Chapter 3. Biomolecules PDF

Exam Review Chapter 3. Biomolecules 1. Importance of carbon compounds a. Most important element to life, fourth abundant element in the universe. b. Most versatile atom, able to form four covalent bonds and therefore forms...

Exam Review Chapter 3. Biomolecules 1. Importance of carbon compounds a. Most important element to life, fourth abundant element in the universe. b. Most versatile atom, able to form four covalent bonds and therefore forms complex biomolecules such as carbohydrates, proteins, lipids and nucleic acids. c. Carbon-based compounds are known as organic molecules. d. Central element in compounds necessary for life. e. Form structural components of living organisms, serve as energy sources. f. Carbon dioxide – greenhouse gas essential for photosynthesis. 2. Hydrocarbons a. Organic molecules consisting of only carbon and hydrogen bonded covalently. b. The simplest hydrocarbon – methane with four hydrogen atoms. c. Methane is the primary component of natural gas, affects surface temperature of Earth, emitted by many natural and man-made sources such as landfills. d. Certain archaea bacteria produce methane - methanogens. e. Carbon chains in hydrocarbons vary in length, branching and presence of double and triple bonds and their locations. f. Organic compounds also form rings as in benzene and cyclohexane. 3. Covalent bonds a. Many large organic molecules are made up of long chains of carbon atoms linked together by covalent bonds. 4. Organic molecules a. Organic biomolecules are grouped into four major types. i. Carbohydrates – sugars and starches. ii. Provides energy to cells, forms body structures. iii. Type of covalent bonds – glycosidic bonds. 1. Simple sugars 1  a. Monosaccharides – glucose, fructose, galactose. b. Disaccharides – lactose, sucrose. 2. Polysaccharides – complex carbohydrates. i. Structural polysaccharides 1. Cellulose 2. Chitin ii. Storage polysaccharides 1. Starch – amylose and amylopectin in plants. 2. Glycogen – branched storage form in animals – in liver and muscles. iv. Lipids 1. Glycerol and fatty acids 2. Ester bond. 3. Includes fats and oils 4. Energy storage, forms plasma membrane and carries messages. v. Proteins 1. Amino acid monomers linked by peptide bonds. 2. Catalyzes chemical reactions in cells, form muscles, helps keep cells in shape, carries messages and materials. vi. Nucleic acids 1. Information molecules – stores genetic information. 2. Nucleotides linked by phosphodiester bonds. 3. Contains genetic information for the construction of proteins, passed on to successive generations. 5. Abiotic origin of life a. Origin of life from non-organic – chemical evolution. b. Lack of oxygen in the prebiotic environment. c. Oparin and Haldane theory – organic molecules could be formed from abiogenic materials in the presence of an external energy source. The Earth’s primitive atmosphere was reducing and contained ammonia, other gases and water vapor. d. Miller and Urey experiment supported the abiogenic theory of life. 6. Functional groups (usually represented as by the letter R) 2  a. Chemical groups that are attached to the carbon skeleton. b. Small reactive groups of atoms which give organic molecules specific chemical properties or contribute to function by affecting their molecular shape and how they interact with other molecules. c. E.g. Hydroxyl group, carbonyl group, carboxyl group, amino group, phosphate group, thiol group. (Know their chemical formulae). 7. Chirality a. Chiral objects – Objects that are mirror images of each other b. Achiral objects – Objects that are mirror images of each other and that can be superimposed. 8. Chiral carbon – carbon atom that is bonded to four different atoms or groups (asymmetric carbon). 9. Isomerism – when two or more compounds have the same chemical formula but exist in two different forms due to some structural or spatial arrangement in their molecular structure. 10. Structural isomers. a. Two molecules with the same chemical formula but atoms are arranged in different ways. b. E.g. Glucose and fructose. 11. Stereoisomers AKA enantiomers. a. Isomers that are mirror images of each other. b. Isomeric molecules that have the same chemical formula but a different three-dimensional spatial arrangement of the atoms. c. E.g. D-glyceraldehyde and L-glyceraldehyde. 12. Dehydration reactions. a. When water molecules are removed, the reaction is called a dehydration reaction. b. A condensation reaction in which water molecules are removed is called a dehydration reaction. c. Macromolecules are formed by condensation reactions by the loss of a water molecule forming a covalent bond between monomeric subunits. 