At its isoelectric point, a protein has what charge

depends on sequence of the protein

PROTEINS AND AMINO ACIDS

What are proteins and what do they do? Examples of protein functions. Structures of Proteins and Amino Acids. Functions of Proteins in Living Organisms. Structure and Function of Enzymes. Chemiosmotic Gradients for ATP Production. Role of Anaerobic Respiration.

Candidates should be able to: (a) state the main roles of carbohydrates, fats and proteins in living organisms: • carbohydrates as an immediate source of energy • fats for insulation and long-term storage of energy • proteins for growth and repair of cells (b) describe and carry out tests for: • starch (using iodine in potassium iodide solution) • reducing sugars (using Benedict’s solution) • protein (using biuret solution) • fats (using ethanol) (c) state that large molecules are synthesised from smaller basic units: • cellulose, glycogen and starch from glucose • polypeptides and proteins from amino acids • lipids such as fats from glycerol and fatty acids (d) explain the mode of action of enzymes in terms of an active site, enzyme-substrate complex and enzyme specificity using the ‘lock and key’ hypothesis (e) investigate and explain the effects of temperature and pH on the rate of enzyme catalysed reactions

LESSON 2 Early Theories on the Origin of Life • Identify the different theories on the origin of life. • Describe each theory and determine their differences What are the characteristics of living things? Before learning about the history of Earth based on geological evidence, early scientists explored the possibilities of how the first life-form existed. There are several theories about the origin of life. Theory of Catastrophism The theory of catastrophism supported by French scientists Georges Cuvier (1769-1832) and Alcide Dessalines d'Orbigny (1802-1857), is said to be a modification of the creation story of the Bible. It states that there have been several living creations from God, each encountered a catastrophe that completely destroyed them. Each new creation consisted of new life-forms, which happen to be different from the previous ones. Theory of Abiogenesis The theory of abiogenesis, or the spontaneous generation theory, states that living things were naturally created from nonliving things such as simple organic compounds. The theory supposes that abiogenesis occurred between 3.8 and 4 Gya. The experiment performed by Stanley Miller in 1953 gave way to many speculations and studies on how life on Earth really began. His research involved a simulation of the possible environment on Earth in the past. He demonstrated how an electric spark (which is a simulation for lightning) when passed through simple organic gases (similar to the early Earth atmosphere), resulted in the formation of amino acids, which are now known as the building blocks of proteins and the components of living tissues. Theory of Biogenesis The theory of biogenesis presented a strong argument against abiogenesis. This theory states that living things come from living things. Experiments of Francesco Redi and Louis Pasteur disproved the thought of spontaneous generation during their time (figure 5-1). Louis Pasteur argued that life comes from preexisting life and not from nonliving material. However, it should be noted that the "abiogenesis" or "spontaneous generation" that he opposed referred to any modern, existing, fully-formed organisms, not the original generation of life. Louis Pasteur's law of biogenesis contradicted the common belief during his time that cattle dung gives rise to flies, or old clothes with rotten food gives rise to mice. The idea of spontaneous generation was popular until near the seventeenth century. Even famous scientists of that period, such as Descartes, Galileo, and Jan Baptista van Helmont, believed in this theory. CIENCE PIONEER Francesco Redi (1626-1697). Francesco Redi is a physician, a naturalist, and a poet. His works challenged the popular theory of spontaneous generation. He disproved the idea that living things may arise from nonliving things. He also worked on toxicology using viper's venom. He discovered and worked on some parasites that caused disease in humans. SCIENCE CAREER Evolutionary Biologist An evolutionary biologist studies the descent of species and the origin of new species of living things. Working as evolutionary biologist means studying and researching species diversity, their interaction with the environment, their adaptation to change, their ancestors, and their possible origins. This career is important in the field of science because it seeks an answer to the questions about how life began on Earth.

