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BCHM 4360 EXAM 3 LATEST EXAM 2025 | ALL
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What are the differences and similarities between miR:miR* and siR:siR* molecules? ---------CORRECT ANSWER-----------------Both have 3' OH and 5' monophosphates and both can undergo post-transcriptional modifications such as methylation siR:siR* molecules are usually fully complementary, but miR:miR* molecules are usually not What are the three main classes of Argonaute proteins? ---------CORRECT ANSWER-----------------1. Argonaute proteins involved in miRNA and siRNA mechanisms in animals, plants, and fungi
- Piwi subclass involved in piRNA mechanisms
- WAGO proteins found in C. elegans What are the four domains of Argonaute proteins and what do they do? ----- ----CORRECT ANSWER-----------------1. PAZ binds the 3' end of bound RNA
- Mid interacts with the 5' end of the RNA
- PIWI is related to RNAse H and interacts with the whole RNA
- PAZ, Mid, and PIWI together orient the bound guide RNA to facilitate its scanning of cellular molecules What is a unique characteristic of piRNA that separates it from miRNA and siRNA? ---------CORRECT ANSWER-----------------Single stranded piRNAs are loaded directly onto Piwi proteins as they are generated - no sorting is required
How are miRNA and siRNA different with regards to the RISC complex? --- ------CORRECT ANSWER------------------miRISC usually pairs initially via a 2 - 8nt "seed" sequence - the 3' end of the miRNA remains tightly bound by the PAZ domain
- siRISC can bind along its full length - this releases the PAZ domain and induces a conformation change that activates the catalytic activity of the PIWI domain What is the purpose of the CRISPR mechanism and how does it work? ----- ----CORRECT ANSWER-----------------Purpose is viral defense in bacteria
- Cleaved foreign DNA is integrated into the CRISPR locus, which contains many repeats of 20-50 nucleotide palindromic sequences
- The CRISPR locus is transcribed and processed by Cas proteins to give short crRNAs
- crRNAs then direct cleavage of complementary RNA in association with various proteins (Cascade complex) How is CsrB RNA an example of how protein-binding RNAs can have a range of biological effects through a range of mechanisms? --------- CORRECT ANSWER-----------------CsrB RNA has multiple GGA binding motifs that can bind the CsrA protein
- CsrA binds to mRNA and blocks translation
- When CsrA is sequestered by CsrB RNA, translation can occur Protein folding can start as soon as the ___ terminus emerges from the ribosome, where the peptide encounters __________. ---------CORRECT ANSWER-----------------N, chaperones
The bacterial secretion system is very similar to ____ targeting in eukaryotes, relying on ______s to recognize and bind hydrophobic signals before handing proteins over to a translocase. ---------CORRECT ANSWER-----------------ER, SRPs True or False: Transport in and out of the nucleus is highly regulated and travel is via nuclear pore complexes (NPCs) ---------CORRECT ANSWER--- --------------True What are inteins? ---------CORRECT ANSWER-----------------Parts of proteins that catalyze their own removal and ligate the flanking pieces
- They often act as a mobile genetic element, moving its own DNA sequence around the genome What are the 4 steps to intein removal? ---------CORRECT ANSWER--------- --------1. A conserved residue (C, S, T) attacks the carboxyl of the previous peptide bond
- The same carboxyl is then attacked by a similar residue in the C-terminal exein
- The amino group of the last intein residue attacks its own carboxyl, separating the intein
- The two joined exeins undergo further attack of amino groups on carboxyl to make a peptide bond What are the three main benefits to RNA processing? ---------CORRECT ANSWER-----------------1. Contribution to regulation of gene activity
- Diversity - many different RNAs can be produced from one gene via alternative splicing
- Quality control
