BIOL 1110 Chapter 5 Structure and Function of Large Biological Molecules PDF

BIOL 1110 Chapter 5: The Structure and Function of Large Biological Molecules By: Dale P. Ledford Northeast State Community College “The only place that success comes before work is the dictionary” Vince Lombardi  Chapter 5 Objectives 1. List the four main classes of macromolecul...

BIOL 1110 Chapter 5: The Structure and Function of Large Biological Molecules By: Dale P. Ledford Northeast State Community College “The only place that success comes before work is the dictionary” Vince Lombardi  Chapter 5 Objectives 1. List the four main classes of macromolecules important to life. 2. Explain the relationship between monomers and polymers. 3. Compare dehydration and hydrolytic reactions and their relationship to monomers and polymers. 4. Describe the structures, functions, properties, the three major groups of carbohydrates and examples of each. 5. Describe the structures, functions and properties of a fatty acid; differentiate between a saturated and unsaturated fatty acid. 6. Describe and differentiate between the structures, functions, properties and types of the four major groups of lipids. 7. Describe an amino acid and a peptide bond. 8. Describe the four types of protein structures, functions, properties and types. 9. Explain how a protein’s shape determines its function. 10. Compare the structures and functions DNA and RNA, noting their similarities and differences.  Objective 5.1 The Molecules of Life There are 4 Classes of Large Biological Molecules: 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids These large molecules are called Macromolecules (example a protein can have a molecular mass of over 100,000 daltons).  Objective 5.2 Some Macromolecules are Polymers Polymer- (poly=many, mere=parts) Large molecules composed of many repeating parts or subunits. Monomers- the building block for a polymer. Macromolecules that are polymers: 1. Carbohydrates 2. Proteins 3. Nucleic acids Lipids are the only macromolecule that does not form polymers.  Objective 5.4 Synthesis and Breakdown of Polymers The building and breaking down of polymers is enhanced by special proteins called enzymes. – Polymers are built up or synthesized by removing water. This is called Dehydration synthesis. – Dehydration reactions produce a covalent bond between the two monomers making a longer chain. – Polymers are broken down by adding water. This is called Hydrolysis. – Hydrolysis reactions results in the breaking of covalent bonds resulting in smaller chains.  Objective 5.5 Carbohydrates Carbohydrates are sugars and polymers of sugars. – They range from simple sugars to more complex carbohydrates. – They are a major source of energy for living systems. – Carbohydrates have a basic chemical formula that have multiples of CH2O. Carbohydrates have a Carbon:Hydrogen:Oygen ratio of 1:2:1. – Example if a carbohydrate has 3 Carbon atoms, it will have 6 Hydrogen atoms and 3 Oxygen atoms.  Objective 5.5 Carbohydrates: Types of Carbohydrates Carbohydrates can exist in 3 classes: 1. Monosaccharides- simplest of all sugars. Have anywhere from 3-7 carbons. Buildings blocks for more complex carbohydrates. 2. Disaccharides- 2 sugars. 3. Polysaccharides- many sugars (3 or more).  Carbohydrates: Classifying Monosaccharides Monosaccharides can be classified by 2 means: 1. The position of the Carbonyl (C=O) group. 1. Aldoses 2. Ketoses 2. The number of carbons (3-7)  Carbohydrates: Classifying Carbohydrates (Position of the Carbonyl) Most of the oxygen atoms in monosaccharides are found in hydroxyl (OH) groups, but one of them is part of a carbonyl The position of the carbonyl (C=O), group can be used to categorize the sugars: – If the sugar has an aldehyde group, meaning that the carbonyl C is the last one in the chain, it is known as an aldose. – If the carbonyl C is internal to the chain, so that there are other carbons on both sides of it, it forms a ketone group and the sugar is called a ketose.  Objective 5.5 Carbohydrates: Classification of Monosaccharaides by Number of Carbons Monosaccharides are described based on the number of carbon atoms they contain: – Triose - Sugar that contains three carbons. – Tetrose - Sugar that contains four carbons. – Pentose - Sugar that contains five carbons. – Hexose - Sugar that contains six carbons. – Heptose- Sugar that contains seven carbons. Each of these can be covalently bonded together to make more complex disaccharides and polysaccharides.  Objective 5.5 Carbohydrates: Monosaccharides The most important monosaccharide in living systems in glucose. Monosaccharides serve as the primary energy source for cells to make energy. Can be used to make more complex carbohydrates.  