AP Biology Name : Chapter 17 Guided Reading Assignment

AP Biology Chapter 17 Guided Reading Assignment 1. What did Garrod mean by “inborn errors of metabolism?” Garrod was the first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell. Garrod postulated that the symptoms of an inherited disease reflect a person’s inability to make a particular enzyme. 2. Describe the Beadle and Tatum experiment with mold in detail – use the diagram below to help. The logic behind both the experiment and the results are critical. Tatum and Beadle where inquiring if individual genes specified the enzymes that function in a biochemical pathway. Working with the mold Neurospora crassa, they isolated mutants that required arginine in their growth medium. Research showed that the mutants fell into three different classes that each was defective in a different gene. This experiment tested there one gene- one enzyme hypothesis and their postulated arginine-synthesizing pathway. In this experiment, they grew their 3 different mutants and four different conditions. Wild Type/ Class 1/ Class 2/ Class 3 Mutants Mutants Mutants 3. What was Beadle and Tatum’s final hypothesis? Beadle and Tatum’s final hypothesis was “ one gene-one polypeptide hypothesis”. 4. Why does the “code” have to be in triplets and not singles or doubles? Triplets of nucleotide bases are the smallest units of uniform length that can code for all the amino acids. If each arrangement of three consecutive bases speficies an amino acids, there are 64 possible code words, which are more than enough to specify all the amino acids. If each nucleotide base were translated into an amino acid, only four of the 20 amino acids would be specified. A two-base sequence would only give 16 possible arrangements, either one would not be enough. 5. What is the template strand? The DNA strand that provides the pattern, or template for ordering the sequence of nucleotides in an RNA transcript. 6. Compare and contrast the codon and anticodon? A codon is a three-nucleotide sequence that specifies a particular amino acid or termination signal; the basic unit of the genetic code. An anti-codon is a nucleotide triplet that recognizes a particular complementary codon on a mRNA molecule. 7. How did Nirenberg “figure out” which amino acids went with which codes? He synthesized an artificial mRNA by linking identical RNA nucleotides containing uracil as their base. The message would contain only one codon in repetition; UUU. Nirenberg added this “poly-U” to a test-tube mixture containing amino acids, ribosomes, and the other components required for protein synthesis. His system translated the UUU into a polypeptide containing man units of the amino acids phenylalanine. From there he determined that the mRNA codon UUU specifies the amino acid phenylalanine. Other amino acids specified by codons went on to be discovered. 8. What is the reading frame? On an mRNA it is the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis. 9. What conclusions can be drawn from the similarities of the genetic code among living organisms? It is a language that is shared by all living things and it must have been operating very early in the history of life. Early enough to be present in the common ancestor of modern organisms. In laboratory experiments genes can be transcribed and translated after being transplanted from one species to another. 10. What is a transcription unit? A region of the DNA that transcribed into an RNA molecule. 11. Describe the prokaryotic promoter and terminator. Promoter- A specific nucleotide sequence in DNA that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place. The terminator is a sequence of nucleotides in DNA that marks the end of a gene and signals RNA polymerase to release the newly made RNA molecule and detach from the DNA. 12. Contrast termination of transcription for prokaryotic and eukaryotic organisms. Bacteria- Transcription proceeds through a terminator sequence in the DNA. The transcribed terminator functions as the terminator signal, causing the polymerase to detach from the DNA and release the transcript, which is available for immediate use of mRNA. Eukaryotes- RNA polymerase 2 transcribes a sequence on the DNA called the polyadenyltion signal sequence , which codes for a polyadenylation signal in the pre-mRNA. Then, at a point about 10 to 35 nucleotides downstream from the AAUAA signal, proteins associated with the growing RNA transcript cut it free from polymerase, releasing the pre-mRNA. 13. Why is important that the promoter be upstream of the transcription unit? It has to start upstream because the mRNA has to be transcribed in a 5’ to 3’ sequence. 14. Why is RNA processing necessary? Both ends of the primary transcript are altered. In most cases, interior sections of the RNA molecule are cut out and the remaining parts spliced together. These modifications produce an mRNA molecule ready for translation. 15. What does adding a 5’ cap and poly A tail mean and why is it important? The 5’ Cap is a modified form of a guanine( G) nucleotide added onto the other 5’ end transcription of the first 20 to 40 nucleotides. At the 3’ end , an enzyme adds 50 to 250 more adenine ( A) nucleotides, forming a poly-A- Tail.. They facilitate the export of the mature mRNA from the nucleus, they help protect the mRNA from degradation from hydrolic enzymes, and they help ribosomes attach 5’ end of the mRNA once the mRNA reaches the cytoplasm. 