18: supercoiling, dna structure, lk

How do proteins recognize specific DNA sequences?

Proteins recognize DNA sequences through hydrogen bond donors and acceptors exposed in the major and minor grooves. The hydrogen bond pattern is unique for each base pair and depends on directionality (e.g., AT vs. TA).

In which groove (major or minor) can proteins discriminate among all four base pairs (AT, TA, GC, CG)?

The major groove.

In the minor groove, what discrimination is possible for DNA base pairs?

Only between AT/TA and GC/CG pairs.

How many base pairs are generally sufficient to create a unique protein binding site in the genome?

As few as four base pairs.

What feature allows certain amino acids to form hydrogen bonds with DNA bases?

Long side chains terminating in polar functional groups.

Which amino acids are commonly involved in DNA-binding due to their ability to form hydrogen bonds?

Asparagine (Asn), Glutamine (Gln), Glutamic acid (Glu), Lysine (Lys), and Arginine (Arg).

How do positively charged amino acids like Arg and Lys assist DNA binding?

They interact with the negatively charged phosphate backbone of DNA, stabilizing binding.

Which groove (major or minor) is narrower and chemically less diverse?

The minor groove.

Name three common structural motifs found in DNA-binding proteins.

Leucine zippers, zinc fingers, and helix-turn-helix motifs.

How is DNA compacted in eukaryotic cells?

DNA wraps around histone proteins to form nucleosomes.

What are histones rich in, and why is it important?

Lysine and arginine residues, which are positively charged and interact with DNA’s negatively charged backbone.

What is the composition of a nucleosome core particle?

Two copies each of histones H2A, H2B, H3, and H4, wrapped by about 146 base pairs of DNA.

What chemical modification of histone tails increases DNA accessibility?

Acetylation of lysine residues.

How does acetylation of histone tails affect histone-DNA interactions?

It neutralizes lysine’s positive charge, weakening histone-DNA binding and making DNA more accessible.

Besides histone modifications, what molecule can regulate DNA compaction?

Long non-coding RNAs (lncRNAs).

What is the typical structure of DNA under normal cellular conditions?

B-form DNA.

How many base pairs per turn does B-form DNA have?

About 10.5 base pairs per helical turn.

What is the pitch (height per turn) of B-form DNA?

Approximately 35.7 angstroms (Å).

What is supercoiling in DNA?

Supercoiling is the formation of additional coils in DNA when its linking number changes from the relaxed state.

What happens to DNA when the linking number decreases (ΔLk < 0)?

It becomes negatively supercoiled (underwound).

What happens to DNA when the linking number increases (ΔLk > 0)?

It becomes positively supercoiled (overwound).

What are topoisomers?

DNA molecules with the same nucleotide sequence but different linking numbers.

How do Type I topoisomerases alter DNA supercoiling?

They cut one DNA strand, change the linking number by ±1, and do not require ATP.

How do Type II topoisomerases alter DNA supercoiling?

They cut both DNA strands, change the linking number by ±2, require ATP, and can introduce negative supercoils.

What special Type II topoisomerase introduces negative supercoils in prokaryotes?

DNA gyrase.

Why is the pattern of hydrogen bonding in DNA direction-dependent (e.g., AT vs. TA)?

Flipping a base pair creates a different arrangement of hydrogen bond donors and acceptors, enabling proteins to distinguish directionality.

What restricts the diversity of amino acids used for DNA recognition by proteins?

Only a limited number of amino acids can reliably serve as hydrogen bond donors or acceptors.

What chemical groups at the end of amino acid side chains form hydrogen bonds with DNA bases?

Amide groups (in Asn, Gln), carboxylates (in Glu), and guanidinium groups (in Arg).

Why are longer side chains beneficial for amino acids in DNA-binding domains?

They can reach into the major or minor grooves to access base-specific hydrogen bonding sites.

How do proteins distinguish AT from TA base pairs in the major groove?

Proteins like those with Asn and Gln residues recognize the unique donor/acceptor pattern of each base orientation.

In non-sequence-specific DNA binding, what part of DNA do proteins primarily interact with?

The negatively charged phosphate backbone.

What are nucleosomes composed of?

DNA wrapped around a histone octamer (2 copies each of H2A, H2B, H3, and H4).

How many base pairs of DNA are typically wrapped around each nucleosome core?

Approximately 146 base pairs.

What role do the N-terminal tails of histones play?

They regulate DNA accessibility through post-translational modifications like acetylation or methylation.

How does acetylation of lysine residues affect the positive charge on histone tails?

Acetylation neutralizes the positive charge, weakening the interaction with DNA.

What effect does acetylation of histones have on transcription?

It increases DNA accessibility, promoting gene transcription.

What structural role do long non-coding RNAs (lncRNAs) play in chromatin organization?

They act as scaffolds or guides to recruit chromatin-modifying complexes.

In what type of duplex is A-form DNA commonly found?

DNA-RNA or RNA-RNA duplexes.

How many base pairs per turn are found in A-form DNA?

Approximately 11 base pairs per turn.

Which DNA form is left-handed?

Z-DNA.

What is the dominant DNA form found inside cells?

B-form DNA.

What structural feature of B-form DNA is critical for protein-DNA interactions?

The presence of distinct major and minor grooves.

What happens to DNA structure if the base pairs per turn deviate from 10.5?

Torsional stress arises, leading to supercoiling.

What is the linking number (Lk) in DNA?

It is the total number of times one DNA strand wraps around the other in a closed circle.

What happens if two turns are removed from a relaxed DNA circle (ΔLk = -2)?

Negative supercoiling forms.

Why is negative supercoiling beneficial for cells?

It makes DNA easier to unwind for replication and transcription.

How does positive supercoiling affect DNA?

It makes DNA more tightly wound and harder to separate.

Which type of topoisomerase introduces negative supercoils into DNA?

Type II topoisomerase, specifically DNA gyrase in prokaryotes.

What energy requirement distinguishes Type I from Type II topoisomerases?

Type I does not require ATP; Type II requires ATP.

What is the typical change in linking number caused by Type I topoisomerases?

±1.

What is the typical change in linking number caused by Type II topoisomerases?

±2.

What types of supercoils can Type I topoisomerases relax?

Both positive and negative supercoils.

What types of supercoils can Type II topoisomerases relax and introduce?

They can relax both types and introduce negative supercoils.