25. DNase I protection assays or DNA footprinting is useful for___________.
(A) determining the start of transcription
(B) preventing contamination of RNA in primer extension samples
(C) determining the location of a DNA binding sequence
(D) monitoring gene expression
(E) determining DNA-protein interactions

1. Restriction endonucleases are commonly used in DNA cloning. Which of the following is not true? (A) Restriction endonucleases are main components of the bacterial restriction- modification (R-M) system. (B) The normal function of the R-M system is to degrade DNA from invading phages. (C) In a R-M system, phosphatases are frequently used to protect the same DNA sequences of bacteria from digestion by the restriction endonucleases. (D) The most useful R-M systems in DNA cloning are the type II system, and the restriction activities do not need ATP as a cofactor. (E) In the type III R-M systems, one enzyme contains two different subunits, one for DNA recognition and modification, and another for DNA cleavage.

2. Which products are made by eukaryotic RNA polymerase III? (A) 28S and 18S rRNA (B) 7SLRNA and 5S rRNA (C) mRNA and tRNA (D) tRNA and 5.8SRNA (E) snRNA and U6snRNA

3. What is the possible outcome of a mutant cell line with reduced levels of TEIIS in transcription carried out by eukaryotic RNA polymerase II? (A) The start site and direction of transcription will be changed. (B) The C-terminal domain (CTD) of RNA polymerase II will not be phosphorylated. (C) The serine residues of histones will not be modified by acetylation. (D) The activity of transcription proofreading will be impaired. (E) The TFILA/TFIID/TFITB complex will dissociate.

4. Which of the following related to eukaryotic ribosomal genes is not true? (A) There are no repetitive sequences. (B) They have a different base composition compared to other nuclear genes. (C) They have a higher GC content compared to other nuclear genes. (D) They are transcribed by RNA polymerases I and III. (E) They are found in the nucleolus.

5. During the activation of a eukaryotic RNA polymerase II (pol II)-dependent promoter, which of the following is the correct order of adding general transcription factors to the initiation complex? (A) TFIIA+TFID, TFIE, TFIB, TFIIF + pol II, TFIIH (B) TFIIA+TFIID, TFIIB, TFIH, TFIIF + pol II, TFITE (C) TFIIF + pol II, TFIIA+TFID, TFIH, TFIIB, TFIIE (D) TFIIA+TFIID, TFIH, TFIB, TFIIF + pol II, TFITE (E) TFIIA+TFIID, TFIB, TFIF + pol II, TFIIE, TFIH

6. Which is not true for the following experimental techniques? (A) DNase I footprinting assay is used to locate the specific protein-binding sites on DNA. (B) In yeast, a temperature sensitive (ts) mutant can exhibit the mutant phenotype at a non-permissive temperature. (C) Yeast one-hybrid analysis is useful for in vivo detection of physical interaction between two proteins. (D) Gel mobility shift assay can be used for determining the ability of a protein to bind to a specific DNA fragment, and measuring the DNA binding affinity of the protein. (E) The far-western blot analysis can be used to determine receptor-ligand interactions, and screen libraries of interacting proteins.

7. Which of the following statement related to TATA-binding protein (TBP) and its associated factors is true? (A) TBP is not required for the TATA-less promoter. (B) TBP-associated factors are universally required for transcription of all RNA polymerase II-activated genes (C) TBP is a transcription factor only required for RNA polymerase I and II regulated genes (D) For RNA polymerase II, TAF1 is responsible for recognizing Inr and DPE in the fly hsp 70 gene and its homologue in yeast contains histone acetyltransferase activity (E) TBP can bind to the major groove of the TATA box.

8. Sigma factors in E.coli. Which of the following descriptions is not correct? (A) σ70 (RpoD) is the primary sigma factor. (B) σ38 (RpoS) is the starvation/stationary phase sigma factor. (C) σ54 (RpoN) is the nitrogen-limitation sigma factor. (D) σ28 (FliA) is the extracytoplasmic/extreme heat stress sigma factor. (E)σ32 (RpoH) is the heat shock sigma factor.

9. Micro RNA. Which of the following descriptions is not correct? (A) The precursor RNA molecules ("primary miRNA", pri-miRNA) fold into stem-loop structures. (B) The double-stranded stem region of pri-miRNA is cut by Dicer to generate pre- miRNA.(C) The pre-miRNA exits the nucleus and is finally trimmed by Dicer to form miRNA. (D) The miRNA is bound by a protein complex, miRISC. (E) One strand of the miRNA binds to the target mRNA.

10. Heterochromatin and euchromatin. Which of the following descriptions is not correct? (A) Heterochromatin is usually located near the nuclear envelope of the nucleus of prokaryotes. (B)Euchromatin is usually located in the center of the nucleus of eukaryotes. (C) The transcription is very low near the nuclear envelope. (D) Heterochromatin is transcriptionally inactive. (E) The center of a nucleus has high levels of transcription taking place.

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