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CHEE 370 (2)


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Chemical Engineering
CHEE 370
Robert Jones

Chapter 3: (51-64) Chemistry of cellular components Diversity lies in the variation of chemistry and arrangement cellular components. 3.1-Strong and weak chemical bonds: Major components in living things: Hydrogen, Oxygen, Carbon, Nitrogen, Phosphorus, and Sulfur. The molecule consists of two and more atoms chemically bonded to each other. Covalent bonds They are strong bonds formed between chemical elements in which electrons are shared more or less equally between atoms. Single, double and triple covalent bonds can form. Monomers: Chemical elements bond to form them. They associate to form polymers. Covalently bonded polymers in living cells are called macromolecules. Hydrogen bonding and polarity Hydrogen bonds: They form as a result of weak electro-static interactions between hydrogen atoms and more electronegative atoms such as nitrogen and oxygen. Because the other atoms will be more electronegative than the hydrogen, this will create a shift in the shared electrons closer to that atom, creating a slight charge separation. An individual hydrogen bond by itself is very weak but many hydrogen bonds together will achieve stability. Water is polar and its molecules tend to associate with one another and remain apart from nonpolar (hydrophobic) molecules. Water is extensively made of hydrogen bonds. Also hydrogen bonds are found in protein which assures its stability. Other weak bonds -Van der Walls forces are weak attractive forces that occur between atoms when they become closer than about 3-4 angstroms; they play an important in binding the substrate to enzymes and in protein- nucleic acid interactions. - Ionic bonds, such as Na+ and Cl- in NaCl are weak electrostatic interactions that support ionization in aqueous solution. -Hydrophobic interactions are also considered weak bonds. They occur when non-polar molecules or non-polar regions of molecules associate tightly in a polar environment. Like Van der Walls forces, hydrophobic interactions help in binding substrates to enzymes, folding of proteins and controlling how different subunits in a multi-subunit protein associate with one another (quaternary structure) to form the biologically active molecule. They also help stabilize RNA. 3.2- An overview of macromolecules and water as the solvent of life Carbons are the major components in all macromolecules. Water on the other hand is the major constituent. 95% of the dry weigh of a cell consists of macromolecules. Carbon can bind to each other and also to other subunits. Different organic compounds have different bonding patterns. Each of these patterns is called a functional group: - Proteins are polymers of monomers called amino acids. They are the most abundant class in the cell dry mass; they play both a structural and an enzymatic role. - Nucleic acids are polymers of nucleotides and are found in two forms, RNA and DNA. RNAs are the next most abundant macromolecule in an actively growing cell. RNA is abundant because there are many types of ribosomes and RNA (mRNA, tRNA). Ribosomes are composed of a mixture of RNAs and protein. DNA is less abundant. - Lipids are formed of both hydrophilic and hydrophobic properties and play a crucial role in the cells such as membranes and storage depots for excess carbon. - Polysaccharides are polymers of sugars, and they are present in the cell, especially in the cell wall. They can exist like glycogen, in the form of a carbon and energy storage in the cell. Water as a Biological solvent Water has two important features that make it an ideal biological solvent. The first feature is the polarity of water which facilitates the dissolving of many macromolecules which are already polar. This also promotes the stability of large molecules because of the increased opportunities for hydrogen bonding. Water also forces the non-polar molecules to aggregate and remain together. The hydrogen bonding gives the water cohesiveness. Water molecules have a big affinity for one another and form arrangements in which hydrogen bonds are constantly forming, breaking and reforming. The cohesiveness of water is responsible for important properties such as high surface tension, and high specific heat. Water expands on freezing to yield a less dense solid form, ice. NON-INFORMATIONAL MACROMOLECULES Play an important role as structural and reserve of water. 