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General Biology notes for Lecture 4

by: CatLover44

General Biology notes for Lecture 4 101-NYA-05

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Is lecture goes over macromolecules, proteins, alpha helix structure, beta pleated sheet structure, denaturation, and polypeptides among other things. I hope they're useful for you!
General Biology 1
Virginia Hock
Class Notes
polypeptides, amino acids, alpha helix, beta sheet, functions of proteins
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This 18 page Class Notes was uploaded by CatLover44 on Sunday September 11, 2016. The Class Notes belongs to 101-NYA-05 at Dawson Community College taught by Virginia Hock in Fall 2016. Since its upload, it has received 12 views. For similar materials see General Biology 1 in Biology at Dawson Community College.


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Date Created: 09/11/16
General Biology Course Number: 201-NYA-05 Lecture no. 4 Date: Wednesday, September 7, 2016 Professor: Dr. Virginia Hock Topics Covered: Macromolecules; properties of organic compounds, dehydration synthesis, hydrolysis, four main classes of biological molecules, amino acids, tertiary structure, quaternary structure, protein denaturation, primary structure, secondary structure, alpha helixes, beta pleated sheets, peptide bonds, polypeptide backbones. Macromolecules • All organisms contain: o nucleic acids; o proteins; o carbohydrates; o lipids. • Organic compounds contain a carbon backbone. o Carbon is a very important element: § Carbon can form four covalent bonds, and it can form with other carbon atoms, as well as many other elements. • Most organic compounds contain oxygen (O) and hydrogen (H), but can also contain nitrogen (N), phosphorus (P), and sulfur (S). • The properties of organic molecules depend on two things: o the arrangement of carbon atoms in a molecule (carbon skeleton); o the other atoms attached to the carbon skeleton (functional groups). § These properties define a molecule’s distinctive chemical properties. § Pay special attention to the carboxyl, amino and hydroxyl groups. § Estradiol and testosterone have similar structures, but they serve completely different purposes. The slightest change in the structure of a molecule can change its function (form fits function). • O, C, H, and N make up 96% of our body’s wet weight percentage. • Biological molecules are made of smaller components that are connected to each other. • An organic compound is a macromolecule, or large molecule. 2 o Macromolecules are made when two large molecules bond together. Examples of macromolecules are RNA, sugars, and fats. • A single unit of a biomolecule is called a monomer, and a string of monomers is called a polymer. o A protein is a string of monomers, not a single monomer. • Chains of polymers are built via dehydration synthesis; a bond forms with the removal of a water molecule. • Chains of polymers are broken via hydrolysis; a bond is broken with the addition of a water molecule. • There are four main classes of biological molecules: 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids 1. Carbohydrates • The class of carbohydrates includes sugars, which can be simple or complex. • Sugars are broken down for energy via cellular respiration, which is demonstrated by the following chemical equation: C 6 12 +66O =26CO + 2H O 2 3 o CO a2d H O a2e formed with the aid of 36 ATP (adenosine triphosphate). o Our liver stores sugar as glycogen. Glycogen is insoluble, and must be broken down into smaller parts before it can enter and leave our cells, while glucose is soluble and can therefore easily be used by out bodies for energy. Also, glycogen is a monosaccharide, and glucose is a disaccharide. o Carbohydrates are found in insects, fungi, animals, bread, starch and sugars. • Sugars are stored as long chains, for short-term energy reserves in muscles and the liver in animals. • Carbohydrates have the following functions in biological systems : o Sugar is a source of energy; o Cellulose provides structure and support. o Sugar is stored as starch in plants. • Carbohydrates have a specific structure: o The chemical formulas for carbohydrates have ratios of 1:2:1 for C, H, and O atoms. o Monomers are simple sugars, while polymers are complex sugars . • There are two types of simple sugars: 1. Monosaccharides, monomers of carbohydrates, that share the same molecular formula (C H 6 12 6xamples of monosaccharides are glucose, 4 galactose, and fructose. Glucose, galactose, and fructose are isomers, meaning the arrangement of atoms is different in each structural formula. 2. Disaccharides, two linked monosaccharides. Examples of disaccharides are sucrose, lactose, and maltose. Memorize this table! Sucrose Glucose + Table sugar Fructose Lactose Glucose + Milk sugar Galactose Maltose Glucose + Brewing sugar Glucose • You have to be able to recognize the different types of disaccharides from their structures. The three disaccharides above are all made of the same elements, but they're arranged in different ways so they're different compounds. • There are two types of complex sugars (or polysaccharides): 1. Storage carbohydrates (starch and glycogen) 5 a. Starch allows for energy storage in plants, and converts excess glucose into starch. b. Animals store excess glucose as glycogen. c. Important: Starch has a branched structure, and glycogen had a highly-branched structure. d. Note: a polysaccharide is a string of many sugar molecules. 