Biochemistry PDF

## SECTION 2-1 CHEMICAL REACTIONS AND ENERGY ### OBJECTIVES - Describe how energy changes are involved in chemical reactions. - Explain how enzymes affect chemical reactions in organisms. - Explain what a redox reaction is. - Describe the use of the pH scale. One important characteristic of all liv...

## SECTION 2-1 CHEMICAL REACTIONS AND ENERGY ### OBJECTIVES - Describe how energy changes are involved in chemical reactions. - Explain how enzymes affect chemical reactions in organisms. - Explain what a redox reaction is. - Describe the use of the pH scale. One important characteristic of all living things is that they use energy. The amount of energy in the universe remains the same over time, but energy can change in form constantly. It is the flow of energy from the sun to, and through, almost every organism on Earth that biologists seek to understand when they study the chemistry of living things. ### CHEMICAL REACTIONS Chemical reactions within living things are linked to favorable conditions. They can be linked, for example, to temperature, or to pH. Chemical reactions within living things are linked to favorable conditions. They can be linked, for example to temperature, or to pH. - **Reactants** are shown on the left side of the equation. - **Products** of the reaction are shown on the right side. In this reaction, the reactants are CO2 and H2O. The products of the reaction are H2CO3. Notice that the number of each kind of atom must be the same on either side of the arrow. In a chemical reaction, bonds present in the reactants are broken, the elements are rearranged, and new compounds are formed as the products. The two-direction arrow indicates that this chemical reaction can proceed either way. Carbon dioxide and water can combine to form carbonic acid, H2CO3, or carbonic acid can break down to carbon dioxide and water. The reaction illustrated in this figure is **reversible**. Because the products of the reaction remain in the blood, the reaction can proceed either from left to right or from right to left. Many reactions are very complex and are interrelated, involving a multistep sequence. Other reactions are rather simple. The one described in Figure 2-1 takes place in your blood. Living things undergo many thousands of chemical reactions as part of their life processes. ## SECTION 2-3 CARBON COMPOUNDS ### OBJECTIVES - Define organic compound and name three elements often found in organic compounds. - Explain why carbon forms so many different compounds. - Define functional group and explain its significance. - Compare a condensation reaction with hydrolysis. All of the many compounds discovered can be classified in two broad categories: **organic compounds** and **inorganic compounds**. Organic compounds contain carbon atoms that are covalently bonded to other carbon atoms and to other elements as well, typically hydrogen, oxygen, and nitrogen. The chemistry of carbon is the chemistry of life. ### CARBON BONDING A carbon atom has four electrons in its outermost energy level. Most atoms become stable when their outermost energy level contains eight electrons. A carbon atom, therefore, readily forms four covalent bonds with other elements. Unlike other elements, however, carbon also readily bonds with other carbon atoms, forming straight chains, branched chains, or rings, as shown in Figure 2-8. This tendency of carbon to bond with itself results in an enormous variety of organic compounds. In the symbolic shorthand of chemistry, each line shown in Figure 2-8 represents a covalent bond formed when two atoms share a pair of electrons. A bond formed when two atoms share a pair of electrons is called a single bond. Carbon can also share two or even three pairs of electrons with another atom. Figure 2-9a shows a model for an organic compound in which six carbon atoms have formed a ring. Notice that each carbon atom forms four covalent bonds: a single bond with another carbon atom, a single bond with a hydrogen atom, and a double bond with a second carbon atom. In a double bond, represented by two parallel lines, atoms share two pairs of electrons. A triple bond, the sharing of three pairs of electrons, is shown in Figure 2-9b. ## SECTION 2-2 WATER ### OBJECTIVES - Describe the structure of a water molecule. - Explain how water's polar nature affects its ability to dissolve substances. - List two of water's properties that result from hydrogen bonding. Water must gain or lose a relatively large amount of energy for its temperature to change. All organisms must maintain homeostasis. Water's ability to absorb large amounts of energy helps keep cells at an even temperature, despite temperature changes in the environment. ### POLARITY Water is an example of a **polar molecule**. In such molecules, the electrical charge is unevenly distributed. The water molecule has a positive side and a negative one, as shown in the models of water molecules in Figure 2-5(a). Notice too in Figure 2-5(b) that the three atoms in a water molecule are not arranged in a straight line as you might expect. Rather, the two hydrogen atoms bond with the single oxygen atom at an angle. Although the total electrical charge on a water molecule is neutral, its polar nature makes it very effective in dissolving many other substances. Water dissolves other polar substances, including sugars and some proteins, as well as ionic compounds, such as sodium chloride, NaCl. ### HYDROGEN BONDING The polar nature of water also causes water molecules to be attracted to one another. The type