http://www.biostudio.com/demo_freeman_protein_synthesis.htm
1. go here: http://learn.genetics.utah.edu/content/molecules/transcribe/
2. type the base that matches the given strand base. 3. have fun! 4 Groups of Organic Compounds Important in Living Organisms:
Carbohydrates Lipids Proteins Nucleotides Organic compound defined – A compound containing carbon (with exception of carbon dioxide); found in all living things. THE CENTRAL ROLE OF CARBON A. The Carbon Backbone - The processes of life are primarily the result of the chemistry compounds of carbon. Because of carbon's tendency to form four covalent bonds in four different directions, carbon can form an unbelievably large number of different compounds of high complexity; organic compounds derive their basic shapes from the carbon atoms; this shape helps determine the compound's function in living systems. B. Functional groups - The structure & behavior of organic compounds also depends on the properties of their functional groups; functional groups are groups of atoms (ex. hydrogen, oxygen, nitrogen, phosphorus, sulfur) attached to the carbon backbone. I. CARBOHYDRATES: A. Structure: generally made up of only three elements: carbon, hydrogen, & oxygen B. Three Principle Classes of Carbohydrates: 1. Monosaccharide a. Structure - composed of single sugar molecule; the atoms in a sugar molecule can form a straight chain or a ring (rings are more common in the body). b. Examples - Glucose, Ribose, Fructose, Galactose d. Functions - monosaccharides are important energy molecules in living things; glucose is the primary energy source for humans & many other animals; also important as building blocks of larger sugars. 2. Oligosaccharides - composed of short chains of monosaccharides; Examples: a. Sucrose (table sugar) is a disaccharide composed of glucose & fructose; sucrose is the form in which sugars are transported in plants. b. Lactose (milk sugar) is a disaccharide composed of glucose & galactose. Sucrose = Glucose + Fructose 2. Polysaccharides - straight or branched chains of many monosaccharide units a. Storage Polysaccharides 1.) Starch - sugar storage in plants. 2.) Glycogen – “animal starch;” principle storage form for glucose in higher animals; this energy storage is short term; lipids are used for long term energy storage. b. Structural Polysaccharides 1.) Cellulose – Principal component of the plant cell wall; also found in the cell walls of algae and fungi. Monosaccharides are bonded together in such a way that the molecule resists breakdown by multicellular organisms. We don’t have the digestive enzymes to break the bonds; however, some microorganisms do have these enzymes; this is why microbes are so important in the gut of a termite, cow, etc.) 2.) Chitin – contains nitrogen; forms the cell wall of some fungi (it’s the same stuff insect exoskeleton’s are made of!) II. PROTEINS A. Protein Structure: 1. Proteins are composed of subunits called amino acids (there are 20 different amino acids that make up proteins). Amino acids contain carbon, hydrogen, oxygen, and nitrogen. Some also contain sulfur. Amino acids have a structure similar to the one below. The R stands for some other atom or group of atoms bonded to the central carbon atom in the molecule. The sequence of amino acids in a chain helps determine the structure & shape of the protein & therefore the function of the protein; there are many possible combinations of amino acids that produce the many different kinds of proteins. H H O N----C----C H R OH 2. Peptide bonds - linkage formed between one amino acid & another amino acid; the name of these bonds is why chains of amino acids are called polypeptides. 3. Producing the three dimensional structure of a protein: We have been discussing proteins as "chains of amino acids." However, the final structure of proteins is not a straight chain of amino acids. Proteins are very complex, three-dimensional molecules, with numerous twists & folds. The amino acid chain of every kind of protein is folded in a very specific way [the chain will twist & fold itself based on the linkage of amino acids in a specific sequence & the environmental conditions (i.e., temperature & pH)]. There are several bonds & forces which give a protein its specific 3-D structure (i.e., hydrogen bonds, ionic bonds, etc.); these bonds link distant parts of the molecule, forming loops, twists, etc. Destruction of a protein's 3-D structure by extreme heat or pH is called denaturation (see "enzymes" on the next page for how this occurs). Analogy for protein structure: Think of a phone cord. Pull it straight (like a straight chain of a.a.), then let it twist, then roll the twisted cord into a ball. (Every type of protein folds and twists in a very specific way.) B. Some Specific Functions of Proteins: 1. Structural Proteins: collagen in connective tissue, keratin in the skin, cytoskeleton in cells 2. Functional Proteins: a. membrane transport proteins – transport substances across the cell membrane b. cell movement – ex. flagellum c. enzymes as catalysts (enzymes speed up the rate of chemical reactions); all life processes are primarily the result of chemical reactions; molecules in living things require enzymes in order to react; without enzymes, chemical reactions in living things can’t occur; see below for more information on enzymes. d. antibodies in the immune response C. Enzymes – a large, globular protein molecule that accelerates a specific chemical reaction. Virtually all chemical reactions that take place in cells involve enzymes!!! Most of a cell’s proteins are enzymes. 