Many of the RNA processing complexes contain both _______ and ___ components. Give an example. ---------CORRECT ANSWER----------------- protein, RNA, RNPs An E. coli precursor encodes __ rRNAs and __ tRNAs. ---------CORRECT ANSWER-----------------3, several The S. cerevisiae precursor encodes __ rRNAs. ---------CORRECT ANSWER----------------- 3 Why is encoding several RNAs in one precursor beneficial? --------- CORRECT ANSWER-----------------ensures that similar amounts of each RNA are made True or False: Exonucleases operate strictly in the 3' to 5' direction during RNA processing. ---------CORRECT ANSWER-----------------False, go both ways Give two examples of endonucleases. ---------CORRECT ANSWER----------- ------RNase III and RNase P 5' trimming of tRNAs is done by which endonuclease? ---------CORRECT ANSWER-----------------RNase P
snoRNAs that direct ribose methylation are _______ snoRNAs. snoRNAs that direct pseudouridylation are ______ snoRNAs. ---------CORRECT ANSWER-----------------box C/D, H/ACA What is the primary purpose of the end modifications of eukaryotic RNAs following transcription? ---------CORRECT ANSWER-----------------protection of mRNAs from nuclease degradation and assisting with protein interactions What are the 5' ends of mRNAs capped with? ---------CORRECT ANSWER- ---------------- 7 - methylguanine nucleotide via a 5'-5' triphosphate linkage What is the 5' cap needed for? ---------CORRECT ANSWER----------------- efficient elongation and termination of the transcript, for mRNA processing and export from the nucleus, and for directing translation What are the three steps for the addition of the 5' cap? ---------CORRECT ANSWER-----------------1. An RNA 5' triphosphate catalyzes removal of a phosphate from the 5' end
- A guanyl transferase attaches a guanosine monophosphate (GMP) to the end in a 5'-5' triphosphate linkage
- The guanine is methylated by a guanine- 7 - methyltransferase The 3' end of most eukaryotic mRNAs have about ___ adenosines added, known as the poly(A) tail. ---------CORRECT ANSWER----------------- 200
Polyadenylation at the _______ site retains multiple regulatory sequences. Polyadenylation at the _______ site eliminates the regulatory sequences. -- -------CORRECT ANSWER-----------------distal, proximal What are the steps for the addition of the poly(A) tail? ---------CORRECT ANSWER-----------------1. Initial cleavage after a CA that lies between a conserved AAUAAA hexamer and a U or GU-rich region
- After cleavage, ~200 adenosines are added by poly(A) polymerase What is responsible for mediating mRNA processing? ---------CORRECT ANSWER-----------------The CTD of the largest subunit of RNA Pol II, RBP __________ is needed to allow RNA Pol II to continue transcription. __________ is needed for efficient transcription termination. --------- CORRECT ANSWER-----------------Capping, polyadenylation How does the CTD of RBP1 sequentially recruit the different processing complexes? ---------CORRECT ANSWER-----------------1. CTD becomes partially phosphorylated on transcription initiation and recruits capping enzyme
- Elongation leads to more phosphorylation of CTD, which recruits splicing machinery
- This also leads to recruitment of the cleavage and polyadenylation complex True or False: Transcription, processing, and translation all occur in the nucleus. ---------CORRECT ANSWER-----------------False: Transcription and processing occur in the nucleus, but translation occurs in the cytoplasm so mature mRNAs must be exported from the nucleus
The energy is the same in both bonds, so the reaction does not require ATP and is easily reversible. What are some characteristics of Group I introns? ---------CORRECT ANSWER-----------------Found in bacteria, viruses, microeukaryotes, and plants. They are ~120-450 nucleotides long Many (but not all) can excise themselves from the primary transcript. What is the mechanism of intron removal for Group I introns? --------- CORRECT ANSWER-----------------In the first transesterification, a free guanosine is the attacking species that detaches the 5' end of the intron from exon 1. In the second reaction, the released end of exon 1 attacks the intron-exon 2 junction, joining the two exons together What are some characteristics of Group II introns? ---------CORRECT ANSWER-----------------Found in bacteria and in organellar genes of plants and fungi ~400-1000 nucleotides long Can also act as mobile genetic elements by reverse splicing, and they often have open reading frames within the introns that assist splicing What is the mechanism for intron removal for Group II introns? --------- CORRECT ANSWER-----------------The 2' OH of a specific A within the intron attacks the exon1-intron junction. Once released, the intron forms a branched lariat intermediate.
What is a similarity between Group I and Group II introns? --------- CORRECT ANSWER-----------------The splice sites are determined by the 3D structure of the intron Eukaryotic genes often have _______ introns, which can be very long ( ________ of bases) and account for up to __ % of a pre-mRNA. --------- CORRECT ANSWER-----------------several, thousands, 90 True or False: Most eukaryotic introns are not self-splicing, so splicing is mediated by the spliceosome, which operates similar to that of Group I introns. ---------CORRECT ANSWER-----------------False: Everything is correct except that the spliceosome operates similar to that of Group II introns What is the spliceosome made up of? ---------CORRECT ANSWER----------- ------several small nuclear ribonucleoproteins (snRNP) What are some short sequence motifs that the spliceosome recognizes for splice sites? ---------CORRECT ANSWER-----------------the 5' and 3' splice sites and a branch-point nucleotide within the intron (like the A in Group II introns) and a polypyrimidine region before the 3' splice site Usually, introns have __ and __ at their ends. ---------CORRECT ANSWER- ----------------GU, AG What are the 5 steps of how the spliceosome works? ---------CORRECT ANSWER-----------------1. The 5' splice site is recognized by U1 and other sequences are bound by non-snRNPs.
Most exons are ____________ (must be included), but some are __________ exons (can be included or not) ---------CORRECT ANSWER--- --------------constitutive, regulated What are cryptic splice sites? ---------CORRECT ANSWER----------------- False splice sites that occur as a result of the simplicity of the sequences defining intron-exon junctions What are the two methods for how the spliceosome recognizes only true splice sites and not cryptic splice sites and how do they work? --------- CORRECT ANSWER-----------------1. Exon definition (mammals)
- The 5' and 3' ends of an exon are brought together by interactions between the U1 and U2 complex. Mutations at a 5' splice site would result in exon exclusion. The exon is typically marked with SR proteins and the introns bound with hnRNPs, which masks cryptic splice sites.
- Intron definition
- Introns are defined by interactions between 5' and 3' bound factors. Mutations at a 5' splice site would reslut in intron inclusion. Describe the similarities between the exon definition and intron definition models? ---------CORRECT ANSWER------------------In both models, the final splicing complex must be one in which the 5' and 3' complexes interact with one another across the intron
- In both models, the 5' and 3' splice sites are marked as they are transcribed, facilitated by RNA Polymerase and splicing components RNA sequence elements that positively affect splicing are called splicing _________. _________ sequences have the opposite effect. Both can either be intronic or exonic (ISS/ESS) ---------CORRECT ANSWER----------- ------enhancers, silencer
What is an example of a silencer protein. ---------CORRECT ANSWER------- ----------Polypyrimidine tract binding protein (PTB) which binds to intron elements and silences neighboring weak introns True or False: Specific nucleotides can be modified, inserted, or deleted during the processing of mRNA. ---------CORRECT ANSWER----------------- True What are the two main common RNA edits? ---------CORRECT ANSWER--- --------------1. Deamination of adenosine to inosine
- Deamination of cytidine to uridine Explain the effects of cytidine to uridine deamination on human apoliprotein B. ---------CORRECT ANSWER-----------------The deamination of a particular cytidine results in the formation of a stop codon, resulting in a shorter version of the protein (APOB48). This occurs in the small intestine and is needed for lipid absorption from food. The long version of the protein (APOB100) is made in the liver, and is involved in cholesterol transport. Describe the mechanism for how the trypanosome mitochondrial mRNA extensive editing works. ---------CORRECT ANSWER-----------------1. 20- 50 nucleotide guide RNAs bind to mRNAs and define insertion and deletion locations
- Guide RNAs first base pair with part of the mRNA. An endonuclease cuts the mRNA at a mismatch, and the guide RNA acts as a template for addition or deletion of uridines.
What is RNase E and what does it do? ---------CORRECT ANSWER---------- -------Endonuclease that is responsible for degradation of bacterial mRNAs, part of the degradosome complex How does eukaryotic RNA degradation work? ---------CORRECT ANSWER- ----------------3' poly(A) tails hinder rather than aid degradation in eukaryotes
- the first step in degradation is often tail shortening by a deadenylase.
