chapter 21
Biochemistry
Introduction
Biochemistry, the chemistry of living systems, is a subject that concerns everyone. How do our bodies extract chemical energy from sugar and other substances? How can we find cures for diseases? The answers to these questions lie in the biochemistry of the human body. To begin to understand how the complex biochemical systems work, we need to know about the kinds of molecules that are important in living organisms. They are often large organic molecules, and they contain atoms and functional groups with characteristics with which we are already familiar.
Chapter Discussion
Proteins are made when amino acids react with each other to form peptide linkages. The carboxyl group of one amino acid reacts with the amino group of another amino acid. A water molecule is removed during the process.
The bond formed between two amino acids is called a peptide linkage. There is an almost endless number of proteins that could be formed from combinations of twenty different amino acids. Each different sequence of amino acids produces a different protein, so the order in which the amino acids occur is important. The order in which amino acids occur is called the primary structure of a protein.
The secondary structure of a protein is the shape the protein chain assumes. Two common secondary structures are the alpha-helix and the pleated sheet.
The tertiary structure of a protein is the three-dimensional shape of the protein molecule. Some proteins are globular in shape, some are elongated. A protein can have several areas of alpha-helix that are separated from each other by bends. The protein folds at each bend, giving the molecule its tertiary structure.
Carbohydrates are a large class of biomolecules composed mainly of carbon, hydrogen, and oxygen. They are a major source of food and serve as structural components in plants. Some carbohydrates are simple sugars, or monosaccharides (such as glucose), some are disaccharides (such as sucrose or table sugar), and some are polysaccharides (such as starch and cellulose).
Nucleic acids store the information necessary for life to continue from generation to generation. The nucleic acid that stores genetic information and transmits information from one generation to the next is deoxyribonucleic acid, or DNA. Another nucleic acid that helps translate the genetic
information into proteins is ribonucleic acid, or RNA. Both DNA and RNA are composed of smaller building blocks called nucleotides. A nucleotide is made from three parts, a five-carbon monosaccharide, a nitrogen-containing organic base, and a phosphate group.
Learning Review
1.What functions do carbon, phosphorus and magnesium perform in the human body?
2.What are two major types of proteins, and how do their functions differ?
3.Which of the amino acids below have hydrophilic and which have hydrophobic side chains?
a.
b.
c.
4.What is the structure of the dipeptide made from the two amino acids below?
5.Show the sequences of all tripeptides that can be made from the amino acids phenylalanine (phe), glycine (gly), proline (pro), and aspartic acid (asp).
6.Explain the difference between the primary, secondary and tertiary structures of proteins.
7.Two types of secondary structures are the α-helix and the pleated sheet. What are the major characteristics of each?
8.Which amino acid plays a special role in maintaining the tertiary structure of proteins?
9.Use a lock and key analogy to explain how an enzyme can catalyze a reaction.
10.What two functional groups are characteristic of monosaccharides?
11.Draw the structure of a tetrose that has an aldehyde functional group.
12.The disaccharide sucrose, or table sugar, is made from which two monosaccharides?
13.What difference between starch and cellulose causes starch to be a food source for humans while cellulose is not?
14.
a.What are the parts of a nucleotide?
b.How do the nucleotides of RNA differ from nucleotides of DNA?
15.Show the structure of a nucleotide.
16.Show why the bases cytosine and guanine and the bases adenine and thymine pair with each other in DNA.
17.How is it thought that DNA reproduces itself?
18.How are proteins synthesized from the DNA code?
19.
a.Draw the structure of the fat made from a molecule of glycerol and three molecules of oleic acid.
b.Would this fat likely be a solid or a liquid at room temperature?
20.Explain how soap cleans away greasy dirt.
21.To form wax molecules, molecules with which two functional groups must combine?
22.The steroids are a diverse group of molecules. What structural feature do they all have in common?
Answers to Learning Review
1.Carbon is the backbone of all organic molecules in the body. Phosphorus is present in cell membranes and plays an important role in energy transfer in cells. Magnesium is required for proper functioning of some enzymes.
2.The two major types are fibrous and globular. Fibrous proteins provide structure and shape while globular proteins perform chemical work.
3.
a.The side chain on tyrosine is a benzene ring that has an –OH substituted for one of the hydrogen atoms. The –OH bond is polar, just as the –OH bond in water is. The polarity of the –OH bond makes the side chain of tyrosine hydrophilic.
b.Aspartic acid has a side chain that has a –CH2 and a –COOH. The –OH bond is polar, and so is the –CO bond. The polarity of the –COOH makes the side chain of aspartic acid hydrophilic.
c.Leucine has a side chain composed entirely of carbon and hydrogen. Carbon-hydrogen bonds are not polar, so the side chain of leucine is hydrophobic.
4.