of attraction that holds two water molecules together in called a **hydrogen bond**, as shown in Figure 2-6. The hydrogen bonds in water exert a significant attractive force, causing water to cling to itself. An attractive force between particles of the same kind is known as **cohesion**. Due to their polarity, water molecules can also be attracted to foreign molecules. **Adhesion** is the attractive force between unlike substances. Together, adhesion and cohesion enable water molecules to move upward through narrow tubes against the force of gravity. This property of water is known as **capillarity**. You have seen capillarity at work if you have observed the flow of water into a flower through its stem, such as is shown in Figure 2-7. ## SECTION 2-4 MOLECULES OF LIFE ### OBJECTIVES - Define monosaccharide, disaccharide, and polysaccharide, and discuss their significance to organisms. - Explain how the sequence of amino acids determines the structure of proteins. - Describe the structure of lipids and their functions. - Describe the essential functions of nucleic acids. Four main classes of organic compounds are essential to the life processes of all living things: **Carbohydrates, Lipids, Proteins, and Nucleic Acids.** You will see that although these compounds are built from carbon, hydrogen, and oxygen, the atoms occur in different ratios in each class of compound. Despite their similarities, the different classes of compounds have different properties. ### CARBOHYDRATES Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen in a ratio of about two hydrogen atoms to one oxygen atom. The number of carbon atoms in a carbohydrate varies. Carbohydrates exist as **monosaccharides, disaccharides, or polysaccharides**. **Monosaccharides** A monomer of a carbohydrate is called a **monosaccharide**. A monosaccharide or simple sugar contains carbon, hydrogen, and oxygen in a ratio of 1:2:1. The general formula for a monosaccharide is written as (CH2O)n, where n is any whole number from 3 to 8. For example, a six-carbon monosaccharide (CH2O)6 would have the formula C6H12O6. The most common monosaccharides are glucose, fructose, and galactose, as shown in Figure 2-13. - **Glucose** is a main source of energy for cells. - **Fructose** is found in fruits and is the sweetest of the monosaccharides. - **Galactose **is found in milk and is usually combined with glucose or fructose. Notice in Figure 2-13 that glucose, fructose, and galactose have the same molecular formula, C6H12O6, but their differing structures determine the slightly different properties of the three compounds. Compounds like these sugars, with a single chemical formula but different forms, are called **isomers**. **Disaccharides and Polysaccharides** In living things, two monosaccharides can combine in a condensation reaction to form a double sugar, or **disaccharide**. As you saw in Figure 2-11, sucrose, which is common table sugar, is composed of fructose and glucose. A **polysaccharide** is a complex molecule composed of three or more monosaccharides. - **Animals** store glucose in the form of the polysaccharide **glycogen**. Glycogen consists of hundreds of glucose molecules strung together in a highly branched chain. Much of the glucose that comes from food is ultimately stored in your liver and muscles as glycogen and is ready to be used for quick energy. - **In plants**, glucose molecules are linked in the polysaccharide **starch**. Starch molecules have two basic forms: highly branched chains that are similar to glycogen and long, unbranched chains that coil, like a telephone cord. The large polysaccharide **cellulose** is also made by plants. Cellulose, which gives strength and rigidity to plant cells, makes up about 50% of wood. In a single cellulose molecule, thousands of glucose monomers are linked in long, straight chains. These chains tend to form hydrogen bonds with each other. The resulting structure is strong and can only be broken down by hydrolysis under certain conditions. ### **PROTEINS:** Proteins are organic compounds composed mainly of carbon, hydrogen, oxygen, and nitrogen, with some containing sulfur and phosphate. Like the other macromolecule, proteins are formed from the linkage of monomers. The skin and muscles of animals are made mostly of proteins, as are many of the catalysts found in both plants and animals. **Amino Acids** The 20 different amino acids, the monomer building blocks of proteins, share a basic structure. As Figure 2-14a shows, each amino acid contains a central carbon atom covalently bonded to four other atoms or functional groups. A single hydrogen atom, highlighted in blue on the illustration, bonds at one site. A carboxyl group, -COOH, highlighted in green, bonds at a second site, an amino group, -NH2, highlighted in yellow, bonds at a third site, and a functional group called the R group, highlighted in red, bonds at the fourth site. The main difference among the different amino acids is found in their R groups. The R group can be as simple as the single hydrogen atom of glycine, shown in Figure 2-14b, or it can be more complex, such as the R group shown in the model of alanine, shown in Figure 2-14c. The differences among the amino acid R groups give different proteins very different shapes. The different shapes allow proteins to perform many different roles in the chemistry of living things **Dipeptides and Polypeptides** Figure 2-15 shows how two amino acids bond to form a dipeptide. In a condensation reaction, two amino acids form a dipeptide and a water