Download PHYS 498 Quiz 1 Solution Starting with double

PHYS 498 Quiz 1 Solution
Starting with double-stranded DNA, explain step-by-step, the process of making RNA and a
protein. Tell about what are (thermodynamically) stable molecules and how to make them
chemically reactive, including small molecules or other molecules/proteins which need to
interact with them.
There are three parts to this question:
1. Transcription of DNA to RNA
2. Translation of RNA to protein
3. Energetics of formation of RNA and protein
Remember the central dogma of molecular biology: DNA makes RNA makes protein
Transcription of DNA to RNA
1. Transcription factors binds DNA (at the promoter region) and recruits RNA polymerase
to form mature transcription complex
2. DNA double helix is unwound, which requires energy
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Any enzyme that unwinds DNA is called helicase. In prokaryotes, the
polymerase itself is a helicase. In eukaryotic DNA, a specific transcription factor
acts as helicase
3. RNA polymerases moves through the DNA strand from 3’ to 5’, producing mRNA from
5’ to 3’ using nucleoside triphosphates (NTPs)
4. The transcription is then terminated and mRNA is released
Translation of RNA to protein
1. Key players: ribosome (30S and 50S subunits), mRNA, aminoacyl-tRNA (or chargedtRNA or just tRNA)
2. Process:
a. Initiation:
i. 30S subunit binds mRNA
ii. fMet-tRNA binds AUG codon at P-site of ribosome
iii. initiation factors (IF1, IF2 and IF3) helps recruit 50S subunit and assemble
initiation complex
b. Elongation:
i. aminoacyl-tRNA bound to EF-tu (elongation factor-thermo unstable)
enters free A-site on ribosome
ii. if there is a mismatch between mRNA codon and tRNA anti-codon, the
tRNA is rejected
iii. when there is a match between the mRNA codon and tRNA anti-codon,
the GTP on EF-tu hydrolyzes, and EF-tu dissociates from tRNA
iv. ribosome catalyzes new peptide bond between the growing peptide chain
at P-site and new amino acid on A-site. It does this through a dramatic
conformational change
v. EF-G binds the ribosome at the A-site. Its GTP hydrolyzes to GDP and Pi
to switch the ribosome to its initial state, ready to accept new tRNA at the
A-site
c. Termination:
i. When the stop codon is encountered, release factor (RF1 or RF2) enters Asite and triggers release of protein from ribosome
ii. Another release factor (RF3) catalyzes release of RF1 or RF2
d. Recycling:
i. RRF (ribosome recycling factor) and EF-G releases mRNA and tRNA
from ribosomes and cause ribosome to dissociate into 30S and 50S
subunits
Energetics of formation of RNA and protein
RNA is formed through covalent bond between nucleotides. The formation of the
phosphodiester bond in RNA requires energy, and this energy is derived from the nucleoside
triphosphates (NTPs). Other than the energy needed for polymerization, there is also an
activation energy that needs to be overcome. This activation energy is reduced by the enzyme
RNA polymerase.
Helicase is used to unwind DNA using the energy derived from ATP hydrolysis
A peptide is formed through condensation reaction between two amino acids, which forms a
peptide bond. This process requires energy, which comes from GTPs that is used by the
ribosome. There is also an activation energy that needs to be overcome when making protein,
and ribosome serves to lower this activation energy to allow proteins to be made more
efficiently
During polymerization, the change in Gibbs free energy (∆G) is positive. This means that the
product has higher energy than the reactants, as shown in Fig 1. The change in enthalpy (∆H) is
positive (unfavorable), while the change in entropy (∆S) is positive (favorable). The magnitude
of ∆H is greater than T*∆S such that the final sign for ∆G is positive (recall that ΔG = ΔH – T ΔS)
Fig 1. Free energy diagram of a condensation reaction with the help of enzyme. The final state has higher energy
than the initial state. Enzymes like DNA polymerase and ribosome help lower activation energy.
Source: http://www.biog1105-1106.org/demos/105/unit3/energychanges.html