Exam 1 Study Guide PDF

Exam 1 Study guide Pre-genetics Material 1. What are the 5 social experiences that the brain treats as physical threats when violated S.C.A.R.F. S🡪 Status, the feel...

Exam 1 Study guide Pre-genetics Material 1. What are the 5 social experiences that the brain treats as physical threats when violated S.C.A.R.F. S🡪 Status, the feeling of knowing that we have equal or higher importance than others C🡪 Certainty, the ability to predict the future or having confidence in what will happen next A🡪 Autonomy, know that we are in control of our surrounding and what happens to us R🡪 Relatedness, a sense of familiarity with other that brings a sense of safety F🡪 Fairness, knowing that we hare treated fairly and no one get priority over us. 2. Describe the difference between the following: a. Skepticism vs denial Skepticism: To doubt the truth of something due to evidence to the contrary. Tends to deepen conversation and debate, leads to better understanding Denial: To refuse to believe something despite supporting evidence and a lack of evidence to the contrary. Tends to shut down conversations and strain relationships b. Correlation vs causation Example: More people who have traffic accidents text a lot Correlation: When two events are related Traffic accidents and texting are both related to age. More young people text and also have less experience behind the wheel and thus get into accidents. Causation: When one event causes another Texting directly causes accidents. People who have accidents admit to texting while behind the wheel taking their eyes away from the road and causes the accident. c. Scientific evidence vs alternative facts Scientific evidence: Evidence bases on objective testing based in the scientific process. Alternative facts: Untruths often told in denial of scientific evidence usually used to sway people into some way of thinking or type of action. 3. What are the three levels of the brain and how are they different? Alligator brain (lower brain): the oldest part of the brain. The first to evolve and first to develop in childhood. This is the seat of basic involuntary functions like breathing and well as the sources of strong primal emotions and the fight/flight/freeze response. Information passed through this portion BEFORE heading to the higher functioning systems. Midbrain: The next level of the brain to evolve and develop. Also the seat of raw emotions and the next place information passes through before moving up to the last portion  Neocortex: The newest portion of the brain and is associated exclusively with humans. This is the seat of logic in the brain and also the last part to receive information after passing through the alligator and mid brain filter. 4. What’s the different between a control group and an experimental group in a clinical study? A control group is the group that is not exposed to a treatment. They are the baseline for comparison for other treated groups. Often considered the “natural state” An experimental group is a group that is exposed to some changed variable. They are the ones that are compared to the natural state to see how the changing variable affects the group. 5. Based on what we discussed in class, what information should be looked at to determine if information provided is trustworthy or not? Publisher Interviews Key words Sources Chapter 8 See previous study guide and quiz 1 Chapter 9-10 1. The genetic material has to store information and be able to express it. What is the relationship among DNA, RNA, and proteins? DNA is the template used to code for the different types of RNA RNA is used to generate proteins 2. Define replication, transcription, and translation, protein processing. In what part of the cell does each process occur? Replication- Creating a new copy of the DNA sequence- Used for cell division and laboratory analysis. Takes place in the nucleus Transcription- Using the DNA template to generate an RNA molecule which is then processed to have the introns removed. Takes place in the nucleus. Translation- Using ribosomal RNA, transfer RNA, and mRNA to generate a polypeptide chain. Takes place in the cytoplasm on the outside of the rough endoplasmic reticulum. Protein processing- Folding of the polypeptide chain into protein with the help of chaperone proteins. Takes place inside the rough endoplasmic reticulum. 3. What is a start codon? What is a stop codon? Do any of them code for amino acids, if so, which ones? A start codon is the 3-base code on mRNA that indicates the starting point of a polypeptide chain. The code is AUG and it codes for Methionine. Stop codons are 3-base codes on mRNA that indicate the end of the polypeptide chain. They code for release factors instead of amino acids. RF1 recognizes the sequence UAA and RF2 recognizes UAG and UGA. 4. Is an entire chromosome made into an mRNA strand during transcription? No. Within each gene are introns that get removed prior to translation and do not contribute to proteins. On each side of genes are spacer regions that contain non-protein coding DNA as well. At the end of each chromosome are telomeres that act as protection to keep genes at the end of chromosome from being frayed. They break down over time (causing aging) and do not code for any proteins. 5. The following segment of DNA codes for a protein. Uppercase letters indicate exons, lower case letters represent introns, and the LOWER band is the template strand. Given that the RNA polymerase would move from left to right: 1. Indicate orientation (5’🡪 3’) for both the template and non-template strands. 2. Write the FINAL processed mRNA strand sequence that would continue on to translation (be sure to include the pieces that get added). 