13. Hydrolysis. a. Polymers are disassembled to monomers by hydrolysis. b. Reverse reaction to dehydration synthesis. 3  c. Addition of water molecules to split the bond between monomeric units. 14. Macromolecules are polymers assembled from monomerric units a. Carbohydrates – Monosaccharides – glycosidic bonds. b. Proteins – Amino acids – peptide bonds. c. Nucleic acids – nucleotides – phosphodiester bonds. 15. Carbohydrates – Major functions. a. Storage polysaccharides – Starch in plant cells and glycogen in animals. b. Structural polysaccharides – cellulose and chitin. c. Monosaccharides – simple sugars; contain three to seven carbon atoms. Trioses, pentoses, hexoses. E.g. glucose, ribose, mannose, galactose, fructose. d. Two monosaccharides polymerize to form disaccharides. e. More than 10 monosaccharides polymerize to form polysaccharides. f. Disaccharides – assembled from two monosaccharides covalently joined by a glycosidic bond by dehydration synthesis. E.g maltose, lactose, sucrose. g. Polysaccharides – polymers consisting of hundreds to thousands of monosaccharide units. i. Starch, glycogen, chitin, cellulose. h. Starch – storage polysaccharide in plants. The simplest form of starch is amylose. Amylopectin is a more complex form of starch which is a branched polymer. i. Glycogen – storage polysaccharide in animals – stored in liver and muscles. Broken down to release glucose units. j. Cellulose – glucose polymers formed from glucose units linked by a beta 1-4 glycosidic linkages. k. Chitin – forms exoskeleton in arthropods – long chain polymer of N- acetylglucosamine, an amino acid derivative of glucose, contains beta 1-4 glycosidic linkage just as cellulose. 16. Lipids a. Large class of biological molecules that have a common feature of being hydrophobic – mix poorly with water. b. Does not include true polymers. 4 c. Three common types of lipids: i. Neutral lipids 1. Stored as energy source. a. Oils – liquid at biological temperatures. b. Fats – semisolids. c. Waxes – water insoluble and solid. 2. Fats are constructed from glycerol and fatty acids a. Glycerol – three-carbon alcohol having a hydroxyl group attached to each carbon. b. Fatty acids – long chain acids (aliphatic) containing a carboxylic acid group. c. Glycerol and three fatty acids are joined by an ester linkage creating a triglyceride. 3. Saturated and unsaturated fats – absence and presence of double bonds respectively. a. Saturated fats are solids at room temperature, most animal fats are saturated. b. Unsaturated fats are liquids at room temperature. Plant and fish fats are unsaturated. ii. Phospholipids 1. Primary lipids of the plasma membrane of cells, the phospholipid bilayer. 2. Phospholipids include a glycerol back bone linked to two fatty acid chains and a polar phosphate group which is linked to another polar group, such as choline or ethanolamine. 3. Fatty acid ends – non-polar hydrophobic 4. Polar group end – hydrophilic – in aqueous environment, the polar ends are exposed to water – extracellular matrix or the cytoplasm. 5. Non-polar fatty acids collect together in regions that exclude water. 6. Phospholipids are amphipathic molecules – substances that contain both hydrophilic and hydrophobic regions. 5  7. Amphipathic molecules spontaneously form bilayers – micelles or a lipid bilayer. 8. Phospholipid bilayers are selectively permeable, act as permeability barriers where different substances have different ability to pass through. iii. Steroids 1. Sterols, containing a single polar hydroxyl group. 2. Derivatives of cholesterol – occur in animal cell membranes. 3. Phytosterols – occur in plant cell membranes. 4. Sex hormones such as testosterone and estradiol are steroids. 17. Proteins – polymers of amino acids linked by peptide bonds. 18. Amino acids – contain amino and carboxylic acid groups (know the general structure of an amino acid. The nature of the functional “R” group affects the solubility of amino acids. 19. Know some basic amino acids and acidic amino acids. 20. Amino acids with sulfhydryl group form disulfide bonds. E.g. cysteine. 