BIO206 Bioinformatics


From the NIH:
“Phenylketonuria (PKU) is an inherited disorder of metabolism that causes an increase in the blood of a chemical known as phenylalanine. Phenylalanine comes from a person’s diet and is used by the body to make proteins. Phenylalanine is found in all food proteins and in some artificial sweeteners. Without dietary treatment, phenylalanine can build up to harmful levels in the body, causing mental retardation and other serious problems.
PKU is inherited in families in an autosomal recessive pattern. Autosomal recessive inheritance means that a person has two copies of the gene that is altered. Usually, each parent of an individual who has PKU carries one copy of the altered gene. Since each parent also has a normal gene, they do not show signs or symptoms of PKU.
Gene alterations (mutations) in the PAH gene cause PKU. Mutations in the PAH gene cause low levels of an enzyme called phenylalanine hydroxylase. These low levels mean that phenylalanine from a person’s diet cannot be metabolized (changed), so it builds up to toxic levels in the bloodstream and body. Having too much phenylalanine can cause brain damage unless diet treatment is started.”
Your task:
You have been provided the genetic information for the PAH gene from NCBI (See URL ‘Transcript’). Use the information pertaining to the transcript to complete the table below.  Also, use it as a reference for answering the following questions where needed. You are also provided, in a separate document, the genetic information for the PAH gene of three patients (Male 1, Male 2, Female 1). Use your knowledge of DNA sequencing and molecular biology to assess the genetic make-up of these patients in the questions below.

You also have been given a ‘Site of Mutations’ image of the 3D structure of the protein of interest and the genetic information of 3 patients which can be found on Quercus.
It is highly recommended to use an online alignment software tool such as Blastn or Benchling.com. You will have to make an account to use for Benchling.com however, it is very user-friendly and is used in other biology courses at UTM.
How to use Benchling.

1.Complete the table using the information obtained from your online search of the National Center for Biotechnology Information (NCBI) search of the NCBI Reference Sequence NM_000277.
Number of bases
Organism
CDS
Enzyme encoded by gene
Chromosome #

2.Using the BLASTn algorithm at NCBI, perform a sequence alignment between the subject sequence (NM_000277) and each of the 3 query sequences provided (Male 1, Male 2, Female 1). Based on the results, complete the table below. (Hint: Check the box labelled “Align two or more sequences” to open the window. In “View Alignment” results change the view to “Query-anchored with dots for identify”.. This will make finding the mutations easier. Complete the table below. You may also use an online alignment software such as BLASTn or Benchling.com. (6)

Mutation, Y or N?    Position of Mutation? (eg. T200C)    Nucleotide Sequence mutated?    Amino Acid sequence change? (eg. M257R)    Type of Mutation?
Male 1
Male 2
Female 1

3.Define the following point mutations:
a.Silent Mutation:
b.Nonsense mutation:
c.Missense mutation:
4.Design a primers that you allow you to introduce a SILENT mutation at position 289 in Female 1. Complete the blanks below (4) and include a schematic of the template, site of mutation and primer sequence

5.Using a BLASTn alignment of patients indicate the following:
E value :
% Indent:
What does E-value measure :

What does Ident measure :

How are E-value and Ident related?

6.Perform a BLASTn search with the provided DNA sequence using the ‘Mouse genomic + transcript” option under Choose Search Set > Database and complete the following table.

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