5’-ACGTTTCGCGATATAGagcgctacactggcgtaCGTAGCATCGATTACTGACcagtcgattacgtacgcaTAGCTAGC-3’ 3’-TGCAAAGCGCTATATCtcgcgatctgaccgcatGCATCGTAGCTAATGACTCgtcagctaatgcatgcgtATCGATCG-5’ mRNA🡪 5’end 5’Cap-ACGUUUCGCGUAUAGCGUAGCAUCGAUUACUGAGUAGCUAGC-3’ poly-A tail 3’end 6. How do promotor regions impact gene regulation? Longer promotor regions, the more tightly the RNA polymerase attaches and thus the more mRNA can be generated and the more protein in generated. Shorter promotor regions result in looser RNA polymerase binding causing it to fall off more often thus less mRNA gets produced and less resulting protein is produced. 7. Explain how the termination sequence of a gene results in RNA polymerase halting mRNA production? The termination sequence of DNA contains a lot of repeat sequence. When that sequence is transcribed into mRNA, it causes the mRNA to for a hairpin like structure. The hairpin changes the shape of the RNA polymerase and make it impossible for the polymerase to stay attached to DNA ending the production of the RNA nucleotide chain. 8. What’s the difference between pre-mRNA and mRNA? Pre mRNA is pre-processed mRNA that still contains introns. mRNA is processed mRNA that has had the introns removed, exons spliced together, a 5’cap added, and a 3’ poly-A tail added. 9. Briefly describe the function of each of the following and state with RNA polymerase produces each: a. rRNA- combines with small proteins to form the large and small subunits of ribosomes that translate mRNA into amino acids. Produced by Polymerase I with the exception of 5S rRNA that is produced by Polymerase III b. tRNA- Carries the amino acid at the amino acid acceptor stem and pairs with mRNA codons at the opposite end called the anticodon. c. mRNA- Caries the code that get translated into amino acid polypeptide chain. 10. What is the different between codons and anti-codons? Provide an example. Codons are 3-base sequences found on mRNA to code for amino-acids. Anti-codons are the 3- base sequences on tRNA that are the compliment of the mRNA codon.  For example if mRNA has the following code UUAGAA, UUA and GAA are two codons. Their compliment, AAU and CUU respectively, are the complimentary anticodon sequences found on two different tRNA. 11. Name the proteins involved in each of the following process: a. Replication initiation i. Origin of replication complex (ORC)- recognizes the origin of recognition and makes an initial opening between the double strands. ii. Helicase- breaks the hydrogen bonds between the complimentary bases. iii. Single stranded binding proteins- bind to the strands of DNA after h-bonds have been broken to keep the strands from rebinding iv. Gyrase- prevents super-coiling of the DNA as it’s opened b. Replication elongation i. Primase- sets down RNA primers along the DNA template strands ii. DNA polymerase- attaches to RNA primers and attached bases as the complementary strand of the template on each side of the open DNA. Construction of complements is done in the 5’ to 3’ direction. This results in a leading and lagging strand. c. Transcription initiation i. RNA polymerase- attaches at the promotor regions and opens the DNA strands d. Transcription elongation i. RNA polymerase- uses DNA template strands to generate mRNA strands. e. Transcription termination i. For genes transcribed by RNA Pol I, there is a specific termination sequence recognized by a protein called Transcription Termination Factor for RNA Polymerase 1 (TTF-1). 1. This protein binds to the recognition sequence AHEAD of the polymerase. 2. When the polymerase reaches the TTF-1 protein, it causes the polymerase and complete mRNA to detach. ii. Genes transcribed by RNA Polymerase II, there is no termination sequence recognized by the polymerase on the DNA. 1. The polymerase will just keep going past the end of the gene 2. Instead there is a restriction site on the mRNA molecule that is recognized by a 5’- exonuclease and causes it to CUT the mRNA at that site releasing the pre-mRNA and nothing extra 3. The rest of the unnecessary RNA is digested by the 5’- exonuclease enzyme and it eats away to RNA until it catches up to the RNA polymerase. Once it reaches the polymerase, it makes the polymerase let go and stops transcription. iii. The mechanisms of termination for RNA Pol III are still not well understood. f. Translation initiation i. 48S initiation complex- Attaches at the 5’ cap, moves through the untranslated region and locates the start codon. Attaches the methionine to the start codon,  releases the initiator proteins from the small ribosomal subunit and triggers a large ribosomal subunit to attach. g. Translation elongation i. Ribosome- moves along the coding region generating the corresponding amino- acid chain sequence. h. Translation termination i. Release factors- RF1 and RF2 recognize stop codons and attach to them when the stop codon enters the A-site of the ribosome. Their binding triggers the release of the ribosome and the end of the polypeptide chain. i. Protein folding i. Chaperones- guide the folding of the polypeptide chains into the final functional protein shape. 12. Draw and name the different parts of an amino acid. Indicate which part defines which amino acid the molecule is? Which parts connect in a peptide bond? H Amino group C Carboxyl group R-group The amino group of one amino acids binds to the carboxyl group of another in a peptide bond resulting in a polypeptide chain. 13. Using the table, determine an ANTI-CODON for Phenylalanine (Phe): Codon combinations for Phe: UUU and UUC Anticodons are the compliment so anticodons are: AAA and AAG respectively. 