21. Proteins have a wide array of functions. a. Structural support, E.g., collagen; component of the ECM b. Catalytic proteins or enzymes, E.g., Catalase, RNA polymerase c. Movement, E.g., Actin and myosin d. Transport E. g., Na+/K+ ATPase e. Cell recognition and receptor molecules, E.g., growth factor receptors f. Regulation of proteins and DNA, E.g., Histones g. Signaling molecules and hormones, E.g., Insulin and glucagon h. Antibodies – immune system. i. Toxins and venoms 22. Protein structure a. Primary the unique sequence of amino acids forming a polypeptide. b. Secondary produced by the twists and turns of the amino acid chain. i. A delicate coil held together by hydrogen bonding between every fourth amino acid. ii. A delicate coil held together by hydrogen bonding between every fourth amino acid. 6  iii. A delicate coil held together by hydrogen bonding between every fourth amino acid. iv. The other secondary structure is the β pleated sheet in which two or more segments of the polypeptide chain lying side by side (called β strands) are connected by hydrogen bonds between parts of the two parallel segments. v. An antiparallel β sheet - In which neighboring hydrogen- bonded polypeptide chains run in opposite directions. vi. A parallel β sheet - In which the hydrogen-bonded chains extend in the same direction. c. Tertiary the folding of the amino acid chain, with its secondary structures, into the overall 3-D shape of a protein. i. The positions of secondary structures, disulfide linkages, and hydrogen bonds play major roles in folding each protein into its tertiary structure. ii. Attractions between positively and negatively charged chemical groups and polar or nonpolar associations also contribute to tertiary structure. iii. When only a single polypeptide chain comprises the functional protein, tertiary structure is the highest level of structure of the protein. iv. The tertiary structure of most proteins is flexible, allowing them to undergo limited conformational changes. v. Conformational changes are important to the function of enzymes, and to proteins involved in cellular movements or transport of substances across cell membranes d. Quaternary when present, is formed from more than one polypeptide chain. i. Quaternary structure is the overall protein structure that results from the aggregation of these polypeptide subunits. ii. E.g. Hemoglobin. e. Protein denaturation. 7  i. Unfolding a protein from its native conformation so that it loses its structure and function (caused by chemicals, changes in pH, or high temperatures) is called denaturation. ii. When a protein in a test-tube solution has been denatured by heat or chemical, it can sometimes return to its functional shape when the denaturing agent is removed. f. Newly synthesized proteins fold into their native states with the help of guide proteins called protein chaperones or chaperonins. g. Functional domains and motifs. i. In many proteins, folding of the amino acid chain (or chains) produces large subdivisions called domains. ii. In proteins with multiple functions, individual functions are often located in different domains. iii. 3-D arrangement of amino acid chains within and between domains produces highly specialized regions called motifs (e.g. Zn-finger motif, leucine zipper motif). 23. Nucleic acids a. Carry genetic information. Nucleic acids store, transmit and help express hereditary information. i. DNA – deoxyribonucleic acid. ii. RNA- Ribonucleic acid. 1. Messenger RNA (mRNA). 2. Ribosomal RNA (rRNA). 3. Transfer RNA (tRNA). b. Nucleic acids are polymers of nucleotides i. Components of a nucleotide – Nitrogenous base (Adenine, thymine, guanine, cytosine), Five carbon sugar (deoxyribose or ribose), phosphate group. ii. Purines – Adenine and Thymine – contain two rings. iii. Pyrimidines – Cytosine, Uracil and Thymine – contain one ring. iv. Uracil is found in RNA in place of thymine. c. Condensation reaction links nucleotides into a polynucleotide chain. d. In a polynucleotide chain, adjacent nucleotides are linked by phosphodiester bonds which covalently link the sugars of the two nucleotides. 8 e. Polynucleotide chains have directionality – one end has a 5’- phosphate, whereas the 3’ end has a hydroxyl group (5’-3’ direction). f. Nucleic acid polymerization is carried out by enzymes known as polymerases (DNA and RNA polymerases). g. Understand the difference between a nucleoside and a nucleotide. i. Nucleoside – the structure that results when a nitrogenous base is attached to a pentose sugar. ii. Nucleotide is nucleoside + Phosphate. h. DNA exists as a double helical arrangement with the backbone formed of sugar and phosphate groups. The center of the helix contains nitrogenous bases which base pair with each other using hydrogen bonds. i. The two polynucleotide chains are wrapped around each other resembling a twisted ladder. j. Other 3D structures are also formed by nucleic acids. For example a clover leaf structure formed by transfer RNA (tRNA). 9