16. Define the following terms: a. RNA splicing- The removal of introns of the transcript that will not be included in the mRNA. b. Introns- A non-coding intervening sequence within a primary transcript during RNA processing; also refers to the region of DNA from which this sequence was transcribed. c. Exons- A sequence within a primary transcript that remains in the RNA after RNA processing; it also refers to the region of DNA from which this sequence is transcribed. d. Spliceosome- A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons. e. snRNP’s - Small nuclear ribonucleoprotines. These particles recognize splice sites. They are located in the cell nucleus and are composed of RNA and protein molecules. f. ribozymes- An RNA molecule that functions as an enzyme, catalyzing reactions during RNA splicing. g. UTR- Untranslated Regions. They are at the ends of the 5’ and 3’ end. They are part of the mRNA that will not be translated into protein, but they have other functions, such as ribosome binding. h. Alternative RNA splicing- A type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns. i. Domains- Independently folding parts of proteins. 17. Describe the structure and function of transfer RNA. The function of tRNA is to transfer amino acids from the cytoplasmic pool of amino acids to a ribosome. It has four-base paired regions and three loops. There is base sequence of the amino attachment at the 3’ end. The The anticodon triple is unique to each tRNA. 18. Why is the enzyme aminoacyl-tRNA synthetase important to translation and protein synthesis? The correct matching up of tRNA and amino acid is carried out by a family of related enzymes called aminooacyl-tRNA synthetases. The active site of each type of aminoacyl-tRNA synthetase fits only a specific combination of amino acid and tRNA. 19. What is “wobble”? Flexibility in the base-pairing rules in which the nucleotide at the 5’ end of a tRNA anticodon can form hydrogen bonds iwht more than one kid of base in the third position ( 3’ end) of a codon. 20. Detail the steps of initiation of translation. 1. A small ribosomal subunit binds to a molecule of mRNA. In a bacterial cell, the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon. An initiator tRNA, with the anticodon UAC, base-pairs with the start codon, AUG. This tRNA carries the amino acid methionine. ( MET) 2. The arrival of large ribosomal subunit completes the initiation complex. Proteins called initiation factors are required to bring all the translation components together. GTP provides the energy for the assembly. The initiator tRNA is in the P site; the A site is available to the tRNA bearing the next amino acid. 21. What are polyribosomes? A group of several ribosomes attached to, and translating, the same messenger RNA molecule. 22. What is an example of a post translational modification of a protein? The protein insulin if first synthesized as a single polypeptide chain but becomes active only after an enzyme cuts out a central part of the chain, leaving a protein made up of two or more polypeptides chains connected by disulfide bridges. 23. What is a signal peptide? A sequence of about 20 amino acids at or near the leading end of a polypeptide that targets it to the endoplasmic reticulum or other organelles in a eukaryotic cell. 24. What is a signal recognition particle? A protein- RNA complex that recognizes a signal peptide as it emerges from a ribosome and helps direct the ribosome to the endoplasmic reticulum by binding to a receptor protein on the ER. 25. You are responsible for the content in Table 17.1 on page 327. 26. Define the following terms: a. Mutations- A change in the nucleotide sequence of an organism’s DNA, ultimately creating genetic diversity. Mutations also occur in the DNA or RNA of a virus. b. Point mutations- A change in a gene at a single nucleotide pair. c. Base pair substitution- A type of point mutation; the replacement of one nucleotide and its partner in the complementary DNA strand by another pair of nucleotides. d. Missense- A base-pair substitution that results in a codon that codes for a different amino acids. e. Nonsense- A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein. f. Insertions- A mutation involving the addition of one or more nucleotide pairs to a gene. g. Deletions- A mutational loss of one or more nucleotide pairs from a gene. h. Frameshift mutation- A mutation occurring when the number of nucleotides inserted or deleted is not a multiple of three, resulting in the improper grouping of the subsequent nucleotides into codons. i. Mutagen- is a physical or chemical agent that changes the genetic material, usually DNA, of an organism and thus increases the frequency of mutations above the natural background level 27. How has a gene been “redefined” and why? The molecular definition of a gene must be broad enough to include the DNA that is transcribed into rRNA, tRNA, and other RNAs that are not translated. These genes have no polypeptide products but play crucial roles in the cell. The new definition is : A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule.