DNA-Protein Interactions and Recognition

Hydrogen bonds are directional, requiring three atoms to be in a straight line. This means the bond strength decreases significantly when the distance between the atoms exceeds 3 Angstroms.

The major groove of DNA is wider and more accessible than the minor groove. This makes it easier for proteins to bind and interact with the bases in the major groove.

DNA binding proteins can recognize specific sequences by forming hydrogen bonds with the bases in DNA. A single amino acid can interact with multiple bases in a base pair or even across adjacent base pairs.

The alpha helix structure is well-suited for DNA binding because its size and shape fit perfectly into the major groove, allowing amino acid side chains to interact with specific DNA sequences.

There is no single universal code for DNA-protein interactions. Protein binding depends on specific combinations of interactions, including hydrogen bonding and other forces.

The CAP protein binds to a specific DNA sequence by acting as a dimer. Each monomer of the dimer contains a DNA binding domain that recognizes half of the target sequence.

To recognize long DNA sequences, the CAP protein uses multiple contacts. Each monomer binds to a specific 11 base pair sequence, and the two monomers together bind to a 22 base pair sequence.

The CAP binding site is the DNA sequence with the highest affinity for the CAP protein. This sequence is recognized by the CAP dimer through specific interactions between the protein's amino acids and the DNA bases.

Proteins interact with DNA through various means, including ionic bonds with the backbone, hydrogen bonds with bases, and van der Waals interactions. These interactions are crucial for protein function and DNA recognition.

Proteins can recognize specific DNA sequences through interactions with bases in both strands. Each amino acid contact involves multiple bases, contributing to the protein's binding affinity.

The CAP protein binds to a specific DNA region through interactions with bases, primarily in positions 4-8. Even if one interaction is removed, the protein retains high affinity for the DNA sequence.

Different proteins exhibit varying tolerance for changes in their binding sites. Some proteins are more flexible, while others, like nucleases, require perfect sequence matches for their function.

The HTH motif is a common DNA-binding structure found in many proteins. It consists of two alpha helices separated by a turn. The recognition helix binds to the major groove of DNA, while the first helix interacts with the DNA backbone.

Many HTH proteins are dimers, meaning they consist of two subunits. The spacing between their recognition helices matches the helical pitch of DNA, allowing for efficient binding.

The spacing between the recognition helices in dimeric HTH proteins is crucial. This spacing must match the DNA helix pitch (3.4nm per turn) to ensure proper binding.

The HTH motif is found in a wide array of protein families, highlighting its importance and versatility in DNA binding. Examples include CAP and many regulatory proteins.

The basic RNA polymerase structure in bacteria, composed of five subunits (including beta and beta prime). It's responsible for synthesizing RNA but lacks promoter recognition and initiation abilities.

A protein in bacteria that attaches to the RNA polymerase core enzyme, forming the holoenzyme. It recognizes the promoter, initiating transcription.

The complete RNA polymerase complex in bacteria, formed by the core enzyme and the sigma subunit. This complex can recognize promoters and begin transcription.

A mechanism that allows RNA polymerase to continue transcribing through terminator sequences, resulting in higher levels of full-length RNA.

A regulatory mechanism where the synthesis of a full-length RNA molecule is controlled by premature termination of transcription, leading to lower levels of the final product.

The process where RNA polymerase stops transcribing DNA into RNA, leading to the release of the newly synthesized RNA molecule.

A mechanism of RNA polymerase termination that relies on specific sequences in the transcribed RNA that form hairpin structures and stretches of U residues, causing the polymerase to pause and dissociate from the DNA.

A mechanism of RNA polymerase termination involving a protein called Rho, which binds to specific sequences in the RNA and uses ATP to unwind the RNA-DNA hybrid, causing the release of the RNA.

A specific sequence within the RNA that is recognized by the Rho protein to initiate Rho-dependent termination.

RNA sequences that can fold into structures and bind to small metabolites, influencing gene expression by altering the formation of terminator structures or affecting translation initiation.

Riboswitches can control transcription by altering the formation of intrinsic terminator structures in response to the presence or absence of specific metabolites.

Riboswitches can also regulate translation by affecting the initiation of protein synthesis in response to specific metabolites.

MRX is a protein complex involved in double-strand break (DSB) repair. It first removes Spo11, an enzyme responsible for the initial break. Then, MRX degrades the strand with the 5' end at the break, leaving the 3' end for homology searching.

Gene conversion is the non-reciprocal transfer of genetic material from one homologous chromosome to another during DSB repair. This means one chromosome's sequence is copied onto the other, while the original sequence remains unchanged.

In DSB repair, the template for repair depends on the cell cycle stage: sister chromatids are used in later stages, while homologous chromosomes are used earlier. This ensures accurate repair by using identical DNA sequences as a template.

HR is a major DSB repair pathway that uses a homologous sequence as a template. The choice of template (sister chromatid or homologous chromosome) influences the outcome of repair.

The immune system generates a vast number of antibodies (over a billion), far more than the number of genes in our genome. This is achieved through VDJ recombination, a process that randomly combines gene segments to create unique antibody genes.

Antibody genes are composed of variable (V), diversity (D), joining (J), and constant (C) segments. These segments are combined in different ways to create unique antibody genes.

The 5' end of an antibody mRNA codes for the N-terminal end of the protein, while the 3' end codes for the constant region of the antibody.

Antibody variable domains are formed by combining V, D, and J segments. These segments are joined together to create a single, unique variable domain sequence.

UV radiation can cause damage to DNA by linking two adjacent thymine bases together, creating a bulge in the DNA strand and disrupting its normal function.

These enzymes repair UV-induced damage by using visible light energy to break the bond between two linked thymine bases, restoring the DNA to its original state.

A type of repair that directly removes the specific damaged base without needing to cut out a section of DNA.

These enzymes repair DNA damage caused by alkylating agents. They work by transferring the alkyl group to a cysteine residue in their active site, becoming inactive in the process.

A broader category of DNA repair that involves removing a damaged section of DNA and replacing it with a new, undamaged copy.

A type of excision repair that removes a larger section of DNA, typically 20-30 nucleotides, including the damaged bases.

A repair method that joins broken DNA ends together without using a template. This can lead to loss of genetic information or mutations.

This system corrects errors made during DNA replication. It identifies mismatched base pairs and removes them, ensuring the correct sequence is restored.