Protein Modeling · Division C · Pearl City MiniSO Invitational · 2021
66 questions · 78 points · 50 min· 7 questions from the original omitted
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The CFTR protein is made up of 1,480 amino acids linked together in a chain. Some humans produce a version of the CFTR protein in which phenylalanine (an amino acid) has been deleted from position 508 of the amino acid chain. Which of the following best predicts how the amino acid deletion will affect the structure of the CFTR protein?
The carbohydrates glucose, galactose, and fructose have the same chemical formula (C₆H₁₂O₆) but different structural formulas, as represented in the figure. Which of the following statements about glucose, galactose, and fructose is most likely true?
Which of the following best describes the effect of a greater number of cysteine amino acids on the stability of the proteins?
A researcher proposes a model of an enzyme-catalyzed reaction in which a reactant is converted to a product. The model is based on the idea that the reactant passes through a transition state within the enzyme-substrate complex before the reactant is converted to the product. Which of the following statements best helps explain how the enzyme speeds up the reaction?
Erwin Chargaff investigated the nucleotide composition of DNA. He analyzed DNA from various organisms and measured the relative amounts of adenine (A), guanine (G), cytosine (C), and thymine (T) present in the DNA of each organism. Table 1 contains a selected data set of his results. Which of the following statements best explains the data set?
Which of the following best describes a characteristic of DNA that makes it useful as hereditary material?
Which statement best describes how the nucleotides are joined to form the polynucleotide?
The p53 protein regulates a cellular response to DNA damage. Based on the diagram above, which of the following best describes the role of p53 in the response to DNA damage?
If a segment of DNA is 5'-TAC GAT TAG-3', the RNA that results from the transcription of this segment will be
Which of the following statements concerning a gene is correct?
The figures show structures of amino acids. Each amino acid has a unique side chain, shown in the boxed portion of each figure. Which amino acid or acids have hydrophobic side chains?
The functional group shown is the ____ group.
Pyruvate kinase, a key enzyme in the glycolysis pathway, is inhibited by the amino acid alanine. The ability of alanine to inhibit the enzyme is not affected by increasing the concentration of substrate. Which of the following best explains the mechanism by which alanine inhibits pyruvate kinase activity?
Alcohol dehydrogenase (ADH) is an enzyme that aids in the decomposition of ethyl alcohol (C₂H₅OH) into nontoxic substances. Methyl alcohol acts as a competitive inhibitor of ethyl alcohol by competing for the same active site on ADH. When attached to ADH, methyl alcohol is converted to formaldehyde, which is toxic in the body. Which of the following statements best predicts the effect of increasing the concentration of substrate (ethyl alcohol), while keeping the concentration of the inhibitor (methyl alcohol) constant?
Which of the following messenger RNA sequences could code for both of the two amino acid sequences below, simply by a shift in the reading frame? . . . . glutamine-glutamine-glutamine . . . . . . serine-serine-serine . . .
The figure shows a protein that contains one disulfide bridge and a covalent bond between the sulfur atoms of two amino acids. Suppose that a point mutation in the gene coding for this protein resulted in a single amino acid substitution from a hydrophilic cysteine to a hydrophobic methionine. Which of the following best explains the most likely effect of such a mutation on the structure and function of the enzyme?
DNA is held together by relatively weak ____ bonds between the nitrogen containing bases, which allows it to be exposed for replication and transcription.
DNA replication is considered semi-conservative because____
Which statement best describes what the role of this molecule will be in protein synthesis?
Which of the following configurations represents a zwitterion?
If hydrogen bonding between two amino acid side chains is sufficient to maintain tertiary and quaternary protein structure, why is the presence of cysteine‒cysteine disulfide bridges important?
The hemoglobin protein has four subunits. Explain what would happen to the structure if it were exposed to high temperatures.
What would likely happen if a hemoglobin molecule exposed to high temperatures was returned to normal temperature?
Auxins are plant hormones that coordinate several aspects of root growth and development. Indole-3-acetic acid (IAA) is an auxin that is usually synthesized from the amino acid tryptophan (Figure 1). Gene Trp−T encodes an enzyme that converts tryptophan to indole-3-pyruvic acid (I3PA), which is then converted to IAA by an enzyme encoded by the gene YUC. Identify the number of the arrow in the figure that represents transcription on the template pathway.
Auxins are plant hormones that coordinate several aspects of root growth and development. Indole-3-acetic acid (IAA) is an auxin that is usually synthesized from the amino acid tryptophan (Figure 1). Gene Trp−T encodes an enzyme that converts tryptophan to indole-3-pyruvic acid (I3PA), which is then converted to IAA by an enzyme encode by the gene YUC. Identify the molecule that would be absent if enzyme YUC is nonfunctional.
Auxins are plant hormones that coordinate several aspects of root growth and development. Indole-3-acetic acid (IAA) is an auxin that is usually synthesized from the amino acid tryptophan (Figure 1). Gene Trp−T encodes an enzyme that converts tryptophan to indole-3-pyruvic acid (I3PA), which is then converted to IAA by an enzyme encoded by the gene YUC. Predict how the deletion of one base pair in the fourth codon of the coding region of gene Trp−T would most likely affect the production of IAA. Justify your prediction.
Identify letter C:
Targeting: Briefly describe and define the role PAM in targeting a DNA sequence in the CRISPR complex
Binding: If the target DNA strand does not match the guide RNA, what happens?
Cleaving: If the DNA-RNA helix forms after the binding event, describe specifically where Cas9 nuclease forms cleavage sites. What is the end result after the cleavage?
DNA Repair: CRISPR-induced double-stranded DNA breaks can be repaired by either nonhomologous end joining (NHEJ) or homology-directed repair (HDR). What are the pros and cons of using NHEJ for DNA repair? List at least one pro and one con.