14. Given the following mRNA sequence, write: a. The DNA template segment that served at the template (with 5’🡪3’) orientation for each  b. The corresponding protein sequence using the table from question 13 c. The tRNA anticodon sequences d. Indicate stop and start codons on the mRNA DNA: 3’- TAC GTA CAA GTC CAC CCG CAT TTG TGA ACT – 5’ mRNA: 5’- AUG CAU GUU CAG GUG GGC GUA AAC ACU UGA – 3’ protein: Start(Met) – His – Val – Gln – Val – Gly – Val – Asn – Thr - Stop tRNA: 3’- UAC GUA CAA GUC CAC CCG CAU UUG UGA ACU – 5’ 15. What are the three binding sites of a ribosome and how do they differ? A-site- The aminoacyl site. The site where new tRNA attaches to it’s corresponding codon P-site- The peptidyl site. The site where the polypeptide chain is anchored. The amino acids on the tRNA in the p-site and a-site. The tRNA in the a-site moves into the p-site and remains attached as the new anchor of the forming polypeptide chain. E-site- The exit site. The now uncharged tRNA in the p-site moves into the e-site where it is released back into the cytoplasm. 16. Describe the 4 levels of protein folding. Primary structure- The simple polypeptide chain Secondary structure- Folding of the polypeptide chain linking amino acids with hydrogen bonds forming either a pleated sheet or helical structure Tertiary structure- helixes or pleated sheets fold in on themselves. Quaternary structure- multiple tertiary structured combine into one lager structure 17. How are prions different from other misfolded proteins? What types of diseases can they cause? Prions are misfolded proteins that act as viruses directly causing diseases like mad cow disease and familial fatal insomnia. They can be familial where they are only inherited genetically and produced during transcription and translation. They can also be infectious where they can be transmitted from organism to organism, find normal versions of themselves and refold them into infectious prion versions. Normal misfolded proteins don’t do the job they’re supposed to, causing a back up in metabolic pathways causing diseases like cystic fibrosis via cascade effect. 18. Do mutations alter proteins folding all of the time? Why or why not? No. Mutations that take place in wobble positions of codons do not cause amino acid changes (and thus protein changes). In addition, mutations in any non-coding region (introns, regions between genes, telomere) also do not affect amino acid sequences. 19. What is a metabolic disease? A metabolic disease is a disease that is a result of a misfolded protein leading to e breakdown in a metabolic pathway. The results in either a build up of a toxic metabolite or a lack of a necessary product in the body. 20. Each compound can have multiple steps along its metabolic pathway. How can changes to one pathway result in different metabolic diseases? Each metabolic pathway has a different substrate and product at each step. Protein issues at any step of a metabolic pathway can cause a different molecule to build up or be lacking leading to different diseases depending on WHICH protein is misfolded. 21. How can we screen for metabolic diseases? i. Check for build of substrates that didn’t get metabolized by the necessary enzyme  ii. Check for deficiency of a product that SHOULD have been produced by a specific enzyme iii. Screen DNA sequences for known mutations leading to misfolded proteins Prokaryotic and viral transcription 1. What are the differences between eukaryotic and prokaryotic gene expression? a. Gene expression is mostly the same with the following differences: b. Prokaryotic genes have an operator region between the gene and promoter. c. They also have multiple genes (associated with one metabolic pathway) for each promoter/operator. d. They have RNA based and Rho dependent transcription termination rather than TTF-1 or exonuclease dependent transcription termination. e. The mRNA has code for multiple proteins on one molecule 2. How are Prokaryotic genes organized? a. 5’ Untranslated region->Promoter->operator-> multiple genes-> 3’ untranslated region 3. Describe RNA based transcription termination. a. Once the RNA polymerase reaches the termination sequence it hits a long series of G’s and Cs , this causes the mRNA to form a hairpin which causes the RNA polymerase to change shape enough that it’s grip is loosened. b. The polymerase then encounters a poly-A sequence, when the U’s are attached, the bonding is weaker and the polymerase and mRNA cannot hold on and both come off. 4. Describes Rho based transcription termination. a. Just like the exonuclease in Eukaryotic RNA polymerase II termination, a Rho protein (that acts as a helicase attaches to the building mRNA at the RUT (Rho Utilization site) and moves along it trailing behind the RNA polymerase. b. The Rho, moving along the mRNA runs into the RNA polymerase. Once it hots ht polymerase, the unbands the mRNA from the DNA and causes the polymerase to detach. 5. What does it mean to be polycistronic mRNA? a. The mRNA contains the code for multiple independent amino acids that fold into different proteins in a metabolic pathway. 6. Describe the viral lytic and lysogenic cycles? a. Lytic cycle: i. The DNA is injected into the host cell, the host genome is destroyed and the transcription and translation machinery starts on the viral DNA producing non- stop (no regulation to stop production). ii. Once the cell is too full of complete viruses, they pop out of the cell, often killing the host cell. b. Lysogenic cycle i. The viral DNA is inserted into the host genome where it is replicated with the host genome during cell division ii. It will remain there until some environmental factor triggers it to switch to the lytic cycle. 7. How are retroviruses different from other viruses and how do they overcome that difference for viral replication? a. Retroviruses have an RNA based genome instead of DNA. b. They have a separate enzyme known as REVERSE polymerase, that transcribes the RNA into DNA and then the normal gene expression process will take place.