Choose the best answer.

1		The collection of proteins that can be produced by a given species is:
			A)	Considered that species' genetic complement.
			B)	Correlated with the size of the organism.
			C)	Called the proteome.
			D)	All of these.
			E)	None of these.
2		A cDNA library:
			A)	Can also be called an expressed sequence tag (EST) library.
			B)	Consists of coding sequences from genes that are expressed.
			C)	Is specific to the set of conditions under which the original mRNA was generated.
			D)	All of these.
			E)	None of these.
3		The technique of subtractive hybridization allows identification of genes that are selectively activated under a certain set of conditions.
			A)	True
			B)	False
4		Which of these questions could be answered using subtractive hybridization?
			A)	What genes are required for basic cellular functions?
			B)	What site is bound by a kidney specific transcription factor?
			C)	What genes are expressed in cardiac but not skeletal muscle?
			D)	All of these
			E)	None of these
5		A single microarray may have a surface area of less than three square inches, yet may contain unique spots of tens of thousands of gene sequences.
			A)	True
			B)	False
6		Which of these might be an advantage to genetic testing of individuals via microarrays?
			A)	Many different potential mutations in a single gene could be tested at once.
			B)	Expression patterns of many different genes can be analyzed simultaneously.
			C)	Microarray analysis can provide information on relative levels of expression of particular genes.
			D)	All of these.
			E)	None of these.
7		Which of these would not be a valid reason that use of microarray technology to differentiate between closely related bacterial species and subspecies is important?
			A)	Certain strains of bacteria are more pathogenic than other related strains.
			B)	Some strains of bacteria are more active in bioremediation than other related strains.
			C)	Infection by different strains of bacteria may require different therapeutic approaches.
			D)	In many cases, critical information about characteristics of a bacterium causing an infection needs to be immediately available.
			E)	All of the above are valid reasons.
8		A cluster analysis is the study of groups of genes that seem to be regulated together.
			A)	True
			B)	False
9		The two most common processes that lead to production of multiple functional proteins from the same DNA sequence are:
			A)	RNA editing and alternative splicing.
			B)	Protein folding and posttranslational covalent modifications.
			C)	Alternative splicing and posttranslational covalent modifications.
			D)	Posttranslational covalent modification and transcriptional regulation.
			E)	RNA editing and base modification.
10		Examples of irreversible posttranslational covalent modification include acetylation and phosphorylation.
			A)	True
			B)	False
11		Which of the following statements regarding the proteome is the most correct?
			A)	A large proportion of the proteome is expressed by each cell of a species.
			B)	Levels of gene expression at the mRNA level generally correlate highly with levels of functional protein.
			C)	The proteins produced by a specific cell depend on cell type and environmental conditions.
			D)	All of the above.
			E)	None of the above.
12		In two dimensional gel electrophoresis:
			A)	Different forms of the same protein will tend to migrate at the same position.
			B)	Up to about a hundred different proteins can be distinguished from each other.
			C)	Proteins with similar functions will be located near each other.
			D)	All of these.
			E)	None of these.
13		Western blotting of 2D gel electrophoresis would be a high resolution method of demonstrating a change in a particular protein as a result of mutation.
			A)	True
			B)	False
14		Which of these conclusions might be drawn from the results of a 2D gel electrophoresis experiment?
			A)	Levels of mRNA expression for two different genes are lower under one set of conditions than another.
			B)	In a mutant cell, the lack of protein expression is due to production of unstable mRNA, which is rapidly degraded.
			C)	A mutation prevents proper posttranslational modification of a protein.
			D)	All of these are reasonable conclusions.
			E)	None of these are reasonable conclusions.
15		Tandem mass spectrometry can be used to determine the specific amino acid sequence of a protein.
			A)	True
			B)	False
16		If computers were not able to access the entire genomic sequence of an organism, which of the following techniques might allow determination of the gene sequence that encodes a particular protein?
			A)	PCR amplification of related gene sequences.
			B)	Hybridization of a genomic library with a degenerate probe.
			C)	Production of synthetic peptides.
			D)	All of these.
