Unit 2 & 3 Bio PDF

Unit 2 - Slides 82-104 Unit 3 – Slides 1-73 What are lethal alleles? - When the recessive or dominant (heterozygous or homozygous) genotype results in the death of the organism What is the ratio of recessive lethal alleles? - 3:0 instead of 3:1 What is the ratio for dominant lethal alle...

Unit 2 - Slides 82-104 Unit 3 – Slides 1-73 What are lethal alleles? - When the recessive or dominant (heterozygous or homozygous) genotype results in the death of the organism What is the ratio of recessive lethal alleles? - 3:0 instead of 3:1 What is the ratio for dominant lethal alleles? - 0:1 instead of 3:1 What is epistasis? - When one specific allele controls the function of another. What is the ratio for epistasis? - 9:3:4, instead of 9:3:3:1 What are multiple alleles? - When dominant alleles can coexist to create a phenotype while still overpowering a recessive allele (e.g., blood types), multiple genes can be necessary to confer a single trait. What is sex-linked inheritance? - Genes located at the sex chromosomes What is X-linked inheritance? - Genes passed through the X chromosome. When is the sex determined? - After 6-8 weeks, the SRY (i.e., sex-determining region of the Y) is activated, which can result in the development of testes. Is the X chromosome responsible for the genes for sex determination? - No, most genes governing the structures expressing one’s sex are found on autosomal chromosomes. Does the father carry the gene for the male reproduction system? - No, it is the mother who carries the genes coding for the penis structure, proving that you can possess genes and not express them. If it skips a generation, what is most likely the inheritance pattern? - Recessive If affected fathers have only affected daughters, what is the most probable inheritance pattern? - X-linked dominant If affected mothers have only affected sons, what is the most probable inheritance pattern? - X-linked dominant What is transcription? - Process of converting DNA to RNA What is translation? - Process of converting RNA to protein What is responsible for transcription? - RNA polymerase What is the difference between the coding and template strand? - 5’ to 3’ is the coding strand, while 3’ to 5’ is the template strand which is used for transcription How does RNA start? - With methionine (TAC) in the template strand What are the three “Stop” codons? - All in 3’ to 5’: ATT, ACT, ATC How does transcription/translation differ between prokaryotes and eukaryotes? - In prokaryotes, mRNA is immediately available and translated into proteins, while in eukaryotes, it is first processed (pre-mRNA à mRNA) to be then translated. What is left out in translation but not in transcription? How many of them are there? - Exons, introns – 1 What are codons? - Triplet of nitrogenous bases that make up the genetic code How are mRNA oriented? - mRNA molecules are always oriented in the 5’ to 3’ direction What strand does the RNA polymerase use to transcribe? - The template strand What makes for a nonheritable mutation? - A non-inheritable mutation occurs in somatic cells, while heritable mutations are present in the allele. What are SNPs? - Single nucleotide polymorphism only impacts one gene but can be for more than one nucleotide. What is a germline? - Sex cells What are the two types of SNPs? - Base substitutions - Frameshift mutation What are the three types of base substitutions, and what do they entail? - Missense mutations: change in nitrogenous base altering the identity of one amino acid, which can have moderate to deleterious effects since it affects the reactive site on the protein - Nonsense mutations: Generates an early stop codon since the nitrogenous base is switched, leading to the shortening of the protein, which can have severe effects - Silent mutation: change in nitrogenous base that does not affect the identity of an amino acid, mostly no effect Give an example as to why missense mutations can be so drastic. - Serine, an uncharged polar A.A., can easily turn into proline, a nonpolar A.A., leading to a significant change in the structure of the protein. What is the basis of frameshift mutation? - It is the insertion or deletion of a nitrogenous base, evidentially leading to a change in the reading frame (a premature stop codon). What is a Large Chromosomal rearrangement (LCRs)? - A mutation with a much larger effect than SNPs, 1000+ nucleotides are changing. What is deletion (LCRs)? - The removal of a segment of a gene can cause disastrous effects on the normal function of cells (e.g., the deletion of chromosome 5 resulting in the disorder named cri-du-chat) What is duplication (LCRs)? - Occurs if a segment is broken from one chromosome and inserted into its homologue. In the receiving homologue, the fragment is added to the alleles (e.g., hemoglobin). What is translocation (LCRs)? - Occurs if the broken segment is attached to a different nonhomologous chromosome (same basis as a crossover in meiosis, but for nonhomologous) [e.g., Burkitt lymphoma, where chromosomes 8 and 14 switch segment] What is an inversion (LCRs)? - Occurs if a broken segment attaches to the same chromosome but in a reversed orientation. [e.g., 5 chromosome pairs show to have been translocated/inverted] What is a UTR? - Untranslated region, the region before/after the coding sequence. What are the three transcription steps? - Initiation, elongation, termination What is a transcription factor? - Proteins with an active site can bind to specific DNA and regulate gene expression by promoting or suppressing gene expression. What is an operator? - Place where repressor attaches, contain the genetic information necessary to start transcription What is a promoter? - Recruits necessary proteins to initiate transcription. Contains DNA sequences such as TATA (24%) on which transcription factors will bind. It is found in eukaryotes and archaea. What is “initiation” in transcription? - Transcription factors bind to the promoter and together recruit RNA polymerase. True or false: Only one transcription factor is necessary to initiate transcription? - False, several