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Bio Block 3 Study guide

by: Bennett Notetaker

Bio Block 3 Study guide Bio 130, 15017

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Covers everything on the pink sheet that is given out at the beginning of each block.
BIO130LEC000:Perspectives in Human Bio
James Lafountain
Study Guide
Genetic code, mutations, Codon
50 ?




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This 5 page Study Guide was uploaded by Bennett Notetaker on Thursday April 7, 2016. The Study Guide belongs to Bio 130, 15017 at University at Buffalo taught by James Lafountain in Spring 2016. Since its upload, it has received 482 views.


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Date Created: 04/07/16
Pink Sheet Answers for Block 3: 1. Transcription happens in the nucleus. Translation of mRNA takes place in the cytoplasm. Within the ribosomes mRNA processing occurs. Newly made proteins will function if folded properly (there are many different factors look at first set of notes). 2. Small and large subunits of ribosomes come together to make functional ribosome after mRNA is translated so that they can bind to the mRNA. Ribosomes split apart once they are done reading mRNA molecule. During initiation RNA polymerase binds to DNA at the promoter region and separates the complementary strand. During elongation RNA is synthesized from the template and RNA polymerase moves along the DNA, elongating the RNA transcript molecule, an enzyme forms the hydrogen bonds between the bases of the DNA strand and the complementary bases of the RNA molecule found in the nucleus. During termination RNA polymerase reaches the terminator region and acts as a termination signal; the enzyme triggers the release of the new RNA. Polysomes are the backbone of mRNA and are where ribosomes are attached and the growing mRNA molecules are translated by these ribosomes. 3. GUG codon matched with val-tRNA anticodon move to site ‘A’ and peptide bond forms linking val 2 and 1. The enzymatic activity of ribosome catalyzes the peptide bond. Elongation continues when ribosome moves, causing val-tRNA to occupy site ‘P’ and then site ‘A’ becomes unoccupied (translocation) so ‘P’ site fills ‘A’ site. 4. The genetic code is the sequence of nucleotides that encodes the information for amino acids in a polypeptide chain. It uses codons. It’s a set of 64 triplet bases or codons that correspond to the 20 amino acids in proteins and signals for initiation=RNA and is 1 codon and termination which is 3 codons or polypeptide synthesis. The 60 other code words are specific for an amino acid. 5. rRNA is the structural and functional components of ribosomes and tRNA helps incorporate amino acids into polypeptide chains, whereas mRNA actually carries the genetic code for synthesis of proteins and that’s why it is considered coding and the other two are not. 6. When a tRNA is ‘charged’ it means that it has an amino acid attached to it and the charged tRNA reads the codon of mRNA during translation. ‘Uncharged’ means no amino acid is attached. Charging occurs within the cytoplasm on the site of the ribosome. 7. Codons are 3 letter code words that exist in the open reading frame of mRNA. An anticodon is a 3-base sequence on tRNA that has to match the codon on mRNA. AUG is the start codon. There are three different stop codons; UAA, UGA, and UAG. A stop codon, tells ribosomes to stop translating. 8. A transcription ‘bubble’ is molecular structure that occurs when a limited portion of the DNA double stranded is unwound this creates the bubble look. Once the polymerase passes it returns to normal. The bubble is related to the DNA template because the mRNA polymerase uses the DNA template to create a RNA transcript. The bubble is related to ribonucleotide used in transcription because the bubble allows the reading of the template strand to happen. This is helpful for the mRNA polymerase to run along the template strand which helps create ribonucleotide bases used in transcription. 9. The trunk of a ‘fir tree’ is the DNA strand and the branches are the RNAs and the increase in length. The RNA polymerase is in the active site of RNAP. 10. The DNA template strand of a gene is CGGATCAT then the sequence of nucleotides in the RNA transcript would be GCCUAGUA. Note that the T gets replaced with a U because typically A matches with T. 11. If the ‘average length’ of a mature mRNA is 1500 bases then there should be about 1500^5 amino acids. 12. There must be 20 amino acids and at least 20 tRNAs to make a polypeptide. A cell’s tRNAs come from transcribed DNA or the nucleus. A cell’s amino acids that are used to make protein come from charged tRNAs. Ribonucleotides come from the anti- codon section of the tRNAs. 13. Chromatin remodeling is related to control of gene expression because gene expression can be activated and inactivated through the condensing process of chromatin remodeling. Histone acetylation or phosphorylation achieves chromatin remodeling because acetylation allows unwinding, while phosphorylation allows for wining. 14. RNAs are transported from the nucleus to cytosol through nuclear pores within the nuclear envelope. Proteins are transported from cytosol to the nucleus through nucleo- cytoplasmic transport. Typically, nuclei have 3000-4000 pores. 15. Conservative missense differs from non-conservative because with conservative missense mutation the product has similar chemical properties with what it is supposed to be, and non-conservative missense mutations are products with different properties with what it is supposed to be. A sense mutation takes a ‘stop’ codon and converts it to a coding codon. Sense mutations lead to longer than normal polypeptides. After a nonsense mutation there are shorter proteins. UAA, UGA, and UAG are the codons found at the site of nonsense mutation. 