Nutrition, Metabolism, and Body Temperature Regulation. Nutrient is a substance that promotes normal growth, maintenance, and repair. Major nutrients are carbohydrates, lipids, and proteins. Other nutrients include vitamins and minerals (and technically speaking, water).Complex carbohydrates (starches) are found in bread, cereal, flour, pasta, nuts, and potatoes .Simple carbohydrates (sugars) are found in soft drinks, candy, fruit, and ice cream.Glucose is the molecule ultimately used by body cells to make ATP.Neurons and RBCs rely almost entirely upon glucose to supply their energy needs.Excess glucose is converted to glycogen or fat and stored .The most abundant dietary lipids, triglycerides, are found in both animal and plant foods.Essential fatty acids – linoleic and linolenic acid, found in most vegetables, must be ingested. Dietary fats help the body to absorb vitamins, a major energy fuel of hepatocytes and skeletal muscle, and a component of myelin sheaths and all cell membranes. Lipids functions in smooth muscle contraction, control of blood pressure and inflammation. Cholesterol stabilizes membranes and is a precursor of bile salts and steroid hormones. The dietary requirements for lipids are higher for infants and children than for adults. The American Heart Association suggests that fats should represent less than 30% of one’s total caloric intake, saturated fats should be limited to 10% or less of one’s total fat intake, and daily cholesterol intake should not exceed 200 mg. Complete proteins that meet all the body’s amino acid needs are found in eggs, milk, milk products, meat, and fish.Incomplete proteins are found in legumes, nuts, seeds, grains, and vegetables. Essential amino acids are the building blocks for nonessential amino acids. Protein supply for nonprotein nitrogen-containing substances. Daily intake should be approximately 0.8g/kg of body weight. All amino acids needed must be present at the same time for protein synthesis to occur. Protein will be used as fuel if there is insufficient carbohydrate or fat available. The rate of protein synthesis equals the rate of breakdown and loss. Anabolic hormones accelerate protein synthesis. Vitamins are organic compounds needed for growth and good health. They are crucial in helping the body use nutrients and often function as coenzymes. Only vitamins D, K, and B are synthesized in the body; all others must be ingested. Water-soluble vitamins (B-complex and C) are absorbed in the gastrointestinal tract . Vitamin B12 additionally requires gastric intrinsic factor to be absorbed. Fat-soluble vitamins (A, D, E, and K) bind to ingested lipids and are absorbed with their digestion products. Vitamins A, C, and E also act in an antioxidant cascade. There are seven minerals are required in moderate amounts . These are calcium, phosphorus, potassium, sulfur, sodium, chloride, and magnesium. Dozens are required in trace amounts. Minerals work with nutrients to ensure proper body functioning. Calcium, phosphorus, and magnesium salts harden bone.

