Chapter+Thirteen

BIOL 160: General Biology Definition Worksheet #6: Chapter 13 Define the following key terms related to DNA structure and DNA replication. 1. Nucleotide: Monomer of nucleic acid, has a five carbon sugar,three phosphate groups and one of four nitrogen-containing bases 2. Pyrimidine (with examples listed): Nitrogen Bases with single carbon rings, Thymine and cytosine 3. Purine (with examples listed): Nitrogen bases with double carbon rings, Adenine and Guanine 4. List of DNA nucleotides: Thyamine (T),Cytosine (C),Adenine(A), and Guanine(G) 5. List of RNA nucleotides: Uracil (U),Cytosine (C),Adenine(A), and Guanine (G) 6. Correct nucleotide pairing in DNA (A pairs with T ) 7. Correct nucleotide pairing in DNA (C pairs with G ) 8. DNA replication: Copies DNA before cell division 9. Semi-conservative: The replicaiton pattern is two parent strands seperate, each a template for a new daughter strand. so you end up after copying with one parent strand and one daughter strand in a replicated DNA. 10. Parent strand of DNA: Original DNA strand 11. Daughter strand of DNA: The new strand of DNA that has been copied from the parent template 12. Function of Helicase enzyme: Breaks open hydrogen bonds between strands. Can go either direction from the origin of replication 13. Function of Primase enzyme: attach short pieces of RNA (10-20 bases) to parent DNA strands in center of repication site, "reads" in 3' to 5' 14. Function of DNA Polymerase enzyme: Joins free nucleotides into a new strand of DNA. Can oly add nucleotidesonto a free 3' end of growing DNA strand, reads strand 3' to 5' and grows 5' to 3' 15. Function of DNA Ligase enzyme: Joins DNA segments on a a discontinuous strand or anywhere there is a gap after replication 16. Okazaki fragments: Fragments of new DNA on the lagging strand. This happens because on lagging strand, the DNA polymerse has to construct the new strand short snippets at a time due to the fact that DNA plymerse can only read the DNA from 3' to 5' end


 * __ CHAPTER 13 __**** : DNA Structure and Function **
 * Timeline of discovery **
 * ** Year ** || ** Scientist ** || ** Discovery ** ||
 * 1869 || ** Johann Miescher ** || found that nucleic contains an acidic substancecomposed mostly of nitrogen and phophorus ||
 * 1875 || ** Frederick Griffith ** || That heat had killed the s cells but had not destroyed their hereditary material ||
 * 1940 || ** Avery-McCarty ** || DNA was indeed the hereditary material ||
 * 1950 || ** Hershey-Chase ** || DNA, not protein, is the material of hereditary common to all life on earth ||
 * 1950's || ** Watson-Crick ** || were the first to come up with a model of DNA ||
 * 1950's || ** Franklin ** || Prepared x-ray crystallographic images of DNA, dimensions and shapes of DNA molecules, Alpha Helix ||

1. Discovery of DNA and its Function (a brief history lesson): A. MOLECULAR BIOLOGY is the study of the molecules found within cells, including the DNA molecule. B. GENETICS is the study of DNA and how it serves as the molecular basis of biological inheritance or heredity. C. In the 1930-40s biologists knew about proteins and the __ 20 __ different amino acids that made them, and that proteins had various structural shapes that influenced their properties and functions. They also knew that DNA existed and that it was made of __ 4 __ different nucleotides. With the number of monomers available to make these two macromolecules, it seemed unlikely that DNA was the genetic information that was passed on to the next generation of cells. D. In the early 1950s numerous biologists were attempting to answer the question of where the genetic information was stored (in the protein molecules or the DNA). To do this they selected a bacteria called //Escherichia Coli// (E. Coli) and a class of viruses called __ Bacteriophage __ that was known to only attack bacteria. E. Viruses were first seen under a microscope in the early 1950s and were commonly used in experiments. Viruses have an outer coat (shell) made of protein and a single molecule of either DNA or RNA, but can’t reproduce on their own. They must infect a living cell, and use that cell’s “cellular machinery” to make more viruses.