16. A frameshift mutation is an effect of a mutation, frameshift mutation is when a letter of the reading frame is either added or deleted. This affects the open reading frame because the codons then will be switched or altered: For example, AAC-CCCAA-CCC. 17. Spontaneous depurination of DNA is when the base from DNA is lost and in its place is an OH group. This process of depurination occurs within the cytosol. Adenine is the base selected to pair with the free hydroxyl generated by depurination when guanine is lost. 18. Common sources of ionizing radiation are X rays, cosmic rays, radon, and gamma rays. Ionizing radiation causes mutation of DNA because it makes the bases GC to turn into TA. The significance of 8-oxo-7, 8 dihydrodeoxyguanine in regards to the generation point of mutations is that free radicals are short-lived entities with unpaired electrons that can damage bases. Antioxidants are protection because it donates electrons to free radicals. Free radicals are uncharged molecules that have an unpaired valence electron. 19. Thymine dimers are when pair thymines are connected and become a single entity due to UV radiation. UV lights does cause these. DNA structure and DNA replication is affected because thymine dimers cause speed bumps for DNA polymerase, these bumps can cause the polymerase to misread. Dimerization does affect transcription of a gene because it can block transcription and DNA replication. 20. DNA repair enzymes essentially fix the nucleotide mutation by detecting, cutting, creating, and replacing mutated sections. This activity is evident in the nucleus. 21. Nitrous acid is a chemical mutagen. It originates in your body from foods that are high in nitrates such as hot dogs, or smoked foods. Nitrous acid figures in generating base substitutions in DNA because it makes AT turn to GC. 22. Genetic disease like Marfan syndrome and cystic fibrosis are so common because the larger a gene is the higher the probability that it will undergo a spontaneous mutation. 23. In terms of the CFTR protein, cystic fibrosis is when chloride cannot get out of the CFTR protein because there is no ION channel, 189000 bases, on chromosome number seven, 1480 amino acids, a transmembrane glycoprotein. This protein is apart of the membrane on lungs pancreas, and skin on chromosome #7. 24. Deletions and missense mutations are involved in producing the two variants of cystic fibrosis that are named deltaF508 and G551D because deltaF508 is when there is a loss of amino acid or deletion. Missense mutation causes protein to misfold, which looks bas so proteolysis destroys it. G551D is when there’s a base substitution. The G gets replaced with aspartic acid (D). This makes the protein but has closed gates when it comes to letting chloride through. 25. Dry, thick mucus blocks airways is the phenotype of the deltaF508. Also, protein is targeted for proteolysis because it is folded oddly. Wild-type CFTR don’t have blocked proteins, chloride can flow through the proteins, chloride can flow through the proteins and therefore do not have thick and dry mucus airways and that’s how the pancreas and lungs are affected. Instead, they are moist and fluid. The wild-type CFTR exhibits complete dominance over a mutant allele. 26. The molecular phenotype of the G551D variant of CF is the protein is altered so that the function is impaired. The CFTR protein gets folded so that the chloride can get through. Kalydaco binds to the CFTR channel to help open up the ion channel and it’s a recessive allele. 27. The protein fibrillin (FBN) in Marfan syndrome is different from the wild-type FBN because the FBN is a mutant dominant gene. The relationship of fibrillin to human growth factors during muscular-skeletal development is that usually long arms, legs, fingers, pinched sternum, and weak joints occur. Marfan syndrome typically finds the heart defective in deaths. This was true for Flo Hyman. The Marfan phenotype is expressed in people heterozygous for the defective gene because the Marfan disease is a dominant gene. FBN is dominant and the wild type is recessive. 28. Huntington disease is autosomal dominant. It’s a large gene passed from parents for a mutation. A looped structure forms in the daughter DNA which causes an increase in CAG repeats. The HTT protein is a strong of nucleotide repeats of CAG, while Htt contains a string of polyglutamine repeats. 29. The mutant HTT is autosomal dominant and HD is evident in the nervous system. 30. The metabolism includes digestion, synthesis, energy conversions coupling release to demand. Enzymes are used to help produce a product once combined with substrate. 31. An enzyme is a protein that catalyzes a specific biochemical reaction and is not altered in the process. The product of one reaction is substrate for the next reaction within the pathway. A downstream product is a substrate for an upstream reaction, creating a loop or cycle. 32. PKU or phenylketonuria was a genetic trait altered by biochemical pathways. The gene is known, it’s a mutations in the PAH gene consisting of nonsense, missense and splicing mutations. To avoid full effects infants are put on a low PKU diet. The Guthrie test uses blood sample from newborn babies within the first week of birth to test their enzymes like B-2 thienylalanine Phe. Bacteria grew due to Phe being converted to tyrosine, which is used for growth. 33. PKU and galactosemia as autosomal recessive disorders are basically two copies of an abnormal gene passed through families. Galactosemia is heritable that is associated with the inability to metabolize sugar. If a galactosemic infant has milk it can be toxic. Florescence emission is a mixture based on fluorimetry and the Beutler tests is based on this of the downstream products of GALT. NADP+ is not fluorescent and is in an oxidized state. NADPH is in a reduced state and is fluorescent.


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