Teaching > BioE131 > BioE131WeeklyExercises > BiologicalSignalExercises

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1. What transformations (or transmissions) of information occur during (a) transcription, (b) translation, (c) splicing, (d) clonal (asexual) reproduction, (e) sexual reproduction, (f) viral infection of a host genome?
2. What's a regulatory sequence? What is a DNA-binding protein ? What's the difference between a cis -acting sequence and a trans -acting sequence?
3. What is a base-pair? How many base-pairs are there in the human genome? How many in the largest and smallest human chromosomes?
4. What is a promoter region? What sort of sequence features are found in (a) bacterial promoters, (b) eukaryotic promoters?
5. What is (a) a transcription factor, (b) a transcription factor binding site? How many base-pairs in a typical transcription factor binding site in the human genome (or another bacterial or eukaryotic genome)? What is specificity in DNA-protein interactions, and what is the structural basis for it?
6. What is the difference between pre-mRNA and mRNA ?
7. What are the (a) nucleus, (b) ribosome, (c) transcription terminator loop, (d) spliceosome?
8. Describe three processes, other than splicing or translation, that can affect the progress of a euykaryotic transcript RNA molecule from nucleus to ribosome. What signals control these processes? Where are these signals located? Find representative examples of such signals. Roughly how many nucleotides (bases) are there each example?
9. What are (a) exons, (b) introns, (c) splice junctions, (d) splice donor sites, (e) splice acceptor sites, (f) the polypyrimidine tract, (g) the ribosome binding site, (h) the IRES (internal ribosome entry site), (i) codons, (j) the genetic code, (k) the start codon, (l) the stop codon, (m) untranslated regions, (n) alternatively-spliced exons, (o) the SECIS element?
10. Name five ways in which translated protein sequences may be chemically modified. What cis -acting signals (binding sites) direct these modifications? How many amino acids are there typically in one such signal?
11. What is cellular signal transduction ? Identify five chemical and/or informational transformations of protein, DNA and/or RNA that may occur during, or after, signal transduction.
12. What is evolutionary homology ? What sort of things can be homologous? What role does homology play in biological scientific inference?
13. What are primary, secondary, tertiary and quaternary structure ? Do these terms relate only to proteins or can you also find examples involving RNA (in which case, what are the differences in interpretation of the terms, if any)?
14. Name three diverse ways in which protein structure confers functional properties.
15. Folded proteins are always linear polymers. True or false? Why?
16. In biological sequences, what is a palindrome ? What is a protein complex , a heterodimer, a homodimer and a tetramer ? What is the relationship between palindromic sequences, and the DNA binding sites for (a) dimeric TF (transcription factor) complexes, (b) tetrameric TF complexes?
17. What does allosteric mean ? What is allosteric regulation ? Give an example of allosteric regulation.
18. What are the signal recognition particle (SRP) and the signal peptide sequence ? How long is the latter?
19. What is the range of lengths of a "typical" protein domain? For example, what is the mean length of a protein domain in the PFAM database, and what is the variance (or other measure of the spread, e.g. the 95th percentiles)?
20. How many amino acids are in a "typical" catalyic enzyme active site? Find an example of the sequence of such an enzyme (e.g. look up the DDE motif , or pick any other catalytic domain). How far apart in sequence are the catalyic amino acids, in your example? (i.e. if you write out the amino acid sequence, how many a.a.'s lie between the active site a.a.'s?)
21. What are (some of) the underlying causes of mutations in DNA? What role/roles is DNA mutation hypothesized to play in cancer, senescence and evolution?
22. What are (a) histones, (b) chromatin, (c) epigenetic regulation? What transformations of biological polymers are involved in epigenetic regulation? What is the histone code ?
23. Name one way in which the sugar code might be more complicated than DNA or protein signals.
24. What are hormones ? How many different hormones are found in humans (roughly)? What different kinds of chemical structure do these hormones have?
25. What are the differences between a protein-coding gene and an RNA-coding gene ? (The latter is sometimes misleadingly called a non-coding gene ... a protein-centric view of the world.)
26. Roughly how many protein-coding genes are there in the genomes of (a) the bacterium Escherichia coli , (b) a human?
27. Roughly how many transcription factor genes are there in the genomes of (a) the bacterium Escherichia coli , (b) a human?
28. What does reverse complement mean?
29. What is (a) an operon, (b) a pseudogene, (c) transfer RNA, (d) micro-RNA ?
30. What is (a) repetitive DNA, (b) an inverted repeat, (c) a tandem repeat, (d) a microsatellite, (e) a retrotransposon, (f) a DNA transposon, (g) LINEs and SINEs, (h) long terminal repeats (LTRs), (i) terminal inverted repeats (TIRs), (j) a target site duplication? What problems does repetitive DNA pose for genome annotation?
31. What is quorum sensing ?
32. What is (a) a lipid raft , (b) a second messenger , (c) a signal cascade ?

Also check the following "general knowledge" questions:

1. What are the effects, and the molecular mechanism of action, of ricin ingestion?
2. Name two pioneers in the history of computing technology who have also had links with mathematical cryptanalysis. Outline (in a sentence) their contributions to computing technology and to cryptanalysis.
3. What is the RNA world hypothesis ? Is there any support for this hypothesis?
4. Sort these scientific discoveries into chronological historical order: existence of micro-RNA; principles of bacterial gene regulation; complete genetic code; complete sequence of the first eukaryotic genome; three-dimensional structure of the ribosome; three-dimensional structure of DNA; theory of evolution; theory of genetic inheritance.
5. Name a technology that has found application in both Signals Intelligence (SIGINT) and Bioinformatics.

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