Cell physiology and Genetics module 1
Sickle cell disease (MOB)
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QUESTIONS (ALBERTS ET AL. MOLECULAR BIOLOGY OF THE CELL
5TH EDITION 6 TH)
1. What’s the approximate size (Mb) of the human genome? (table 4-1)
~3000 Mb
2. What’s the approximate number of protein-encoding genes in the human
genome?
~20,000
3. Why is it so difficult to find/predict protein coding genes in the human genome
compared to the yeast genome? (Fig 4-13/15/17)(4-13/15/62)
The gene density in the human genome is much lower than in the yeast genome
4. What is on the DNA level next to small mutations in the DNA an
important driving force in (genome) evolution? (fig 4-86/87)(4-75/76)
Gene duplication events
5. What is meant with a gene family (give an example), how (by which process)
are they created, and what are pseudogenes? p255/ p228
A gene family is a group of genes which are highly similar; an example is the
globin gene family, where hemoglobin subunits (α and β) and globins from ) and globins from
other species strongly resemble each other. Pseudogenes are genes which have
a similar sequence as another functional gene (duplication event), but which is
inactive as it lost its activity by mutations during evolution.
6. What is meant with gene ontology (GO)? briefly describe the three
vocabularies (ontologies) that are used to describe gene products.
Gene ontology is the annotation and classification of genes; the three
ontologies used to describe gene products are molecular functioning,
biological role/goal/purpose and localization within the cell.
7. Indicate the exons and introns of the ß-globin gene on the genomic DNA in the
picture below, mark the beginning and end of the protein coding sequence and
mark on the primary RNA transcript the positions of all the sequences that are
relevant for RNA processing of the transcript of the gene. What do the numbers
in the figure indicate? (fig 4-7/6-21/22/28) (4-7/6-20/21/27)
, E I E I E
The numbers in the figure above indicate the nucleotides that are included in the
final transcript (e.g. nucleotides 1-31 are included in exon 1, while exon 2 delivers
nucleotides 32-105, etc.)
8. What is/are the essential molecular difference(s) (at the DNA and protein
level) between Sickle Cell Disease and β) and globins from -Thalassemia’s?
SCD: a qualitative problem of synthesis of an incorrectly functioning globin
which causes red blood cells to sickle. SCD is caused by a specific mutation
which (usually) replaces Glu-6 with Val-6;
β) and globins from -Thalassemia: a quantitative problem of too few globins being synthesized.
A wide range of mutations (point mutations, deletions) cause abnormalities
in transcription, slicing, mRNA stability and/or translation.
9. Why is Sickle Cell Anemia quite common in Africa?
Heterozygosity for SCD offers protection against malaria, which commonly
occurs in Africa; however, due to this positive selection for the SCD allele, it
won’t be wiped out of the gene pool. The result is that relatively much
homozygous recessive individuals are born, that have SCD itself as a trait.
10. What is the major role of the general transcription factors? (fig 6-16/table 6-3)
(6- 14/table 6-3)
Enabling RNA polymerase-II to bind, thereby facilitating initiation of
transcription of a gene. They mark the start site for RNA pol-II.
11. What is the major role of consensus sequences like the TATA box found in
the vicinity of the transcription start site of eukaryotic protein coding genes?
(fig 6- 17)(6-16)
Sequences like the TATA box can be recognized and bound to by specific
general transcription factors (such as TBP, TATA-binding protein), that can
bind to and assemble the entire transcription machinery, including other
GTFs and RNA polymerase-II itself.
12. What is the role of the 5’ and 3’ non-coding regions of an mRNA? (fig 6-22)
(6- 22)
The 5’ non-coding region binds the 5’ cap, which is enzymatically added to
the mRNA. The 3’ non-coding region contains the recognition sequence for
poly-A synthetase, which will add a poly-A tail to the 5’ end of the mRNA.
,13. Describe the role of the C-terminal domain (CTD or tail) of RNA polymerase II
in RNA processing.
The CTD stimulates elongation of the mRNA transcript upon phosphorylation;
furthermore, it carries all the proteins involved in premature-mRNA
modification (capping proteins, splicing proteins, 3’-processing proteins).
14. Explain what the effect will be of a mutation in the ‘branch point A residue’ in
the first intron of the beta globin gene on splicing of a pre-mRNA and on the
synthesis of beta globin (fig 6-26) (6-25)
The branch point is necessary for splicing, as it is involved in lariat formation; if
this branch point is mutated, slicing of this first intron will be disabled. As a
result, a new coding sequence is retained in the mature mRNA, which could
cause a frame shift (if the intron isn’t a multiple of 3). Dysfunctional or non-
functional beta globin will be produced.
, 15. What is the present day advantage of the presence of introns in genes? (fig 6-27)
(6-26)
Introns allow alternative splicing; therefore, multiple variants of a specific
protein can be produced. This is especially useful for cells with a different
speciation, that each require an altered variant of the protein for their
functioning.
16. What is the major role of the short consensus sequences present at 5’- en 3’ splice
junctions in a eukaryotic pre-mRNA? (fig 6-28) (6-27)
These sites are recognition sites for spliceosomes; they signal the beginning and
end of introns.
17. What’s the function of a spliceosome and what sort of molecules form the
functional core of the spliceosome? (fig 6-29) (6-28)
The spliceosome is responsible for the removal of introns from pre-
mRNA. The spliceosome is formed by small nuclear RNA’s (snRNA)
and associated proteins, which forms snRNP’s (small nuclear
ribonucleoproteins).
18. Explain why splicing has to occur at exactly the correct positions, and what are to
two basic principles the cellular machinery uses to accomplish this? (fig 6-30) (6-
29)
If splicing were not to occur at exactly the correct positions, pieces of coding
DNA (exons) could get lost, and a disastrous frame shift could occur (yielding a
dysfunctional protein as product).
1) Base pairing of snRNP’s with splice junctions
2) Rearrangements requiring the same splice site by different snRNP’s, thereby
increasing accuracy
19. Briefly describe the major events in the RNA splicing reaction (see fig below).
What is the purpose of the rearrangements that occur during splicing (fig 6-30)
(6-29) and what type of molecules catalyze the splicing reaction?
U1 snRNP recognizes the 5’ splice site, while some proteins recognize the
branch point (A); the proteins calls an U2 snRNP, which binds to the branch
point (the proteins are released); finally, some more snRNP’s are gathered and
the formation of the lariat is initiated; the branch point reacts with the 5’ splice
site. The purpose of the rearrangements is increased accuracy in splice-site
selection by the spliceosome. The splicing reaction is catalyzed by snRNP’s,
which are units that consist of snRNA’s and proteins.
