Question

How many structures can you find to use as a starting dataset if you wanted to study how proteins interact with DNA. Assume that you will require only high resolution structures for the study (at least 2.5 Angstroms resolution). For the study, you plan to use structures that were only solved by X-ray crystallography. (Select the closest number if the exact number is not available) *

between 1000-1500

between 2700 - 4000

172

371

between 450 - 950

What is the UniProtKB? *

The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.

The UniProt Knowledgebase (UniProtKB) is the universal protein information center.

The UniProtKB is a database of unique protein sequences.

The UniProtKB is a database of conserved protein sequences.

The UniProtKB is a database of protein 3D structures using the Cartesian coordinate format.

Retrieve the database entry for the protein BPSL1549 from the GenBank database. What organism is the protein from? *

Burkholderia pseudomallei

Pseudomonas aeruginosa

Vibrio cholera

Burkholderia mallei

E. coli

Search the GenBank database for the database entry with the following accession number: MN908947. Select from the list below answers that are TRUE statements pertaining to that database entry. *

It is a nucleotide sequence composed of ~29,903 bp

The data is a genome sequence.

The data is the genome sequence of SARS-CoV-2

The data entry is from the order Nidovirales.

The data entry is from the order Coronavirales

The genome sequence was reported by Wuhan et al in the journalNature, 579, published in 2020.

The genome was isolated from patients who had suffered severe breathing difficulties that in some cases were fatal.

The organism caused a bacterial pneumonia that presented as a severe and acute respiratory symptoms.

The sequence was deposited into the GenBank database on 18 May 2020 and is the newest version of the COVID-19 sequence available.

Answer 1

How many structures can you find to use as a starting dataset if you wanted to study how proteins interact with DNA. Assume that you will require only high resolution structures for the study (at least 2.5 Angstroms resolution). For the study, you plan to use structures that were only solved by X-ray crystallography. (Select the closest number if the exact number is not available) *

between 450 – 950

(These much structures can be used as starting dataset to study protein interaction with DNA)

What is the UniProtKB? *

The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.

(It contains information about a protein such as amino acid sequence, protein name with description, taxonomic information, citation information as well as annotation information. UniProtKB contains two sections:

1. UniProtKB/Swiss-Prot (reviewed and manually annotated)

2. UniProtKB/TrEMBL (unreviewed and automatically annotated))

Retrieve the database entry for the protein BPSL1549 from the GenBank database. What organism is the protein from? *

Burkholderia pseudomallei

(It is an un-characterized protein from Burkholderia pseudomallei (strain K96243).This protein negatively regulates the helicase activity.

Search the GenBank database for the database entry with the following accession number: MN908947. Select from the list below answers that are TRUE statements pertaining to that database entry. *

It is a nucleotide sequence composed of ~29,903 bp. TRUE

The data is a genome sequence. TRUE

The data is the genome sequence of SARS-CoV-2 TRUE

The data entry is from the order Nidovirales. TRUE

The data entry is from the order Coronavirales FALSE

The genome sequence was reported by Wuhan et al in the journalNature, 579, published in 2020. TRUE (But the author name is “Wu” instead of “Wuhan”).

The genome was isolated from patients who had suffered severe breathing difficulties that in some cases were fatal. TRUE (The genome was isolated from a patient who worked at seafood market and was admitted to the Central Hospital of Wuhan on 26 December 2019 when he suffered a severe respiratory syndrome that included fever, dizziness and cough)

The organism caused a bacterial pneumonia that presented as a severe and acute respiratory symptoms. FALSE

The sequence was deposited into the GenBank database on 18 May 2020 and is the newest version of the COVID-19 sequence available. FALSE (The sequence was deposited on 18^th March, 2020)