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Biochemistry (Biology, Chapter 3, for Honors Chem summer work) Carbon Compounds Section 1 The hundreds of thousands of different molecules in living things are made mostly of just four different elements: _____________________________________________________. Of these, ____________ is the one that forms the basic structure, or framework of these molecules. Carbon is able to form large and complex molecules, allowing for great diversity of life. Carbon Bonding A carbon atom has ____ electrons in its outermost (highest) energy level. Therefore, a carbon atom readily forms __________________________ with other atoms, resulting in an enormous variety of organic compounds. By having four “connection points,” molecules made of carbon can branch out and become very complex. Even molecules made of just carbon and hydrogen can form a variety of shapes: Label each shape: Carbon rings are often simplified by just drawing a pentagon or hexagon. = Further variety is achieved by the types of covalent bonds that carbon can form. In a typical covalent bond, atoms share two electrons (often referred to as one pair of electrons.) When it shares ______________, it forms a _____________________. When it shares ______________, it forms a _____________________. In any combination of single, double & triple bonds, there will always be a total of four bonds from a single carbon atom. Page 1 Functional Groups Functional groups are groups of atoms that are found together in the same arrangement so often, that they are given special names. When a functional group occurs, it gives its molecule predictable characteristics. Analogy: If you see a person wearing a suit, carrying a briefcase and talking on a cellphone while walking down a city street in the business district, you might conclude he is a business administrator in a large company. If you see a woman in a long white dress with a veil and carrying flowers, you can tell she is getting married. In the same way, certain combinations of elements in a molecule, tell us something about the molecule. The Hydroxyl Group One important functional group is the _____________________, —OH which makes a molecule __________. Polar molecules are ______________, (“water-loving“) and are soluble in water. When found on a simple carbon-based molecule, a hydroxyl group makes that molecule into an “alcohol.” There are many kinds of alcohols. One common alcohol is called ethanol, and this is the molecule found in alcoholic beverages. More functional groups are presented here. Fill in the missing information from the text. Common Functional Groups Name Structure Effect on molecule Examples (from the molecules on next page.) Hydroxyl Carboxyl Amino Phosphate (mildly acidic) (alkaline) (acid) Notes: • The structure of a functional group is drawn with one bond to the side that does not appear to be connected to anything. This is to indicate that the functional group is bonded to some larger molecule. The functional group is not a molecule and it does not exist all by itself. • A carboxyl group has an —OH as part of its make up. However, this —OH is not a hydroxyl group. An —OH is only called a hydroxyl group when it is not part of a larger functional group. • Not all molecules with an —OH are alcohols. For example, sugars such as glucose contain many —OH, but they are not alcohols. • A molecule is a three-dimensional object that can be drawn from any angle. Although we usually write a functional group in one direction, such as —OH, it might be drawn on the other end of a molecule, such as HO—. Also, the bond between the O and the H might be drawn: x—O—H. All of these are representations of the hydroxyl group. • A carboxyl group is sometimes drawn as —COOH, but really the two O branch out in different directions, as shown in the text. Page 2 Find, circle, & label the functional groups in the molecules below. Ethanol A fatty acid, a component of fats. An amino acid, for making proteins Glucose, a sugar. ATP Butyric acid, a fatty acid Page 3 Large Carbon Molecules Many large carbon compounds are made from simpler subunits joined together. monomer: polymer: Analogy: if you are building with Lego blocks, each individual Lego would be like a monomer. A stack of Legos or a wall of Legos, would be like a polymer. Monomers Polymers macromolecules: When two monomers bond together, some atoms need to be removed to provide a location for the new bond. In the molecules of living things, the atoms that are removed are an oxygen and two hydrogens, which form a molecule of ______________. condensation reaction (also called dehydration synthesis): In the diagram above, circle the H from glucose and the –OH from fructose that could be removed to form H2O (water) when the two monomers are bonded together. The opposite process happens when large molecules are broken down into monomers. This happens when we digest our food. For every monomer that breaks apart from the larger molecule, a water molecule is used from the surrounding environment (instead of created.) Hydrolysis: (We are skipping the section called Energy Currency.) Page 4 Molecules of Life Section 2 There are four main categories of organic compounds essential to living things. They are all built primarily from carbon, hydrogen and oxygen. These atoms occur in different amounts and in different arrangements in each category, giving each its own set of unique properties. You are likely familiar with these names from your knowledge of nutrition. (We are covering only carbohydrates and proteins. We are not doing Lipids