PROTEIN STRUCTURE? 1. AMINO ACID SEQUENCE 2. PHYSICAL & CHEMICAL CONDITIONS OF THE PROTEIN’S ENVIRONMENTS SUCH AS: SALT CONCENTRATION TEMPERATURE IF ENVIRONMENTS ARE ALTERED WEAK CHEMICAL BONDS AND INTERACTIONS WITHIN PROTEIN MAY BE DESTROYED This change is known as “DENATURATION” DENATURATION DENATURATIONS Most protein become DENATURED if they are transferred from an aqueous environment to a nonpolar solvent such as: ETHER or CHLOROFORM The polypeptide chain refold so that its HYDROPHOBIC region faces outward. DENATURATIONS Other denaturing agents disrupts: HYDROGEN BOND IONIC BONDS and DISULFIDE BRIDGES Excessive HEAT also cause DINATURATION PROTEIN FOLDING IN THE CELL Protein folding system is not simple. Most proteins go through several intermediate structures on their way to stable shape. Crucial to the folding process are CHAPERONINS There are protein molecules that assist in proper folding of other proteins. CHAPERONIN CHAPERONINS segregate new peptides from the influences of the cytoplasmic environment while it folds. Misfolding of polypeptides is a serious problem in cells. Many disease are associated with misfolding of peptides such as: Alzheimer’s Parkinson’s Mad Cow Disease etc NUCLEIC ACIDS NUCLEIC ACIDS Amino acid sequence of a polypeptide is programmed by the unite of inheritance known as GENE. GENE consist of DNA Which belong to the class of compounds known as NUCLEIC ACIDS. NUCLIC ACIDS are polymers made of monomers called NUCLEOTIDES THE ROLE OF NUCLEIC ACIDS There are two types of NUCLEIC ACIDS: DEOXYRIBONUCLEIC ACID (DNA) RIBONUCLEIC ACID (RNA) These Nucleic Acids enable living organisms to transfer information form one generation to the next. DNA is the genetic material that organism inherit from their parents. DNA provide directions for its own replications DNA, also directs RNA synthesis and through RNA, controls protein synthesis. THE ROLE OF NUCLEIC ACIDS The DNA is not directly involved in running the operations of the cell. DNA----m RNA-----r RNA-- Protein In EUKARYOTIC cell, DNA reside in nucleus and ribosome in cytoplasm PROKARYOTIC cells lack nuclei but still use m RNA to convey a message from DNA to ribosome. THE COMPONENTS OF NUCLEIC ACIDS Nucleic acids are macromolecules that exist as polymers called polynucleotides. A nucleotide is composed of three parts: a nitrogenous base a five carbon sugar one or more phosphate groups NUCLEOSIDE A portion of a nucleotide without any phosphate groups is called a NUCLEOSIDE NUCLEOTIDE There are two families of nitrogenous bases: PYRIMIDINES PURINES PYRIMIDINE The members of Pyrimidine are: CYTOSINE (C) THYMINE (T) URACIL (U) PURINES Purines are larger, a six membered ring fused with a fiver member ring. Purines are: ADENINE GUANINE Adenine, Guanine, and Cytosine are found in both DNA and RNA Thymine is found only in DNA Uracil is found only in RNA In DNA, DEOXYRIBOSE sugar is attached with nitrogenous base. In RNA, RIBOSE is the sugar To complete the construction of a nucleotide, a phosphate group is attached to the 5 carbon of the sugar