Carbohydrates: Glucose and its Isomers Glucose is a hexose with the formula (C6H12O6). Other common monosaccharides include galactose (which forms part of lactose, the sugar found in milk) and fructose (found in fruit). Glucose, galactose, and fructose have the same chemical formula, but they differ in the organization of their atoms, making them isomers of one another. Fructose is a structural isomer of glucose and galactose, meaning that its atoms are actually bonded together in a different order. Glucose and galactose are enantiomers of each other.  Carbohydrates: Ring Forms of Sugars Many five- and six-carbon sugars can exist either as a linear chain or in one or more ring- shaped forms. These forms exist in equilibrium with each other, but equilibrium strongly favors the ring forms (particularly in aqueous, or water-based, solution). For instance, in solution, glucose’s main configuration is a six-membered ring. – Over 99% of glucose is typically found in this form.  Objective 5.5 Carbohydrates: Disaccharides Disaccharides are two monosaccharides held together by a special covalent bond called a glyosidic linkage. – This is the result of a dehydration synthesis between the 2 monosaccharides. – A disaccharide will posses only 1 glyosidic linkage. – A polysaccharide will possess at least 2 or more. Examples: 1. When two glucose molecules form a glyosidic linkage the result in maltose sugar, a major component of beer. 2. When a glucose and a fructose bond this creates sucrose, or table sugar. 3. When a glucose and a galactose bond, this creates lactose, or milk sugar.  Objective 5.5 Carbohydrates: Dehydration in Carbohydrates  Objective 5.5 Carbohydrates: Polysaccharides Polysaccharides (many saccharides) are polymers of many simple sugars. Some polysaccharides are used from energy storage, some for structure. – Storage polysaccharides: 1. Starch- used by plants to store excess sugars. (polymer of glucose). 2. Glycogen- used by animals to store excess sugars. (polymer of glucose). – Structural polysaccharides: 1. Cellulose- used in plants to make cell walls (polymer of glucose). 2. Chitin- used in the exoskeleton arthropods (insects, crawfish etc.) (a polymer of glucose).  Objective 5.5 Carbohydrates: Starch There are two kinds of starch: 1. Amylose- unbranched starch 2. Amylopectin- somewhat branched starch.  Objective 5.5 Carbohydrates: Types of Polysaccharides  Objective 5.6 Lipids Lipids function in various ways: 1. Energy storage 2. Insulation 3. Hormones Lipids are hydrophobic molecules. Lipids do not form polymers. Lipids are mostly composed of hydrocarbons (though there are exceptions). We will discuss 3 major groups of lipids (though others exist): 1. Fats 2. Phospholipids 3. Steroids  Objective 5.6 Lipids: Fats (Glycerides) Although not polymers fats are composed of subunits. 2 subunits of fats: 1. Glycerol- an alcohol, containing hydroxyl groups (-OH). 2. Fatty acids- a hydrocarbon chain possessing a carboxyl group (-COOH) at one end. Fatty acids are held to the glycerol with an ester linkage (result of dehydration synthesis). Generally have a C:H ratio of 1:2 Fats contain variable numbers of fatty acids: 1. If it contains 1 fatty acid chain it is called a monoglyceride. 2. If it contains 2 fatty acid chains it would be a diglyceride. 3. If it contains 3 fatty acid chain it is called a triglyceride.  Objective 5.6 Lipids: Saturated Fats vs. Unsaturated Fats The hydrocarbon chains of fatty acids can have different structures: 1. Saturated fats- posses no double covalent bonds, therefore all of the carbon can have the maximum number of hydrogens possible (saturated with hydrogens). These are solid at room temperature. 2. Unsaturated fats- posses at least 1 double covalent bond. Therefore, all of the carbons do not posses all of the hydrogens possible (unsaturated with hydrogens). Causes the fatty acid tails to have a kink in them. These are liquid at room temperature.  Objective 5.6 Lipids: Saturated Versus Unsaturated Fats  Objective 5.6 Lipids: Fats and Nutrition A diet rich in saturated fats has been shown to increase the risk of cardiovascular disease. Unsaturated fats can have the Hydrogens artificially moved from Cis to Trans to make them more solid. – Such as Crisco and Olestra. These trans-fats have been shown to increase heart disease and other cardiovascular issues.  Objective 5.7 Lipids: Phospholipids Cells could not exist without phospholipids. – They are an essential component of the cell membrane. Phospholipids contain: 1. Tail: (Hydrophobic) A diglyceryde (2 fatty acid tails). 2. Head: (Hydrophilic) 1. A phosphate group 2. A Choline 3. A Glycerol  Objective 5.7 Lipids: Phospholipid Bilayer The hydrophilic heads interact with water, but not dissolve. The hydrophobic tails do not interact with water and are excluded from water. When in water they self assemble into a phospholipid bilayer.  Objective 5.6 Lipids: Steroids Steroids are lipids composed of 4 fused rings. – 3, 6 Carbon rings and 1, 5 Carbon ring. All steroids contain this basic steroid skeleton. However different functional groups attached to the steroid skeleton create new steroids. Types of Steroids: 1. Cholesterol is an important steroid in animals (shown to the right). 