The Effects of Climate Change on Biodiversity, Exams of Biology

Download The Effects of Climate Change on Biodiversity and more Exams Biology in PDF only on Docsity! Molecular Biology Final Exam Question and Answers (a) What occurs during transcription? Describe this process in your own words. (b) What is the difference between transcription and gene expression? (c) What is the most common step of regulation for transcription? (Sec 19.1) - a) Transcription produces an RNA chain representing a copy of one strand of a DNA duplex b) Transcription is the first step of gene expression c) Determination of whether or not a transcribe is a gene What do the terms "upstream" and "downstream" mean? (You will need to be familiar with these and the other terms defined on p. 470) (Sec 19.1) - Upstream: Sequences in the opposite direction from expression Downstream: Sequences preceding farther in the direction of expression within the transcription unit. Coding strand and template strand - Coding Strand: The strand that is the exact same as the mRNA Template strand: the strand that is copied by the polymerase In what direction does RNA polymerase move along the template strand? Are nucleotides added to the 3' or 5' end of the growing RNA chain? (Sec 19.2) - RNA polymerase moves 5'- 3' while the nucleotides are added to the 3' end Describe the three stages of transcription. What steps are involved in each stage? (Sec 19.3) - Initiation: Promotor is recognized, bubble is created, and RNA synthesis begins Elongation: as the bubble moves along the DNA; Termination: RNA transcript is released and the bubble closes In bacteria, RNA polymerase is loosely bound to DNA all the time. (a) What component is necessary to change the affinity of RNA polymerase for DNA? (b) How is the affinity of RNA polymerase altered by this component? (Sec 19.4 and 19.6) - a) Sigma Factor b) The sigma factor reduces the affinity for sequence-independent binding and confers specificity for promoters (a) What is a promoter? (b) What are the key features of a bacterial promoter? (c) Why is the -10 box AT rich? (Sec 19.7) - a) The site where RNA polymerase binds the DNA. b) Purine at the start point, the hexameter TATAAT centered at ~10, and another hexameter centered at ~35. c) Located upstream (a) What does "consensus sequence" mean? (b) Is there any bacterial promoter in vivo that has a perfect match for the consensus sequence? Why or why not? (c) How do mutations in promoters affect transcription? (Sec 19.7 and 19.8) - a) An idealized sequence in which each position represents the base most often found when many actual sequence are compared b) no, only related by one or two subunits c) Effect the level of expression of the gen they control without altering the gene products themselves. (a) What are the two types of transcription terminators in bacteria? (b) Why is "pausing" necessary for both kinds of termination? (Sec 19.11, 19.12, and 19.13) - a) Rho Factor and intrinsic termination b) Unknown (a) What is an RNA hairpin? (b) What type of sequences are required for an RNA hairpin to form? (Sec 19.11, 19.12) - a) An RNA sequence that can fold back on itself forming double stranded RNA b) G-C rich region near the base of the stem and needs a unit rich in U residues (a) What does it mean to say that bacteria have "coupled transcription/translation"? (b) Why is this possible in bacteria but not in eukaryotic cells? (c) What process is also occurring to a bacterial transcript at the same time (as transcription and translation)? (Sec 19.17) - a) The process in bacteria where a message is simultaneously being translated while it is being transcribed b) Bacterial mRNA is usually unstable, while eukaryotic mRNA isn't c) Ribosomes beging translating an mRNA (a) Besides having more than one RNA polymerase, what are two major differences between transcription in eukaryotes and bacteria? (b) Describe the significance of each of these differences. (Sec 20.1) - a) Eukaryotes: take place on chromatin and cannot read DNA Bacteria: takes place on a DNA template and can read DNA sequence to find and bind to its promoter splicing apparatus? (b) Describe the function of this site. (Sec 21.3 and Sec 21.5) - a) Branch site b) Lariat intermediate is formed in splicing by joining the 5' nucleotide of the intron to the 2' position of the adenine (a) What are the two main stages of splicing? How do they occur? (Sec 21.5 and Fig 21.5) - a) 5' exon is cleaved off and then joined to the 3' exon b) Lariat intermediate forms; 2 transesterification reactions (a) What is the name of the large ribonucleoprotein complex that carries out splicing? (b) List the four major types of components in this complex. (Sec 21.6 and Fig 21.7) - a) Spliceosome b) 5sRNAs, 41 proteins, 70 splicing factors, and 30 other proteins (a) What is the first step of splicing (carried out by U1 snRNP)? (b) How was this determined experimentally? (Sec 21.7 and Fig. 21.9) - a) Binding U1 snRNP to the 5' splice site via RNA b) Mutations that abolish function of the 5' splice