Self-assessment questions

The questions all follow the same convention: questions in this font can be answered from the text of the pages of the topics in the module and are potentially useful in helping you to decide whether you need to study the topic at all. Questions in dark green range slightly outside the confines of the topic but the answers should lie within the module as a whole. Questions in red require some work in libraries or on the Web.
  1. Biological chemistry in time and space
  2. Molecules: structures, isomers, chirality, representations of molecular structures
  3. Equilibrium and reactions
  4. The biological and chemical literature
  5. Macromolecules; primary structures and conformations
  6. Genomes, gene expression and protein biosynthesis
  7. Metabolic, regulatory and neural networks
  8. Classification and ontologies in the biological sciences
  9. Recombination, repair, rearrangement and evolution
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Topic 1

  1. Draw a straight line representing the "history of everything" from the big bang to the present day.
    • what is the approximate length of the line in years?
    • mark the approximate position of the supposed origin of life on earth
      •
    • Mark on the line approximately the positions corresponding to origins of the classes Oo4 - Oo7 of Chandler's semiotics
      •
  2. Within an order of magnitude what are the sizes in mm (millimetres) of an oxygen molecule (O2), a small globular protein, a small virus, a bacterium?
  3. Define (or give examples) of the word, "ecoment"; differentiate between a biolgist's use of the word, "cell" and the class Oo5 of Chandler: speculate wildly (but briefly!) on why Chandler might have eschewed the biologist's definition.
  4. Give one example each of the importance in biochemistry of interactions between a macromolecule and (a) a smaller molecule and (b) another macromolecule.
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Topic 2

  1. What is the valency of Se?...
  2. ... and what is the significance in biochemistry of the molecule shown below?
             H2NCH(CH2SeH)CO2H
  3. What is the shape of each of the following?
    • an ammonium ion (NH4+)
    • ethylene (H2C=CH2)
    • H2C=C=CH2 (it doesn't matter what it's called)
    • an oxonium ion (H3O+)
  4. What does SMILES stand for? and
    what are the SMILES strings for methane, ethane, benzene, phenol and     D-glyceraldehyde?
  5. Define (or explain briefly with examples) enantiomer, geometric isomer, diastereoisomer.
  6. Complete the following table (C6H5- is phenyl)
    Rough formula types of isomerismacidic, basic?reducing/oxidising
    CH3CH2OH    
    C6H5-OH    
    CH3CH2NH2    
    CH3CH=O    
    CH3C(=O)OH    
    HO(O=)C-CH=CH-C(=O)OH    
    (CH=O)-CHOH-CH2OH    
    (CH2OH)2C=O    
  7. Which of the molecules in the pictures below contain chiral C atoms?
  8. What is the relationship between CH3CH=O ("acetaldehyde") and CH2=CH2OH ("vinyl alcohol")?
  9. Write down the products if each of the following is hydrolysed.
    • CH3(C=O)NHCH3
    • CH3(C=O)OCH3
    • (HO)2P(=O)OCH3
    • CH3CH(OCH3)2
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Topic 3

Note: questions in bold are important.
  1. What is the molarity (M) of pure water?
  2. Glycerol is CH2OH-CHOH-CH2OH
    • What is the RMM of glycerol?
    • What is the mass of glycerol (in g) in 250 ml of a 150 mM glycerol solution?
  3. So far we have looked at rather small molecules. What would be the mass of 1 mol of a large protein of RMM 105?
    4.
  4. Look at the acetic acid/acetate saga. Note that if we add a strong acid to such a buffer, we substract the concentration of strong acid from [OAc-] and add the value to [HOAc] and likewise with a strong base we add the value to [OAc-] and subtract it from [HOAc]. Assume the pK is 4.0. We have a solution of 100 mM HOAc and 120 mM NaOAc in our buffer.What are the effects of adding ....
  5. Re-write the text of the account of buffers using as an example a solution of NH3 and NH4Cl.
    Specifically, what is the form of the equation
         "pH = pK + log10(something-or-other)" in this case?
  6. Rate constants etc.:
    • What is the equation ("kt = ln(something)") for the bimolecular reaction of A and B?
    • How would the answer to that differ if a and b were equal?
  7. Define or explain briefly, free energy, free energy change, standard free energy change.
    What is the free energy change for a reaction at equilibrium and how does this differ from the free energy change for a reaction not at equilibrium?
  8. Write (hopefully short !) essays on
    • transition states
    • the significance of the parameter A in the Arrhenius equation
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Topic 4

These are exercises in using the Web.... do not infer that that the answers themselves are crucial to understanding bioinformatics. Following our rules, they should all be in red.
  1. What type of sea creature contains vanadate that replaces, to some extent, phosphate in animals such as ourselves?
  2. Name one human protein that contains copper ions.
  3. Find a tutorial on chemcial reaction rates.
  4. What is the geographical, as opposed to biological, significance of the word "wombat"?
  5. Where is the largest taxonomic resource in Belgium?
  6. What are the modern terms for the following?
    • muriatic acid
    • spirits of salt
    • old yellow enzyme
    • new yellow enzyme
    • Zwischenferment
  7. What is the full and correct chemical name for the substance biochemists call GTP?
  8. What are the chemical components of fusel oil?
  9. What is "fuller's earth" and why is not referred to as "Fuller's earth"?
  10. What is the importance of Streptomyces rimosus in the pharmaceutical industry?
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Topic 5

  1. What are differences (if any) between
    • a peptide bond and an amide bond
    • an O-glycoside and an N-glycoside
    • α and β anomers
    • a nucleotide and a nucleoside
  2. Name one or more amino acid(s) that are in some sense similar to
    • methioine
    • glutamic acid
    • tryptophan
  3. name or describe a phosphomonoester and a phosphodiester
  4. Print out the following pictures and draw an approximate scale (Å):
  5. Now do question 4 again using the correct sizes
    6.
  6. Have a look at RasMol. It can be obtained from www.umass.edu/microbio/rasmol/getras.htm and elsewhere (try Google).
  7. Here is a DNA sequence 5'-to-3' left-to-right
    ACATAAACATGGGACCCAA
    Write down the sequence of the complementary strand also 5'-to-3' left-to-right.
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Topic 6

  1. Explain the terms diploid and allele
  2. What is a ribozyme?
  3. In what forms of life would you expect to find ...?
    • introns
    • polycistronic mRNA
  4. Explain the concept of "template" in gene expression
  5. Describe qualitatively (e.g. pseudocode) a method for looking up the Genetic Code in a computer program.
  6. Explain what is meant by "reading frame".
  7. In our example of reading frames one of us (!) felt confident in writing down 10 amino acids in the reading frames labelled "2" but only felt able to write donw 9 in the case of reading frames "3". Why was this?
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Topic 7

  1. Look at the description of Michaelis-Menten kinetics
    • A competitive inhibitor has the effect of increasing KM: sketch the graph for this hypothetical enzyme in the presence of such an inhibitor
    • What is the value of [S] when v = Vmax/2 ?
    • Vmax and KM can be calculated by doing a non-linear regression to fit v versus [S] data to the equation. In the era before everday use of computers, biochemists used to plot 1/v as a function of 1/[S] to obtain a straight line that could be fitted by hand.
      1. Sketch such a graph and label Vmax and KM
      2. However this is an inaccurate method: why?
  2. Discuss briefly with examples anhydrides and esters of phosphoric acid.
  3. Name or describe one reaction or process in which a favourable overall free energy change is achieved by the hydrolysis of GTP rather than ATP and speculate on how the resultant GDP might be re-converted to ATP.
  4. In an important metabolic reaction, glucose-6-phosphate is oxidised in a REDOX reaction
    • What is glucose-6-phosphate oxidised to?
    • what is the oxidant in this case?
  5. Referring to one of the metabolic maps in the text....
    • What is the metabolic importance of chorismic acid (or "chorismate")?
    • In which of the following organisms does chorismic acid metabolism actually occur?
      • carrots
      • rabbits
      • mushrooms
      • earthworms
      • common bacteria
    • describe 2 different mechanisms whereby micro-organisms can take up up ammonia (NH3) from the medium in whcih they are growing.
  6. Write short essays/notes on the following topics
    • Transcriptional and translational control in different types of organism
    • The importance of the cro gene to lambdoid phages
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Topic 8

  1. A chef in a large restaurant or hotel decides to sort out the enormous number of pans that have been accumulated over the years. Design an Adansonian scheme for helping the chef differentiate frying pans, sauce pans, woks, griddle pans....
  2. Without drawing a time scale, sketch a phylogenetic tree for the following: bumble bee, gold fish, earth worm, star fish, pig, cat.
  3. What is the time scale in question 2?
    • For what taxonomic purpose(s) are mtDNA sequences useful?
    • Comment on the inheritance of mtDNA.
  5. What macromolecular studies would be useful for studying relationships between
    • conifers
    • zoöplankton
    • daisies and related plants
    • isolates of HIV
  6. Comment on mistakes which would be made by putting execessive taxonomic reliance on the toxicity of different species of snake on the basis of the extent to which they are venemous.
  7. Use the link provided to answer these questions about enzymes
    • What is EC 2.1.1.1 ?
    • How many EC numbers describe DNA polymerases?
    • What is the EC number for rhodanese?
    • How does the EC cope with "restriction enzymes"?
  8. Name one other Web site for relating EC numbers to enzymes.
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Topic 9

  1. In the case of the fictitous (and rather implausible!) fish how might the frequency of recombinants between genes 1-9 be related to the spacing between the genes ?... and how was this used in "classical genetics"?
  2. Explain the terms
    • gene
    • allele
    • linkage group
  3. Explain the terms
    • transposon
    • plasmid
    • resolution (in relation to transposition)
  4. Be prepared to discuss the molecular a clinical implications of drug resistance.
  5. Name 2 drug resistance mechanisms used in bacteria of clinical importance
  6. Name/describe 3 ways in which DNA damage can arise in vivo... and
  7. name/describe repair mechanisms for your 3 examples (question 6).
  8. In experiments with experimental micro-organimsms, caffeine is not in itself mutagenic but it enhances the mutagenicity of mutagens including UV light. Speculate plausibly on the mechanism for this effect of caffeine.
    • What sort of chemical is caffeine?
  9. What is "Darwinism": hypothesis, wild guess, belief... or what?
  10. Name 3 factors that might account for a very rapid generation of species diversity over a relatively short period of time.
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