hw 11

You are carrying out a chromatin immunopreciptation experiment. At the step where you are supposed to add the antibody to your protein of interest, you accidentally add a mixture of antibodies that someone was storing in the lab. What will your results show? DNA will still be isolated, but it will correspond to DNA that was bound by any protein recognized by the antibody mixture.Correct DNA will not be isolated. Proteins that do not bind to DNA will now be inaccurately identified. DNA will be isolated nonspecifically.

DNA will still be isolated, but it will correspond to DNA that was bound by any protein recognized by the antibody mixture.

A multiple sequence alignment is shown for a protease that is highly conserved among species. What amino acid do you predict is essential for function of the protease? Dots are indicative of gaps where the sequences do not line up. Species 1 WEDSSNQLRKEWWYFPGCCNQTTSAALLPGE Species 2 WEDSSNQ..............WYFPGCCNQTTSAALLPGE Species 3 WEDSSNQLRKEWWYFPGCCNQTTSAAL......... Species 4 WCCSSNQLRKEWWYLGGCCNFSSSSSLLPGE Species 5 GED........QLRKEWVCFP.............QTTSARRLPGE Species 6 WEDSSNQLRKEWWYFPGCCNQTTSAAGGPGE A in position 26 Q in position 7 P in position 16 E in position 2 W in position 13

Q in position 7

Assemble the following fragments (5'-3') of sequence into a contig. Report you answer using all capital letters. TATACGG AATGCAA ACGGAAT TATACGGAATGCAAACGGAAT TATACGGAATGCAA ACGGAATAATGCAATATACGG TATACGGATACGCA

TATACGGAATGCAA

What allows chain termination to occur at each base of the template during an automated sequencing reaction? The presence of a relatively high concentration of dNTPs The presence of a relatively low concentration of ddNTPs The presence of a relatively high concentration of ddNTPs The presence of a relatively low concentration of dNTPs

The presence of a relatively low concentration of ddNTPs

Why does incorporation of a dideoxynucleotide into a growing DNA polymer terminate strand synthesis? There is no longer a free 3' phosphate to which to add the next nucleotide. There is no longer a free 5' phosphate to which to add the next nucleotide. There is no longer a free 5' hydroxyl to which to add the next nucleotide. There is no longer a free 3' hydroxyl to which to add the next nucleotide.

There is no longer a free 3' hydroxyl to which to add the next nucleotide.

The output from an automated sequencing reaction shows a series of fluorescent peaks, when considering the data output, why are some peaks larger than others? a) Chain termination occurred more frequently at the base corresponding to a large peak, producing a relatively larger fluorescent signal. b) The primer had multiple bases that were fluorescently labeled for products corresponding to the larger peaks. c) Some fluorescent colors are brighter than others. d) More bases were fluorescently labeled in the DNA strands corresponding to the larger peaks.

a) Chain termination occurred more frequently at the base corresponding to a large peak, producing a relatively larger fluorescent signal.

A new technician loaded the pyrosequencing machine with the typical reagents, plus a mixed solution of the four DNA nucleotides. What is likely to occur? a) The machine will not be able to read the correct DNA sequence. b) If the nucleotides are in perfectly even proportions, the machine will still be able to read the DNA sequence. c) The machine will read the DNA sequence but will run out of nucleotides in 1/4 the usual time. d) The machine will read the sequence but will repeat some nucleotides and skip others.

a) The machine will not be able to read the correct DNA sequence.

In automated fluorescent sequencing, what would happen if the fluorescently labeled ddATP was inadvertently omitted from the reaction? a) The sequence would end where the first thymine was encountered on the template DNA strand b) The sequence would end where the first adenine should be incorporated c) Thymines in the template DNA strand would not be represented in the sequencing results d) DNA polymerase does not function without equal concentrations of the four nucleotides

c) Thymines in the template DNA strand would not be represented in the sequencing results

1. Genes derived from the same ancestral gene. 2. Two homologous genes found in different species 3. Two or more homologous genes found in the same organism 4. Two or more paralogs in a single organism.

homologous, orthologs, gene family, paralogs

Based on this phylogenetic tree, which species of flightless bird listed below is most closely related to the cassowary?

kiwi

The figure shows three of the many different phylogenetic trees that could be drawn to describe the evolution of a short DNA sequence. Each arrow indicates a mutation, for instance A3→C means the A at position 3 was changed to a C. Look at each tree. If you apply the principle of parsimony, which tree represents the most likely evolutionary relationship? Note: The tree at the top is Tree A, the middle tree is Tree B, the bottom tree is Tree C.

tree c