and Nucleic Acids.) Carbohydrates (Sugars, starch, and plant fiber are common types of carbohydrates.) carbohydrates: organic compounds composed of ________________________. Example: glucose is C6H12O6 Draw a molecule of glucose: Notes about Names • Understanding the word origin of a name will help you remember the name and will also help you remember facts about the topic. • Look at the word “carbohydrate.” • The first part of the word comes from “carbon.” • The second part of the word is “hydrate.” This should make you think of water. You already know that words like hydration, dehydration and dehydrated have to do with how much water you have in your body. If you look at the chemical formulas of different carbohydrates, you will see that the hydrogen (H) and the oxygen (O) are always in a 2:1 ratio, just like in water: H2O • You will see below that carbohydrates are also called “saccharides.” This name comes from the Greek word for sugar: saccharum. Carbohydrates can exist as: • ______________________: a single subunit (a monomer) • ______________________: two monomers bonded together • ______________________: multiple monomers in a longer chain Page 5 Monosaccharides Monosaccharide: Chemical formula: usually C6H12O6 These are also called “simple sugars.” The three most common monosaccharides are: (see diagrams in text) • • • All have the same chemical formula ( ) but _____________________________. This is a common occurrence in Chemistry. When two substances have the same chemical formula, but the atoms are arranged differently, the two substances are called isomers of each other. isomers: chemical substances with the same chemical formula but different molecular structures. Disaccharides disaccharide: a sugar made of two monosaccharides. Examples: Sucrose : this is the typical white sugar that you likely have in your kitchen at home. Made of the monomers _______________ and ________________. (in textbook.) Lactose : this is one of the sugars found in milk. Made of the monomers ______________ and ________________. (research!) Note that when two monosaccharides bond to form a disaccharide, it is done by the process of dehydration synthisis. Page 6 Polysaccharides Polysaccharide : a carbohydrate made of 3 or more monosaccharides. (Usually made of hundreds or thousands.) Ex 1: Glycogen Structure : Purpose : Ex 2: Starch Structure: hundreds of glucose monomers. Two forms: § long coiled chain. § Branched chain (similar to glycogen.) Purpose: storage of glucose in plants, usually in the fruits, roots, or seeds. (think of foods that you might already know are “starchy” such as grains and potatoes.) Ex 3: Cellulose Structure: thousands of glucose molecules linked in long chains. The chains are then further connected to each other by hydrogen bonding between them, making a strong rigid structure. Purpose: Page 7 Proteins proteins: • organic compounds composed mainly of…_________________. (what 4 elements) • • polymers, formed from monomers called _____________________. Examples of proteins: Amino Acids There are ______ different amino acids. All have the same basic structure of four different groups arranged around a central carbon: 1. 2. 3. 4. The “R group.” This is the part that varies among the 20 amino acids. For example, the diagrams below show that glycine’s R-group is “H.” And alanine’s R-group is “-CH3” Alphabet Analogy: The 26 letters of the English alphabet can be combined in different ways to make hundreds of thousands of words. Depending on the choice and order of letters, the words can have different meanings and different functions. The similar idea with proteins is that each protein is made of a different combination of the 20 amino acids. The choice and order of the amino acids, and the behavior of their different R-groups, creates a variety of protein molecules with a wide variety of functions. Dipeptides and Polypeptides dipeptide: two amino acids joined by a covalent bond. peptide bond: + H 2O Note that when two amino acids bond together, it is by the process of dehydration synthisis. Page 8 polypeptide: a long chain of amino acids (100’s or 1000’s of them) bonded together to make a protein. A polypeptide refers simply to the long chain of amino acids, similar to the idea of beads strung together on a necklace. The molecule is not officially called a “protein” until the chain folds upon itself to make a threedimensional shape. Certain amino acids in the chain, depending on their R-groups, can make a second bond with another amino acid at a distant location on the chain, causing the molecule to be locked into a specific shape. These various shapes are what give each protein its specific function. Tool Analogy: many tools are made of the same few materials: steel, with a wood or plastic handle. Examples are a hammer, screwdriver, pliers, needle, fork, knife, and a wrench. Although they are all made of the same materials, they have different functions because of their different shapes. Functions of proteins: It is impossible to make a simple list of the functions of proteins. There are thousands of proteins and thousands of functions. As with tools, there are so many functions because of all the different shapes that can be made. A few are listed here: • Body structures (hair, horns, skin, nails) • Muscle movement • Antibodies that target germs for destruction • Hemoglobin: carries oxygen in the blood • Hormones: cause chemical reactions in target cells • Receptors in the cell membrane: receive the message from a hormone • Enzymes: their shape creates a mini-environment for another chemical reaction. Page 9