Exercise 1: What is DNA?
Q1: What are the names of the 4 different DNA bases, and their single letters identifier?
Adenine (A), Cytosine (C), Guanine (G), Thymine (T)
Q2. How many nucleotide base pairs are there in this fragment of DNA?
16
Tip: count the base pairs in the 3D structure window, whilst you hover the mouse cursor over the bases in one of the sequences in the alignment window.
Q3. From step 9, are the DNA strands parallel or anti-parallel?
Anti-parallel
Tip: If you compared the position of the first base in strand A and strand B (as viewed in the alignment window) they are in fact at the opposite ends of the double helix (as viewed in the 3D structure window). Because they start at different ends of the helix.
Q4. Look at the shape of the purines and pyrimidines in the structure viewer, how are they different to each other?
Purines and pyrimidines are nitrogenous bases.
Purines (adenine and guanine) coloured pink are two-carbon nitrogen ring bases.
Pyrimidines (cytosine and thymine) coloured cyan are one-carbon nitrogen ring bases.
Q5. In Step 11, what direction is the strand turning, clockwise or anticlockwise?
The B-form double helix of DNA, as proposed by Watson and Crick, rotates clockwise (right-handed).
Exercise 2: What are codons?
Q6. When an amino acid residue is selected in the protein sequence, why are three nucleotide bases highlighted by a black box in the DNA coding sequence panel?
The black box highlights the three nucleotide bases codons present in DNA. The set of three adjacent nucleotides (triplet) code for a specific amino acid residue during protein synthesis.
Q7. What DNA triplet bases are associated with leucine at residue 3, 10 and 12?
3= ctc
10=ttg
12= ctg
Q8. Would you expect them to be the same?
No, as there are 6 different triplet combinations that code for leucine (tta,ttg, ctt, ctc, cta, ctg)
Exercise 3: What is RNA?
Q9: What are the names of the four different RNA bases?
Adenine (A), Cytosine (C), Guanine (G), Uracil (U)
Q10. How does RNA and its nucleotides differ from those of DNA?
DNA and RNA are polymers made up of nucleotide sub-units. The nucleotide consists of a phosphate group, a 5-ring sugar, and a nitrogenous base. DNA contains a deoxyribose sugar and has a thymine base. RNAs contains a ribose sugar and has an uracil base.
RNAs are usually single-stranded.
Exercise 4: Viewing human myoglobin protein
Q11. How many amino acid residues are there in the human myoglobin protein?
149
Tip: Either scroll to the end of the sequence, place the mouse cursor on the last residue leucine (L) and look at the status box in the bottom left-hand corner of the alignment window.
Or read the information in ID sequence name as the sequence name has the start and end position of the sequence appended to the name.
Q12. How many alpha-helix regions are there in the structure?
Rotating the 3D structure, there are 6 distinct alpha-helix regions and one very short alpha-helix region.
Exercise 5: Compare myoglobin proteins from different species
Q13. Which animal has the most similar sequence compared to the human myoglobin?
The gorilla as they share the same branch in the tree. Looking at the sequences in the alignment window, they are the same except at residue 23 where there is a proline in human myoglobin and serine in gorilla myoglobin.
Q14. Looking at the tree window, are the groupings what you might expect?
Yes, the primates group together as they have similar myoglobin, the birds group together, the dolphin and whale have similar myoglobin.
Q15: From the tree which animal has the most similar myoglobin to humans?
The gorilla when you review the sequences in the alignment window, they are the same except at residue 23 where there is proline in humans and serine in gorillas.
Q16: From the tree, compared to humans which animal has the least similar myoglobin?
Ostrich.
The ostrich and chicken have their own branch away from the other animals, so they are the most different from human myoglobin. But the ostrich with a branch distance score of 44 is larger than the distance score of 22 for chicken.
The tree reflects the similarity between the sequences. The numbers on the trees are distances scores. They can be added together to allow comparison. The smaller the distances scores, the greater the sequence similarity.
Exercise 6: Viewing a range of proteins with different biological functions
Q17. How many different protein amino acids are found in nature?
Proteins found in the human body are constructed from a set of 20 amino acids.
Although there are hundreds of amino acids found in nature, only 20 are present in naturally occurring proteins.
Q18. What is the name of the amino acid that is represented by the letter A?
Alanine
Q19. What is the chemical formula of the amino acid glycine (G)?
C2H5NO2
Exercise 7: What are exons & introns?
Q20. How many exons are in the HBB gene?
5
The exons are coloured cyan. Probably the easiest way is to count the cyan bands in the overview window.
Each exon is numbered, and this information can be seen by hovering the mouse cursor over the exons in the alignment and a yellow tooltip opens.
Tip: The overview window contains a red box that reflects the bases that are displayed in the alignment window. Click & drag the red box to scroll along the sequences in the alignment window.
Q21. What is the main difference between exons and introns?
Genes are made up of protein-coding regions called exons, separated by regions called introns. Introns do not encode proteins but appear to play a role in regulation and gene expression.
Exercise 8: Viewing the coding DNA of the HBB gene & its protein product
Q22. What nucleotide triplet codon code produces the glutamic acid at residue 7?
gag
Q23. In the mutated HBB protein, what amino acid replaces the glutamic acid at residue 7?
The glutamic acid amino acid residue (E) at residue 7 (highlighted in red) is replaced with valine (V).
Placing the mouse cursor on residue 7 in the alignment opens a yellow tooltip that contains this information.
Q24. Does every person with this HBB gene mutation get sickle cell anaemia?
No.
Sickle cell disease is caused by a mutation in the haemoglobin-beta gene found on chromosome 11. The disease is autosomal recessive which means that only people with 2 copies of the sickle cell gene, one on each chromosome 11, have the condition.
Q25. What happens to the red blood cells of people with sickle cell anaemia?
Under low oxygen conditions, the haemoglobin with homozygote mutations has a tendency to form polymers, this process is called sickling. These polymer filaments distort the cell into the characteristic crescent shape. I recommend this video on the subject:
Q26. What evolutionary advantage does heterozygote sickle cell mutation (only 1 of the HHB genes have the mutation) infers on people in countries such as Africa?
Individuals with the heterozygote sickle cell mutation in areas with persistent malaria outbreaks appear to have a distinct advantage. This is why individuals with heterozygous alleles are far more common in these areas.