Module+Three

BIOL 160: General Biology Definition Worksheet #6: Chapter 13 Define the following key terms related to DNA structure and DNA replication. 1. Nucleotide 2. Pyrimidine (with examples listed) 3. Purine (with examples listed) 4. List of DNA nucleotides 5. List of RNA nucleotides 6. Correct nucleotide pairing in DNA (A pairs with ____) 7. Correct nucleotide pairing in DNA (C pairs with ____) 8. DNA replication 9. Semi-conservative 10. Parent strand of DNA 11. Daughter strand of DNA 12. Function of Helicase enzyme 13. Function of Primase enzyme 14. Function of DNA Polymerase enzyme 15. Function of DNA Ligase enzyme 16. Okazaki fragments  || || ||  || ||  || ||  || ||  || ||  || 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 ____ 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 ____ 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 _____________________________ 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.
 * __ CHAPTER 13 __**** : DNA Structure and Function **
 * Timeline of discovery **
 * Year ** ||
 * Scientist ** ||
 * Discovery ** ||
 * Discovery ** ||
 * Johann Miescher ** ||
 * Frederick Griffith ** ||
 * Avery-McCarty ** ||
 * Hershey-Chase ** ||
 * Watson-Crick ** ||
 * Franklin ** ||

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

What did these results show about the nature of 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 ________________________ 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 _____________________ groups. 4. The two strands are connected by ___________________ bonds formed between the nitrogenous bases. 5. Nitrogenous Bases: a. Two of them are called _______________________ and have a **single ring** structure. They are Thymine (T) and Cytosine (C) b. Two of them are called _______________________ 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 _____________________ and the amount of Guanine (G) was exactly the same as the amount of __________________ 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 _____ hydrogen bonds while Cytosine and Guanine are connected with ____ 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 _____________________________.  phosphate -5’3’- sugar sugar -3’5’- phosphate

B. RNA Structure: 1. RNA is formed from building blocks called _________________________, 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 _____________________ 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 _________________ (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. =

_____ 1. The basic chemical unit of a nucleic acid _____ 2. A polymer of nucleotides _____ 3. The two kinds of nucleic acids _____ 4. The three parts of every nucleotide _____ 5. A pair of these forms a “rung” in the DNA ladder _____ 6. Used to “label” DNA and protein in experiments _____ 7. RNA base that is not found in DNA _____ 8. Two alternating parts that form the nucleic acid “backbone” or “posts” in the DNA ladder _____ 9. The four bases in DNA _____ 10. The DNA base complementary to T _____ 11. Links adjacent nucleotides in a polynucleotide chain _____ 12. The substance a phage leaves outside its host cell _____ 13. Ribose in RNA and deoxyribose in DNA _____ 14. Links a complementary pair of bases together _____ 15. The four bases in RNA _____ 16. The DNA base complementary to G _____ 17. Describes the overall shape of a DNA molecule _____ 18. The sequence of these encodes DNA information _____ 19. Eukaryotic chromosomes consist of this and DNA || A. Adenine B. Base C. Covalent bond D. Cytosine

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 polynucleotide guanine (G) sugar-phosphate backbone pyrimidine bases adenine (A) complementary base pair hydrogen bond cytosine (C) sugar (deoxyribose) phosphate group thymine (T) purine bases double helix**

 6. DNA ______________________________ 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 ____________________________ 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 ______ and C pairs with ______). B. There are several key enzymes needed for DNA replication to occur, each with a specific function to perform. 1. ________________________: 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 ________________________________: 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 _______________________ 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 _________________________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 other; remember that in DNA, (A) pairs with ___ and (C) pairs with ___. 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 __________________________ 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 ____________________ end toward the 3’ or __________________ 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”.

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 ___________________ 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 _____________________ 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 _______________________________ 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 ______________________: 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 B. 5′ end of parental strand C. 3′ end of daughter strand D. 5′ end of daughter strand  E. DNA polymerase enzyme F. DNA ligase enzyme G. Helicase enzyme H. location where Helicase enzyme works I. location where DNA ligase enzyme works

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).