are necessary to do so When does initiation begin in transcription? - Once RNA polymerase binds to the DNA What happens during elongation in transcription? - DNA is unwound while new complementary RNA bases are added to newly formed RNA strand What is a dimer? - Hybrid of DNA-RNA double-helix When can a dimer be found? - After transcription, the DNA rapidly rewinds to a double-stranded molecule. What is the step where RNA polymerase is released? - Termination What do you find after the termination of transcription in eukaryotes? - Pre-mRNA still must be processed. What is RNA polymerase I in Eukarya? - Transcribe DNA into rRNA (ribosomal) What is RNA polymerase II in Eukarya? - Enzymes used to transcribe protein-coding genes (mRNA) What is RNA polymerase III in Eukarya? - Enzymes used to transcribe DNA into tRNA (transfer) and some parts of rRNA What are the three differences between eukaryotes and prokaryotes in transcription? - No transcription factor, RNA polymerase binds directly to promoters - There is no pre-mRNA processing - Termination is done either by the mRNA sequence binding to itself in a hairpin shape or by a protein factor that terminates transcription. Paint a picture in your head of tRNA. What does an amino acid chain start and end with? - Starts with an N-terminus end and ends with a C-terminus end What is an anticodon? - Trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule Describe polypeptide synthesis. - The anticodon is antiparallel to the mRNA’s codon - The amino acid is attached to the 3’ end of tRNA How many tRNAs are there? - 61 (one for each codon except the STOP codons) How does tRNA bind to mRNA? - Complementary base pairs What is the role of ribosomes? - Facilitate the interaction between tRNAs and mRNA molecule and hold the chain of growing A.A. Consists of the 1% of enzymes that are not proteins. How is the anticodon read? - 3’ to 5’ (complementary to 5’ to 3’ of RNA) Where do tRNA molecules enter the ribosome? - The aminoacyl site (A) Where is the transfer of amino acid from tRNA to polypeptide chain done? - The peptidyl site (P) Where is the “empty tRNA exit? - The exit site (E) What does the modified guanine at the beginning and end do? - The UTR protect the ends of the mRNA, it acts as the end of a zipper, making it possible for the ribosome to insert into the start piece. What is the first step of translation, and what does it consist of? - Initiation: after having latched on the ribosome, methionine provides energy by bond breaking (GTP) to quickly start the search for the correct reading frame What is the second step of translation, and what does it consist of? - Elongation consists of four sub-steps. - I) After the reading frame is established, A.A. can start to be used - II) The peptidyl transferase facilitates the bond between A.A. and tRNA - III) Due to the effect of the peptidyl transferase, A.A. break off tRNA but stays attached to the previous A.A. - IV) New tRNA enters the ribosome until the STOP codon How does elongation differ between prokaryotes and eukaryotes? - It is much slower in eukaryotic cells due to the larger variety in proteins and their complexity What is the final step of translation, and what does it consist of? - Termination is indicated by the stop codon, but the tRNA does not associate with it; release factors do (a placebo of tRNA). T/F: a single ribosome is responsible for a single mRNA. - False, multiple ribosomes, called polysome, simultaneously translate a single mRNA since it is a fragile molecule which degrades easily T/F: Proteins are formed by the translation of mRNA. - False, the result of translation is a chain of polypeptides. To have a fully formed protein, the polypeptide needs to be arranged by chaperons. T/F: Genes expressed in all cells are called housekeeping genes - True What is one of the main functions of E.coli? - Three genes that control the metabolism of lactose T/F: One of the three genes in lactose can be transcribed without the others - False, all the genes are under the control of the same promotor. What is an operon? - Sequence of gene, promotor and operator involved in a metabolic pathway What will happen if lactose is absence of lactose to the lac transcription? - The lac repressor, encoded by lacI, binds to the receptor, preventing transcription What binds to the receptor if lactose is present and what results from it? - Since the affinity of the lac repressor is not 100%, ß-galactosidase will already be formed and have converted some of the lactose to allolactose, the repressor’s inhibitor. With the “suppression” of the repressor, lactase transcription results. How is the repressor inhibited in lactase? - Allolactose enters the binding site for the inducer and makes the repressor come off the operator What is a system like lactose transcription called? - Inducible system, the neutralization of a repressor What does catabolism mean? - Degradation of molecules, which produces energy (e.g., lac) What does anabolism mean? - Construction of molecules, which consumes energy (e.g., trp) How does the trp repressor differ from the lac repressor? - The trp repressor is inactive and will not normally stop the production of trp unless there is already trp while the lac repressor is active, meaning it will suppress transcription unless lactose is present. Why is trp produced unless there is already some and not lac? - Trp is an essential amino acid, it cannot hurt to have more, while lac is not necessarily the main source of glucose. T/F: The lac operon is said to be repressible, while the trp operon is said to be inducible - False, the lac operon is said to be inducible since it is normally inhibited, while the trp operon is said to be repressible since the repressor needs to be activated. ^ In short, describe the relation between lac operons and trp operons. - Lac present: repressor à not activated à transcription happens - Lac absent: repressor à activated à transcriptions do not happen - Trp present: repressor à activated à transcription does not happen - Trp absent: repressor à not activated à transcription happens