PDB Molecule of the Month (December): Hepatitis C Virus Protease/Helicase
What mechanisms do RNA viruses (like Hepatitis C) use to hijack healthy cells?
What role does the helicase complex play in this molecule?
The active site of Hepatitis C virus protease does not have a deep pocket like other active sites. How did medical chemists overcome this challenge?
Which of the amino acids could form disulfide bonds with another amino acid in the chain to stabilize the tertiary structure of the protein?
Which of the amino acids could participate in hydrophobic interactions with another amino acid in the chain to stabilize the tertiary structure of the protein?
Below are three different representations of phosphoglycerate kinase. For each letter describe the type of structure listed and the defining feature it highlights of the protein.
RNA transcribed from the CRISPR locus and cleaved into individual targeting fragments:
Short segments of RNA used to direct the DNA-cutting enzyme to the target location in the genome:
A natural repair process used to repair broken DNA, which relies on a DNA “template” with homology to the broken stretch of DNA. This usually occurs during or after DNA synthesis, which provides this template
A class of engineered restriction enzymes generated by the fusion of a transcription activator-like effector DNA-binding domain (that binds to a specific DNA sequence) to a DNA-cleavage domain (nuclease) to be used as a genome-editing tool
A metal-dependent DNA-specific endonuclease that produces double-stranded DNA fragments:
Single-stranded DNA nuclease (HD domain) and ATP-dependent helicase and required for interference.
What is the difference between Cas9 and dCas9?
Describe the role of base pairing during DNA microarray analysis, RNA sequencing, and CRISPR-Cas9 editing.
Which chemical group is most likely to be responsible for an organic molecule behaving as a base?
Visualize the structural formula of each of the following hydrocarbons. Which hydrocarbon has a double bond in its carbon skeleton? (*should be subscripts)
Choose the term that correctly describes the relationship between these two molecules:
Identify the asymmetric carbon in this molecule:
Which of the molecules shown has an asymmetric carbon?
Which carbon is asymmetric?
Where would you expect a polypeptide region rich in the amino acids valine, leucine, and isoleucine to be located in a folded polypeptide?
A biochemist isolates, purifies, and combines in a test tube a variety of molecules needed for DNA replication. When she adds some DNA to the mixture, replication occurs, but each DNA molecule consists of a normal strand paired with numerous segments of DNA a few hundred nucleotides long. What has she probably left out of the mixture?
The spontaneous loss of amino groups from adenine in DNA results in hypoxanthine, an uncommon base, opposite thymine. What combination of proteins could repair such damage?
Which is most likely the Ramachandran plot for glycine?
What Ramachandran plot (from the figure above) best represents this molecule?
In 1918, an epidemic of sleeping sickness caused an unusual rigid paralysis in some survivors, similar to symptoms of advanced Parkinson's disease. Years later L-dopa, a chemical used to treat Parkinson's disease, was given to some of the patients. L-dopa was remarkably effective at eliminating the paralysis, at least temporarily. However, its enantiomer, D-dopa was subsequently shown to have no effect at all, as is the case for Parkinson's disease. In a few sentences, describe how the effectiveness of one enantiomer and not the other illustrates structure guiding function.
If 30% of the nucleotides in a single-stranded RNA molecule are adenine, then what percent are expected to be thymine?
Antigens are foreign proteins that invade the systems of organisms. Vaccines function by stimulating an organism's immune system to develop antibodies against a particular antigen. Developing a vaccine involves producing an antigen that can be introduced into the organism being vaccinated and which will trigger an immune response without causing the disease associated with the antigen. Certain strains of bacteria can be used to produce antigens used in vaccines. Which of the following best explains how bacteria can be genetically engineered to produce a desired antigen?
Genetic engineering techniques can be used when analyzing and manipulating DNA and RNA. Scientists used gel electrophoresis to study transcription of gene L and discovered that mRNA strands of three different lengths are consistently produced. Which of the following explanations best accounts for this experimental result?
The sequences for two short fragments of DNA are shown above. Which of the following is one way in which these two segments would differ?
A student analyzed a viral genome and found that the genome had the following nucleotide composition. • 28% adenine • 20% thymine • 35% cytosine • 17% guanine
Which of the following best describes the structure of the viral genome?
Which of the following best illustrates the flow of information required for the synthesis of proteins encoded in the genome of a retrovirus?
The next few questions will relate to this passage and figure.
The structure of the TRPV1 protein consists of several transmembrane domains that are embedded in the membrane as well as a carboxy-terminus and an amino-terminus that are located inside the cell. TRPV1 is activated by several stimuli, including the binding of capsaicin, a chemical found in chili peppers. Capsaicin enters the cell by simple diffusion and then binds to one of the transmembrane domains of TRPV1, which opens the ion channel. The opening of the TRPV1 channel allows Ca²⁺ ions to enter the cell, leading to the activation of the enzyme calcineurin. Calcineurin removes phosphate groups from the phosphorylated form of the transcription factor NFAT2, which is typically found in the cytoplasm. Once dephosphorylated, NFAT2 moves into the nucleus, where it blocks the transcription of another protein, ATF3. ATF3, when active, prevents the cell cycle regulatory protein pGoG from inducing apoptosis and blocking cell division (see figure). Low extracellular pH activates TRPV1 through the binding of H⁺ ions to TRPV1.
Based on the information and figure above: Describe the properties, including the location, of the site of TRPV1 that allow H⁺ ions to bind.
Describe the specific location in the cell where ATF3 protein is produced.
Researchers claim that many cancers include a mutation in the gene encoding pGoG. Support the researchers' claim.