Was wondering If anyone know where i could find answers to these study guide que

Question

Was wondering If anyone know where i could find answers to these study guide questions, there were posted couple weeks ago and were deleted later:

Thanks in advance! - Will +rep right away if you could find any <3

Transcription II – RNA Processing

• How is eukaryotic mRNA processed after its synthesis (list four types of modification)? Do these modifications occur in prokaryotes too (which?)?

• What type of linkage links the mRNA cap to the main body of mRNA?

• What is splicing of mRNA? What type of chemical reaction that produces splicing and its intermediates? What functional group is the nucleophile, what is the electrophile? What is a lariat intermediate? What are snRNPs and spliceosomes? What is their function?

• What type of particles are involved in splicing? How is the splicing machinery guided to the exon-intron splice junction?

• Which two enzymes are involved in termination of eukaryotic transcription?

• What is the role of the CTD of Pol II in processing of eukaryotic mRNA? Which types of processing are facilitated by phophorylated CTD?

• What is the role of alternative splicing in gene expression? You should be able to predict, in principle, which and how many alternatively spliced mRNAs can be produced from a primary transcript that contains several introns and splice sites.

• What is the life cycle of a retrovirus, such as HIV? How do retroviral protease inhibitors block the replication of HIV?

• What are the various enzymatic activities of reverse transcriptase? What does AZT do?

Translation (Chapter 27)

• Structure of tRNA: Where are amino acids attached? Where are anticodons located? What does the 5’ end consist of? What is a constant feature of the 3’ end? How can the overall secondary and the tertiary of tRNA be described? How does a tRNA recognize its codon? What does the term “charged tRNA” mean?

• Is there one codon for every amino acid? What are “wobble bases?” (Keep in mind directionality when dealing with anticodon sequences.)

• What set of enzymes implements the genetic code?

• What are the steps during the attachment of amino acids (AA) to tRNA? Name two. Be familiar with the terminology (e.g. Ala-tRNA, fMet-tRNAfMet, AA-tRNAAA).

• What is the composition of prokaryotic and eukaryotic ribosomes (subunits, rRNA, >10 proteins each subunit, not exact number)

• What are the phases of protein synthesis? How can these phases be subdivided (steps?)? What is the function of Shine Dalgarno sequences?

• What is most commonly the first amino acid in prokaryotic proteins, what in eukaryotic proteins?

Material for Exam III up to this point                                                                                                         

• Which factors are involved in each step of translation (IF1, 2, 3; EF-Tu, -Ts, -G; RF1, 2,3 RRF)? Which of these factors requires metabolic energy and what is the source of metabolic energy?

• What are the key differences between prokaryotic and eukaryotic translation (size of ribosomes, first amino acid, polycistronic mRNA in bacteria, function of cap and poly-A tail in eukaryotic mRNA)?

Control of Gene expression I

• At what levels can the expression of genes be controlled? What is the meaning of the terms “constitutive expression regulated expression, induction and repression”?

• In the Jacob and Monod model of bacterial gene regulation what is the function of the regulator gene, the operator, the promoter? What are structural genes? What is “polycistronic mRNA”? Explain the role of an inducer. What chemical compound is the inducer of the lac operon?”

• What possible alternative possibilities exists for the functions of regulator genes and their products? What alternative functions can small molecules have that bind to the products of regulatory genes?

• Name an example of a positive gene regulator of the lac operon (name the DNA binding protein and the small molecule that regulates DNA binding)?

Control of Gene Expression II

• Name four key differences between bacterial and eukaryotic control of gene expression.

• What is the function of histones? What types of amino acids (their charge) are involved in DNA binding? What is the function of nucleosomes? What is the meaning of the terms chromatin, euchromatin, and heterochromatin? (see lecture 23)

• Name three key events at the level of DNA and of chromatin organization that mediate gene regulation. Among these, name a key event that regulates binding of DNA to histones.

• Name two downstream effects of histone acetylation.

• What is the function of each of the following components of transcription activation: promoter, TATA box, basal transcription factors, enhancers transcription factors (or actovators), Co-activators, mediator, archetectural regulators, chrmatin-remodeling engine?

• Name a drug that antagonizes the action of estrogen. At what level does it act? How could the action of such a drug be beneficial (name disease)?

• Which percentage of the human genome codes for proteins (exons)?

• What is the meaning of the following terms: miRNA, RNAi, siRNA, stRNA?

Explanation / Answer

Attachement of amino acid to tRNA and charged tRNA There occurs a esterification reaction between the 3' or 2' -hydroxyl group of the terminal adenylate of tRNA to the amino acid and forms an aminoacyl-tRNA.The enzyme called aminoacyl-tRNA synthetase (aaRS) catalyzed the process . There are 20 aminoacyl-tRNA synthetase, one for each amino acid and there is a specific aaRS for each tRNA. This esterification reaction is called charging of the tRNA.

Protein synthesis

firstly, the charged tRNA, mRNA, and ribosomal subunits come together and form the initiation c complex. This consists of a peptidyl binding site (P site) and an aminoacyl binding site (A site).

The initiator RNA, binds to the mRNA start codon, AUG. To add additional amino acids to the polypeptide chain, a second charged tRNA must come in and have its anticodon bind to the next mRNA codon in the vacant A site.

The P site and A site which are nearby, forms a stable peptide bond by reacting the carboxy terminus of the amino acid in the P site with the amino terminus of the of the amino acid on the tRNA in the A site. .

The complex moves along the RNA in a process called translocation which causes the tRNA in the P site to be displaced. The tRNA in the A site then moves into the P site so another charged tRNA can move into the A site. This process continues until the stop codon is reached the polypeptide chain is released from the ribosome.

The Shine-Dalgarno sequence  This sequence is required for ribosomal binding and protein synthesis to occur in prokaryotic cells. It is also known as the ribosome binding site.

The anticodon region of a transfer RNA is a sequence of three bases. They are complementary to a codon in the messenger RNA. In the translation, the pairing between its anticodon and the messenger codon brings the ribosome.

miRNA, RNAi, siRNA,stRNA

miRNA meaning microRNA is a small non-coding RNA molecule generally found in plants, animals and some viruses.It functions in RNA silencing and post-transcriptional regulation of gene expression.

RNAi i.e RNA interference is a biological process. here RNA molecules inhibit gene expression, by causing the destruction of specific mRNA molecules.

Small or short interfering RNA (siRNA) is the most commonly used RNA interference (RNAi) tool for inducing short-term silencing of protein coding genes. siRNA is a synthetic RNA duplex designed to specifically target a particular mRNA for degradation.

Small temporal RNA (abbreviated stRNA) regulates gene expression during roundworm development by preventing the mRNAs they bind from being translated.

Composition of prokaryotic and eukaryotic Ribosomes

Prokaryotic ribosome composed of 65% rRNA and 35% ribosomal proteins.

Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. Their small subunit has a 16S RNA subunit (consisting of 1540 nucleotides) bound to 21 proteins. The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins.

Eukaryotic ribosomes have an rRNA-to-protein ratio close to 1.

Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S) subunit. Their 40S subunit has an 18SRNA (1900 nucleotides) and 33 proteins.

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