Question

The initiation phase of eukaryotic transcription via RNA polymerase II is considered an assembly and disassembly process. Which types of biochemical interactions-hydrogen bonding, ionic bonding, covalent bonding, and/or hydrophobic interactions-would you expect to drive the assembly and disassembly process? How would temperature and salt concentration affect assembly and disassembly?

Short answer

In the assembly and disassembly process of the transcription complex, hydrogen bonding, ionic bonding, and hydrophobic interactions play a key role whilst covalent bonding is usually not involved. The process is sped up by increased temperatures and can be stabilized by moderate salt concentrations, but too high temperatures or salt concentrations can disrupt it.

Step-by-step solution

Identifying the Biochemical Interactions

The assembly and disassembly of the transcription complex involve various biochemical interactions. Covalent bonding is usually not involved as it is stronger and needs energy to break; this is not typically feasible for processes demanding quick assembly and disassembly. Primary interactions include the non-covalent types: Hydrogen bonding, ionic bonding, and hydrophobic interactions.

Effect of Temperature

Temperature affects the rate of biochemical reactions. Increasing the temperature typically speeds up the assembly and disassembly process by increasing kinetic energy which then intensifies the biochemical interactions. However, if the temperature is too high, it may destabilize the proteins, disrupting the process.

Impact of Salt Concentration

Salt concentrations can affect ionic and hydrogen bonds, which are vital for the assembly and disassembly of the transcription complex. Moderate salt concentrations usually stabilize these interactions, but high salt concentrations can disrupt them because they screen the charges and reduce the capacity for these types of interactions to take place.

Key concepts

RNA Polymerase II

RNA Polymerase II is a crucial enzyme in eukaryotic cells responsible for transcribing DNA into messenger RNA (mRNA). This process, known as transcription, is the first step of gene expression.
RNA Polymerase II is made up of multiple subunits that work together to bind to a particular region of DNA and initiate transcription.
Unlike prokaryotic RNA polymerase, RNA Polymerase II requires various additional factors for its proper function, including general transcription factors which assist in the formation of the transcription complex.
These transcription factors help position RNA Polymerase II correctly at the gene's start site and help in pulling apart the DNA strands to start synthesizing RNA.

Biochemical Interactions

Biochemical interactions are the forces that enable the assembly and disassembly of macromolecules, such as proteins and nucleic acids, necessary for biological processes.
In transcription, several types of non-covalent interactions play key roles.
These interactions help form the intricate structures needed for function while allowing flexibility and enabling dynamic processes like initiation and termination of transcription.
Key biochemical interactions include:

• Hydrogen bonding
• Ionic bonding
• Hydrophobic interactions

Covalent bonding is generally not used for these processes due to its strength and stability, making it unsuitable for rapid assembly and disassembly.

Hydrogen Bonding

Hydrogen bonding is a type of chemical bond where a hydrogen atom is attracted to an electronegative atom like oxygen or nitrogen.
In the context of transcription, hydrogen bonds assist in stabilizing the structure of nucleic acids and proteins.
They are weak individually but collectively provide significant strength.
As they are relatively easy to break and reform, they are ideal for processes requiring high dynamics, such as those involved in the transcription process.

Ionic Bonding

Ionic bonding involves the electrostatic attraction between positively and negatively charged ions.
In the assembly of the transcription complex, ionic interactions help stabilize structures by neutralizing charge imbalances and maintaining the proper folding of protein subunits.
The sensitivity of ionic bonds to changes in environmental conditions, such as salt concentration, makes them effective for dynamic cellular processes.
These bonds can be disrupted by high salt concentrations, which interfere by crowding around charge sites and breaking the attraction between ions.

Hydrophobic Interactions

Hydrophobic interactions occur between nonpolar molecules or parts of molecules that associate together to avoid contact with water.
In the context of transcription and protein folding, these interactions help stabilize the structure by driving nonpolar side chains to the interior, away from the aqueous environment.
Such interactions are crucial in maintaining the tertiary and quaternary structures of proteins involved in transcription.
Hydrophobic interactions are fundamental in facilitating the association and dissociation of molecules within the transcription apparatus, affecting the assembly and disassembly processes.