F. Hershey/Chase labeling experiment
 * Organic molecule || Composition || Labeled || Labeled stuff ended up where? ||
 * protein || High sulfur content || 35S || viruses capsule outside ||
 * DNA or RNA || High phosphorus content || 32P || bacteria inside ||

What did these results show about the nature of the genetic material? The DNA from the bacteriophage was injected into the bacterial cells showing that DNA is the genetic material

2. There are numerous words used to descibe DNA or sections of DNA. A. Chromatin: all of the DNA molecules in a cell + associated proteins B. Chromosome: //a single strand of DNA// + proteins attached C. Gene: on section of a chromosome that contains the genetic instructions for making a specific protein. D. DNA triplet: a group of three nucleotides (building blocks or monomers) used to make DNA E. Nucleotide: 5 Carbon sugar (ribose or deoxyribose) + phosphate group + nitrogenous base. monomers (building blocks) of DNA. 3. DNA & RNA structure: (some of this is a review from chapter 3) A. DNA Structure:  1. DNA is formed from building blocks called __ Nucleotides __ 2. The molecule is a double strand and has a “right handed” twist called an alpha-helix. 3. Each strand has a backbone made of alternating deoxyribose sugar and __ Phosphate __ groups. 4. The two strands are connected by ___ Hydrogen bonds__ __formed between the nitrogenous bases.__ __5. Nitrogenous Bases:__ __a. Two of them are called Pyramidine __ and have a **single ring** structure. They are Thymine (T) and Cytosine (C) b. Two of them are called __ Purines and have a **double ring** structure. They are Adenine (A) and Guanine (G)__ __c. Edwin Chargaff by 1952, had__ __discovered that the amount of Adenine (A)__ __was exactly the same as__ __ Thyamine __ __and the amount of Guanine (G) was exactly__ __the same as the amount of Cytosine __ leading them to determine that they must pair up together. It was later discovered that the reason was the number of hydrogen bonds that could form between the nitrogenous bases. d. Adenine and Thymine are connected with __ 2 __ hydrogen bonds while Cytosine and Guanine are connected with__ 3 __ hydrogen bonds. An easy way to remember this is to think about A T and T (telephone), since there are two T’s, then A and T are connected with 2 bonds. Also think about “C” and “G” sound like THREE, and the letter C is the third letter in the alphabet so C and G are connected with 3 bonds. e. The A-T, G-C pairing allows the two backbones of the DNA double helix to always be 2.3 angstroms apart from each other!!! This makes the two “legs” of the DNA ladder EQUIDISTANT apart!! Makes for smooth winding of the double helix. f. One of the most important insights attributed to James Watson (of the famous Watson/Crick team) comes in the discovery that the two strands of DNA are arranged in //opposite orientations.// On one strand the last group is a sugar group called the 3’ (three prime) end and on the opposite strand the last group is a Phosphate group called the 5’ (five prime) end. These numbers are based on the numbering of the carbons on the sugar molecule. Because the DNA strands are arranged in this way they are described as being __ Nucleotide Pairing. __ phosphate -5’3’- sugar sugar -3’5’- phosphate

B. RNA Structure: 1. RNA is formed from building blocks called __ Ribonucleotides __, which contain the following three parts: - a ribose sugar (OH is present on carbon #2) - a nitrogenous base (A, U, C or G) - a phosphate group 2. The molecule consists of a Single strand of nucleotides. 3. The sugar-phosphate backbone is the same as with one of the DNA strands except the sugar ribose is used in place of the sugar deoxyribose. 4. The only other difference is that the nucleotide Thymine (T) does not exist in RNA, rather it is replaced by the nucleotide __ Uracil __ (U), which has almost the same molecular structure as Thymine.