CARBOHYDRATES Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen in a ratio of about one carbon atom to two hydrogen atoms to one oxygen atom. The number of carbon atoms in a carbohydrate varies. Some carbohydrates serve as a source of energy. Other carbohydrates are used as structural materials. Carbohydrates can exist as monosaccharides, disaccharides, or polysaccharides. Monosaccharides A monomer of a carbohydrate is called a monosaccharide (MAHN-oh-SAK-uh-RIED). A monosaccharide—or simple sugar— contains carbon, hydrogen, and oxygen in a ratio of 1:2:1. The gen- eral formula for a monosaccharide is written as (CH2O)n, where n is any whole number from 3 to 8. For example, a six-carbon mono- saccharide, (CH2O)6, would have the formula C6H12O6. The most common monosaccharides are glucose, fructose, and galactose, as shown in Figure 3-6. 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. Notice in Figure 3-6 that glucose, fructose, and galactose have the same molecular formula, C6H12O6, but differing structures. The different structures determine the slightly different properties of the three compounds. Compounds like these sugars, with a single chemical formula but different structural forms, are called isomers (IE-soh-muhrz). SECTION 2 OBJECTIVES ● Distinguish between monosaccharides, disaccharides, and polysaccharides. ● Explain the relationship between amino acids and protein structure. ● Describe the induced fit model of enzyme action. ● Compare the structure and function of each of the different types of lipids. ● Compare the nucleic acids DNA and RNA. VOCABULARY carbohydrate monosaccharide disaccharide polysaccharide protein amino acid peptide bond polypeptide enzyme substrate active site lipid fatty acid phospholipid wax steroid nucleic acid deoxyribonucleic acid (DNA) ribonucleic acid (RNA) nucleotide C HO H C H OH C OH H C CH2OH H C H OH O Glucose C OH C O H OH C OH H CH2OH C H CH2OH Fructose C H HO C OH H C OH H C CH2OH H C H OH O Galactose Glucose, fructose, and galactose have the same chemical formula, but their structural differences result in different properties among the three compounds. FIGURE 3-6 Copyright © by Holt, Rinehart and Winston. All rights reserved. 56 CHAPTER 3 Disaccharides and Polysaccharides In living things, two monosaccharides can combine in a condensa- tion reaction to form a double sugar, or disaccharide (die-SAK-e-RIED). For example in Figure 3-4, the monosaccharides fructose and glu- cose can combine to form the disaccharide sucrose. 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. Plants store glucose molecules in the form of the polysaccha- ride starch. Starch molecules have two basic forms—highly branched chains that are similar to glycogen and long, coiled, unbranched chains. Plants also make a large polysaccharide called cellulose. Cellulose, which gives strength and rigidity to plant cells, makes up about 50 percent of wood. In a single cellu- lose 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 be broken down by hydrolysis only under certain conditions. PROTEINS Proteins are organic compounds composed mainly of carbon, hydrogen, oxygen, and nitrogen. Like most of the other biological macromolecules, proteins are formed from the linkage of monomers called amino acids. Hair and horns, as shown in Figure 3-7a, are made mostly of proteins, as are skin, muscles and many biological catalysts (enzymes). Amino Acids There are 20 different amino acids, and all share a basic structure. As Figure 3-7b 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 in the illustration, bonds at one site. A carboxyl group, —COOH, highlighted in green, bonds at a second site. An amino group, —NH2, highlighted in yel- low, bonds at a third site. A side chain called the R group, high- lighted in red, bonds at the fourth site. The main difference among the different amino acids is in their R groups. The R group can be complex or it can be simple, such as the CH3 group shown in the amino acid alanine in Figure 3-7b. The differences among the amino acid R groups gives different proteins very different shapes. The different shapes allow pro- teins to carry out many different activities in living things. Amino acids are commonly shown in a simplified way such as balls, as shown in Figure 3-7c. (a) Many structures, such as hair and horns are made of proteins. (b) Proteins are made up of amino acids. Amino acids differ only in the type of R group (shown in red) they carry. Polar R groups can dissolve in water, but nonpolar R groups cannot. (c) Amino acids have complex structures, so, in this and other textbooks, they are often simplified into balls. FIGURE 3-7 (b) Alanine (an amino acid) (c) Simplified version of amino acid CH3 H N OH C C H O H (a) Copyright © by Holt, Rinehart and Winston. All rights reserved. BIOCHEMISTRY 57 H H N C C OH H O H CH3 H2O Glycine Alanine H N OH C C H O H H H N C C H O H CH3 N OH C C H O H (a) (b) (a) The peptide bond (shaded blue) that binds amino acids together to form a polypeptide results from a condensation reaction that produces water. (b) Poly- peptides are commonly shown as a string of balls in this textbook and elsewhere. Each ball represents an amino acid. FIGURE 3-8 Substrate Products Enzyme 1 2 3 In the induced fit model of enzyme action, the enzyme can attach only to a substrate (reactant) with a specific shape. The enzyme then changes and reduces the activation energy of the reaction so reactants can become products. The enzyme is unchanged and is available to be used again. 3 2 1 FIGURE 3-9 Dipeptides and Polypeptides Figure 3-8a shows how two amino acids bond to form a dipeptide (die-PEP-TIED). In this condensation reaction, the two amino acids form a covalent bond, called a peptide bond (shaded in blue in Figure 3-8a) and release a water molecule. Amino acids often form very long chains called polypeptides (PAHL-i-PEP-TIEDZ). Proteins are composed of one or more polypep- tides. Some proteins are very large molecules, containing hun- dreds of amino acids. Often, these long proteins are bent and folded upon themselves as a result of interactions—such as hydrogen bonding—between individual amino acids. Protein shape can also be influenced by conditions such as temperature and the type of solvent in which a protein is dissolved. For exam- ple, cooking an egg changes the shape of proteins in the egg white. The firm, opaque result is very different from the initial clear, runny material. Enzymes Enzymes—RNA or protein molecules that act as biological catalysts—are essential for the functioning of any cell. Many enzymes are proteins. Figure 3-9 shows an induced fit model of enzyme action. Enzyme reactions depend on a physical fit between the enzyme molecule and its specific substrate, the reactant being catalyzed. Notice that the enzyme has folds, or an active site, with a shape that allows the substrate to fit into the active site. An enzyme acts only on a specific substrate because only that substrate fits into its active site. The linkage of the enzyme and substrate causes a slight change in the enzyme’s shape. The change in the enzyme’s shape weakens some chemical bonds in the substrate, which is one way that enzymes reduce activation energy, the energy needed to start the reaction. After the reaction, the enzyme releases the products. Like any catalyst, the enzyme itself is unchanged, so it can be used many times. An enzyme may not work if its environment is changed. For example, change in temperature or pH can cause a change in the shape of the enzyme or the substrate. If such a change happens, the reaction that the enzyme would have catalyzed cannot occur.

RNA translation. The genetic information in DNA is used to synthesize proteins through the processes of RNA Transcription and RNA Translation. The sequence of three-letter code words in the gene determines the sequence of amino acids in a polypeptide chain. RNA Transcription DNA serves as a template for the synthesis of RNA. There are 3 major types of RNA that participate in the process of proteins synthesis. 1.5% of the genome encodes for proteins via mRNA, but an unknown % of the genome codes for noncoding RNA (ncRNA)

