Sickle Cell Anemia
An example of why:
a change in protein can lead to disease a change in DNA can lead to a change in
protein
Ground Rules for Class Discussions and Workshops
Be on time. Speak so that everyone from front to
back can hear you. Listen when others are speaking. If it’s review for you, use you intellect
to hear it in a new way. Write down your answers or
consolidate to print.
What do you already know about hemoglobin?
What is the function of hemoglobin? What class of biomolecules does
hemoglobin belong to? What are the symptoms of sickle cell
anemia? Is sickle cell anemia hereditary?
What does that tell us?
Symptoms of Sickle Cell Anemia
pain episodes strokes increased
infections leg ulcers bone damage yellow eyes or
jaundice early gallstones lung blockage
kidney damage and loss of body water in urine
painful erections in men (priapism)
blood blockage in the spleen or liver (sequestration)
eye damage low red blood cell
counts (anemia) delayed growth
Website for Amino acid interactive Workshop
Amino acids – everyone open to this page
http://www.biomed.curtin.edu.au/biochem/tutorials/AAs/AA.html
Power of the R Groups Note the one letter and 3 letter abbreviations for your amino
acid(s). Identify the atoms in red, blue, white, gray, and other colors Find the carboxy group, amino group, beta carbon, R group Categorize the amino acids – and be able to say why – some fit
in more than one category! Aromatic Aliphatic, unbranched Aliphatic, branched Polar Positively charged (basic) Negatively charged (acidic) Small Has a sulfur atom in the R group Hmm?
Which are hydrophobic vs. hydrophilic? Which would attract each other if brought together? Which would repel? Which would likely fold to the interior in an aqueous
environment? Which would likely fold to the exterior in a lipid environment?
Alpha helix is the “default”Ala, Glu, Leu
Beta sheetBranched R groupsVal, Thr, IleHelix disrupters with close H bond participants:Ser, Asp, Asn
Turns (not shown): Gly, Asp, Pro
The Nucleic Acids: DNA and RNA
DNAsynthesized from deoxynucleotide triphosphates
(dNTPs)
RNAsynthesized from nucleotide triphosphates
(NTPs)
DNA sequence Write the primary sequence of the DNA displayed in 3B from the 5’ to the 3’ end of both strands
Website for interactive workshop for DNA analysis
Translation exercise Translate the following sequence using the codon
table: ATG GTG CAC CTG ACT CCT GAG GAG AAG TCT GCC GTT
ACT Perform same procedure on the sequence below
using a software program: ATG GTG CAC CTG ACT CCT GTG GAG AAG TCT GCC GTT
ACT http://us.expasy.org/tools/dna.html How many nucleotides have changed in the codon
in boldface? What is the amino acid difference in the two
sequences? What is the quality of that difference with respect to
R groups?
The early evidence that sickle cell anemia is caused by an amino acid change in hemoglobin. Tryptic digest: the protease trypsin cleaves C terminal to lysine and arginine.
Summary
DNA (mutated = changed)
RNA (mutated)
Protein (possibly mutated)
Remember: Mutation is not always “bad”! For example: Mutation → Evolution → An additional normal genome
Multiple sequence alignment for cytochrome C – mutation and conservation
Human protein accession number AAA35732 (see next slide)
Dog protein accession number XP_532493
Yeast protein number from structure database 1YCC
CLUSTAL W PROGRAM
Hemoglobin HBB1
>gi|4504349|ref|NP_000509.1| beta globin [Homo sapiens] MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN ALAHKYH
FASTA format for a protein sequence in single letter code
How to prepare the sequences for the MSA on ClustalW
For Human and Dog Go to NCBI Select to search the protein database from the dropdown
menu Enter the Accession Number (previous slide) and GO Click on the link Change the display to a FASTA file Copy the FASTA output for both species into a single text
file. Make sure the header is separate from the sequence. For Yeast
Clink on the link, find the FASTA format and copy into the same file
Copy or upload the file into ClustalW
Workshop due as email to me by 9AM Wednesday, 6/24.
1. Give the answers to questions/challenges from slides within today’s PowerPoint.
2. Print out your ClustalW results and add a short paragraph discussing how Clustal W gives you a clue as to which part(s) of the Cytochrome C protein you would hypothesize are most important to its function (which is/are the same in all 3 organisms). Start your paragraph as a hypothesis as to which parts are most important, and write your discussion as a defense of your hypothesis.
3. What is the chromosomal location of the gene that causes sickle cell anemia?
4. What is the name of the gene? 5. State the nucleotide change and amino acid change that leads to sickle cell
anemia (there may be more than one change that gives rise to the disease)6. If sickle cell anemia is so devastating, why has it lasted in the population
for such a long time? Give a molecular, mechanistic, evolutionary explanation (you may have to do a little research to get this). What does the sickled molecule do that the normal molecule can’t?
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