Amino acids are the building blocks of proteins. There are 20 amino acids that most commonly occur in proteins. Based on the functional group making up their side chain, or R group, amino acids are classified as acidic, basic, or neutral. The physical and chemical properties of the R group determine the unique characteristics of each amino acid. Acidic amino acids have acidic R groups. Their electrically charged R groups make these molecules highly soluble in water. (GLUTAMIC ACID) Acidic R groups contain a carboxylic acid functional group, -COOH. Basic amino acids have basic R groups. Their electrically charged R groups make these molecules highly soluble in water. (ARGININE, LYSINE) Basic R groups contain an amino (not amide) functional group, -NH2, which attracts a proton to form -NH3. Neutral (neither acidic nor basic) amino acids can be further classified as nonpolar or polar. The neutral nonpolar amino acids have R groups that contain no charged atoms; most of these amino acids are not water soluble. The neutral polar amino acids have R groups that have a dipole moment. The partial charges in their R groups make these molecules generally water soluble. Neutral polar R groups are neither acidic nor basic, but they contain a highly electronegative atom such as oxygen, nitrogen, or sulfur. (ASPARAGINE, CYSTEINE, GLUTAMINE, SERINE, THREONINE, TYROSINE) Neutral nonpolar R groups contain mostly carbon and hydrogen (alkyl groups). They may also contain nitrogen or sulfur, but the effect of those atoms is diminished due to the size of the alkyl portion. (ALANINE, PHENYLALANINE, METHIONINE, PROLINE, VALINE, TRYPTOPHAN) It important for you to understand how amino acids are classified, rather than just looking up the answers to this tutorial in your book. The hints provided here will teach you how to figure out the classifications without looking them up. That way you won't have to memorize them when you are tested on this material. Protein structure is conceptually divided into four levels, from most basic to higher order: Primary structure describes the order of amino acids in the peptide chain. Secondary structure describes the basic three-dimensional structures, -helices and -sheets. Tertiary structure describes how the secondary structures come together to form an individual globular protein. Quaternary structure results from individual proteins coming together to form multi-subunit protein complexes. PRIMARY ? sequence of amino acids in protein SECONDARY ? describes alpha & beta formed by hydrogen bonding between backbone atoms located near each other in the protein TERTIARY ? when protein folds into 3D shape stabilized by interactions between side-chain R groups QUATEMARY ? result of 2+ protein subunits assembling to form larger biologically active protein complex Most proteins are folded into a complex globular shape. Each protein molecule consists of one or more chains of amino acid monomers. The amino acids are linked by peptide bonds, so a protein polymer is often called a polypeptide. Because they are so complicated, proteins are usually described in terms of four levels of structure. Each protein has a unique primary structure? a particular number and sequence of amino acids making up the polypeptide chain. Twenty different amino acids are used to build proteins. Theoretically, the various amino acids could be linked in almost any sequence, forming an almost infinite variety of different proteins. Click on the magnifying glass (in the lower right corner) to see primary structure in more detail. Secondary structure results from hydrogen bonding between atoms along the polypeptide backbone. Oxygen and nitrogen atoms along the backbone are highly electronegative, giving them partial negative charges, and leaving nearby hydrogen atoms with partial positive charges. These negatively and positively charged atoms are attracted to one another at regular intervals along the chain, causing parts of the protein to twist or fold back upon itself. In most proteins, parts of the polypeptide chain are coiled or folded, forming twists and corrugations. This is secondary structure. The turns and folds of secondary structure contribute to the protein's overall shape. One kind of secondary structure is the alpha helix, where the chain twists. Another is the pleated sheet, where the chain folds back on itself or where two regions of the chain lie parallel to one another. Click on the magnifying glass to examine secondary structure in more detail. Superimposed on primary and secondary structure is tertiary structure, irregular loops and folds that give the protein its overall three-dimensional shape. Click on the magnifying glass to see tertiary structure in more detail. Some proteins consist of two or more polypeptide chains. The fourth level of protein structure-- quaternary structure-- results from the combination of two or more polypeptide subunits. Click on the magnifying glass for a more detailed look at quaternary structure. Proteins-- the purple blobs in this closeup of an animal cell-- are the most complicated molecules known. A cell contains thousands of kinds of proteins, which carry out a variety of