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


 * //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. <span style="font-family: "Times New Roman","serif"; font-size: 12pt;"> BIOL 160: General Biology Definition Worksheet #7: Chapter 14 Define the following terms related to transciption and translation. 1. Anticodon 2. Codon 3. Elongation stage 4. Frame-Shift mutation 5. Gene 6. Initiation stage 7. mRNA molecule 8. Mutation 9. Promotor region of a gene 10. rRNA molecule 11. RNA polymerase 12. Substitution mutation 13. tRNA molecule 14. Terminator region of a gene 15. Termination stage 16. Transcription 17. Translation 18. Triplet <span style="font-family: "Times New Roman","serif"; font-size: 12pt;">
 * __ CHAPTER 14 __**** : From DNA to RNA to PROTEIN Molecules: **

1. Cells cannot survive unless they are constantly replacing enzymes and other proteins. The instructions for making these molecules are referred to as the “Genetic Code” and are found within the DNA molecules (chromosomes). 2. DNA Replication (covered in chapter 13) only occurs when a cell is actively preparing to divide. This is the only time the DNA is completely unwound and an exact copy is made. For the majority of the time, the DNA strands only unwind in specific areas to expose the genetic code for a specific protein that is needed. 3. The small section of a DNA strand that codes for a specific protein is called a _________________, and is the functional unit of heredity. This is why the study of heredity is called genetics. 4. The process of producing a protein molecule from the instructions encoded in the DNA molecules requires two steps: A. ______________________________: is the first step, where the DNA message is copied into a complementary code called ________. This process occurs inside the nucleus as DNA __never__ leaves the nucleus. B. ______________________________: is the second step that must occur. In this process the RNA molecule leaves the nucleus (after it has been modified slightly) through pores in the nuclear envelope. The RNA makes its way to a ribosome where it directs the assembly of amino acids into a polypeptide (protein) chain. This process therefore occurs in the cytoplasm of the cell.

5. TRANSCRIPTION: Converting DNA into RNA A. This is a process that converts one nucleic acid into another nucleic acid making a complementary copy. This is like a “medical transcriptionist” converting a “voice message” in say English to a “written message” still in English. The two forms are of the same language, but in a different form. B. Remember that DNA and RNA are similar and yet different: 1. They are both made of subunits called __________________________. (they are both classified as polynucleotides). 2. DNA is a _____________ strand, RNA is a ______________ strand. 3. DNA uses the sugar _________________ RNA uses the sugar ____________. 4. DNA uses nucleotides A, C, G & ___, RNA uses nucleotides A, C, G & ___.
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RNA Strand

DNA Template

C. Given the following DNA sequence, what is the complementary RNA transcript that would be produced by transcription of the DNA? TAC AAG ATA ACA TTT GTC ATT _____ _____ _____ _____ _____ _____ _____ (RNA transcript)

D. There are three types of RNA molecules produced in the nucleus that are all formed by transcription of different sections (genes) of the DNA sequence: 1. _________________________ RNA (mRNA): has the genetic instructions for making a specific protein (polypeptide). This is like the __“blue-print”__ for the project that will ultimately make a protein molecule. 2. ________________________ RNA (rRNA): contains the genetic instructions for making a Ribosome that will ultimately take part in the formation of the new protein molecule. The Ribosome in a sense acts like the __factory__ (or an assembly line in a factory) where the blue-print will be read and assembly of the protein will take place. 3. ________________________ RNA (tRNA): contains the genetic instructions for making a specific carrier molecule that will attach to a specific amino acid in the cytoplasm and deliver it to the Ribosome for assembly into a protein molecule. The tRNA molecule in a sense acts like the __workers__ in the factory, reading the blue-print.