= 4. Match the following terms with the correct description listed. Note that some answers are used more than once, and some questions have multiple answers. =

__ I __ 2. A polymer of nucleotides __ E,O __ 3. The two kinds of nucleic acids __ B,K,P __ 4. The three parts of every nucleotide __ B __ 5. A pair of these forms a “rung” in the DNA ladder __ N __ 6. Used to “label” DNA and protein in experiments __ R __ 7. RNA base that is not found in DNA __ P,K __ 8. Two alternating parts that form the nucleic acid “backbone” or “posts” in the DNA ladder __ A,D,G,Q __ 9. The four bases in DNA __ A __ 10. The DNA base complementary to T __ C __ 11. Links adjacent nucleotides in a polynucleotide chain __ M __ 12. The substance a phage leaves outside its host cell __ P __ 13. Ribose in RNA and deoxyribose in DNA __ H __ 14. Links a complementary pair of bases together __ A,D,G,R __ 15. The four bases in RNA __ D __ 16. The DNA base complementary to G __ F __17. Describes the overall shape of a DNA molecule __ B __18. The sequence of these encodes DNA information __ M __19. Eukaryotic chromosomes consist of this and DNA || A. Adenine B. Base C. Covalent bond D. Cytosine
 * __ J __ 1. The basic chemical unit of a nucleic acid

E. DNA
F. Double helix G. Guanine (G) H. Hydrogen bond I. Nucleic acid J. Nucleotide K. Phosphate L. Polynucleotide M. Protein N. Radioactive isotope O. RNA P. Sugar Q. Thymine (T) R. Uracil (U) ||

5. Review the structure of DNA and use the following terms to label this diagram.


 * nucleotide (11) polynucleotide (12)guanine (G) (7) sugar-phosphate backbone (1) pyrimidine bases (13) adenine (A) (6) complementary base pair (5) hydrogen bond (9) cytosine (C) (10) sugar (deoxyribose)(3) phosphate group (2) thymine (T) (8) purine bases (14) double helix (4)**



6. DNA **Replication** __is a step by step process used by the cell to copy the DNA prior to cell division.__ __A. There are several key events that occur in the process.__ __1. The double helix strand of DNA is unwound forming two parallel strands.__ __2. Hydrogen bonds that link the complementary nitrogenous bases of each strand are broken, separating the two strands from each other.__ __3. The “main enzyme” used to copy DNA is DNA plymerase (although there are other equally imporant enzymes needed for the process to occur). Each strand then acts as a template for the synthesis of a complementary strand of DNA.__ __The process is described as being__ **semiconservative** __because the original strands of DNA (the “parent” strands) remain intact while the new companion strands (the “daughter” strands) are assembled according to the__ __base pairing rules (A pairs with__ **T** and C pairs with **G**__).__ __B. There are several key enzymes needed for DNA replication to occur, each with a specific function to perform.__ __1.**DNA Helicase**__ __: these enzymes attach themselves to the DNA at numerous locations, unwind the double helix and break the hydrogen bonds, separating the double strands of DNA, forming little “bubbles” in the chain called “bubbles of replication”. This is where the DNA is copied.__ 

__ There can be 1000’s of these bubbles of replication forming along the length of a DNA molecule at the same time, which shortens the amount of time needed to copy the DNA since part of the DNA can be copied in each bubble at the same time.__

__At the two ends of each bubble of replication where the two unwound sections of DNA join to form the double helical DNA are areas called “replication forks”, so named because it resembles a “fork in the road” where a road divides and takes two different paths. Each bubble of replication therefore has two replication forks.__ 