1. Why are enzymes needed? In order for particular molecules to react with one another, they must be in close proximity & must collide with sufficient force to overcome the mutual repulsion of their negatively charged electron clouds & to break existing chemical bonds within the molecules. The force with which they collide depends on their kinetic energy (energy of motion). Most chemical reactions require an initial input of energy to get started, which increases the kinetic energy of the molecules, enabling a greater number of them to collide with sufficient force. In the chemistry lab, we can supply this energy with heat. In a cell, many different reactions are going on at the same time, therefore heat cannot be used as it would be nondiscriminatory (it would affect many reactions at the same time). Cells get around this problem by using enzymes, which serve as catalysts (they get the chemical reactions going). The enzymes form a temporary association with the molecules that are to react, bringing them close to one another & weakening the existing chemical bonds, making it easier for new ones to form. 2. Enzyme Structure & Function - Enzymes are large, complex, globular proteins consisting of one or more polypeptide chains. The molecules that enzymes acts on are known as the substrates. Enzymes are folded to form a groove or pocket (called an active site) on their surface into which the substrate fits & where the chemical reactions take place. See diagram below: 3. Effects of Temperature & pH on Enzyme Function 1. Temperature: As the temperature increases, so does the rate of enzyme catalyzed reactions, but only up to a certain point. At high temperatures, the enzymes are denatured (due to the vibration of molecules at high temperatures, the bonds that maintain the enzyme's structure are broken & the protein unfolds). If denaturation is severe, the damage to the enzyme is irreversible. 2. pH: The shape of the enzyme depends partly on attraction between positively & negatively charged amino acids. As the pH changes (acidic - more H+, basic - fewer H+), these charges change, changing the shape of the enzyme & its function. Remember: the optimum pH for most enzymes is 6-8. (exception: the stomach which has a pH of 2) Note: All proteins can be denatured by heat and extreme pH. III. PEPTIDOGLYCAN This molecule has both protein and polysaccharide components and it forms the cell wall of eubacteria. It may be one or several layers thick. It is an extremely strong protective covering. Glycan strands in all eubacteria are made of alternating units of 2 modified sugars, N-acetylglucosamine (NAGA) and N-acetylmuramic acid (NAMA). (It’s structure is similar to a chain link fence!) More later! IV. LIPIDS A. General Structure - all lipids are mostly nonpolar (hydrophobic) & are insoluble in polar solvents such as water; lipid structure varies greatly & is discussed below for each type. B. Some General Functions: 1. long term energy storage (example: glycerides); energy is stored in the chemical bonds; excess carbohydrates, proteins or fats are converted to triglycerides & are stored in adipose (fat) tissue. 2. structural (example: phospholipids make up the cell membrane of cells) C. Types of Lipids: 1. Lipids with Fatty Acids – Glycerides & Phospholipids: a. Glycerides 1.) Structure: classified as mono-, di-, & triglycerides, depending on the number of fatty acids attached a single glycerol molecule; glycerol has 3 carbon atoms & 3 hydroxyl (OH) groups; fatty acids are long, nonpolar chains composed of hydrogen & 4 to 24 carbon atoms, with a carboxyl (COOH) group at one end. a.) Saturated fatty acids - all carbons in the fatty acid tails are joined together by single carbon to carbon bonds & as many hydrogen atoms as possible are linked to the carbons (the carbons are said to be "saturated" with hydrogens); triglycerides with many saturated fatty acids are solid at room temperature; occur mostly in animal tissues, but also in a few plant products; examples: butter, lard, cocoa butter, palm oil, coconut oil; the liver produces cholesterol from some breakdown products of saturated fats. b.) Unsaturated fatty acids - one or more double bonds occur between carbon atoms in the fatty acid tails; this cuts down on the number of hydrogen atoms that can bond to the carbons; liquids at room temperature; the double bonds create a kink in the shape of the molecule prevent the fatty acids from packing close together & becoming solidified; unsaturated fatty acids are more common in plants; monounsaturated fatty acids are better for you that the polyunsaturated ones; the poly’s can produce compounds called trans fatty acids, which increase the risk of heart disease. A triglyceride molecule: H H H H H H H H H H H H--C---O---C--C—C--C--C--C—C—C—C—C--C—H saturated f.a. O H H H H H H H H H H H H H H H H H H H H H--C---O---C--C—C--C--C--C--C—C—C—C—C--H saturated f.a. O H H H H H H H H H H H H H H H H H H H H H—C---O---C—C—C—C==C—C—C—C—C—C—C---H unsaturated f.a. H O H H H H H H H H 2.) Functions of Glycerides a.) Energy - For most organisms and cellular microorganisms, sugars in excess of