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Bioinformatics Practice Test Questions: Functional Genomics & Proteomics

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Avg score: 64% • Most missed: “Which of the following is untrue regarding the classic yeast two-hybrid method?”

Functional genomics: Studies the function and expression of the genome, including how genes and intergenic segments contribute to metabolic pathways. It also studies how different segments of an organism work together to produce a phenotype. Proteomics: Studies the interactions, function, composition, and structures of proteins and their cellular activities. It focuses on identifying when and where proteins are expressed in a cell to establish their physiological roles. Proteomics provides a better understanding of the structure and function of the organism than genomics. Topics... Show more

Functional genomics: Studies the function and expression of the genome, including how genes and intergenic segments contribute to metabolic pathways. It also studies how different segments of an organism work together to produce a phenotype.
Proteomics: Studies the interactions, function, composition, and structures of proteins and their cellular activities. It focuses on identifying when and where proteins are expressed in a cell to establish their physiological roles. Proteomics provides a better understanding of the structure and function of the organism than genomics.

Topics include: Sequence – Based Approaches, Microarray-Based Approaches, Comparison of SAGE and DNA Microarrays, Technology of Protein Expression Analysis, Post Translational Modification, Protein Sorting, & Protein Interactions.

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Bioinformatics Practice Test Questions: Functional Genomics & Proteomics

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1. It is important to use bioinformatics tools to predict sites for posttranslational modifications based on specific protein sequences. However, prediction of such modifications can often be difficult because the short lengths of the sequence motifs associated with certain modifications.

TrueFalseMaybeCan't Say

2. Which of the following is untrue regarding EST Index Construction?

The process includes a preprocessing step that removes masks repeatsThere is no screening of vector contaminantsThe goal of the EST databases is to improve the quality of the sequence information so the data can be used to extract full-length cDNAsThe goal of the EST databases is to organize and consolidate the largely redundant EST data

3. Which of the following is incorrect about a microarray?

It is the most commonly used global gene expression profiling methodArray of immobilized DNA oligomers cannot be cDNAsEach oligomer is spotted on the slide and serves as a probe for binding to a unique complementary cDNAIt is a slide attached with a high-density array of immobilized DNA oligomers representing the entire genome of the species under study

4. Which of the following is incorrect about Data Collection?

The two-color microarray uses multiple dyes at timesThe most common type of microarray protocol is the two-color microarrayThe cDNAs are obtained by extracting total RNA or mRNA from tissues or cells and incorporating fluorescent dyes in the DNA strands during the cDNA biosynthesisThe expression of genes is measured via the signals from cDNAs hybridizing with the specific oligonucleotide probes on the microarray

5. Accurate prediction of _____ bonds may also help to predict the _____ dimensional structure of the protein of interest.

nitrogen, twooxygen, threenitrogen, threedisulfide, three

6. Which of the following is untrue regarding expressed sequence tags (ESTs)?

ESTs can also facilitate the unique identification of a gene from a cDNA libraryEST libraries can be easily generated from various cell lines, tissues, organs, and at various developmental stagesIdentification of cDNA clone is difficultAlthough individual ESTs are prone to error, an entire collection of ESTs contains valuable information

7. Which of the following is untrue about SAGE Genie?

It provides an interface for visualizing human gene expressionIt allows matching of experimentally obtained SAGE tags to known genesIt is an NCBI web-based programIt doesn’t filter out linker sequences from experimentally obtained SAGE tags

8. Which of the following is a wrong statement?

The modifications in eukaryotic cells include proteolytic cleavage; formation of disulfide bonds; addition of phosphoryl, methyl, acetyl, or other groups onto certain amino acid residuesThe modifications in eukaryotic cells doesn’t include attachment of oligosaccharides or prosthetic groups to create mature proteinsIn eukaryotic cells most modifications take place in the endoplasmic reticulum and the Golgi apparatusTo assume biological activity, many nascent polypeptides have to be covalently modified before or after the folding process

9. It has been estimated that up to 11% of cDNA clones may be chimeric.

Can't SayFalseTrueMaybe

10. The justification behind Rosetta stone method is that when two domains are fused in a single protein, they have to be in _______ proximity to perform a common function.

extremely closeclosedistantextremely distant

11. Cysteine doesn’t make predictions by building profiles.

Can't SayFalseTrueMaybe

12. ExPASY contains a number of programs to determine posttranslational modifications based on MS molecular mass data.

Can't SayMaybeTrueFalse

13. Which of the following is incorrect regarding 2D-Page?

It works to separate proteins by isoelectric points (pI)The gel is run in one direction in a pH gradient under a non-denaturing conditionIt separates proteins by charge onlyIt stands for Two-dimensional polyacrylamide gel electrophoresis

14. A disulfide bridge is a unique type of _____ modification in which _____ bonds are formed between cysteine residues.

posttranslational, covalenttranslational, ionictranslational, covalentposttranslational, ionic

15. Which of the following is not one of the training sets in SignalP?

ProkaryotesGram-positive bacteriaGram-negative bacteriaEukaryotes

16. Which of the following is untrue regarding UniGene?

The overlapping EST sequences are computationally processed to represent a set of expressed genesOverlapping EST sequences are computationally processed to represent a single expressed geneEach cluster is a set of overlapping EST sequencesIt is an NCBI EST cluster database

17. The signal sequences have a _________ consensus but contain some specific features. They all have a ______ core region preceded by one or more positively charged residues.

strong, hydrophilicweak, hydrophobicweak, hydrophilic

18. An alternative approach to determining protein–protein interactions is to use a large-scale affinity purification technique that involves attaching fusion tags to proteins and purifying the associated protein complexes in an affinity chromatography column.

Can't SayMaybeTrueFalse

19. If the bait and prey proteins _______ they bring the DNA-binding and trans-activation domains in such close proximity that they reconstitute the function of the transcription activator, turning ____ the expression of a reporter gene as a result. Which of the following is not the correct pair of blanks?

do not interact, onphysically interact, onstop interacting, offdo not interact, off

20. Which of the following is incorrect regarding 2D-Page?

One of the challenges of this technique is the separation of membrane proteinsThe stained gel can be scanned and digitized for image analysisNot all proteins can be separated by this method or stained properlyMembrane proteins are largely hydrophilic and readily solubilized

21. ExPASY is a comprehensive proteomics web server with a suite of programs for searching peptide information from the SWISS-PROT and TrEMBL databases.

MaybeCan't SayTrueFalse

22. Which of the following is incorrect about k-Means Clustering?

k-means clustering produces a dendrogramIt classifies data through a single step partitionIn this method, data are partitioned into k-clusters, which are prespecified at the outsetIt is a divisive approach

23. Comparing two-dimensional gel images from various experiments can sometimes pose a challenge because the gels, unlike DNA microarrays, may shrink or warp.

MaybeCan't SayFalseTrue

24. The signal sequences are typically _______ residues long, rich in _____ charged residues such as arginines as well as hydroxyl residues such as serines and threonines, but devoid of ______ charged residues.

28 to 80, negatively, positively28 to 80, positively, negatively300 to 800, negatively, positively300 to 500, positively, negatively

25. Which of the following is incorrect regarding the Protein Identification through Database Searching?

The purpose of the database search is to find exact or nearly exact matchesEven in reality, the protease digestion is always perfect in MSBioinformatics programs can be used to search for the identity of a protein in a database of theoretically digested proteinsMS characterization of proteins is highly dependent on bioinformatic analysis

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