E. There are several important enzymes needed for Transcription to occur, just like in DNA replication, each with a specific function to perform. 1. ____________________________: attaches to the helix strands of DNA and break the hydrogen bonds, separating the double strands, forming a little “bubble” in the DNA chain. Unlike DNA replication, only __one__ bubble forms at a specific location on a specific chromosome where the genetic instructions are located for the specific protein needed to be synthesized. Once the “bubble” forms, the enzyme moves down the chain in __one__ direction increasing the size of the “bubble”. This works much like the clasp of a zipper opening it up. 2. __________________________________: attaches to the DNA and begins to “read” the DNA molecule, forming a strand of RNA. a. Unlike the DNA Polymerase enzyme in DNA replication, this enzyme only reads __one__ strand of the original DNA molecule, not both, and only reads a small section of the DNA strand, not the entire strand. b. Like DNA Polymerase, this enzyme also only “reads” the original DNA strand of nucleotides from the _____ end toward the _____ end of the original DNA molecule.

c. The new RNA molecule is “growing” from the ____ end to the ____ end. d. Unlike the DNA Polymerase enzyme, this enzyme uses the nucleotide _______________ (U) instead of ______________(T) as the complement to Adenine (A) e. Each gene is responsible for regulating its own activity. <span style="height: 132px; margin-left: 125px; margin-top: 15px; position: absolute; width: 276px; z-index: -6;">

F. Transcription can be divided into three distinct stages: 1. INITIATION STAGE: a. At the beginning of each gene there is a region of the DNA called the ____________________ DNA that signals the RNA Polymerase enzyme where to attach to the DNA strand. b. This stage begins as the enzyme attaches to the DNA strand and begins to “read” the original DNA “message”. c. At the very end of the promoter DNA is a specific set of nucleotides that signals the start of the actual set of instructions. This is called the “start signal”. 2. ELONGATION STAGE: a. This is the process where the ___________________________ enzyme continues to “read” the DNA strand, creating the complementary mRNA strand. b. As the process continues, the RNA strand gets longer and longer as more and more nucleotides are added to the strand. 3. TERMINATION STAGE: a. At the end of each gene there is a region of the DNA called the TERMINATOR DNA that signals the RNA Polymerase enzyme that the end of the gene (genetic sequence for a particular protein) has been reached and it is now time to detach from the DNA strand. b. At the very beginning of this section is a specific set of nucleotides that signals the end of the actual set of instructions called the “stop signal” and the RNA Polymerase enzyme stops reading the DNA sequence.