molecule. Amino acids can bond to each other one at a time, forming a very long chain called a **polypeptide**. **Proteins** Proteins are very large molecules, containing hundreds of amino acids strung together. Often these long protein molecules are bent and folded upon themselves as a result of interactions, such as hydrogen bonding, among individual amino acids. Protein shape can also be influenced by conditions, such as temperature, or the type of solvent in which a protein is dissolved. When you cook an egg, heat changes the shape of proteins in the egg white. The firm, opaque result is very different from the clear, runny material you began with. **Enzymes** Enzymes, organic molecules that act as catalysts, are essential for the functioning of any cell. Most enzymes are proteins. Figure 2-16 shows a model of enzyme action. Enzyme reactions depend on a physical fit between the enzyme molecule and its substrate, the reactant being catalyzed. Notice in Figure 2-16a that the enzyme and substrate have shapes that allow them to fit together like a lock and key. The linkage of the enzyme and substrate causes a slight change in the enzyme's shape, shown in Figure 2-16b, which is called **induced fit**. This shape change probably weakens some chemical bonds in the substrate, which is one way that enzymes reduce activation energy. After the reaction, the enzyme releases the products, as shown in Figure 2-16c. Like any catalyst, the enzyme itself is unchanged, so it can be used many times. An enzyme may fail to work if its environment is changed in some way. For example, a change in temperature or pH can cause a change in the shape of the enzyme or the substrate. If this happens, the reaction that the enzyme would have catalyzed cannot occur. ### **LIPIDS** Lipids are large, nonpolar organic molecules that do not dissolve in water. Lipid molecules have a higher ratio of carbon and hydrogen atoms to oxygen atoms than carbohydrates have. Lipids store energy efficiently. Lipid molecules have large numbers of carbon-hydrogen bonds, which store more energy than the carbon-oxygen bonds common in other organic compounds. **Fatty Acids** Fatty acids are unbranched carbon chains that makeup most lipids. The model in Figure 2-17 shows that a fatty acid contains a long straight carbon chain (from 12 to 28 carbons) with a carboxyl group, -COOH, attached at one end. The two ends of the fatty acid molecule have very different properties. The carboxyl end of the fatty acid molecule is polar and is thus attracted to water molecules. Because of this attraction, the carboxyl end of the fatty acid molecule is said to be **hydrophilic** or "water loving.” In contrast, the hydrocarbon end of the fatty acid molecule is nonpolar. This end tends not to interact with water molecules and is said to be **hydrophobic** or “water fearing.” In **saturated fatty acids**, like palmitic acid, which is pictured in Figure 2-17, each carbon atom is covalently bonded to four atoms. The carbon atoms are, in effect, full, or “saturated.” In contrast, you can see from the structural formula of a molecule of linoleic acid, shown in Figure 2-17, that the carbon atoms are not bonded to the maximum number of atoms that they can bond to. Instead, they have formed double bonds within the carbon chain. This type of fatty acid is said to be **unsaturated**. ### **NUCLEIC ACIDS** Nucleic acids are very large polymers that store and transmit genetic information. They are made up of smaller repeating subunits called nucleotides. Each nucleotide consists of three parts: * **A five-carbon sugar** * **A phosphate group** * **A nitrogen-containing base** There are two main types of nucleic acids: deoxyribonucleic acid, or DNA, and ribonucleic acid, or RNA. **DNA** DNA is the genetic material of all living things. It is a large, double-stranded helix, as shown in Figure 2-18. The two strands of DNA are held together by hydrogen bonds between pairs of nitrogenous bases. The nitrogenous bases in DNA are adenine, guanine, cytosine, and thymine. The nitrogenous bases pair up specifically: A always pairs with T, and G always pairs with C. This pairing is known as **complementary base pairing**. The sequence of the nitrogenous bases within the DNA molecule contains the genetic information that makes each organism unique. The sugar in DNA is deoxyribose, which is a five-carbon sugar. **RNA** The primary function of RNA is to direct protein synthesis, as shown in Figure 2-19. RNA is a single-stranded molecule that is shorter than DNA. The sugar in RNA is ribose, which is a five-carbon sugar with a hydroxyl group at the 2' position. RNA uses the same nitrogenous bases as DNA except that uracil replaces thymine. The sequence of bases in RNA is complementary to the sequence of bases in DNA. The genetic information coded in DNA and RNA is expressed through complex processes involving a variety of enzymes. The sequence of bases in DNA determines the sequence of amino acids in proteins, which in turn determines the proteins' shape and function. ## **SECTION 2-3 REVIEW** 1. What is an organic compound. 2. What property allows carbon compounds to exist in a number of forms? 3. What is an organic compound? 3. Define functional group and give an example. 4. How does a polymer form? 5. How does a polymer break down? 6. CRITICAL THINKING Scientists can determine the age of a substance using a method that compares the amounts of different forms of carbon atoms present in the substance. Is this method more useful for organic substances or inorganic substances?