			E)	None of these.
17		Which of these concerns would apply to functional protein microarrays but not antibody microarrays?
			A)	Antibodies recognize relatively short peptide sequences from a protein, and presence of the same peptide sequence in several proteins is possible.
			B)	Three dimensional structure of a protein is essential for correct function, and the process of microarray preparation may interfere with this structure.
			C)	Certain functions, such as structural support of a cell, may not be amenable to analysis on a microarray.
			D)	All of these apply to functional protein microarrays but not antibody microarrays.
			E)	All of these apply equally to both types of microarrays.
18		Functional protein microarrays can identify protein functions only if their sequence is known.
			A)	True
			B)	False
19		Which of the following pieces of information would not be required for a computer program to determine exon/intron structure of a gene?
			A)	A table correlating codons to amino acids.
			B)	The nucleotide sequence of the mRNa.
			C)	Splice site signals for the species under study.
			D)	All of these pieces of information would be requireD. E. None of these pieces of information would be requireD. This would be a required piece of information; at least the start and stop codons must be recognized by the computer program to identify potential open reading frames.
20		How many potential open reading frames are present in a DNA sequence?
			A)	One.
			B)	Three.
			C)	Six.
			D)	More than six.
			E)	None of these.
21		A computer program must be written in a specific language in order for the computer to understand what needs to be done.
			A)	True
			B)	False
22		You have cloned a new gene from your favorite species of experimental organism, which has had very few genes cloned so far. Which of the following techniques would you expect to provide information about the function of this gene?
			A)	Comparison of regulatory sequences to other DNA sequences in this organism.
			B)	Comparison of regulatory sequences to DNA sequences from other organisms.
			C)	Comparison of the gene sequence to other DNA sequences in this organism.
			D)	Comparison of the gene sequence to DNA sequences from other organisms.
			E)	None of these.
23		Why might you want to search a database for a protein motif?
			A)	A specific motif may impart a specific function to the molecule. You could then identify groups of proteins that may have similar functions.
			B)	Presence of a specific motif in several proteins indicates that they are likely to be all from the same species.
			C)	Absence of a specific motif from one of a pair of otherwise similar proteins indicates that they are produced by alternative splicing of the same gene.
			D)	All of the above.
			E)	None of the above.
24		Which of these would not be an example of sequence element?
			A)	A recognition site for binding of a particular transcription factor.
			B)	A restriction endonuclease cut site.
			C)	An open reading frame.
			D)	A stop codon.
			E)	None of these.
25		In an analysis of eukaryotic gene, you identify several nonoverlapping open reading frames, but they are not all in the same frame. Which explanation makes the most sense?
			A)	By random chance, a second reading frame within the gene also has an open reading frame.
			B)	This gene includes introns which are not multiples of three.
			C)	This is a mutant allele that has had several small insertions.
			D)	All of these.
			E)	None of these.
26		Identification of a gene that does not fit the typical patterns for eukaryotic gene structure would not have a dramatic effect on bioinformatics.
			A)	True
			B)	False
27		Homologous genes:
			A)	Would be expected to have very similar sequences in related organisms.
			B)	Would be expected to be more similar in distantly related organisms than in organisms that are closely related.
			C)	May have become similar to each other by random mutation.
			D)	All of these.
			E)	None of these.
28		A multiple sequence alignment of related genes can identify amino acids required for protein function.
			A)	True
			B)	False
29		You clone a novel gene from your favorite experimental organism, and identify the sequence of the gene itself and the protein. You would like to know if this gene is regulated by any known transcription factors. Which technique would be best suited to provide you evidence to address this question?
			A)	BLAST analysis of the protein sequence.
			B)	BLAST analysis of the DNA from the coding sequence.
			C)	BLAST analysis of the DNA from the upstream regions.
			D)	None of these.
30		Secondary structure of RNA molecules:
			A)	Depends on complementary base pairing.
			B)	Is generated by covalent bonding between sections of the RNA molecule.
			C)	Can be described as interactions between portions of the backbone of the molecule.
			D)	Does not have an impact on function of the molecule.