<span style="font-family: "Times New Roman","serif"; font-size: 12pt;"> G. Several modifications (finishing touches) are made to the pre-RNA strands before they leave the nucleus. 1. A _____________ (methyl and phosphate groups) is added to the 5’ end of the RNA strand. These groups will help the final mRNA attach itself to the Ribosome. In a sense, it also protects the beginning of the set of instructions like a hat protects the head. 2. A ______________ is added to the 3’ end of the RNA strand. This will generally contain anywhere from 100-300 Adenine (A) nucleotides (often called a poly-A tail). This strand of nucleotides will combine with proteins and coil up. The longer the tail and the more coiled it becomes influences how long the mRNA will function in the cytoplasm. If only a small amount of the protein is needed, a short tail will be attached, if much of the protein is needed, a long tail will be attached. 3. ___________________ of the RNA strand are removed (snipped out). These sections of a gene are not needed for making a specific protein. By removing these sections, different cells can use the same gene to make 10 or more different proteins. Think of these as sections that are “__in__ the way” or need to stay “__in__side the nucleus”. 4. ____________________ of the RNA strand are sliced together (reconnected) to form the final version of the mRNA. Once these are reconnected the mRNA is ready to leave the nucleus. Think of these as sections that need to be “__ex__ported” from the nucleus as part of the final message.
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Perhaps an analogy may help. To save space in a cookbook, there is one basic cookie recipe that contains all the necessary ingredients (flour, sugar, eggs, oil, baking soda, etc.) and any ingredient you may ever want to add to a cookie (chocolate chips, oatmeal, raisins, coconut, nuts, peanut butter, M&Ms, etc.). If you choose to make peanut butter chocolate chip cookies, you will need to keep some of the ingredients, and eliminate others. Those that you keep would be like the “exons” while those you choose to eliminate would be like the “introns”. This process allows you to make many different types of cookies with one very general recipe. 6. TRANSLATION: Deciphering the mRNA genetic code into a protein molecule. A. The connection between genes and proteins is found in the protein-building “words” found in the mRNA molecules. B. In the English language “words” can be of any length, however the genetic code on the mRNA strand is always “read” by the Ribosomes __________ nucleotides at a time. This is because the DNA nucleotides (four of them A,T,C,G) must code for 20 different amino acids. 1. If it was a 1:1 ratio, there could only be 4 amino acids (41=4). 2. If two nucleotides were used in any order, there could be 16 different amino acids (42=16), still not enough. 3. If three nucleotides were used in any order, there could be 64 different amino acids (43=64). Three is all that is needed to give more than enough information, since there are only 20 different amino acids. 4. A group of three nucleotides on a DNA strand is called a TRIPLET. 5. A complementary group of three nucleotides on a mRNA strand is called a ___________________. In other words, “the secret ‘CODE is ON’ the mRNA strand”, or described another way, “the DNA’s ‘message’ on the mRNA is in a secret ‘code’. 6. <span style="height: 495px; left: 0px; margin-left: 271px; margin-top: 22px; position: absolute; width: 397px; z-index: -5;"> To understand a “secret code” one needs a “code book”. For protein synthesis, the code book is for the CODONS on the mRNA, __not__ for the DNA triplets. 7. As mentioned, there are 64 different “3-letter” combinations possible. 8. Each 3 letter (nucleotide) sequence codes for __one__ particular amino acid. 9. The table at the right shows the different combinations possible and the amino acids for which each codes. a. Some combinations code for the same amino acid (there are 64 possibilities, but only need to make 20 amino acids, so no need to let them go to waste). b. One codon signals the START of the message. It is _______. c. There are three codons that signal the END of the message. They are: _______, _______, and _______.

C. Given the following mRNA sequence that is complementary to a section of the original DNA molecule, use the table of mRNA Codons from the textbook or on the previous page to determine the amino acid sequence of the polypeptide chain. AUG UUC UAU UGU AAA CAG UAA _____ _____ _____ _____ _____ _____ _____ (Amino acid sequence) D. The tRNA molecule also has a group of 3 nucleotides that is complementary to the CODON on the mRNA, and is called an _______________________. E. The CODON on the mRNA is complementary to the TRIPLET on the original DNA, and is also complementary to the ANTICODON on the tRNA; therefore the ANTICODON is essentially the __same genetic code__ as the original DNA. This is how the tRNA molecule knows which amino acid to transport to the Ribosome. F. The tRNA molecules attach to special enzymes in the cytoplasm which helps them link to specific amino acids. The tRNA then transports the specific amino acid to the rRNA (Ribosome) where it joins to other amino acids by a peptide bond, ultimately forming a polypeptide (protein) molecule. G. Translation can also be divided into three distinct stages: 1. ________________________ STAGE: this gets everything ready to begin. a. to begin the process of converting the mRNA message into a protein chain, the mRNA binds to a ______________________. b. the ribosome begins to move along the mRNA strand “looking” for a specific mRNA codon called the ___________ codon (AUG). c. an ___________________ tRNA molecule arrives at the Ribosome and the anti-codon on the t-RNA forms hydrogen bonds with the “start” codon on the m-RNA strand. 2. _________________________ STAGE: this is the work in progress. a. a second t-RNA molecule brings its amino acid to the ribosome and hydrogen bonds form between the anti-codon (on the tRNA) and the codon (on the mRNA). b. while the two amino acids are held closely together, a ________________ bond forms between the two amino acids c. once this very strong bond forms, the initiator t-RNA separates from its amino acid AND the ribosome and leaves to go “find” another amino acid in the cytoplasm. d. the ribosome moves down the mRNA strand and the process continues. e. as the process continues the protein chain gets longer and longer by linking together more and more amino acids. <span style="font-family: "Times New Roman","serif"; font-size: 12pt;"> 3. _________________________ STAGE: this ends the process of translation. a. the elongation stage continues until the ribosome reaches a specific codon called the _____________ codon. Since there is no tRNA that recognizes this message, the process stops. b. Special proteins known as __________________ FACTORS trigger the mRNA and protein to break away from the Ribosome.

