Golden Gate Invitational — Protein Modeling

“Hi, is this the Krusty Krab?” (Free response, no points–just checking if you’re awake J )

Which of the following locations on a DNA strand is accessible to DNA binding proteins?

Which of the following describes the structure of a zinc finger domain best?

Which of the following quantities is minimized during protein folding (which thermodynamic quantity drives folding)?

Which of the following is an accurate statement about prions?

When studying a particular DNA binding domain, you find that there are two alpha helices associated with DNA binding. You also finds that the motif is regulating transcription. What amino acid would you be likely to find in these alpha helices?

The structure described in the above question is an example of what general structural motif?

What DNA modification process are CpG islands particular subject to?

Which of the following amino acid residues would most likely be found in close proximity to a DNA or RNA binding site on a protein?

What does the presence of local but nonglobal minima in a conformational free energy diagram indicate about a particular proteins folded state?

Protein domains such as SH2 which recognize phosphorylated tyrosine residues might be involved in which of the following cellular processes?

Which of the following statements is accurate about higher dimensional structures in macromolecules?

Define the contact order of a protein as a measure of how far apart in the primary sequence are residues which interact in the native state (normalized for protein size). Which of the following statements is true?

Scientists analyze protein folding in both a normal water environment and a deuterated heavy water environment. They find that the mass of the native state in both of these environments is different, with the mass in the deuterated water being slightly higher. Which of the following could be a plausible explanation?

WT lambda repressors contain two (Gly46 and Gly48) glycine residues in the middle of an alpha helix. What effect would G46/48A substitution mutations have on folding kinetics and why?

Zidovudine (shown below) is an anti-HIV drug. What is a reasonable function for this drug?

How does phosphorylation of a protein allosterically affect its enzymatic activity?

Histidine is commonly used to tag proteins for affinity chromatography and extraction/purification. What common metal do they bind to preferentially?

You’ve discovered two proteins which cannot be resolved to appreciable degree on a mass based SDS-PAGE gel. You know that one protein has many more glutamic acid and aspartic acid residues than the other protein. What technique would you use to separate these two proteins on a gel? What property do you separate these proteins by?

You run a protein on a PAGE gel and find a band of mass approx. 45 kDa. After running it on an SDS PAGE gel you find a band of much stronger intensity at a mass of approx. 15 kDa. What amino acid (other than methionine) would you expect to find with almost absolute certainty in this protein, and what can you say about the structure of this protein (is it monomeric, dimeric, etc.)?

Name three different interactions that stabilize protein structure.

Due to their aromatic R groups, what special interaction can phenylalanine and tyrosine engage in?

What does CRISPR stand for?

In what organism was the SpyCas9 nuclease first isolated?

List each of the three steps of the CRISPR-Cas9 immune system IN ORDER and describe each briefly (one sentence max per step) (2 for correct order, 2 for each description)

Which domains are mutated in the dCas9 enzyme?

What is the function of Cas6e/Cas6f enzymes in Type I CRISPR-Cas mediated immunity and what structure on pre-crRNA transcripts do they recognize?

What naturally occurring RNA complex is replaced by sgRNA in genomic editing?

dCas9 has potential use as which of the following?

Which strand of DNA is cleaved by the RuvC domain of Cas9?

An single H840A mutation in only the HNH domain of Cas9 creates what molecule, and what does this molecule do?

Which of the two methods of cellular DNA repair of DSB’s is less error prone and why?

About how many nucleotides down or upstream of the PAM site does the Cas9 endonuclease cut DNA?

Some Anti-CRISPR proteins function by inhibiting Cas9 recognition ability. How might they do this?

For what specific purpose have some Anti-CRISPR proteins been used in CRISPR-Cas9 mediated genomic editing?

What gene encodes the cytidine deaminase protein and what is the function of this protein? What specific nucleobases are involved?

Cytidine deaminase is thought to be efficient near areas of DNA breakage. What might this imply about errors in CRISPR-Cas9 mediated genomic editing?

After cytidine deaminase acts on a DNA strand, what process must occur to ensure that all the nucleotides in both strands are deoxyribonucleotides?

The image A shows a segment of a large protein near a segment of a nucleic acid. Is the nucleic acid (on the left) a strand of DNA or RNA, and how do you know (max 1 sentence explanation)? Blue atoms are nitrogen, red atoms are oxygen, beige atoms are carbon, the backbone atoms of both structures and hydrogens are not explicitly shown.