2. Sex Hormones: 1. Testosterone 2. Estrogens  Objective 5.8 Proteins Almost all functions of the body require proteins. Proteins are more 50% of the dry weight of living things. Proteins have the functions of: 1. Speeding up chemical reactions in the body. 2. Defense 3. Storage 4. Transport 5. Cellular communication 6. Movement 7. Structural support  Objective 5.6 Proteins: Protein Functions  Objective 5.8 Proteins: Enzymes A special kind of protein that act as biological catalysts that speed up reactions. Enzymes regulate metabolism in the body without being consumed.  Objective 5.7 Proteins: Amino Acids The building blocks of proteins. All amino acids have 4 things in common: 1. A central carbon 2. An amino group 3. A carboxyl group 4. A hydrogen All Amino acids have 1 place where they are all different: 1. The variable R group. (also called side chains). A polypeptide is a polymer of amino acids. Some proteins are composed of various polypeptides.  Objective 5.7 Proteins: Classifying Amino Acids Based on R Groups There are 20 amino acids found in living things. The physical and chemical properties of the side chains (R groups) of each amino acid determine the unique properties of that amino acid, impacting its role in a polypeptide. Proteins: Classifying Amino Acids Based on R Groups (The 5 Types) Amino acids are grouped based on the properties of their side chains. – There are 5 main types with some subtypes 1. Non-polar (hydrophobic) “GLAMP TVIP”: Glycine, Leucine, Alanine, Methionine, Phenylalanine, Tryptophan, Valine, Isoleucine, Proline. 2. Hydrophilic (polar) “TCSy-TAG: Tyrosine, Cysteine, Serine, Threonine, Asparagine, Glutamine. 3. Electrically charged (hydrophilic): 1. Acidic (negatively charged) “GA” Glutamate, Aspartate 2. Basic (positively charged) “HAL” Histidine, Arginine, Lysine 4. Aromatic (has rings) “TTP”: Tyrosine Tryptophan Phenylalanine. 5. Sulphur containing- Methionine, and Cysteine.  Objective 5.7 Proteins: Classifying Amino Acids Based on R Groups  Objective 5.7 Proteins: Amino Acids Continued There are 20 amino acids used in all living things. These are the building blocks of all proteins for all life on Earth. Amino Acid Abbreviations and One Letter Code  Objective 5.7 Proteins: Building Proteins The covalent bond between two amino acids is called a peptide bond. – The result of a dehydration synthesis between two amino acids. Two amino acids link carobxyl group to amino group. This allows for a dehydration synthesis. Because of this any sequence of amino acids have a C terminus (carboxyl end) and an N terminus (amino end).  Objective 5.8 Proteins: Protein Structure and Function A protein's structure determines its function. – A polypeptide may not be biologically active unless it folds in a particular shape. The amino acid sequence determines this shape. 1. Proteins can be nearly spherical is shape called globular proteins. 2. Proteins can also be long and thin called fibrous proteins.  Objective 5.8 Proteins: 4 Levels of Protein Structure Proteins have 4 levels of structure that they may or may not possess: 1. Primary 2. Secondary 3. Tertiary 4. Quaternary  Objective 5.8 Proteins: 4 Levels of Protein Structure (Primary Structure) The amino acid sequence. All proteins have primary structure – Because all proteins are made of amino acids, and the sequence of amino acids is the primary structure. The primary structure can form up into further proteins structures because of the arrangements of the R groups.  Objective 5.8 Proteins: 4 Levels of Protein Structure (Secondary Structure) Forms a coiled or folded pattern. – Result from the hydrogen bonds between repeating parts of the polypeptide backbone/constiuents/residues, not the R groups. Two secondary structures: 1. Alpha (α) helix- a coiled shape. Forms when hydrogen bonds form every 4 constituents. – This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon. 2. Beta (β) pleated sheet- two or more segments of polypeptides lying side by side are connected via hydrogen bonds. Secondary structures create fibrous proteins.  Objective 5.8 Proteins: 4 Levels of Protein Structure (Tertiary Structure) Results from the interactions of side chains or R groups, not polypeptide backbone. – Tertiary proteins are primarily globular. – Usually they will contain Sulphur (disulfide bridges).  Objective 5.8 Proteins: 4 Levels of Protein Structure (Tertiary Structure Continued) Various interactions hold together tertiary structure – Such interactions could be: 1. Hydrophobic interactions- non-polar parts fold inward. 2. Van der Waals interactions 3. Hydrogen bonds between R groups. 4. Disulfide bridges- form when two amino acids contain sulfhydryls/sulfur form a covalent bond. 5. Ionic bonds  Objective 5.8 Proteins: 4 Levels of Protein Structure (Quaternary Structure) Two or more polypeptide chains bonded together. – It could be two or more secondary units. – Two or more tertiary units. – Or a combination of each.  