- After this, decapping enzymes remove the 5' cap and 5' to 3' exonucleases degrade the RNA, or the exosome catalyzes exonuclease activity in the 3' to 5' direction Describe what happens to transferrin receptors when iron is low and when it is high. ---------CORRECT ANSWER-----------------High - mRNAs encoding the receptor are degraded as there is no need to import more iron Low - receptor mRNA is protected from degradation by Iron Regulatory Proteins (IRP1/IRP2) that bind to stem-loop Iron Response Elements (IRE) Foreign nucleic acids are removed by RNA interference (RNAi) in __________ and CRISPR interference in __________. ---------CORRECT ANSWER-----------------eukaryotes, bacteria What happens to defective endogenous RNAs? ---------CORRECT ANSWER------------------In eukaryotes, ribosomes on defective RNAs are marked by interaction with proteins such as the EJC, which recruit RNAses to degrade the RNA
- In bacteria, stalled ribosomes are recognized by a complex containing tmRNA, which allows the ribosome to finish translation using the tmRNA as a template (also recruits RNases)
What is the RNA-recognition motif (RRM)? ---------CORRECT ANSWER----- ------------Also known as RNA-binding domain (RBD) or ribonucleoprotein (RNP) domain, this is where the RNA binds proteins
- Has alpha helices and four beta sheets in a sandwich, very adaptable and can bind RNAs that have different structures What are KH and PAZ? ---------CORRECT ANSWER-----------------ssRNA binding motifs
- KH domains have an RNA-binding groove formed by two alpha helices and one beta strand
- PAZ domains have a pocket formed from beta strands and an alpha helix (this pocket interacts with the single stranded overhangs of the siRNA
- PAZ domains are found in many RNAi proteins like Dicer What are unique about RNase III family enzymes? ---------CORRECT ANSWER-----------------Have dsRNA-binding domains
- Alpha helix and two loop regions that interact with three grooves on the dsRNA True or False: RNA-binding proteins often have more than one binding motif. ---------CORRECT ANSWER-----------------True What are three examples of RNA-binding motifs? ---------CORRECT ANSWER-----------------1. The eukaryotic PUF protein family, including Pumilio 1, has repeats of a two-helix motif with conserved amino acids, each interacting with a single nucleotide
- Some RNA-binding proteins need to have small regions rich in lysine and arginine
- Some proteins with the zinc finger DNA-binding domains also bind to RNA
A single tRNA doesn't recognize all the codons for a specific amino acid. Different tRNAs that carry the same amino acids are called ____________. ---------CORRECT ANSWER-----------------isoacceptors True or False: The first two positions on the mRNA are read by strict Watson-Crick base-pairing with positions 2 and 3 of the anticodon --------- CORRECT ANSWER-----------------True What is wobble pairing and what does it mean with regards to tRNA? --------
- CORRECT ANSWER-----------------The third position of the codon allows some pairing deviations, means that non-Watson-Crick interactions can occur and thus that each codon does not need its own tRNA (40 tRNAs for the 61 codons) Why do similar amino acids have similar codons? ---------CORRECT ANSWER-----------------Mutations that change the amino acid that is encoded will result in an amino acid with similar characteristics which generally won't affect the resulting protein too much _______________ attaches amino acids to tRNAs. ---------CORRECT ANSWER-----------------aminoacylation True or False: aminoacylation does not require ATP. ---------CORRECT ANSWER-----------------False
What is the two-step mechanism for aminoacylation? ---------CORRECT ANSWER-----------------1. The amino acid is activated by attachment of AMP, releasing pyrophosphate and providing energy.
- Enzyme then transfers the amino acid to the 2' or 3' OH of the ribose of the terminal adenosine on the tRNA 3' CCA tail The correct amino acid for a tRNA is referred to as _______. --------- CORRECT ANSWER-----------------cognate Loading of amino acids onto tRNA is very _______ with fewer than one error per _____ aminoacylation events. ---------CORRECT ANSWER--------- --------accurate, 100000 How do aminoacyl-tRNA synthetases recognize tRNAs? ---------CORRECT ANSWER-----------------sequence and structural features called identity elements How does the editing site prevent non-cognate amino acids from binding? - --------CORRECT ANSWER-----------------It can accomodate the pre-transfer amino acid, in which the activated amino acid is hydrolyzed if it is incorrect, or post-transfer, in which the amino acid is cleaved from the tRNA. What is the main difference between Class I and Class II aminoacyl tRNA synthetases? ---------CORRECT ANSWER-----------------Class I usually recognizes the minor groove of the acceptor stem, Class II the major groove
- Class I attach amino acids to the 2' OH of the terminal ribose, class II to the 3' OH