site can be suppressed by compensating mutation in U1 snRNA that restore base pairing. Explain how the presence of introns in a gene may aid in export of the mRNA product to the cytoplasm. (Sec 21.9) - They may prevent transport to the cytoplasm so that transport happens only after splicing is complete. (a) Where are Group I and Group II introns found? (b) How is their splicing different from premRNA splicing? (Sec 21.10) - a) Organelles and bacteria b) They can self-splice (a) Describe alternative splicing (in general). (b) Considering alternative splicing, how accurate is the "one gene: one polypeptide" principle that we discussed in Chapter 2? (Sec 21.11) - a) The production of different RNA products from a single product by changes in the usage of splicing junctions. b) Doesn't work for alternative splicing. (a) Describe the 3' end of a mature mRNA. (b) How is this 3' end generated? (c) What are the functions of this 3' end? (Sec 21.14) - a) Poly A tail b) Cleavage and polyadenylation c) Protects the mRNA from degradation by 3' to 5' exonuclease and a binding site for PABP; helps with translation initiation. (a) What molecule brings in an amino acid to add to the growing polypeptide chain? (b) How does this molecule "read" the mRNA? (Sec 24.2) - a) aminoacyl-tRNA b) By interactions with the rRNA that brought the previous amino acid. (a) What are the three sites on the ribosome that are occupied by tRNA? (Include the letter abbreviation and the full word that gives each site its name.) (b) In what order does the tRNA molecule proceed through these sites? (c) What occurs at each site? (Sec 24.2) - a) A site (aminoacyl-tRNA), P site (peptidyl-tRNA), and E site (deacylated tRNA) b) A site --> P site --> E site c) A site: aminoacyl-tRNA enters to base pair with codon. P site: the tRNA carrying the nascent polypeptide chain. E site: Briefly hold deacylated tRNA before their release Protein synthesis requires accuracy at several stages. Describe three types of errors that can potentially occur during translation. (Sec 24.3) - 1. It can place there wrong amino acid on its tRNA 2. charge its amino acid with the wrong tRNA 3. Frameshift (a) Which ribosomal subunit binds first during translation? (b) What additional proteins are also needed for initiation to occur? (c) What tRNA starts the polypeptide chain? (Sec 24.4 and 24.5) - a) 30s b) Initiation factors: IF-1, IF-2, and IF-3 c) N-formyl-methionyl-tRNA (a) What is the Shine-Dalgano sequence and what is its function? (b) How is this sequence initially "recognized" by the ribosome? (Sec 24.6) - a)The polypurine sequence AGGAGG centered about 10 bp before the AUG initiation codon. The function of this sequence is Paire with its rRNA complement during mRNA ribosome binding to allow translation b) Aligns ribosome with start codon (a) In eukaryotic cells, what is the major mechanism by which the ribosome binds to mRNA and finds the start codon? (b) What is another (minor) pathway by which ribosomes can bind to eukaryotic mRNA? (Sec 24.7) - a)Eukaryotic 40S ribosomal subunits bind to the 5' end of mRNA and scan the mRNA until they reach an initiation site. b) IRES: internal ribosomal entry site During the translation process, what is the function of elongation factors (EF-Tu in bacteria; eEF1α in eukaryotes)? (Sec 24.8) - Brings aminoacyl-tRNA to the A site. (a) What catalytic molecule of the ribosome is responsible for formation of the peptide bond? (b) What is this type of activity called? (Sec 24.9) - a) Ribosomal RNA b) Peptidyl transferase (a) What are termination codons? (b) How many are there? (c) What are their sequences? (d) Are there termination tRNAs? (e) How does translation termination occur? (Sec 24.12) - a) Cause polypeptide translation to terminate b) 3 c) UAG, UAA, and UGA d) no e) Occurs when the stop codon encounters a ribosome (a) The ribosome is a ribonucleoprotein. Is there more RNA or more protein in the ribosome (based on mass)? (b) Describe three important functions of the rRNA components. (Sec 24.1 and others) - a) More RNA b) 1. Catalyze peptide bond formation 2. Forming contacts between ribosomal subunits 3. Interactions with r-proteins (a) How many codons comprise the genetic code? (b) How many of them code for an amino acid (c) What is the function of the other ones? (Sec 25.1 and 25.2) - a) 64 b) 61 c) Start and stop codons (a) Describe the degeneracy of the genetic code. (b) How does this degeneracy minimize the effect of mutations? (Sec 25.2) - a) multiple codons are for one amino acid b) This means that the nucleotide in the last position have little or less meaning. (a) What is an anticodon and where is it located? (b) Where is a codon located? (c) Which position of the anticodon pairs with the 3rd position of the codon (if both are written 5' to 3')? (Sec 25.3) - a) Complementary to the codon. Located on tRNA b) RNA? c) the first position of the anticodon pairs with the 3rd position of the codon (a) What is the "wobble hypothesis"? (b) How is it consistent with the third-base degeneracy of (a) For positive control of the lac operon, what is the natural inducer? (b) For negative control of the lac operon, what is the natural inducer? (Sec 26.3, 26.4, 26.11) - a) cAMP b) allolactose (a) What is an operator? (b) Why does the lac operon need three operators? (Sec 26.9) - a) The site on DNA at which a repressor protein binds to prevent transcription from initiation at the adjacent promoter b) Three operators are have higher levels of repression The trp operon is regulated by the trp repressor and by tryptophan. (a) Is the trp operon an example of positive or negative regulation? (b) Is tryptophan an inducer or a corepressor? (Sec 26.12) - a) Negative b) Inducer The trp operon is also regulated by attenuation. (a) Describe the attenuation of the trp operon. (b) What happens when trp-tRNA is abundant? (c) What happens when trp-tRNA is in short supply? (Sec 26.13) - a) Attenuation is the second negative feedback in trp operon b) Terminatoin occurs c) RNA polymerase can continue into the structural genes Three major steps involved in transcription initiation: - 1. Chromatin is opened 2. Basal transcription factors bind 3. RNA polymerase binds and initiates transcription TBP - TATA Binding protein. Help position promoter and polymerase can induce kink in DNA All polymerases need this Polymerase I promoter elements - Bipartite promoter: core promoter plus upstream element TBP is part of SL1 Polymerase II promoter elements - Core promoter: BRE ~35, TATA box ~25, Inr (initiation region), DPE (downstream promoter element) TATA: 6ss promoters must have DPE TBP: is part of TFIID which binds at TATA box Displays most variation Polymerase III promoter elements - Internal promoters: Type I: box A and C, Type II: box A and B Upstream promoter TBP is part of TFIIIB which binds at start point What is the mediator complex - Coactivator that initiates polymerase II Which RNA polymerase requires mediator complex - Polymerase II Three mRNA processing events: - 5' capping, splicing, and 3' poly A polymerase Review feature of transcription worksheet - Which enzyme is responsible for transcritption of heterogeneous nuclear RNA? - RNA polymerase II Which RNA polymerase utilizes bipartite promoters - RNA polymerase I Which of the following promoter elements are required for an RNA polymerase II core promoter - a TATA box and Inr element or Inr and DPE element Enhancers and silencers are _____________-acting sequences - cis Which of the following statements is NOT true about mediator complex: a. It promotes phosphorylation of the C-terminal domain of RNA pol II b. It associates with RNA pol II near the start point of transcription c. It can interact with transcription factors bound to enhancers d. It remodels chromatin near the start point of transcription - It remodels chromatin near the start point of transcription Which enzyme is responsible for transcription of tRNA - RNA pol III Which of the following is not true of transcription in eukaryotes: a. RNA pol reads the DNA directly b. Chromatin remodeling is required c. Basal transcription factors find to the core promoter d. There are three different RNA polymerases - RNA polymerase reads the DNA directly Which RNA polymerase has the largest group of transcription factors: - RNA Polymerase II Which word best describes the expression of housekeeping genes? - Constitutive The transcription starts when RNA polymerase binds to the.... - Promoter Which statement best describes the role of E. coli RNA polymerase sigma factor? - Sigma factor increases the affinity of RNA polymerase for promoter sequences Which step of gene expression is most commonly regulated - Initiation of transcription How many strands of DNA are copied during transcription - 1 The term downstream refers to - DNA sequences that lie within the coding region of a gene Which of the following statements is false about a cis-acting sequence: a. It affects the activity of sequences on its own molecule of DNA b. It does not encode a protein c. A promoter is an example d. It encodes a diffusible product that acts on any copy of a target sequence - It encodes a diffusible product that acts on any copy of a target sequence Full name and function of: mRNA, tRNA, and rRNA - mRNA: messenger RNA. template for protein synthesis tRNA: transfer RNA: carry amino acid to peptide chain rRNA: ribosomal RNA: form peptide bond Which of the following ways does U1 snRNP participate in splicing initiation - Base- Pairing between U1 snRNP and the 5' splice site Which of these consensus sequences allows the splicing apparatus to bind to the mRNA? - GU...AG In eukaryotic cells, initiation of translation of mRNA relies on - the small ribosomal subunit binding to the 5' cap Which type of tRNA occupies the E site of a bacterial ribosome - Deacylated tRNA Termination of translation requires - a stop codon What is unique about Group I and Group II introns - Self-Splicing What is a ribonucleoprotein - RNA and protein Give two examples of a ribonucleoprotein from chapter. 21 and 24 - Ribosome and spliceosome