62. Which of the following represents the sequence of the template strand?" A. 5'--GAAGACTAACATTCA--3' B. 5'-- ACTTACAATGTAGUA--3' C. 5'-- CTTCTGATTGTAAGT--3' D. 5'--ACTTACAATCAGAAG--3' E. 5'--TGAATGTTAGTCTTC--3'

For each of the following sequences, place a check mark in the appropriate space to indicate the process most immediately affected by deleting the sequence. Choose only one process for each sequence (i.e., one check mark per sequence). Process most immediately affected by deletion RNA Sequence deleted Replication Transcription Translation processing a. ori site b. 3' splice site consensus c. Poly(A) tail d. Terminator e. Start codon f. -10 consensus g. Shine-Dalgarno

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2. H. Gobind Khorana deciphered the genetic code by (1) chemically synthesizing DNA molecules of known sequence, (2) using this synthetic DNA as a template to produce RNA in a reaction involving RNA polymerase and dNTPs, then finally (3) using this RNA in an in vitro translation experiment with the ribosome and amino acyl-tRNA (aa-tRNA) building blocks to produce peptides. For each single-stranded deoxyribonucleotide sequence Khorana synthesized (shown below), a single polypeptide was produced in the in vitro translation step (3): (1) Synthetic DNA d(TTT)n d(CCC)n d(AAA)n d(GGG)n d(AAACCC)n d(AC)n d(ACA)n a. (2) RNA encoded by synthetic DNA (3) Peptide product composition polylysine polyglycine polyphenylalanine polyproline Equal F and G Equal C and V polycysteine Fill in the RNA sequences that were produced by RNA polymerase in column (2). b. When Khorana conducted this work, one looming question in the field was whether or not the genetic code is overlapping or non-overlapping. In a…

b. Now do this AGAIN assuming that the DNA and RNA templates are read right to left. DNA strand C DNA strand T G A MRNA codon C|A U TRNA anticodon G A polypeptide TRP

(11) If you design a gRNA with the sequence, GGU AUC AUU GCA CUG ACC AG, in theory which position of the nucleotide in the genomic DNA sequence below will be cut by Cas9 protein, which may lead to a knockout due to an error in DNA repair? The starting and the end coordinate positions of the DNA fragment on the chromosome are indicated at the beginning and end of the sequence, respectively. 110,001 ATC GGT ATC ATT GCA CTG ACC AGA GGC TAC 110,030 A) Between 110,023 (G) and 110,024 (A) B) Between 110,021 (C) and 110,022 (A) C) Between 110,020 (C) and 110,021 (C) D) Between 110,009 (C) and 110,010 (A)

A. Diagram a short single strand of DNA 5’ -AA-GG- 3’. Show the chemical structure of the phosphoribosyl backbone and the attachment point for nucleotides added as “A” or “G”. B. Diagram the product of digestion was a restriction enzyme to cut this sequence between the A and G.

A mutation has occurred to a wild type mRNA sequence:   Wild Type: 5’-AUG-UUG-CAA-GCG-3’  The new mutated sequence: 5’-AUG-UUG-UAA-GCG-3’  What kind of mutation has occurred? a)Silent mutation b)Missense mutation c)Nonsense mutation d)Frameshift mutation

36.Start with two exons and an intervening intron. Include the cap and poly-A tail in your starting pre-mRNA. Show 2’-OH, 3’-OH, O-P-O phosphodiester bonds for the two transesterification reactions that splice exon 1 and exon 2. Be sure to include the branchpoint A and intron consensus sequences. You will need to show where the incoming -OH attacks the O-P-O bond to allow correct splicing in the lariat and between exons. Make your arrows precise. Show the lariat with the consensus sequences. Whenever possible, show 5’ and 3’ ends. Explain the fate of the lariat after it forms?

I. The DNA template, 3'–CGTTACCCGAGCOCGTACGATTAGG–5', was exposed to a mutagen, resulting in the following three templates. 2. A. 3'–CGTTACCCGAGCCGTAACGATTAGG-5' nserti on leuding to frame shift B. 3-CGTTACCCGATCCGTACGATTAGG–5' Point - Transversin C. 3'-CGTTACCCGAGCCGTTCGATTAGG–5' Transition I. Transcribe and translate each template and write down the primary sequence of the resulting polypeptide/protein. Describe how each of the mutations will affect the final protein product from the corresponding template. N met -gla - Ser- Ala -cys -Stup-d Predict whether gene expression (from initiation of transcription to final protein product) would be faster in a prokaryotic or eukaryotic cell. Explain your answer.