3.3- Polysaccharides Carbohydrates: they are organic compounds that contain carbon, hydrogen, and oxygen in ratio of 1:2:1. Glucose (C H O ) is the most abundant sugar on earth .Pentose (C5) are important 6 12 6 because their role as structural backbones of nucleic acids. Hexoses (C6) are the monomeric constituents of cell wall polymers and energy reserves. Derivatives of simple carbohydrates are formed when the hydroxyl group on the sugar is replaced. For example, the important cell wall polymer peptidoglycan contains the glucose derivative N-Acetylglucosamine. Glycosidic bond Polysaccharides are carbohydrates containing up to 100 or 1000 monosaccharides. These are connected by covalent bonds called glycosidic bonds. 2 monosaccharides: disaccharide, 3 monosaccharides: trisaccharide, several more monosaccharides: oligosaccharide, long chain of monosaccharides: polysaccharide. Glycosidic bonds can form in two different geometric orientation, a and b. The 1-4 a orientation functions as important carbon and energy reserves in bacteria, plants and animals. The 1-4 b orientation are present in stiff plant and algal cell wall component. Complex Polysaccharides Polysaccharides can also combine with other classes of macromolecules such as proteins and lipids to form polysaccharides, glycoproteins and glycolipids. They play an important role as cell-surface receptors. They reside on the external surface where they are in contact with external environment of cells. Glycolipids are and important compound of the cell wall of gram negative bacteria. 3.4- Lipids Lipids are amphipathic which means that they both show hydrophilic and hydrophobic properties. Fatty acids are major constituents of Bacteria and Eukarya lipids. By contrast, lipids of Aarchaea contain a hydrocarbon side chain not composed of fatty acids. Fatty acids contain both hydrophobic and hydrophilic components. Fatty acids consist of fatty acids bonded to C3 alcohol glycerol. Triglycerides and complex lipids Simple lipids are also called triglyceride because three fatty acids are bonded to a glycerol unit. Complex lipids are simple lipids that contain additional elements such as phosphorus, nitrogen, sulphur or small hydrophilic organic compounds such as sugars. Ex: phospholipids, they play an important role in the cytoplasmic membrane. Lipids aggregate to form membranes. The hydrophilic glycerol portion is in contact with external environment and cytoplasm while hydrophobic region remains imbedded inside the membrane. This makes the membrane an ideal permeability barrier. INFORMATIONAL MACROMOLECULES The sequence of monomers in nucleic acids carries genetic information and the sequence of monomers in proteins carries structural and functional information. Nucleic acids and proteins are thus informational macromolecules. 3.5- nucleic acids DNA=Deoxyribonucleic acid RNA= Ribonucleic acid They are macromolecules composed of monomers called nucleoids. DNA and RNA are polynucleotides. A nucleotide is composed of three components: - A pentose sugar: Ribose in RNA or Deoxyribose in DNA. - A Nitrogen base - A molecule of phosphate, PO 43- Nucleotides The nitrogen bases of nucleic acids belong to two classes: - Purine bases: adenine (A) and guanine (G). They contain two fused heterocyclic rings. - Pyrimidine bases: thymine (T), cytosine (C), and uracil (U). They contain a single six- membered heterocyclic ring. - G, A, C are present only in DNA. T is only present in DNA and U only in RNA. Nucleotides consist of a nitrogen base attached to a pentose sugar by a glycosidic linkage between carbon atom 1 of the sugar and nitrogen of the base, either the nitrogen atom labeled 1(in a pyrimidine base) or 9(in purine base). Without the phosphate the molecule is called nucleoside. Nucleotides are thus nucleosides containing one or more phosphates. Nucleotides also play a role in energy production in ATP and in metabolism by inhibiting or simulating the activities of certain enzymes or metabolic events. Nucleic acids Polynucleotides consist of nucleotides covalently bonded via phosphate from carbon 3- called the 3 (3 prime) carbon of one sugar to 5 carbon of the adjacent sugar. The phosphate linkage is called a phosphodiester bond because a phosphate connects 2 sugar molecules by ester linkage. The sequence of nucleotides in a DNA or RNA is called its primary structure. DNA It is double stranded. Each chromosome consists of two strands of DNA. Hydrogen bonds play a role in linking the two strands. Hydrogen bonding is most stable when adenine bonds with thymine (A-T) by two hydrogen bonds and (C-G) with 3 hydrogen bonds. RNA They are single stranded molecules but can fold upon themselves in regions where complementary base pairing is possible to form folded structures called secondary structures. Four classes of RNA exist: 1. Messenger RNA: carries the genetic information of DNA in a single stranded molecule complementary in base sequence to that of a DNA. 2. Transfer RNA; tRNA: converts the genetic information found in the mRNA
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