2. Structural carbohydrates (cellulose and chitin) a. Cellulose provides structure in plants b. Chitin is found in fungal cell walls, and the skeletons of insects and other arthropods. 6 c. Important: the complex structure of cellulose gives rigidity to the structure of plants. d. Herbivores eat only plants, which contain cellulose in their cell walls, but they don't produce the enzymes that decompose cellulose. Instead, they have bacteria in their digestive systems which contain the enzymes that break down cellulose. i. Termites have protests that contain the enzyme they need to break down cellulose. ii. Note: all the parts of a plant or tree contain cellulose. 2. Lipids • ATP is used by our cells for energy. Our bodies make it from food. Food is converted into sugar, which is converted into fats, which make up proteins, which eventually make ATP. o In a protein cell, the cell uses ATP to release ions. • All lipids are non-polar, meaning they are insoluble in water. o They have little to no affinity to water (hydrophobic). • Lipids are very different from each other with respect to their forms and functions, even though they are mostly made of C and H atoms. 7 • There are three different types of lipids: 1. Neutral fats: a. have different structures and functions, but they are all hydrophobic (water-fearing) and are therefore non-polar. b. Include fats, but also phospholipids and steroids. c. The functions of fats in animals are long-term energy reserves in fat tissues, the maintenance of body temperature (insulation), protection of vital organs, and buoyancy. i. Fat provides our kidneys with the property of shock absorbency. ii. Neutral fats are found in hormones and steroids, such as Estradiol and progesterone. • Fat is constructed from two kinds of smaller molecules; 1 molecule of glycerol, and 1 to 3 molecules of fatty acids, o The number of fatty acids ranges from 1 to 3. o 3 fatty acids strung together make up a triglyceride. Triglycerides are made via dehydration synthesis. • Saturated fats are easily stacked together, and are solid at room temperature. Stearic acid is an example of a saturated fat. 8 • Unsaturated fats don't stack well, and are liquid at room temperature. Oleic acid is an example of an unsaturated fat. 2. Phospholipids: a. Are the main constituent of cell membranes in biological systems; i. Cell membranes are made of phospholipids, which have hydrophilic heads and hydrophobic tails. ii. This particular structure prevents certain things from entering our cells. b. Their structures are similar, but not the same as those of neutral fats (2 molecules of fatty acids, 1 glycerol molecule,and 1 phosphate molecule); c. Consist of hydrophilic (water-loving) heads, and hydrophobic (water- fearing) tails, so when they are placed in water, they form a bi-layer with a shield of water-loving heads protecting the water-fearing tails. 9 d. The diagram below demonstrates the structures of phospholipids in the cell membranes of plants, animals, bacteria, and protists: 3. Steroids a. Cholesterol, a type of steroid, makes up cell membranes, and the components of vitamins and hormones, such as growth hormones, and the sex hormones (estrogen, progesterone, testosterone); b. Are made from sterol, which are multiple rings of carbon atoms. Several types of molecules are made in our bodies from sterol. i. You don't need to memorize steroids, but you should recognize their structures. 10 3. Proteins • Proteins are the workhorses in the cell. o Their functions include coordinating the movement of substances in and out of cells, catalyzing reactions in cells, acting as messengers or receptors, and protecting our bodies from diseases § Enzymatic proteins accelerate certain chemical reactions. For example, digestive enzymes catalyze hydrolysis of bonds in food molecules. § Defensive proteins provide protection from diseases. For example, antibodies deactivate to help destroy viruses and harmful bacteria. § Storage proteins store amino acids. For example, casein (protein found in milk) is he major source of amino acids for baby mammals. Plants have storage systems in their seeds. Ovalbumin is he protein found in egg whites, which is used as the amino acid for developing embryos. § Hormonal proteins direct an organism's activities. For example, insulin is produced by the pancreas and causes other organs to absorb glucose which allows it to regular blood sugar concentration. § Receptor proteins let cells communicate with each other. They respond to chemical stimuli. For example, receptors in a nerve cell detect 11 signalling molecules released by other nerve cells (think of neurotransmitters). § Contractile and motor proteins are what allow us to move. Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin are responsible for muscle contraction. § Structural proteins provide support. For example, keratin makes up hair, feathers and horns, while insects and spiders use silk to make their cocoons and webs. § Collagen and elastin proteins provide a fibrous support for connective tissues in animals. • Proteins are made of amino acids (monomers). o Proteins are found in meat and nuts. o Cartilage is a protein, and glucagon is a protein hormone that's made by the pancreas. o Proteins allow muscle tissues to contract and expand. o Proteins are very complex polypeptides that are formed when two polypeptides are combined. • All amino acids have the same basic structures which can be classified by: o The amino group, the carboxyl group, and the R-group, which is variable. 