Name_____________________________________________PD_______________DATE____________ Biology DNA Structure and Function Worksheet Guide Part 1: DNA Structure Previously we have discussed the processes of cell division, DNA replication during S phase of interphase, and the structures of chromosomes. While discussing these topics we often referred to chromosomes and DNA. Now you will learn more about DNA structure and how it serves as the instructions for the cell. The structure, type and functions of a cell are all determined by chromosomes that are found in the nucleus of a cell. These chromosomes are composed of tightly condensed DNA, the acronym for deoxyribonucleic acid. This DNA determines all the characteristics of an organism, and contains all the genetic material that makes us who we are. This information is passed on from generation to generation (heritable) in a species so that the information within them can be passed on to offspring to be used as instructions for cell activities. DNA Double Helix Structure of DNA and Nucleotides DNA is arranged into a double helix structure where two strands of DNA are spiraled around each other to form a “twisted ladder” shape. Each strand is composed of monomers called nucleotides. The following diagram illustrates a nucleotide, the building blocks of DNA Nitrogenous Base (Adenine, Cytosine, Thymine, or Guanine) (pentose sugar) There are four different types of nucleotides possible in a DNA sequence, adenine, cytosine, guanine and thymine (can be abbreviated A, C, G and T). There are billions of these nucleotides in our genome (the complete set of genetic material present in a cell or organism). These 4 nucleotides make up the “letters” of the instructions that allow a gene to code for the production of a protein. Each individual has a unique sequence of nucleotides, making every individual human on Earth unique. 1. What does DNA stand for? ____________________________________________________ 2. What is the function of DNA in the cell? 3. What structures within the nucleus of a cell contain the DNA (hint: humans have 46!) _____________________ 4. What is the shape of a DNA molecule? ___________________________________________ 5. What are the monomers of a DNA molecule? ________________________________________ 6. Draw a nucleotide below and label its 3 parts. 7. What are the four different nitrogenous bases that make up deoxyribonucleic acid? 8. Genes (segments of DNA instructions) code for the production of what macromolecule? ___________________ One key feature of DNA, discovered by Erwin Chargaff, is that the nitrogenous base Adenine always pairs with Thymine, and Guanine always pairs with Cytosine in two opposite DNA strands of a double helix. This is known as Chargaff’s Rule. The matching nitrogenous bases are held together by hydrogen bonds. The term used to describe the idea that DNA strands always match each other A with T and G with C is the vocabulary term complementary. This fact allows DNA to easily copy itself without making any mistakes. Mistakes made in the instructions of DNA during replication are known as mutations. When Watson and Crick discovered the structure of the DNA molecule, they determined that the two strands of a DNA double helix actually run in opposite directions. One strand runs in the 3’ to 5’ direction (referring to how the carbons in the deoxyribose sugar are named), and the opposite strand runs in the 5’ to 3’ direction. The term used to describe the opposite orientation of DNA strand is anti-parallel. 9. What does it mean that the two DNA strands are complementary? 10. Chargaff’s rule states that the DNA of any species contains equal amounts of ______________ and______________, and also equal amounts of __________________ and ___________________. 11. What type of bond holds the matching nitrogenous bases of two DNA strands in a double helix together? 12. What does it mean that the two DNA strands are anti-parallel? 13. Use the image at the right to complete the following: Circle a nucleotide. Label the sugar and phosphate. Identify the missing complementary bases that are not already labeled. Label the 3’ and 5’ ends of each strand. Label the hydrogen bonds holding base pairs together. 14. Write the complementary sequence for the matching DNA strand: 3’ A A T T C G C C G G T A T T A G A C G T T A T G G C 5’ ________________________________________________ 15. Write the complementary sequence for the matching DNA strand: 5’ T T T A A G C G T C G A T A T T G G G C A C A T G G 3’ ________________________________________________ Part 2: DNA Replication DNA replication, or the copying of a cell's DNA, is no simple task! There are about 6.5 billion base pairs of DNA in your genome, all of which must be accurately copied when any one of your trillions of cells divides. Remember that DNA is replicated during the S phase of Interphase. The basic mechanisms of DNA replication are similar across organisms. Let's take a look at the process, and at the proteins and enzymes that carry out replication, seeing how they work together to ensure accurate and complete replication of DNA. DNA replication is semiconservative, meaning that each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand. This process takes us from one starting molecule to two template DNA strands, with each newly formed double helix containing one new strand and one old strand. DNA Replication is semi-conservative The dark strands in this picture are the newly made DNA strands. Notice how the new double helices are made up of an old template strand and a newly made DNA strand A T A T G C C G T A T G T T T A G C 16. For each strand of the new replicated DNA, label them as either template strands (from the original DNA) or the replicated strands. 17. During what phase of the cell cycle is DNA replicated? _______________________________ 18. What does it mean that DNA replication is semiconservative? 19. What is true about the base pair sequence of the two new DNA double helices? Part 3: Enzymes involved in DNA replication One of the key molecules in DNA replication is the enzyme DNA polymerase. Remember, enzymes are proteins that catalyze (speed up) chemical reactions by lowering the activation energy of the reaction. DNA polymerases are responsible for synthesizing DNA: they add nucleotides one by one to the growing DNA chain, using only bases that are complementary to the template. Here are some key features of DNA polymerases: They always need a template (old DNA strand to read) They can only add nucleotides to the 3' end of a DNA strand (build new DNA 5’ to 3’ – downhill) They require a pre-existing chain or short stretch of nucleotides called a primer to get started with DNA replication. They proofread, or check their work, removing the vast majority of mistakes (mutations) made accidentally How do DNA polymerases and other replication factors know where to begin? Replication always starts at specific locations on the DNA, which are called origins of replication and are recognized by their sequence. Helicase is the first replication enzyme to load on at the origin of replication. Helicase's job is to move the replication forks forward by "unwinding" the DNA (breaking the hydrogen bonds between the nitrogenous base pairs). DNA polymerases can only add nucleotides to the 3' end of an existing DNA strand. How, then, does DNA polymerase add the first nucleotide at a new replication fork? Alone, it can't! The problem is solved with the help of an enzyme called primase. Primase makes an RNA primer, or short stretch of nucleic acid complementary to the template that provides a 3' end for DNA polymerase to work on. A typical primer is about five to ten nucleotides long. The primer primes DNA synthesis, i.e., gets it started. Once the RNA primer is in place, DNA polymerase "extends" it, adding nucleotides one by one to make a new DNA strand that's complementary to the template strand. DNA polymerases can only make DNA in the 5' to 3' direction, and this poses a problem during replication. A DNA double helix is always anti-parallel; in other words, one strand runs in the 5' to 3' direction, while the other runs in the 3' to 5' direction. This makes it necessary for the two new strands, which are also antiparallel to their templates, to be made in slightly different ways. One new strand, which runs 5' to 3' towards the replication fork, is the easy one. This strand is made continuously, because the DNA polymerase is moving in the same direction as the replication fork. This continuously synthesized strand is called the continuous strand. The other new strand, which runs 5' to 3' away from the fork, is trickier. This strand is made in fragments because, as the fork moves forward, the DNA polymerase (which is moving away from the fork) must come off and reattach on the newly exposed DNA. This tricky strand, which is made in fragments, is called the discontinuous strand. The small fragments left over from the discontinuous strand are then linked together by the enzyme ligase (think linkase!). 20. What is an enzyme? 21. Identify the jobs of each of the following enzymes in DNA replication. Helicase – Primase – DNA polymerase – Ligase – 22. Explain what 3’ and 5’ means, and why this leads to the production of continuous and discontinuous strands.