Tutorial 4: Biopolymers, Protein, DNA and RNA
Question1: [Transcription and Translation]
What is the main difference between transcription and translation?
We have both transcription and translation process in the protein synthesis.
Transcription
Translation
Takes place in the
nucleus
Takes place in the cytosol
Requires RNA
polymerase
Requires the aid of 40s and 60s
subunit of ribosomes
Produces mRNA from
DNA
Produces protein from mRNA
Question2: [Protein structure and functionality]
Describe the four level of protein structure.What is an alpha helix and beta sheet?
 Primary structure - the amino acid
sequence of the peptide chains.
 Secondary structure - highly regular sub-
structures (alpha helix and strands of
beta sheet) which are locally defined.
 Tertiary structure - three-dimensional
structure of a single protein molecule; a
spatial arrangement of the secondary
structures. It also describes the
completely folded and compacted
polypeptide chain.
 Quaternary
structure - complex of
several protein molecules or polypeptide
chains, usually called protein subunits in
this context, which function as part of
the larger assembly or protein complex.
Any protein is made of a sequence of amino acids? Suppose you have a
sequence of amino acids, do you have a protein with a particular biofunctionality? Why?
No. The functionality is determined by the shape
(3D structure) of protein. A given sequence of
amino acids may give rise to different shapes,
therefore different functionalities.
The shape of protein depends on the sequence
of amino acids, the nature of the primary solvent
(water or lipid), the concentration of salts, the
temperature, and etc.
Raswin (Software to study of the protein structure via protein crystals)
Question3: [Protein Denaturation]
(i) Give an example from daily life where denaturation can be observed.
 Cooking an egg
 When egg white is heated up, the protein molecules start to unfold in a
process called denaturation which leads to long strands of amino acids
that can easily entangle with each other and form new (weak) bonds.
http://www.sumanasinc.com/webcontent/animations/content/proteinstructure.html
(ii) After eating eggs for breakfast, you return in the evening, dunk the dirty dishes in
water, and notice the yellow streaks remain "dried on." However, after soaking a while,
the complex of various egg yolk molecules easily "washes off."What has happened?
Heating denatured the egg protein molecules,
unorganized condensation reactions then
formed bonds in the drying egg, and soaking
in water eventually resulted in hydrolysis
reactions where water broke these bonds.
Question4: [Protein Combinations vs Number of atoms in Universe]
(i) If we proclaim that we need as many different possible proteins as there are atoms in
the universe, then how long would a protein need to be? (For simplicity we assume that
there are 20 different amino acids and that all protein has equal length-equal number of
monomers.)
 The number of atoms in the universe is approximately 1078. (note: more
details approximation will not make a conceptual difference compare)
 There are 20 amino acids used to synthesize a protein.
 Let define x as the length of the protein
 20x = 1078 (assumption: reading forward and backward is different)
→ x log 20 = 78
→ x = 59.95 ≈ 60
 So, the length of the protein is (ONLY) 60 so that we can have as many
different possible proteins as there are atoms in the universe.
Question4: [Protein Combinations vs Number of atoms in Universe] (continue)
(i) Will your result in part (i) changes significantly if we relax the constraint on the
length of the protein, i.e. you can consider protein with variable length or number of
monomer.
 If proteins allowed to be of different length, then the number of
combinations of proteins Npcan be synthesized up to a certain maximum
length x is N  201  202  203  ....20x   x 20k  1

p
 Recall the geometric sum,
 So,
n 1
 k 0
 ark  a
k 0
r 1
r 1

n
 20x 1  1 
  1  1078
N p  
 20  1 
 20x 1  19 1078  1  1  19  1078


ln(19)  ln(1078 )
 x 1 
 60.94  x  59.94
ln 20
 So, we need the protein with a maximum length of about 60. The result is
qualitatively similar to the part (i).
Question5: [Entropy and Disorderness]
A physical quantity, entropy-S, is often employed to quantify the degree of disordering for
a thermodynamic system. Let  be the number of allowed states of N particles in the
system. S can be then given by S  k B ln  where kB is the Boltzmann constant. If a
polypeptide consists of 4 amino acids, and each amino acid has only one degree of
freedom, calculate the entropy of the molecule for the following cases:
(i) The four amino acids are all different;
S  kB ln 4!
(ii) There are two types of amino acids, sharing the equal number of amino acids;
 4! 
  k B ln6 
S  k B ln
 2!2! 
The 2! (factorial) in the denominator is due to the
redundancy.We have 2 pairs repeated twice.
(iii) All of the 4 amino acids are the same.
S  kB ln1  0
Entropy is important to study the amount of
information encoded in the DNA, etc (next lesson)
Question6: [Codon System, pat year test2]
Consider Figure 16.10 in the textbook. If I claim that the next codon on the mRNA
strand consists of the nucleotide combination TCC, what would that tell us about the
mRNA strand? Explain in no more than 3 short sentences! (2 marks)
This is not a valid mRNA strand since Thymine (T)is not the nucleotide for
RNA. During the replication (transcription), all the Thymine (T) is changed
to another base, Uracil (U).
Question7: [RNA and Replication]
Can RNA polymerase read DNA in both directions? If not, why?
The function of RNA polymerase is to produced RNA by reading a section of
DNA. DNA is directional and consequently, RNA polymerase can read DNA in
only one direction, namely from 3’ to 5’ (otherwise, the product would not
uniquely defined).
Question9: [“Non-coding” RNA]
What is the “non-coding” RNA?
A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a
protein.
Non-coding RNA genes include transfer RNA (tRNA) and ribosomal RNA
(rRNA), small RNAs such as snoRNAs, microRNAs, siRNAs and piRNAs
Question10: [DNA and Codon systems (past year exam)]
(i) Consider the standard genetic code. Which sequence(s) of nucleotides (i.e. which
codon) code(s) for the amino acid tyrosine? (If there is more than one, list them all).
(2 marks)
Both UAU and UAC give
the amino acid tyrosine.
(ii) Next, consider a possible alien genetic code. Assume the codons are of
length 5 and the number of different nucleotides is 3, how many amino
acids could be coded for taking into account the necessity of a start and a
stop codon? (2 marks) There might be redundancy here. Since the codon
system (alien) is different compare to human
5
being, we only know the maximum possibility in
number of amino acid here.
3  2  241