12 o Amino acids have the amino and carboxyl groups. • There are 20 common amino acids which all contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. You don't need to memorize them. Just remember that their forms are all the same except for R-groups; R-Groups are the only functional groups that change. Proline is different from the other amino acids listed below because it's the only one that doesn't contain H N. 3 • Polypeptides are chains of amino acids that were created via dehydration synthesis. As the chain grows, a polypeptide is created. • Many amino acids are connected by peptide bonds, and eventually form polypeptides. • The repeating structure of atoms forms the polypeptide backbone with side chains (R-Group) coming out of it. 13 • All polypeptides have an N-terminus, which is a free amino end, and a C-terminus, which is a free carboxyl end. o These make polypeptides polar (soluble in water, hydrophilic) • The shape of a protein is essential to its function. Amino acids are linked together in specific ways to create distinct patterns. • Proteins can spontaneously change their shapes depending on the order and arrangement of amino acids. • There are 4 structural levels of proteins: o Primary structure: the specific unique sequence of amino acids that make up a protein (polypeptide). The order of the amino acid is determined by the nucleotide of the gene that encodes the protein; they are genetically determined. Even a small change in the primary structure of a protein can change the way it works. Remember: form determines function. § Proteins with primary structures are made of amino acids that are bound together by peptide bonds in a linear fashion. This structure is the most important of all structures because it determines the form 14 and function of the protein by determining how its amino acids are arranged. § Sickle-cell anemia occurs when one amino acid is substituted for another (glutamic acid is replaced by valine, which is less polar than glutamic acid, in hemoglobin, causing some blood cells to be smaller than others. Since there aren't enough healthy red blood cells to carry oxygen in our bodies, we become ill). o Secondary structure: classified by the coiling or folding of amino acids within a polypeptide. Coiling and folding occurs because hydrogen bonds form at regular intervals within a molecule. Hydrogen bonds (H-bonds) form between the amino and carboxyl groups in the polypeptide’s backbones. § Coiling and folding: • contributes to a protein’s conformity; • can be in the alpha helix (coiling) or beta sheet form (folding). Alpha helix (coiled) § Hydrogen bonds hold cells in shape in alpha helix structures, and hold neighbouring strands of sheet together in beta sheet structures. (No covalent bonding, and the hydrogen bonds are stronger when many 15 hydrogen bonds are present. Like a telephone cord, once tension is released, the fivers can recoil and hydrogen bonds can reform. § alpha helix bonds are mostly common in keratin (alpha keratin), which makes up our hair and nails as well as wool. Beta pleated sheet (folded) § Beta sheets are strong, but not elastic. The distance between folds is fixed by the covalent bonds in the polypeptide backbone; they can stretch but can't twist (these are stronger than alpha helixes). H-bonds bond the adjacent length of polypeptides for beta sheets. • Folded sheets make up the core of globular proteins, and also make up some fibrous proteins such as fibroid, which is the silk that spiders use to spin webs. • Globular structures are formed from hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions. o Tertiary structure: formed when more forces are holding the protein together. Examples of these forces are hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions. o All of the above forces between amino acids can occur in one protein. 16 o The 3-D structure of a protein is determined by which forces are acting between the R-groups of amino acids. § Hydrogen bonds occur between hydrogen and fluorine, hydrogen and oxygen, and hydrogen and nitrogen; § Ionic bonds result from charged particles (ions with + or – charge) § Hydrophobic interactions occur between two non-polar molecules § Covalent bonds occur when atoms share electrons. Disulfide bonds are covalent. o Quaternary structure: the fusion of two or more polypeptides. § Quaternary structures are formed by interactions between polypeptide chains that contain protein. • Hemoglobin in a globular protein with 4 polypeptide subunits • Collagen is a fibrous protein made of 3 helical polypeptides coiled together to create a strong rope-like structure. • Many proteins have 2 or more polypeptide chains that form one macromolecule. Ø Proteins are affected by their environment, and they can break down (disruption or destruction). This is denaturation, which can be temporary or permanent. 17 o Denaturation can disrupt the normal alpha-helix and beta sheets in a protein, and uncoil them it into a random shape. o Denaturation reactions aren't strong enough to break the peptide bonds, so the primary structure remains intact. o Alcohol, heat, acids, and bases can denature proteins. In most cases, once a protein is denatured, it doesn't work properly anymore (its functionality is compromised). Disinfecting alcohols work by denaturing bacteria. o H-bonds, which occur in both the secondary and tertiary structures, can be denatured by alcohol. Ø Ribosomes are very important: they have a quaternary structure, use RNA to make other proteins, and are made in the nucleolus of cells. o Our bodies need RNA and some proteins to produce proteins. 18


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