Review Questions DNA Part I

1. What are the functions of the nucleic acids? The nucleic acids are used by cells for information storage, specifically DNA and RNA. Another nucleic acid, ATP stores chemical energy for the cell.

2. What is the monomer of the nucleic acids? The monomer of the nucleic acids is the nucleotide. A nucleotide is composed of three parts: a pentose sugar, a nitrogenous base, and a phosphate group.

3. What is the polymer of the nucleic acids? The polymer of the nucleic acids is the polynucleotide. A polynucleotide is a chain of nucleotides covalently bonded to each other.

4. What is the function of DNA? DNA is deoxyribonucleic acid. DNA is a spiraling pair of polynucleotides found in all cells. The shape of the molecule is described as a “double helix”. The DNA carries the information for building proteins. The sequence of nucleotides in a DNA molecule determines the sequence of amino acids in a polypeptide of a protein. A DNA molecule is a collection of recipes for making proteins. Since proteins are the machinery of life, DNA is the recipe for making an organism.

5. What is the function of RNA? RNA is ribonucleic acid. RNA is a single polynucleotide chain. RNA builds the proteins based on the recipe in the DNA. RNA is the builder of organisms. 6. What is the function of ATP? Adenosine triphosphate (ATP) is a nucleic acid molecule that remains a single nucleotide. Unlike a DNA or RNA nucleotide, the ATP nucleotide has three phosphate groups attached to its ribose sugar. All living beings run their cells on ATP. The universal battery, ATP is an energy-storing molecule. All the food an organism consumes (carbohydrates, lipids, and proteins) are degraded into their individual monomers. The monomers are then broken apart atom by atom. The chemical energy freed from the reaction is stored in ATP as chemical bonds between the phosphate groups. An individual ATP molecule doesn’t hold a lot of energy. What makes ATP useful as an energy bank is that the energy can easily be accessed and released by a cell.

7. Describe the ATP cycle. ATP is not made from scratch every time it is needed. ATP is recycled. When a cell needs a burst of energy, it will break off a phosphate group from ATP. Now the molecule is ADP (adenosine diphosphate). ADP is converted back to ATP by the cell adding energy and a phosphate group. The energy for reattaching the phosphate group comes from the energy extracted from the chemical bonds of food. 8. Where is DNA located in a cell? Within the cells of animals, plants, fungi, and protists, DNA is stored in the nucleus. Bacteria lack a nucleus and so store their DNA in a portion of the cytoplasm called the nucleoid region.

9. What is a chromosome? A chromosome is a very long piece of DNA. A typical chromosome contains hundreds of genes. 10.What is a gene? Technically, a gene is a length of DNA that codes for a polypeptide. Later in the semester, we will modify this definition.

11. Describe deoxyribose, the pentose sugar subunit in the nucleotides of a DNA molecule. Deoxyribose is a five-carbon monosaccharide. Biochemists have mapped the molecule by numbering each carbon in the sugar. Next to the number, there is also what looks like an apostrophe. For example, the first carbon in ribose is called the 1’ (one prime) carbon. The term “prime” refers to the apostrophe. The apostrophe represents that the carbon is part of a carbohydrate. For every kind of nucleotide, the nitrogenous base is always attached to the 1’ carbon, the phosphate group is always attached to the 5’ carbon, and the 3’ carbon always holds a hydroxyl group (–OH). 12.Explain the formation of the sugar-phosphate backbone. The DNA molecule looks like a twisted rope ladder. The sides of the ladder are called the sugar-phosphate backbone. Each nucleotide is attached to the one above by means of a covalent bond between the phosphate group and the 3’ carbon. The repeating pattern of sugar hooked to phosphate hooked to sugar gives the backbone its name. Just like other organic compounds, the sugar-phosphate backbone is built by dehydration synthesis. 13.Explain how the DNA molecule is anti-parallel. A DNA molecule is described as “anti-parallel” because one polynucleotide is oriented in the opposite direction to the other. A DNA molecule kind of resembles a divided highway with traffic moving in opposite directions. 14.Describe the 5’ strand and 3’ strand. Since DNA is anti-parallel, one polynucleotide is oriented with the 5’ end of the ribose sugars pointing up and the 3’ end pointing down. This is the 5’ strand. The other polynucleotide is oriented in the opposite direction with the 3’ end pointing up and the 5’ end pointed down. This is called the 3’ strand.

5’ strand 3’ strand

15.So what is the leading strand? lagging strand? A synonym of the 5’ strand is the leading strand. The 3’ strand is also known as the lagging strand. 16.Describe Chargaff’s Rules. Back in the 1940’s, Edwin Chargaff, an Austrian American biochemist, examined the relative amounts of adenine, guanine, cytosine, and thymine in the DNA of a variety of organisms. Chargaff compared the amounts of these bases in everything from bacteria to humans. What stood out was that for each species, the amount of adenine always equaled the amount of thymine. Likewise, the amount of guanine was the same as cytosine. The pattern is constant regardless of the species, and so it is known as “Chargaff’s rules”. Later, in the early 1950’s, James Watson and Francis Crick concluded from Chargaff’s rules that in the DNA molecule every adenine binds to thymine and every guanine always binds to cytosine forming rungs of the double helix.

17.Describe the complementary bases. Adenine and thymine are complementary, meaning they go together. The same goes for guanine and cytosine. Adenine and guanine are both purines (nitrogen bases composed of double rings). Cytosine and thymine each are single-ring bases so they are pyrimidines. You may notice that in each complementary pair of bases there is one purine and one pyrimidine. This arrangement insures that the DNA molecule maintains a constant width down the length of the molecule. If complementary bases were two purines, the molecule would be too wide and with two pyrimidines it would be too narrow. Why does A only bond to T? The bases are bonded to each other by weak hydrogen bonds. A is bound to T with two hydrogen bonds. G is bound to C with three hydrogen bonds. If A tried to bond with C, C would fall off because it needs three hydrogen bonds. If G tried to bond with T, G requires three hydrogen bonds and so won’t stay attached to T. This difference in the number of hydrogen bonds for each complementary pairs keeps them A-T and C-G.