2. A. Proteins stick to DNA through hydrogen bonds. Draw your choice of a correctly hydrogen bonded Watson and Crick base pair. B. Draw your choice of any amino acid side chain correctly hydrogen bonded to the available edge of the base pair.
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- 1. Label the drawing at the right with the terms nucleotide, base pairing rules, and double helix. Write each term and draw a line that connects the term to the appropriate part of the drawing. AX P 010101010 80 Р PDP TCXA D. D C GXC P 0 CXG P P D A ICXA D P G D D CXG D TCXA DL D TCXA 0101010 D CXG P AXT D P P P P D 0 D P P P GCD LON A1) a) Sketch an A-form helix and a B-form helix, highlighting the differences between them. Indicate the bases and backbone as lines. Label the major and minor grooves. 2) Sketch a ribose in the pucker that is expected in RNA. 3) Sketch a 2’ deoxyribose in the pucker that is expected in DNA. 4) Draw a GCG triplet (GC Watson-Crick), with perfect geometry. Draw the bases only, with dR’s at the N-9 positions of the purines (Gs) and at the N1 positions of the pyrimidine (C)13. please answer, i'll give thumbs up
- 11) Examine the following two DNA sequences. Sequence 1: ATGCGATGCTAGCAT Sequence 2: ATGCGATGATAGCAT If both of these sequences code for proteins, how might the function of protein 2 differ from the function of protein 1? Use the table below for assistance. U C A G บบน UUC UUA UUG CUU CUC CUA CUG U Phe GUUT GUC GUA GUG Leu Leu AUU AUC lle AUA AUG Met or Start Val Ceweg 232 www... UCU UCC UCA UCG CCU CCC CCA CCG ACU ACC ACA ACG C GCU GCC GCA GCG Ser Pro Thr Ala CAU CAC CAA CAG A AAU AAC AAA AAG UAU U UAC C UAA Stop UGA Stop A UAG Stop UGG Trp G Tyr GAA GAG His Gin Asn Lys GAU GAC Asp G c] Glu UGU UGC CGU CGC CGA CGG AGU AGC AGA AGG GGU GGC GGA GGG Cys Arg Ser Arg Gly U C A G U C A G U C A G by Calin me press A) Protein 1 and protein 2 will function exactly the same. B) Protein 1 will be shorter than protein 2, so they will not function the same. C) Protein 2 will be shorter than protein 1, so they will not function the same. D) Protein 2 has a different sequence, so it will function…Name a.) ( pair. Indicate hydrogen bonds with dashed lines, number the atoms in the bases according to IUPAC convention, and circle the pyrimidine. Additionally, indicate where the sugar is attached to the base, the major groove, and the minor groove. 8.) Looking at the bases from above, draw a Watson-Crick C-G base b.) ( triple helix (shown below). In this triple helix, a third strand binds in the major groove via base pairs with the existing Watson-Crick bases. This additional base pair is called a Hoogsteen base pair and is indicated by an asterisk followed by the third base. On your drawing add a cytosine in the appropriate location to indicate a CG*C base pair. , it is possible for nucleic acids to form a structure known as a c.) ( between turns, glycosidic bond conformation and sugar conformation differs between A-form DNA and Z-form DNA, Which one is PNA? Indicate (possibly using a table) how the strand width, distance1.Calculate the average number of nucleotide pair per micrometer of DNA double helix using the dimensions proposed by Watson and Crick. 2. Considering the number of base pairs, compute for the actual length of the given DNA strand in micrometer. (1m = 10,000Ao) 3' C G A C T A C 5' 5' G C T G A T G 3'
- 2. Dr. Kim at Ewha Research Center performed shotgun Sanger sequencing on an unknown DNA sample, and obtained the following reads (12 reads). Since the length of each read is quite short, Dr. Kim ran the original sample in a gel electrophoresis, and realized that the original DNA is just 50 base pairs long. (Please note that the resolution of gel electrophoresis is not so good. Thus, we cannot figure out the exact length of DNA using gel electrophoresis in the real world.) 1) САСТС ССAGT GTACC T 3) GGAGT CAАТC GC 5) GGCTG TGCTT GG 7) GATGG CTGTG 9) CAGTG TAССT GCA 11) TGCAA GCCGA G 2) AGCCG AGATG GCTG 4) CTGCA AGCCG A 6) CTTGG AGTCA ATCGC 8) САСТС ССAG 10) GCTGT GСТTG G 12) TGCTT GGAGT (a) Find the sequence of the original DNA (reconstruction), and align each read with the reconstructed DNA sequence. (hint: put all reads on a ppt slide, and move them around to find overlaps.) (b) Calculate coverage at each nucleotide position of the reconstructed DNA, i.e., how many reads cover that…2. Dr. Kim at Ewha Research Center performed shotgun Sanger sequencing on an unknown DNA sample, and obtained the following reads (12 reads). Since the length of each read is quite short, Dr. Kim ran the original sample in a gel electrophoresis, and realized that the original DNA is just 50 base pairs long. (Please note that the resolution of gel electrophoresis is not so good. Thus, we cannot figure out the exact length of DNA using gel electrophoresis in the real world.) 1) САСТС ССAGT GTACC T 3) GGAGT CAАТC GC 5) GGCTG TGCTT GG 7) GATGG CTGTG 9) CAGTG TACCT GCA 11) TGCAA GCGA G 2) AGCCG AGATG GCTG 4) CTGCA AGCCG A 6) CTTGG AGTCA ATCGC 8) САСТС ССAG 10) GCTGT GCTTG G 12) TGCTT GGAGT (a} Find the sequence of the original DNA (reconstruction), and align each read with the reconstructed DNA sequence. (hint: put all reads on a ppt slide, and move them around to find overlaps.) (b) Calculate coverage at each nucleotide position of the reconstructed DNA, i.e., how many reads cover that…In the Watson-Crick structure of DNA, the: a. adenine content of one strand must equal the thymine content of the same strand. b. nucleotides are arranged in the A-form. c. purine content (fraction of bases that are purines) must be the same in both strands. d. two strands are parallel. e. the strands are complementary to each other.
- Describe the d=features of the following DNA-binding domains and how they interact with DNA. Helix-turn-Helix Zinc Finger Leucine Zipper Helix-loop-Helix10.) Draw a double-stranded DNA molecule (using different colors for each) model should clearly represent the sequence: A G T A C C G G G C A A Note: It should include items to represent - sugar molecules - phosphate molecules - 4 distinct nitrogenous base molecules (Adenine, Thymine, Cytosine, and Guanine) - two types of bonds between these moleculesHere is the cartoon representation and Ramachandran plot of a small DNA-binding protein, 80-residues in length. In its Ramachandran plot, 58 residues fall in the a region; 20 residues fall in the region; 2 residues fall in the L region. No residues fall in the disallowed region. The polypeptide termini are labelled. 11. Approximately what percentage of the protein is a-helix? A. 38% B. 42% C. 58% D. 72% 12. What percentage of the protein is B-sheet? A. 0% B. 25% C. 75% D. 100% 13. What percentage of the protein is regular structure? A. 3% B. 42% C. 58% D. 97% 14. What percentage of the protein is irregular structure? A. 0% B. 42% C. 75% D. 97% 15. How many domains are present? A. 1 B. 2 C. 3 D. 4 100 16. How many subunits are present? A. 1 B. 2 C. 3 D. 4