7. Any change in the DNA sequence that alters the genetic code and may change the protein being produced is called a _______________________________. If the protein is essential for metabolism or cell structure, the cell may also be altered, and in some cases become cancerous. A. There are two main types of mutations that occur in the cell: 1. ________________________________ MUTATIONS: these occur when one nucleotide is wrongly paired with another nucleotide. The effects may or may not change the desired amino acid in the final protein (remember more than one codon can signal for some amino acids) and therefore will not be evident or if it does change the code, the effects are generally less sever than the other types of mutations because only one codon and therefore only one amino acid is affected. 2. __________________________________ MUTATIONS: occur when an additional nucleotide is added to the sequence (___________________) or one nucleotide is removed from the sequence (_____________________). The effects of this type of mutation are very severe because many codons are affected.
 * For a typical protein molecule, this entire process of translation takes about 20 seconds. The mRNA strand remains intact and may come in contact with another ribosome and begin translation before the first one is even finished. In this way, many proteins can be made quickly. Eventually, the mRNA breaks down and is recycled to make new DNA or RNA strands in the nucleus.

B. There are a number of known factors that may cause mutations: 1. _____________________________: most commonly caused by x-rays. 2. _______________________________: most commonly caused by ultraviolet rays from the sun (or tanning beds). 3. _________________________ AGENTS: natural and synthetic chemicals that attach to the nitrogenous bases or phosphate groups in DNA.

<span style="font-family: "Times New Roman","serif"; font-size: 12pt;"> C. Mutations change the meaning of the coded genetic message. Using the genetic code chart, translate the following mRNAs into amino acid sequences and answer the questions that follow. 1. **Original mRNA nucleotide sequence:** <span style="height: 67px; margin-left: 70px; margin-top: 9px; position: absolute; width: 545px; z-index: -4;">

a. What would be the correct amino acid sequence formed from this mRNA?

2. **Base Substitution Mutation (*)** **in the original mRNA:** Only one nucleotide is changed in this mutation (labeled with the *), where the letter ‘A’ in the above sequence was __replaced__ with the letter ‘C’. <span style="height: 66px; margin-left: 70px; margin-top: 17px; position: absolute; width: 551px; z-index: -3;"> ** * **

a. What is the new amino acid sequence formed from this mRNA?

b. How many amino acids remained the same after the mutation occurred?

c. How many changed as a result of this mutation?

d. Why are all of these types of mutations not necessarily harmful?

3. **Frame Shift (insertion) Mutation (*) in the original mRNA:** Only one nucleotide was changed in this mutation (labeled with the *), where the letter ‘G’ was __inserted before__ the letter ‘A’. <span style="height: 64px; margin-left: 62px; margin-top: 22px; position: absolute; width: 576px; z-index: -2;"> ** * **

a. What is the new amino acid sequence produced from this mRNA?

b. How many amino acids remained the same as a result of this mutation?

4. Which mutation had the greatest effect on the protein chain and why? <span style="font-family: "Times New Roman","serif"; font-size: 12pt;"> 8. REVIEW the “Key Concepts” to know about Protein Synthesis:

A. Converting DNA into RNA and finally into a Protein chain takes place in several steps: 1. ____________________________: takes place in the nucleus and converts the DNA into RNA. It involves 3 stages: a. __________________________: RNA Polymerase attaches to one section of a DNA strand and begins to “read” the DNA. b. __________________________: RNA Polymerase continues to “read” the DNA strand creating a longer and longer RNA molecule. c. __________________________: RNA Polymerase stops “reading” the DNA and releases the RNA molecule. 2. _________________________ of the RNA: before the molecule can leave the nucleus, several changes need to be made. a. A _____________ is added to the 5’ end b. A _____________ is added to the 3’ end c. _______________ are removed from the RNA molecule d. _______________ are reconnect (spliced together) to form the finished mRNA molecule 3. ________________________: takes place in the cytoplasm (specifically at a ribosome) and converts RNA into Protein. It also involves three stages: a. _________________________: mRNA attaches to the ribosome and the initiator t-RNA attaches to the mRNA. b. _________________________: additional tRNA molecules deliver specific amino acids to the ribosome, allowing them to form strong peptide bonds to other amino acids, and the new protein chain grows in length. c. _________________________: a stop codon is reached on the mRNA and release factors allow the mRNA and protein to break free from the ribosome. B. There are three different types of RNA with very different functions: 1. __________________ RNA (mRNA): carries the secret CODE out of the nucleus and delivers it to the ribosomes 2. ___________________ RNA **(**tRNA): finds the correct amino acid in the cytoplasm that is required and delivers it to the ribosome, matching its anticodon to the codon on the mRNA 3. ___________________ RNA (rRNA): the organelle where the actual protein is assembled

9. This chapter summarizes the key steps in the flow of genetic information from DNA to protein. We will fill this diagram in together in class as a final review. <span style="height: 821px; margin-left: 0px; margin-top: 18px; position: absolute; width: 625px; z-index: -1;"> <span style="font-family: "Times New Roman","serif"; font-size: 12pt;">
 * //Sample Test Questions for Chapter 14://**

1. Where in the cell does transcription take place? a. nucleus b. cell membrane c. ribosome d. chromosome e. mitochondria

2. When RNA is made, the RNA base ____ always pairs with the base ____ in the original DNA molecule. a. U……T b. T……G c. U……A d. A……U e. T……A

3. The sequence of three nucleotide nitrogenous bases can specify the identity of a. a specific gene b. a single DNA molecule c. a single protein molecule b. a single amino acid molecule c. all of the above

4. The transfer of genetic information from mRNA to a polypeptide is called a. translation b. transcription c. initiation d. elongation e. replication

5. At one point as a cell carried out its regular functions, the nucleotide CTA was paired with the nucleotide GAT. This pairing occured a. in a double-stranded DNA molecule b. during translation c. when an mRNA codon paired with a tRNA anticodon d. it is impossible to say with the information given

6. If the nucleotide sequence of a section of DNA strand is “GTAACT”, which of the following choices is the correct nucleotide sequence found on the corresponding strand of mRNA copied? a. CATTGA b. GUAACU c. GTAACT d. CAUUGA e. GAUUCA

7. Which of the following enzymes catalyzes the linking together of RNA nucleotides to form an mRNA molecule? a. RNA ligase b. RNA polymerase c. ribosome d. reverse transcriptase e. tRNA enzyme

8. When DNA replication occurs, DNA polymerase always reads the template strand of the original DNA molecule in which direction? a. From the 3’ to the 5’ b. From the 5’ to the 3’ c. one strand of DNA reads in one direction (3’ to 5’) while the other strand of DNA reads in the other direction (5’ to 3’)

9. A gene is a. the same thing as a chromosome b. the information for making a polypeptide c. made of RNA d. made by a ribosome e. made of protein

10. A messenger RNA molecule for making a protein is made in the nucleus and sent out to a ribosome. The ribosome reads the mRNA message and makes a protein containing 40 amino acids. The mRNA strand consists of at least how many nucleotides? a. 30 b. 40 c. 120 d. 360

11. True or False: The nitrogenous bases that pair together to connect the two parallel strands forming DNA (or in other words the “rungs” of the DNA ladder) are held together by covalent bonds.

12. Which of the following changes occur before eukaryotic mRNA leaves the nucleus? a. a nucleotide cap is added to the strand b. the molecule is spliced c. a long nucleotide tail is added to the strand d. all of the above e. only A and C are true statements