functions. In most cases, a protein's function depends on its complex three-dimensional structure. Click on each protein to see a demonstration and description of its function. Note how function depends on protein shape and changes in shape. STRUCTURAL PROTEINS ? have many functions. Like tent poles and ropes, they shape cells and anchor cell parts. They may serve as tracks along which cell parts can move. They bind cells together, making organized units such as muscles, ligaments, and the tendons that bind muscles to bones. The silk of spiders and the hair of mammals are also structural proteins. SIGNAL PROTEINS ? Include hormonal proteins that help coordinate an organism's activities by acting as signals between cells. For example, insulin, a hormonal protein secreted by the pancreas, signals an animal's cells to take in and use sugar. The hormone receptor is also a protein. RECEPTOR MOLECULES ? bind to signal molecules and can then emit second messengers which trigger changes inside a cell. Receptors are thus important links in the system of communication among cells. Some signal molecules, such as hormones, are also proteins. TRANSPORT PROTEINS ? carry molecules from place to place. The example shown here allows certain solute molecules to enter the cell. Hemoglobin is the transport protein that carries oxygen in the blood. SENSORY PROTEINS ? detect environmental changes such as light, and respond by emitting or producing signals that call for a response. GENE REGULATORY ? proteins bind to DNA in particular locations and control whether or not certain genes will be read. This allows cells to become specialized for different functions and respond to changes in their surroundings. An ENZYME is a protein that changes the rate of a chemical reaction without itself being changed into a different molecule in the process. Enzymes promote and regulate virtually all chemical reactions in cells. The immune system makes defensive proteins called antibodies that bind to invaders (such as the virus shown here) and mark the foreign objects for destruction. This is a closeup view of a DNA polymer, one of two twisted strands that make up a DNA molecule. Cells make nucleic acid polymers by linking together four kinds of monomers called nucleotides. Each nucleotide consists of a sugar (deoxyribose in DNA), a phosphate group, and a nitrogen-containing base-- abbreviated G, A, C, or T. Like letters in a sentence, the sequence of nucleotides in a nucleic acid carries information. The DNA of every organism has a unique nucleotide sequence. This illustration shows only a tiny segment of DNA, which may be millions of nucleotides in length. DNA normally consists of two strands of nucleotides that twist around one another, forming the famous double helix. The strands are held together by hydrogen bonds between pairs of nitrogenous bases. The base A always pairs with T, and C always pairs with G. This is a closeup view of an RNA polymer. RNA looks a lot like DNA, except it is typically single-stranded, contains a different sugar (called ribose), and has the base uracil (U) instead of thymine (T). RNA is copied from part of a DNA molecule, so it is shorter than DNA-- dozens to thousands of nucleotides. If a DNA double helix is 100 nucleotide pairs long and contains 25 adenine bases, how many guanine bases does it contain? 75 (100 nucleotide pairs are a total of 200 nucleotides. Because of base pairing, if there are 25 adenine there must also be 25 thymine. This leaves 200?50 = 150 nucleotides to be divided evenly between guanine and cytosine.) Ahe building block of a nucleic acid, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and a phosphate group. The nucleic acids DNA and RNA are made from chains of nucleotides. Nucleotides consist of three components: a five-carbon sugar (either ribose or deoxyribose), a nitrogenous base attached to the sugar?s 1'-carbon, and a phosphate group attached to the sugar?s 5'-carbon. ribose deoxyribose has one less O atom phosphate purine Identify three possible components of a DNA nucleotide. deoxyribose, phosphate group, thymine DNA: deoxyribose, thymine BOTH: adenine, cytosine, phosphate, guanine RNA: ribose, uracil DNA is used for storage of genetic information. The presence of deoxyribose as the sugar in DNA makes the molecule more stable and less susceptible to hydrolysis. The 2'-oxygen on the ribose found in RNA makes RNA much more susceptible to breakdown. It is important that mRNA be easily broken down, to ensure that the correct levels of protein are maintained in the cell. DNA, or deoxyribonucleic acid, contains the genetic information that is used by all living things to produce their biomolecules essential for life. DNA is a double helix, with two strands. The two strands are held together by hydrogen bonds between complementary nitrogenous bases. The two strands are always complementary, ensuring that the DNA can be replicated accurately. The two complementary DNA strands always run in opposite directions: One runs from 5' to 3', and the other runs from 3' to 5', if you are looking along the strand, as seen in the image.
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