__Small protein molecules attach to the parent strands of DNA once they are separated from each other to prevent them from reconnecting and winding back together forming the double helix.__ __The helicase enzymes continue to move down the DNA molecules in both directions increasing the size of the “bubbles of replication”. This works much like the clasp of a zipper opening it up. Because the helicase enzymes work in both directions, they are described as being NOT directional dependant.__ __ 2.__ PRIMASES__: these enzymes attach to the parent DNA strands in the center of the bubbles of replication at a site called the “origin of replication”. They begin to “read” the parent DNA strands in the 3’ to 5’ direction and attach about 10 complementary RNA nucleotides (found floating around in the nucleus) together and to the parent DNA, to create a working template (primer) to get the process started. This is much like painting with a “primer” before adding the finished coat of paint. Because the DNA-RNA strands are arranged in an anti-parallel orientation, the new RNA primer “grows” (is formed) in a 5’ to 3’ direction.__

__This step in DNA replication is essential because the DNA polymerase enzyme that actually copies the DNA can only add DNA nucleotides to the__ __3’ end of an existing nucleotide chain. The RNA nucleotides of the primer will later be removed and replaced with DNA nucleotides. Because the primase enzyme can only “read” the original DNA templates in the 3’ to 5’ direction, the enzyme is described as being directionally dependant.__ __3. DNA__ **Polymerase**__: these enzymes are the “main” enzymes that “read” the original (parent) DNA strands and using DNA nucleotides (found floating around in the nucleus) begin to “grow” (create) new (daughter) DNA strands forming two DNA molecules.__ __a. These enzymes are responsible for forming__ **covalent**_ bonds between the sugar group of one nucleotide and the phosphate group of a neighboring nucleotide to creat the very strong sugar-phosphate “backbone” of the DNA molecule. They are also responsible for forming other; remember that in DNA, (A) pairs with **T**___ and (C) pairs with__ **G**_. b. This enzyme is also described as being directionally dependant since it can only “read” the original DNA strand of nucleotides from the 3’ (sugar) end toward the 5’ (phosphate) end of the original DNA molecule. c. Since the two strands of DNA are oriented in opposite directions they are also described as having an **antiparallel** __arrangement. At the same time the original (parent) strand is being “read” in the 3’ to 5’ direction, the new (daughter) strand is forming or “growing” in the 5’ or__ __**phosphate** end toward the 3’ or__ **sugar** end. d. At each bubble of replication, there are two of these enzymes actively working on the two strands of DNA at the same time, but are moving in opposite directions following the Helicase enzymes as they continue to open up the bubbles of replication making them larger. These initial replications began as soon as the bubbles are large enough for the enzymes to function properly and the RNA primers have been created.  e. When looking at one of the forks of replication, only one of the original DNA strands is oriented in the 3’ to 5’ direction. Only on this strand is the DNA polymerase enzyme able to immediately begin creating the complementary DNA strand as it “reads” the original DNA in the 3’ to 5’ direction adding DNA nucleotides to the RNA primer. It will continue this process uninterupted following the Helicase enzyme. Due to this fact, this newly created DNA strand is called the “leading strand” or the “continuous strand”.
 * hydrogen**_bonds between the complementary DNA nucleotides on the parent and daughter DNA strands that will link the two strands together forming a new double-stranded DNA molecule. The two strands of DNA (original and newly created) are complementary to each

f. The other strand of DNA in the replication fork is oriented in the 5’ to 3’ direction so the RNA primer is oriented in the reverse direction and DNA replication is not able to begin immediately in this fork of replication. This strand of the original DNA must wait for the **helicase**___ enzyme to make the bubble of replication larger before DNA replication can begin on this strand. As the bubbles of replication continue to grow in__ __size, additional__ **primase**___ enzymes attach to the remaining portion of the original (parent) DNA strand that has not been copied and begin to make the RNA primers. Since they are “directionally dependant” they must read the DNA in the 3’ to 5’ direction. This is in the opposite direction than the Helicase enzyme is moving down the DNA molecule.__ __Once the primer is formed, another__ **DNA polymerase**_ enzyme will begin to make a complementary copy of the DNA. Remember, these enzymes are also “directionally dependant” and can only read the DNA from the 3’ to 5’ direction. Once they reach an RNA primer on this strand, the enzymes will break free; leaving short segments of DNA copied alternating with RNA primers. This part of the fork of replication is called the “lagging strand” (because it must wait to get started) or the “discontinuous strand” (because it has alternating DNA and RNA on the daughter strand formed). The fragmented sections of DNA separated by RNA are called “Okazaki Fragments” in honor of the scientist who first discovered them. 

g. Additional DNA Polymerase enzymes double check the process (proofread the DNA) correcting any mistakes and removing the RNA primers and replacing them with the correct DNA nucleotides.