Objective 5.8 Proteins: 4 Levels of Protein Structure (Quaternary Structure Continued) Proteins: Protein Structure Summary Proteins: Visualizing Protein Structures  Objective 5.8 Proteins: Hemoglobin 3D Structure  Objective 5.8 Proteins: Protein Structure and Function  Proteins: Protein Structure and Function Normally a protein’s structure is determined by the primary structure of amino acids. This determines how the protein folds, which determines its function. However other conditions determine protein shape: 1. pH 2. Salt concentration 3. Temperature  Proteins: Protein Structure and Function Loss of protein structure is called denaturation. – Proteins unravels and losses it’s native structure. – This results in loss of function. Caused by changes in: 1. pH 2. Salt concentration 3. Temperature Substances that denature proteins disrupt the various interactions that hold the protein together. Renaturation- The conversion of a denatured protein back into its native 3D structure. Proteins: Protein Denaturation  Proteins: Protein Folding Proteins use other proteins called chaperonins to aide in the folding into their final active conformations. Misfolded proteins can have serious impacts of the cell. – Misfolded proteins called prions that cause disease. Ex: mad cow disease.  Nucleic Acids The primary structure of proteins are coded for in the genes of our DNA. DNA and RNA are two types of Nucleic acids. Nucleic acids are polymers composed of monomers called nucleotides. Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA): – DNA is the genetic material of life. – DNA provides direction for its own replication. – DNA directs mRNA and protein synthesis called gene expression.  Nucleic Acids: Gene Expression DNATranscriptionmRNAT ranslationProtein: – Most of your DNA is stored up in the nucleus of your cells. – A molecules of mRNA is produced from your DNA. – The mRNA leaves the nucleus into the cytoplasm. – The proteins are made from the mRNA molecules using ribosomes.  Nucleic Acids: Structure of Nucleic Acids Nucleic acids are polymers called polynucleotides (many nucleotides). The monomers of nucleic acids are nucleotides. Each nucleotide is joined together by a phosphodiester linkage. – A phosphate group links the two sugars of two nucleotides together. – This creates a sugar phosphate backbone. Nucleotides are composed of a 3 parts: 1. A 5 carbon (pentose) sugar 2. A nitrogenous base 3. A phosphate group Each nucleotide only contains 1 phosphate The side of the nucleotide without a phosphate is called the nucleoside.  Nucleic Acids: Structure of Nucleic Acids (Nitrogenous Bases) There are 2 groups of nitrogenous bases: 1. Pyrimidines- has 1, 6 membered ring (“CUT”). DNA- Cytosine and Thymine (all have a Y in it). RNA- Cytosine and Uracil. 2. Purines- has a 2-ring structure, a 6 membered ring fused to a 5 membered ring. DNA and RNA- Adenine and Guanine “All Good”.  Nucleic Acids: Structure of Nucleic Acids (Pentose Sugars) DNA- the pentose sugar of DNA is Deoxyribose. – Deoxyribose because it lacks an oxygen on the second carbon in the ring (2’ carbon). RNA- the pentose sugar is Ribose.  Nucleic Acids: Ribose and Deoxyribose These two are very similar in structure, with just one difference: – The second carbon of ribose bears a hydroxyl group, while the equivalent carbon of deoxyribose has a hydrogen instead. The carbon atoms of a nucleotide’s sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”), as shown in the figure above. In a nucleotide, the sugar occupies a central position, with the base attached to its 1′ carbon and the phosphate group (or groups) attached to its 5′ carbon.  Nucleic Acids: DNA and RNA Structure DNA is a double (2) stranded molecule. RNA is a single (1) stranded molecule. RNA exists in 3 types: 1. mRNA- takes the DNA information to the ribosomes to be made into proteins. 2. tRNA- transfers amino acids to the ribosomes. 3. rRNA- makes up the ribosomes that produce proteins. Remember that Ribose and Deoxyribose is a pentose sugar because they contain 5 carbons. – The backbones of sugar and phosphate attach from the 5th (5’) carbon to the 3rd (3’)carbon. The double strands of DNA go from 5’-3’ on one side and 3’-5’ on the other side of the strand. Example: – 5’ ATGCACG 3’ – 3’ TACGTGC 5’ This results in the antiparallel arrangement of DNA. Nucleic Acids: DNA and RNA Structure (Part 2)  Nucleic Acids: DNA and RNA Base Pairing In DNA Purines will bind to Pyrimidines. – Adenine (A) and Thymine (T) will bind together. And they will have 2 hydrogen bonds between them. – Guanine (G) and Cytosine (G) will bind together. And they will have 3 hydrogen bonds between them. – “Apples on the Tree, Car in the Garage”. In RNA Uracil replaces Thymine – Uracil of an RNA molecule will bind the Adenine of a DNA molecule. This happens in gene expression. The nitrogenous bases that bind with each other are said to be complimentary.