Lipids are large, nonpolar organic molecules. They do not dissolve in water. Lipids include triglycerides (trie-GLIS-uhr-IEDZ), phospho- lipids, steroids, waxes, and pigments. Lipid molecules have a higher ratio of carbon and hydrogen atoms to oxygen atoms than carbohydrates have. Because lipid molecules have larger numbers of carbon-hydrogen bonds per gram than other organic com- pounds do, they store more energy per gram. Fatty Acids Fatty acids are unbranched carbon chains that make up most lipids. Figure 3-10 shows that a fatty acid contains a long 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 different properties. The carboxyl end is polar and is thus hydrophilic or attracted to water molecules. In contrast, the hydro- carbon end of the fatty-acid molecule is nonpolar. This end tends not to interact with water molecules and is said to be hydrophobic (HIE-droh-FOH-bik), or “water fearing.” In saturated fatty acids, such as palmitic acid, which is shown in Figure 3-10, each carbon atom is covalently bonded to four atoms. The carbon atoms are in effect full, or saturated. In contrast, linoleic acid, also shown in Figure 3-10, has carbon atoms that are not bonded to the maximum number of atoms to which they can bond. Instead, they have formed double bonds within the carbon chain. This type of fatty acid is said to be unsaturated. Triglycerides Three classes of lipids important to living things contain fatty acids: triglycerides (fats), phospholipids, and waxes. A triglyceride is composed of three molecules of fatty acid joined to one molecule of the alcohol glycerol. Saturated triglycerides are composed of saturated fatty acids. They typically have high melting points and tend to be hard at room temperature. Common dietary saturated triglycerides include butter and fats in red meat. In contrast, unsaturated triglycerides are composed of unsaturated fatty acids and are usually soft or liquid at room temperature. Unsaturated triglycerides are found primarily in plant seeds where they serve as an energy and carbon source for germinating plants. Phospholipids Phospholipids have two, rather than three, fatty acids attached to a molecule of glycerol. They have a phosphate group attached to the third carbon of the glycerol. As shown in Figure 3-11, the cell membrane is made of two layers of phospholipids, called the lipid bilayer. The inability of lipids to dissolve in water allows the mem- brane to form a barrier between the inside and outside of the cell. Hydrophilic “head” Phospholipids Hydrophobic “tail” Phospholipids Water Water The lipid bilayer of a cell membrane is a double row of phospholipids.The “tails” face each other.The “head” of a phospholipid, which contains a phosphate group, is polar and hydrophilic.The two tails are two fatty acids and are nonpolar and hydrophobic. FIGURE 3-11 H C H C O OH H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H C H H H H C H H C H H C H H C H H C H C O OH H C H H C H H C H C H C H C H H C H H C H C H H C H H C H C H H H H C H Fatty acids have a polar carboxyl head, highlighted in purple, and a nonpolar hydrocarbon tail, highlighted in green. FIGURE 3-10 Palmitic acid Linoleic acid mb06se_bchs02.qxd 5/18/07 10:49 AM Page 59 60 CHAPTER 3 1. Compare the structure of monosaccharides, dis- accharides, and polysaccharides. 2. How are proteins constructed from amino acids? 3. How do amino acids differ from one another? 4. Describe a model of enzyme action. 5. Why do phospholipids orient in a bilayer when in a watery environment, such as a cell? 6. Describe how the three major types of lipids differ in structure from one another. 7. What are the functions of the two types of nucleic acids? CRITICAL THINKING 8. Applying Information Before a long race, run- ners often “carbo load.” This means that they eat substantial quantities of carbohydrates. How might this help their performance? 9. Recognizing Relationships High temperatures can weaken bonds within a protein molecule. How might this explain the effects of using a hot curling iron or rollers in one’s hair? 10. Applying Information You want to eat more unsaturated than saturated fats. Name examples of foods you would eat more of and less of. SECTION 2 REVIEW Waxes A wax is a type of structural lipid consisting of a long fatty-acid chain joined to a long alcohol chain. Waxes are waterproof, and in plants, form a protective coating on the outer surfaces. Waxes also form protective layers in animals. For example, earwax helps pre- vent microorganisms from entering the ear canal. Steroids Unlike most other lipids, which are composed of fatty acids, steroid molecules are composed of four fused carbon rings with various functional groups attached to them. Many animal hor- mones, such as the male hormone testosterone, are steroid com- pounds. One of the most familiar steroids in humans is cholesterol. Cholesterol is needed by the body for nerve and other cells to func- tion normally. It is also a component of the cell membrane. NUCLEIC ACIDS Nucleic acids are very large and complex organic molecules that store and transfer important information in the cell. There are two major types of nucleic acids: deoxyribonucleic acid and ribonucleic acid. Deoxyribonucleic acid, or DNA, contains information that deter- mines the characteristics of an organism and directs its cell activi- ties. Ribonucleic (RIE-boh-noo-KLEE-ik) acid, or RNA, stores and transfers information from DNA that is essential for the manufactur- ing of proteins. Some RNA molecules can also act as enzymes. Both DNA and RNA are polymers, composed of thousands of linked monomers called nucleotides (NOO-klee-uh-TIEDS). As shown in Figure 3- 12, each nucleotide is made of three main components: a phosphate group, a five-carbon sugar, and a ring-shaped nitrogenous base.

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