34. Non-coding RNA. Which of the following descriptions about the non-coding RNA is not correct?
(A) Non-coding RNAs are classified into two major categories: structural and regulatory non-coding RNAs.
(B) Structural non-coding RNAs comprise of siRNAs and miRNAs.
(C) Regulatory non-coding RNAs are further divided into three classes, small, medium and long non-coding RNAs.
(D) Short non-coding RNA with a size between 20-50 nucleotides. Medium non- coding RNA with a size between 50-200 nucleotides.
(E) Long non-coding RNA with maximum regulatory potency containing greater than 200 nucleotides.

1.Enhancer function underlies regulatory processes by which cells establish patterns of gene expression. Which of the following descriptions about enhancer is not correct? (A) Enhancer works as cis-regulatory elements to mediate spatiotemporal control of gene expression. (B) Enhancers can be identified using a reporter gene. Once a reporter gene is integrated near an enhancer, its expression reflects the expression pattern. (C) Next-generation sequencing (NGS)-based approach called RNase-seq enables identification of enhancers. (D) Enhancer help recruit RNA polymerase II to promoters and can attract various chromatin-modifying enzymes to DNA. (E) Enhancer is distal sequences that lie upstream or downstream of the core promoter and recruit transcription factors

2.The DNA polymerases are the workhorses for replication of genomic information in living cells. Which of the following descriptions about their biotechnological applications is not correct? (A) During polymerase chain reaction (PCR), DNA polymerases often extend misprimed targets and primer-dimers, which are common sources of nonspecific amplification. (B) During PCR, hot-start DNA polymerases reduce nonspecific amplification, increase yields, and allow convenient room temperature setup for high-throughput applications. (C) Although archaeal DNA polymerases are extremely heat-stable, they may bc slow in synthesizing DNA due to lower processivity. (D) High-fidelity DNA polymerases are enzymes with strong proofreading activity based on their 3'→5' exonuclease activity. (E) DNA polymerases can be engineered with high specificity by introducing a strong DNA-binding domain of another protein without compromising polymerase activity.

3. Which of the following components or events is not involved in epigenetic gene regulation? (A) Histone acetylation (B) Heavy methylation of promoter regions (C) Ubiquitin-mediated degradation of transcription factors (D) Nucleosome sliding (E) Chromatin opening and closing

4. Agrobacterium-mediated T-DNA delivery of CRISPR/Cas9 expression cassettes is an advanced tool for genome editing in plants. Which of the following descriptions about this technique is not correct? (A) Only the T-DNA region is transferred from agrobacterium into the host plant's nuclear DNA genome. (B) The virulence region of the Ti plasmid encodes proteins to form a membrane- spanning DNA transporter called the type IV secretion system (T4SS). (C) CRISPR/Cas9 cleaves foreign DNA via two components, Cas9 and sgRNA. (D) The sgRNA is a synthetic RNA containing a 5'-end with a 20-nt sequence that acts as a guide sequence to identify the target sequence accompanied by a protospacer adjacent motif (PAM) sequence. (E) When a template is present, nonhomologous end-joining (NHEJ) can be activated and results in gene replacement or knock-in.

5. Which of the following statements about small RNA is not correct? (A) Small RNAs are short, non-coding RNA molecules that can regulate gene expression. (B) Small RNAs can regulate gene expression in the nucleus via chromatin- dependent gene silencing. (C) Most small interfering RNAs (siRNAs) are generated through multiple processing steps from longer primary transcripts produced by RNA polymerase II. (D) Most microRNAs (miRNAs) form imperfectly complementary stem-loop structures, pair imperfectly with sites in the 3' untranslated region of their target mRNAs. (E) Both miRNAs and siRNAs are produced from longer RNA precursors through the activity of ribonuclease IlI-like nucleases called Dicer in animals and DICER- LIKE (DCL) in plants.

6. Which of the following descriptions about homeobox genes is not correct? (A) They are a group of genes regulates development in multicellular organisms. (B) The DNA binding motif in homeobox genes is typically a 180 base pair DNA sequence which encodes a 60 amino acid homeodomain that acts as transcriptional regulator. (C) The use of chromatin immunoprecipitation sequencing can identify genes bound and modulated by homeodomain protein (D) Yeast one-hybrid can be used for testing homeodomain protein-protein interactions. (E) The homeobox Hox genes arrange on chromosomes in the same order as their expression domains along the body axis.

7. Which of the following descriptions about protein translation is not correct? (A) Terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during translation (B) Upstream open reading frames generally hinder translation of the main open reading frame (ORF) (C) Ribosome density along ORFs can be studied with high resolution by sequencing of ribosome-protected mRNA footprints, a method known as ribosome footprinting. (D) Mass spectrometry-based methods can provide estimates of synthesis and degradation rates for a substantial fraction of proteins. (E) The direct method for analysis of the de novo protein synthesis is to detect the isotope-labeled amino acids incorporated into newly synthesized proteins.

8.Which of the following descriptions about electrophoretic mobility shift assay (EMSA) is not correct? (A) It is used to detect protein complexes with nucleic acids. (B) Solutions of protein and nucleic acid are combined and the resulting mixtures are subjected to electrophoresis under native conditions through polyacrylamide or agarose gel. (C) The distribution of species containing nucleic acid is deternined usually by autoradiography of 32P-labeled nucleic acid (D) Protein-nucleic acid complexes migrate more faster than the corresponding free nucleic acid. (E) The electrophoretic mobility of a complex provides little direct information about the location of the nucleic acid sequences that are occupied by protein.

9. Which of the following sequence(s) in mRNA can form base pairing with the 3' end of 16S rRNA? (A) Kozak sequence (B) Shine-Dalgarno sequence (C) TATA Box sequence (D) Internal Ribosome Entry sequence (E) PolyA sequence

10. Which of the following sequence(s) contain AUG? (A) Kozak sequencc (B) Shine-Dalgarno sequence (C) TATA Box sequence (D) Internal Ribosome Entry sequence (E) PolyA sequence

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