what can be stored as glycogen are converted into fats for more permanent storage; this is not the case in bacteria! b. Phospholipids 1.) Structure - 2 fatty acids & 1 phosphate group are linked to a glycerol molecule; a small polar group is linked to the phosphate group; this results in a molecule with a dual nature - the molecule has a nonpolar, hydrophobic end & a polar, hydrophilic end. 2.) Function: Structural. The phosphate end of the molecule & its polar group are called the "head" of the molecule; the two fatty acids are called the "tails" of the molecule; the head is hydrophilic ("water-loving"), while the 2 fatty acid "tails" are hydrophobic ("water-fearing"). This arrangement forms the structural basis of cellular membranes & is called the phospholipid bilayer. Phosphate Head (polar) 2 Fatty AcidTails (nonpolar) V 2. Lipids without Fatty Acids: Steroids a. Structure - different from other lipids; they consist of 4 interlocking carbon rings with numerous hydrogens attached; while they have no fatty acids, they are still nonpolar & hydrophobic, so they are classified as lipids. b. Some Examples: 1.) cholesterol - important component in eukaryotic cell membranes & serves as the starting material for the synthesis of other steroids. Not found in the cell membranes of bacteria with the exception of the Mycoplasms. V. NUCLEOTIDES A. Structure: nucleotide = phosphate(s) + monosaccharide + a nitrogen-containing compound (called a base); it’s the bases that spell out the genetic message in DNA & RNA). B. Functions: 1. Nucleotides are the basic subunits of nucleic acids such as a. DNA (deoxyribonucleic nucleic acid) - carrier of the genetic message - makes up chromosomes in the nucleus of the cell. b. RNA (ribonucleic acid) - transcribes genetic message present in DNA & produces proteins from it. 2. Nucleotides also make up the adenosine phosphates (ex. ATP - adenosine triphosphate – used for energy molecule in the cell). 3. Nucleotides make up some coenzymes (ex. NAD & FAD); these molecules function as electron carriers in some biochemical reactions; they are called the cell’s “reducing power.” We’ll talk about this more in the metabolism chapter. When molecules of inorganic acids, bases, or salts dissolve in water of body cells, they undergo ionization or dissociation (they break apart into their individual ions).
1. Acids & Bases Generally Defined Acid - Defined as a solute that releases H+ ions in a solution [ex. HCl - hydrochloric acid dissociates into H+ ions & Cl- ions] Base - Defined as a solute that removes H+ ions from a solution; many release OH- ions in this process. [ex. Mg(OH)2 - magnesium hydroxide dissociates into OH- ions & Mg++ ions]. 2. pH Scale - Fluids are assigned a pH value (0 -14), which refers to the hydrogen ion concentration present in the fluid. The hydrogen ion concentration is abbreviated as [H+]. a. acid - pH below 7.0; base - pH above 7.0; neutral - pH = 7.0 b. pH = - log [ H+ ] (formula for calculating pH) c. It is a common misconception to think that as the [H+] increases, the pH also increases! The rule is: As [H+] increases, pH decreases! This can be seen from the following example: solution A: [H +] = 1 x 10-2 or 0.01 pH = -log[1 x 10-3] = 2 solution B: [H+ ] = 1 x 10-8 or 0.00000001 pH = -log[1 x 10-4] = 8 (A quick way to find the pH of these solutions is to look at the exponent or count the number of decimal places in the [H+]) Solution A is more acidic than Solution B - Solution has a higher [H+] than Solution B (0.001 > 0.0001); therefore, Solution A has a lower pH than B. When you think about a pH value, think that this number is really the number of decimal places in the hydrogen ion concentration. The larger the number, the more decimal places there are, indicating a smaller hydrogen ion concentration. 3. Buffers - help maintain a constant pH by removing or adding H+ ions; the pH inside living systems is generally between 7.35-7.45 (exception: the hydrochloric acid in the digestive system makes the pH here 2-3); this pH range is important, as many biochemical reactions take place only within this range; buffers can combine with hydrogen ions &/or release them, & so help stabilize the pH. Hydrophilic & hydrophobic interactions underlie several properties of water that are biologically important. 1. Temperature-Stabilizing Effects:
Note: The temperature of a substance is a measure of how fast its molecules are moving; the higher the temperature of a substance, the faster its molecules are moving. a.) heating water - It takes considerable heat to raise the temperature of water because the hydrogen bonds between the water molecules restrict the movement of the molecules; in order for the temperature of water to rise, a number of H bonds must be broken - this takes a lot of energy. This resistance to temperature change helps living cells to maintain a relatively constant temperature; this is important because biochemical reactions take place within a narrow temperature range (this has to do with the action of enzymes). This resistance to temperature change also helps organisms that live in aquatic or marine environments. 2. Water As a Solvent - the polarity of water is also responsible for water's capacity as a solvent (something that dissolves something else); water is an excellent solvent for ions & other polar molecules (solutes) in cells. |