Drewniak 1

Katarzyna (Kasia) Drewniak

Biol 2281.301
1/23/2023
Experiment 1: The use of the Internet to analyze nucleic acid and protein sequences
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Question 1). In the alignment report, locate the sequence with accession code BC007075.1. What
is the name of the gene (1pt)? Note: a long code may be posted: gi|13937928|BC007075.1

This is a homo sapiens hemoglobin beta, mRNA(cDNA clone MGC:14540 is the name of
the gene.

Question 2).
a. What are the Max score and E-value for the similarity between this sequence
(BC007075.1) and the first query sequence (131 nucleotides) (1 pt)?

The mas score is 237 and the E-value of 3e-58 for the 131 nucleotide.

b. What are the Max score and E-value when you use (last) 60 nucleotides to perform a
Nucleotide BLAST search (1 pt)? (hint: You need to scroll down the page more to find
(BC007075.1) when shorter sequence is used)

The max score is 109. And E- Value 3e-20. For the 60 nucleotides.
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Question 3). Click on the accession code (BC007075.1) to obtain information about this DNA
sequence. Under the section of " Articles about the HBB gene"; Click "see all" and find an article
published on Viruses. 2022 Mar 15;14(3):611. What is the title of this article (1pt)? (If you
would like to read the full text of the article, and it is not available through this link, you can
obtain it through UTD library links)

A BioID-Derived Proximity Interactome for SARS-CoV-2 Proteins is the title.

Question 4)
a. On the information page for (BC007075.1), could you find out information whether
this clone is a cDNA clone or genomic DNA clone? (1pt, hint: look under
“definitions” at the top of the page).

Yes, you can find out whether it is cDNA clone or genomic DNA clone because it
states it under the definition.

b. Do you think there is any intron in the reported nucleotide sequence at the very
bottom of the page (1pt, review the definition of Complementary DNA (cDNA) and
intron using the link of Glossary in NCBI:
https://www.ncbi.nlm.nih.gov/books/NBK21106/

No there are no introns because this is complementary DNA meaning it has gone
through splicing.

Question 5). How many alpha chains and beta chains are present in a normal adult hemoglobin
tetramer (1pt)?
The normal adult hemoglobin tetramer consists of two alpha chains and two beta chains.

Question 6). What is the disease caused by Absence of beta chain (1 pt)?

The disease caused by the absence of beta chain is beta-zero-thalassemia.

Question 7). On which chromosome is the beta hemoglobin gene located (1 pt)?
It is on chromosome 11.
Question 8)
a. From biochemical analysis, it was determined that the human beta hemoglobin protein
contains about 150 amino acids (aa).  Based on this information, which one of the
ORFs displayed on website is most likely the correct one, RF1 or RF2 (1 pt)?

RF1 is most likely because it has a length of 147 amino acids.

b. How many amino acids are translated in the correct reading frame (1 pt)?

There is one reading frame.

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Question 9). How many amino acids are identical (displayed in red) between the query (47
amino acids) and the consensus sequence (cd08925) in this conserved domain of Hb-beta-like
(1pt)?

There are 30 identical amino acids between query and the consensus sequence.

Question 10) What polypeptide chains are present in hemoglobin A (HbA) (1pt)?

The polypeptide chains present in hemoglobin A are two alpha-chains and two beta-
chains.

Question 11): To determine the evolutionary relationships among the organisms you can
compare the amount of time to a common ancestor. Scroll down to find phylogram tree based on
the alignment.
a. Which protein shares the highest similarity with human hemoglobin subunit beta
(HBB_HUMAN) (0.5pt)?
_HBB_Rabit shares the highest similarity with human hemoglobin subunit beta.

b. Which protein shares the least similarity with human hemoglobin subunit beta
(HBB_HUMAN) (0.5pt)?
HBA human shares the lest similarities to HBB human.
c. Insert a screen shot of Phylogenetic tree with parameters selected as below (1pt):
Tree type: Phylogenetic tree Layout: Horizontal Phylogram with
aligned labels
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