Deck 22: Bioinformatics and Omics

Question 1

Bioinformatics is _________.

A) the application of information science to biology
B) the computational branch of molecular biology
C) about searching vast biological databases available on the internet
D) using computational tools to compare nucleic acid sequences and protein sequences
E) all of the above

Answer 1

all of the above

Question 2

The term _____ refers to study of the structure, function, and evolution of all the genes of an organism.

A) lipidomics
B) proteomics
C) genomics
D) metabolomics
E) all of the above

Answer 2

genomics

Question 3

Bioinformatics has developed as a distinct field due to _______.

A) solving the human genome
B) advances in software and computing power
C) implementation of high-throughput nucleic acid sequencing techniques
D) advances in mass spectrometry techniques that make it possible to analyze large molecules
E) all of the above

Answer 3

all of the above

Question 4

The genome is consistent across an entire organism, because all the cells of an organism contain ____.

Question 5

The _________ is the collection of all of the RNA molecules in an organism, cell, or tissue.

A) proteome
B) transcriptome
C) lipidome
D) interactome
E) kinome

Question 6

The _____ is the collection of all the proteins in an organism, cell, or tissue. The half-lives of proteins vary depending on the cellular treatment during an experiment.

A) metabolome
B) kinome
C) lipidome
D) proteome
E) interactome

Question 7

When running cell-based experiments a large number of biochemical processes are taking place simultaneously and can continue after sample collection, confounding the results while additional samples are being harvested. To stabilize the composition of the reaction mixture researchers can ____.

A) add a cocktail of inhibitors to the mixture
B) separate the mixture
C) evaporate the mixture
D) dilute the mixture
E) all of the above

Question 8

Biological systems are always in flux. The ________ change the most on a short time scale.

A) proteome and genome
B) genome and lipidome
C) metabolome and kinome
D) transcriptome and proteome
E) glycome and interactome

Question 9

The kinome is highly transient because it is a collection of ______ modifications of biomolecules made by kinases upon cell stimulation.

A) esterification
B) hydrolysis
C) condensation
D) phosphorylation
E) none of the above

Question 10

______ is related to the novel expression of the genes due to environmental factors without changes in the genetic code.

Question 11

______can detect novel gene transcripts, gene fusions, and single-nucleotide variants.

A) Microarray technology
B) RNA sequencing
C) DNA sequencing
D) PCR
E) none of the above

Question 12

Protein sample preparation for mass spectrometry analysis, MALDI-TOF, includes (sometimes) ______.
I. protein labeling
II. protein sequencing
III. mixing with a matrix
IV. protein migration
V. protein separation

A) I and II
B) II and III
C) I, III and V
D) III, IV and V
E) II, III and IV

Question 13

The most common programming languages used in developing bioinformatics tools are:
I. JavaScript
II. LabVIEW
III. R
IV. Python
V. BASIC-PLUS

A) I
B) II
C) III
D) I, III and IV
E) III and V

Question 14

The _____ is an international nucleotide sequence repository maintained jointly by the U.S. National Center for Biotechnology Information (NCBI), the European Molecular Biology Laboratory (EMBL), and the DNA Data Bank of Japan (DDBJ).

A) GenBank
B) PDB
C) Entrez Gene
D) PubMed
E) PubChem

Question 15

A cDNA sequence is the ___________ region of a gene.

A) regulatory
B) protein-coding
C) untranslated
D) epigenetic
E) none of the above

Question 16

________ is used to determine related sequences, to establish phylogenetic information, and to recognize tertiary motifs of proteins.

A) Processing
B) Sequence alignment
C) Similarity search
D) Cross-referencing
E) none of the above

Question 17

________ are made with short nucleotide sequences that are used as probes. The abundance of transcripts in a sample is determined by binding _____ transcripts to the probes and detecting the intensity of the signal.

A) Microarrays; fluorescently-labeled
B) Slides; color-coded
C) Tags; fluorescently-labeled
D) Samples; color-coded
E) none of the above

Question 18

A prokaryotic coding sequence includes information on coordinates of the ____ .
I. promoter elements
II. ribosome binding site (RBS)
III. open reading frame (ORF)
IV. introns

A) I and II
B) I and III
C) II and IV
D) I, II and III
E) III and IV

Question 19

The National Center for Biotechnology Information (NCBI) site,
Https://www.ncbi.nlm.nih.gov/, can be searched by __________.

A) GeneID
B) name of protein
C) accession number
D) GI number
E) all of the above

Question 20

Use the NCBI site (
Https://www.ncbi.nlm.nih.gov/) and search for GI: 631226408, without choosing a particular database. The answer to your search is a ___________.

A) nucleic acid sequence
B) protein
C) book
D) journal citation
E) all of the above

Question 21

Use the NCBI site (
Https://www.ncbi.nlm.nih.gov/) and search for NP_001278826.1, without choosing a particular database. The answer to your search contains access links to ___________.
I. labratory information
II. the protein sequence of insulin preproprotein
III. the Gene ID: 3630
IV. clinically significant information
V. references

A) I and II
B) II and III
C) II, III and IV
D) II, III and V
E) none of the above

Question 22

Use the NCBI site (
Https://www.ncbi.nlm.nih.gov/) and search for NP_001278826.1, without choosing a particular database. Click on the protein link. This protein ________.

A) is of human origin
B) is 110 amino acids long
C) contains three protein segments: insulin B chain, C-peptide and insulin A chain
D) has a protein sequence that starts with a methionine
E) all of the above

Question 23

BLAST is a(n) ___________ that uses FASTA format protein sequences or nucleic acid sequences.

A) ionization assignment tool
B) molar mass tool
C) modeling tool
D) local alignment search tool
E) none of the above

Question 24

ExPASy is a bioinformatics website that contains numerous tools. Among them is the ProtParam tool,
Https://web.expasy.org/protparam/. Go to this site, type in the amino acid sequence without spaces, and calculate some physical and chemical parameters for the following peptide sequence:
Choose the correct answers from the list given.
I. theoretical pI 6.90
II. molecular weight 3430 (g/mol or DA)
III. number of negatively charged residues (Asp + Glu) is 4
IV. number of proline residues is 3
V. number of histidine residues is 3

A) I and II
B) I and III
C) II and IV
D) III and V
E) II and V

Question 25

ExPASy is a bioinformatics website that contains numerous tools. Among them is the Reverse Translate tool at
Http://www.bioinformatics.org/sms2/rev_trans.html. Go to this site, type in the peptide to find the cDNA sequence that encodes it:
The answer is a ___ base sequence that starts with ______.

A) 30; ytngtngar
B) 30; tcgatcgat
C) 90; tttgtgaac
D) 90; cgctgtatc
E) 60; ctggtggaa

Question 26

MALDI-TOF is used to characterize __________.

A) food additives
B) proteins
C) pesticides
D) hydrocarbons
E) none of the above

Question 27

A _______ can be a protein that is either increased in concentration or might be misfolded in a disease state and can help in diagnosing a disease.

A) biomarker
B) sequence
C) cluster
D) fluorescent probe
E) dye

Question 28

The National Institutes of Health (NIH) is the largest biomedical research center in the World. It is funded by the US government and its yearly budget is $41.7 billion (fiscal year 2020). This yearly budget is used for funding __________.

A) intramural research
B) extramural research
C) RO1 grants
D) Early-Stage Investigator grants
E) all of the above

Question 29

The National Institutes of Health (NIH) is responsible for biomedical and _________ research and it comprises ___ different institutes and centers.