5.To help you determine all the sequences, begin with one of the amino acids, and write all the possible sequences beginning with this one amino acid. Then choose another amino acid, and write all the sequences that begin with the second amino acid. Continue until you have written sequences that begin with each of the amino acids given.
phe-gly-pro / gly-phe-pro / pro-gly-phe / asp-phe-prophe-gly-asp / gly-phe-asp / pro-gly-asp / asp-phe-gly
phe-pro-gly / gly-pro-phe / pro-phe-asp / asp-pro-phe
phe-pro-asp / gly-pro-asp / pro-phe-gly / asp-pro-gly
phe-asp-pro / gly-asp-pro / pro-asp-phe / asp-gly-phe
phe-asp-gly / gly-asp-phe / pro-asp-gly / asp-gly-pro
6.The primary structure of proteins is the amino acid sequence. The secondary structure of proteins is the arrangement of the protein chain or the arrangement of the amino acids to form an α-helix or a pleated sheet. How the α-helices or pleated sheets are bent in relation to one another is the tertiary structure of a protein.
7.In the α-helix the amino acids are coiled like a spiral staircase. This makes a long region of protein. Areas of protein with lots of α-helix are springy and elastic. In a pleated sheet, protein chains are bent back one or more times to form a sheet of protein chains. Pleated sheets are strong and resistant to stretching.
8.The amino acid cysteine helps proteins maintain their unique tertiary structures. The –SH side chains of two cysteine molecules can react to form a disulfide linkage that holds the protein chain in a fixed tertiary structure.
9.For some enzymes it is believed that the enzyme has a shape that fits the shape of the substrate, just like a key fits a lock. When the enzyme and the substrate join together, a reaction occurs. The enzyme then releases the product that has formed.
10.Monosaccharides all have hydroxyl and carbonyl functional groups. The carbonyl can be either an aldehyde or a ketone.
11.There are several tetroses with an aldehyde group. The structure of one is presented below.
12.Sucrose is made from the monosaccharides glucose and fructose.
13.Both starch and cellulose are made from glucose molecules. The way the glucose molecules are joined together in starch is different from the way they are joined in cellulose. Enzymes in our bodies can break the links between glucose molecules in starch, but not in cellulose.
14.
a.All nucleotides are made from a phosphate group, a nitrogen-containing organic base, and a five-carbon sugar.
b.In RNA, the sugar is ribose while in DNA the sugar is deoxyribose. Some of the organic bases also differ between DNA and RNA. DNA and RNA have cytosine, adenine and guanine. Thymine is found only in DNA, and uracil is found only in RNA.
15.
16.Cytosine and guanine pair with each other in DNA because the hydrogen-bonding sites on the molecule are complementary. The three hydrogen bonds between the two molecules hold cytosine and guanine together. Adenine and thymine molecules on complementary DNA strands are also held together by hydrogen bonds. Two hydrogen bonds form between adenine and thymine molecules.
17.There is evidence to show that two complementary DNA chains unwind and that new strands are made by pairing bases along the old chains. The end result is two new chains, each complementary to the old one.
18.DNA stores the information required to produce proteins needed by organisms. A length of the DNA chain called a gene contains the information for one protein. The DNA transmits the information it contains by synthesizing a chain of RNA called messenger RNA (mRNA). Once the mRNA has been produced, it moves away from DNA to the site of protein synthesis. The mRNA and small bodies called ribosomes begin the synthesis of protein. Another kind of RNA, called transfer RNA (tRNA), brings up amino acids one by one to join them on the end of the growing protein chain. The mRNA contains the information that determines which amino acids join, and in what order.
19.
a.
b.Fats made of unsaturated fatty acids are often liquids at room temperature. This fat would likely be a liquid at room temperature because oleic acid is an unsaturated fatty acid.
20.Soap molecules are the anions of long chain fatty acids. Each soap molecule has two parts. The carboxylate head has a negative charge and is attracted to polar water molecules. The remainder of the molecule is a long hydrocarbon tail that is not attracted to water. The hydrocarbon tail is hydrophobic. When soap is added to water, the hydrocarbon tail does not want to associate with the polar water molecules, so tails from many soap molecules associate together to form a soap micelle in which the polar heads face outward toward the water.
Much of the dirt we wish to remove is greasy dirt. This kind of dirt is not washed away by water because it is hydrophobic. When soap micelles come in contact with greasy dirt, the dirt is lifted from the surface and enters the inside of the micelle. The hydrophobic dirt would rather be in contact with the hydrophobic hydrocarbon tails than with water. The soap micelles that contain the greasy dirt are washed away with water.
21.Waxes are esters with long carbon chains. Esters are made from a carboxylic acid and an alcohol.
22.All steroids have a basic ring structure called the steroid nucleus. Each steroid has different substituents on the rings.