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. TranscriptionTranslation 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 bio- functionality? 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. Raswin (Software to study of the protein structure via protein crystals) 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.

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. (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 (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 20 x = (assumption: reading forward and backward is different) → x log 20 = 78 → x = ≈ 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 N p can be synthesized up to a certain maximum length x is Recall the geometric sum, So, 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 where k B 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; (ii) There are two types of amino acids, sharing the equal number of amino acids; (iii) All of the 4 amino acids are the same. Entropy is important to study the amount of information encoded in the DNA, etc (next lesson) The 2! (factorial) in the denominator is due to the redundancy. We have 2 pairs repeated twice.

Question6: [Codon System, pat year test2] Consider Figure 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).

Question8: [RNA and Catalysis] Why is it so that RNA can be reasonably efficient catalyst? RNA can form base-pairs, i.e. A-U and C-G The fact that RNA is single- stranded (mostly), while yet it can form base-pairs, make it possible to “fold on itself”, giving rise to a huge number of possible conformations. Thus, such flexibility may make RNA a better enzyme as compared to DNA

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) (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) Both UAU and UAC give the amino acid tyrosine. There might be redundancy here. Since the codon system (alien) is different compare to human being, we only know the maximum possibility in number of amino acid here.