4. DNA **ligase**__: these enzymes are responsible for sealing-together the gaps between the DNA backbones created by the Okazaki fragments forming a continuous daughter DNA strand. Since these enzymes do not technically “read” the original DNA strand but simply create covalent bonds between the sugar-phosphate groups of neighboring nucleotides forming the backbone, they are NOT directionally dependant.

7. The following diagram represents a replication fork undergoing the process of DNA replication. Match each of the lettered choices below with the numbers in the boxes on the diagram below. Some choices may not be used and others may be used more than once.

A. 3′ end of parental strand **1** B. 5′ end of parental strand C. 3′ end of daughter strand **3** D. 5′ end of daughter strand  E. DNA polymerase enzyme **4** F. DNA ligase enzyme G. Helicase enzyme H. location where Helicase enzyme works **7** I. location where DNA ligase enzyme works **6**

8. Give two reasons why in DNA replication, the nucleotides Thymine (T) always pairs with Adenine (A) and Cytosine (C) always pairs with Guanine (G). **Thymine and cytosine are pyrimidines. Adenine and guanine are purines.**

9. Explain how the following words are related and place them in their correct order from largest to smallest: Chromatin, Chromosome, DNA triplet, Gene, and Nucleotide **All are components of DNA. Nucleotide, DNA triplet, gene, chromosomes, chromatin.**


 * //Sample Test Questions for Chapter 13://**

1. Viruses that infect bacteria are called a. parasites b. bacterioviruses c. bacteriophages d. retroviruses

2. TRUE or FALSE: The nitrogenous bases called //purines// have a single ring structure, whereas those called //pyrimidines// have a double ring structure.

3. Which of the following are nitrogenous bases called //pyrimidines//? a. adenine and guanine b. thymine and cytosine c. thymine and adenine d. uracil and guanine e. both A and D

4. Which of the following correctly ranks the structures in order of size from smallest to largest? a. nucleotide- codon (triplet)- gene- chromosome b. chromosome- gene- codon (triplet)- nucleotide c. nucleotide- chromosome- gene- codon (triplet) d. chromosome- nucleotide- gene- codon (triplet) e. gene- chromosome- codon (triplet)- nucleotide

Which of the following is/are differences between RNA and DNA molecules? a. RNA uses the sugar ribose whereas DNA uses the sugar deoxyribose b. RNA uses the nucleotide Uracil whrease DNA uses Thymine c. RNA is a single strand of nucleotides whereas DNA is a double strand d. all of the above are differences between the two

5. TRUE or FALSE: The “backbone” of a DNA molecule consists of alternating sugar and phosphate groups held together by hydrogen bonds.

6. DNA replication occurs a. whenever a cell makes protein b. to repair gene damage caused by mutation c. before a cell can divide d. whenever a cell needs RNA e. in the cytoplasm of a eukaryotic cell

7. TRUE or FALSE: DNA polymerase “reads” the original DNA molecule from the 3’ to the 5’ direction.

8. 8. Which of the following enzymes is responsible for breaking the hydrogen bonds between the DNA strands and creating the “bubbles of replication”? a. DNA helicase b. DNA ligase c. DNA polymerase d. DNA primase

9. The nucleotide sequence of one small section of a DNA strand is “GTAACG”. Which of the following is the correct nucleotide sequence found on the corresponding strand of DNA? a. GTAACG b. CATTGC c. CUTTGC d. CAUUGC e. GCAATG

10. TRUE or FALSE: Okazaki fragments are commonly found on the “leading strand” during DNA replication.