Chapter+Fourteen


 * Chapter 14 Module 3 **

Kelsey........ pg.15 words..15-18.. pg..24,25... done 5/13/12
BIOL 160: General Biology Definition Worksheet #7: Chapter 14 Define the following terms related to transciption and translation. 1. Anticodon- A set of 3 nucleotides in a tRNA, base pairs with an mRNA codon 2. Codon- a nucleotide base triplet that codes for an amino acid or stop signal during translation 3. Elongation stage- ribosomes assembles a polypeptide chain as it moves along the mRNA, threading the strands between its two subunits 4. Frame-Shift mutation -- when extra bases are inserted into the DNA 5. Gene ** - Heritable unit of information in DNA, occupies a particular location on a chromosome ** 6. Initiation stage ** - Mature mRNA binds with small ribosomal subunit after leaving the nucleus and entering the cytoplasm ** 7. mRNA molecule ** - Messenger. An RNA that carries a protein building message ** 8. Mutation Small permanent change in DNA, a source of new alleles and life's diversity 9. Promotor region of a gene facilitates the transcription for a specified gene 10. rRNA molecule Contains genetic instructions and delivers them to the Ribosome for protein synthesis 11. RNA polymerase enzyme that catalyzes transcription of DNA into RNA 12. Substitution mutation a DNA nucleotide is substituted for another DNA nucleotide on a transcript. May or may not affect the identity of the amino acid. 13. tRNA molecule finds the correct amino acid in the cytoplasm that is required and delivers it to the ribsome, matching its anticodon to the codon of the mRNA. 14. Terminator region of a gene a specific genetic sequence inserted in a seed of DNA 15. Termination stage: ** The stage that ends the process of both Translation and Transcription. At the end of each gene there is a region called the termination region that lets the RNA polymerase enzyme that the strand has ended. ** 16. Transcription: ** The process by which an RNA is assembled from nucleotides using a gene region in DNA as a template. This is the first step in protein synthesis. ** 17. Translation: ** At ribosomes, information encoded in an mRNA guides synthesis of a polypeptide chain from amino acids. This is the second stage of protein synthesis. ** 18. Triplet: ** The complementary three base sequences in DNA. **


 * __ 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 gene_, 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. transciption __: is the first step, where the DNA message is__ __copied into a complementary code called__ a codon. __This process occurs inside the nucleus as DNA__ never __leaves the nucleus.__ __B.__ Translation : 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 nucleotides __. (they are both classified as polynucleotides).__ __2. DNA is a__ double helix _ __strand, RNA is a__ single strand. 3. DNA uses the sugar deoxyribose _ RNA uses the sugar ribose. 4. DNA uses nucleotides A, C, G &** T **_, __RNA uses nucleotides A, C, G &__ ** U_ **.
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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...(DNA) AUG UUC UAU TGT AAA CAG TAA ..(.RNA)

(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. Messenger _ 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. Ribosomal 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. Transfer 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. Helicase DNA : 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. Nucleotide bases __: 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__ 5' _ __end toward the__ 3' _ __end of the original DNA molecule.__

__c. The new RNA molecule is “growing” from the__** 3' ** __end to__** 5' ** __the__ __end.__ __d. Unlike the DNA Polymerase enzyme, this enzyme uses the nucleotide__ __e. Each gene is responsible for regulating its own activity.__ 
 * __ uracil __**(U) instead of __** thymine **(T) as the complement to Adenine (A)__

__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 ** PROMOTER **__ __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__ ** RNA POLYMERASE ** 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.

G. Several modifications (finishing touches) are made to the pre-RNA strands before they leave the nucleus. 1. A ** METHYLATED CAP **(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 __ **TAIL** 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.__ ** INTRONS **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. ** EXONS **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 3 __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 codon. __ _. 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.  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 AUG ___.__ __c. There are three codons that__ __signal the END of the message.__ __They are:__ UAA, UAG __,__ __and__ UGA.

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

Start, Phe, Tyr, Cys, Lys, Gln, Stop (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 anticodon ___.__ __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.__ Initiation __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 ribosomal subunit __. b. the ribosome begins to move along the mRNA strand “looking” for a specific mRNA codon called the start __codon (AUG).__ __c. an__ initiator 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. Elongation 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.

3. _ Termination STAGE: this ends the process of translation. a. the elongation stage continues until the ribosome reaches a specific codon called the _ stop codon. Since there is no tRNA that recognizes this message, the process stops. b. Special proteins known as release __FACTORS trigger the mRNA and protein to break away from the Ribosome.__

__**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.**__ __**7. Any change in the DNA sequence that alters the genetic code and may change the**__ __**protein being produced is called a mutation **__**. 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. Base pair substitution 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. Frame Shift __MUTATIONS: occur when an__**
 * __additional nucleotide is added to the sequence ( insertion ___) or**
 * one nucleotide is removed from the sequence ( deletion ). The effects of this type of mutation are very severe because many codons are affected.**


 * B. There are a number of known factors that may cause mutations:**
 * 1. ionizing radiation _: most commonly caused by x-rays.**
 * 2. non ionizing radation ___: most commonly caused by ultraviolet rays from the sun (or tanning beds).__**
 * __3.__ harmful environmental ___ AGENTS: natural and synthetic chemicals that attach to the nitrogenous bases or phosphate groups in DNA.__**


 * __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:__

__**a. What would be the correct amino acid sequence formed from this mRNA?**__ med-pro=askp=asn-ile-lys-stop

__**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’.__**  __ * __

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

med-pro-asp-his-ile-lys-stop __**b. How many amino acids remained the same after the mutation occurred?**__ 6 __**c. How many changed as a result of this mutation?**__ 1 __**d. Why are all of these types of mutations not necessarily harmful?**__ It only affects one amino acid and may or may not change the desired amnio acid in the final protein because more than one codon can signal for some amino acids.

__**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’.__**  __ * __

__**a. What is the new amino acid sequence produced from this mRNA?**__ med-pro-asp-glu-tyr-stop-val

__**b. How many amino acids remained the same as a result of this mutation?**__ 3 __**4. Which mutation had the greatest effect on the protein chain and why?**__ Frame Shift because only one letter was added which changed the rest of the amino acid sequence.

__**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.**__ ** Transcription __: takes place in the nucleus and converts the DNA into RNA. It involves 3 stages:__**
 * __a.__ Initiation : RNA Polymerase attaches to one section of a DNA strand and begins to “read” the DNA.**
 * b. Elongation __: RNA Polymerase continues to “read” the DNA strand creating a longer and longer RNA molecule.__**
 * __c.__ Termination : RNA Polymerase stops “reading” the DNA and releases the RNA molecule.**
 * 2. Modifications of the RNA: before the molecule can leave the nucleus, several changes need to be made.**
 * a. A Guanine Cap is added to the 5’ end**
 * b. A Poly-A tail is added to the 3’ end**
 * c. Introns __are removed from the RNA molecule__**
 * __d.__ Exons 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. Initiation : mRNA attaches to the ribosome and the initiator t-RNA attaches to the mRNA.**
 * b. Elongation : 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. Termination : 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. Messenger __RNA (mRNA): carries the secret CODE out of the nucleus and delivers it to the ribosomes__**
 * __2.__ Transfer 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. Ribosomal __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.__**

__//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