dna structure, chromosomes, and chromatin organization in eukaryotes

What are the basic building blocks of DNA?

Nucleotides, which consist of a phosphate group, sugar, and nitrogenous base.

What forms the sugar-phosphate backbone of DNA?

The sugar and phosphate groups of nucleotides.

What are the four nitrogenous bases found in DNA?

Adenine (A), Thymine (T), Cytosine (C), and Guanine (G).

How are DNA strands formed?

Nucleotides are linked by covalent bonds between the sugar of one nucleotide and the phosphate of the next.

What is the directionality of DNA strands?

DNA strands run from the 5′ end to the 3′ end.

What type of bond connects the nucleotides in the DNA backbone?

Phosphodiester bonds connect the 5′ carbon of one sugar to the 3′ carbon of the next.

How do the two strands of DNA interact?

They run in opposite directions (antiparallel) and are held together by hydrogen bonds between complementary base pairs.

Which bases pair together in DNA?

Adenine (A) pairs with Thymine (T) and Guanine (G) pairs with Cytosine (C).

What is the structure of the DNA double helix?

Two antiparallel strands twist around each other, with sugar-phosphate backbones on the outside and base pairs forming the interior.

What is the significance of the major and minor grooves in DNA?

They are important for protein-DNA interactions.

How many chromosomes do humans have?

Humans have 46 chromosomes, organized into 23 pairs.

How do human chromosomes compare to chimpanzee chromosomes?

Humans have 46 chromosomes while chimpanzees have 48; the key difference is chromosome 2, which is fused in humans.

What is a karyotype?

A karyotype is an arrangement of chromosomes in numerical order, used for genetic analysis and diagnosis.

What is the total size of the yeast genome (S. cerevisiae)?

Approximately 12.5 million nucleotide pairs.

How many genes are found in the yeast genome?

About 6600 genes on 16 chromosomes.

What is the role of exons and introns in eukaryotic genes?

Exons are coding sequences that specify amino acids, while introns are noncoding regions interspersed between exons.

What is the process of gene expression?

DNA is transcribed into RNA, which is then translated into protein.

What happens to the RNA produced by some genes?

For a minority of genes, the RNA itself is the final product and does not undergo translation.

What is the evolutionary significance of chromosome fusion in humans?

Chromosome fusion is a major evolutionary event that distinguishes humans from other primates, despite high genetic similarity.

What does the term 'antiparallel' refer to in DNA structure?

It refers to the orientation of the two DNA strands running in opposite directions (5′ to 3′ and 3′ to 5′).

What is the importance of the DNA double helix structure?

It provides stability and allows DNA to be densely packed while remaining accessible for replication and transcription.

What is the final product for a minority of genes?

The RNA itself, as seen in gene C, where expression ends after transcription.

What determines whether genes produce proteins or functional RNAs?

The role of the gene.

What are the three essential DNA elements for eukaryotic chromosomes?

Origins of replication, centromere, and telomeres.

What occurs during interphase of the cell cycle?

The cell is metabolically active, expressing genes, synthesizing proteins, and duplicating chromosomes.

What happens during the M Phase of the cell cycle?

Mitosis and cytokinesis occur, where chromosomes condense, segregate, and the cell divides.

What is the role of the centromere during mitosis?

It holds duplicated chromosomes together and attaches them to the mitotic spindle for segregation.

What are telomeres and their function?

Special sequences at chromosome ends that ensure complete replication and stability.

What is a duplicated mitotic chromosome composed of?

Two identical sister chromatids, each with a full DNA molecule and associated proteins.

What is the structure of a nucleosome?

DNA wrapped around a histone octamer, forming the basic repeating unit of chromatin.

What is the appearance of condensed chromatin?

It appears as a thick, irregular fiber with dense regions of staining.

What does the 'beads-on-a-string' structure of chromatin represent?

Nucleosomes connected by linker DNA, showing the fundamental structure of chromatin.

How many nucleotide pairs of DNA are included in each nucleosome?

About 200 nucleotide pairs.

What happens to nucleosomes during experimental breakdown?

Nuclease digestion cleaves linker DNA, releasing individual nucleosome core particles.

What is the diameter of a nucleosome core particle?

Approximately 11 nm.

What is the basic structure of DNA?

A 2-nanometer-wide double helix.

What is the width of the 'beads-on-a-string' chromatin?

11 nm.

What is the width of the packed nucleosome chromatin fiber?

30 nm.

What is the approximate size of a fully condensed mitotic chromosome?

About 1400 nm.

What stabilizes the 30-nm chromatin fiber?

Histone H1 and nonhistone chromosomal proteins.

What is the significance of the chromatin structure in gene regulation?

It regulates DNA accessibility for processes like transcription and replication.

What is the primary function of histone H1 and condensin proteins?

They organize and maintain the compaction of DNA into tightly packaged chromosomes for accurate segregation during mitosis.

What are looped domains in chromatin?

Looped domains are structures formed by chromatin fibers that help compact DNA while keeping certain regions accessible for gene regulation.

What role do chromosome loop-forming clamp proteins play?

They anchor the bases of loops in looped domains, creating stable points that hold the loops in place.

How do chromatin-remodeling complexes regulate DNA accessibility?

They modify nucleosome positioning using energy from ATP hydrolysis to loosen and reposition DNA wrapped around nucleosomes.

What is the significance of ATP hydrolysis in chromatin remodeling?

ATP hydrolysis provides the energy needed to slide DNA along the histone octamer, controlling access to specific DNA sequences.

What are the chemical modifications that can occur on histone tails?

Histone tails can be modified by acetyl groups, methyl groups, and phosphate groups.

What is the 'histone code'?

The pattern and combination of histone tail modifications that influence chromatin recognition and behavior by the cell.

What effect does trimethylation at Lysine 9 (K9) have on chromatin?

It leads to heterochromatin formation and gene silencing.

What is the difference between heterochromatin and euchromatin?

Heterochromatin is tightly packed and transcriptionally inactive, while euchromatin is loosely packed and transcriptionally active.

How does heterochromatin formation begin?

It begins when certain nucleosomes acquire heterochromatin-specific histone tail modifications, marking the region as transcriptionally inactive.

What role do specialized heterochromatin proteins play?

They recognize and bind to modified histone tails, recruiting enzymes that spread these modifications to adjacent nucleosomes.

What is the function of barrier DNA sequences in chromatin?

They block the spread of heterochromatin modifications into euchromatin, ensuring that active chromatin regions remain accessible.

What is the overall structure of interphase chromosomes?

Interphase chromosomes contain a mosaic of chromatin states, alternating between compact heterochromatin and open euchromatin.

What is the role of ATP-dependent chromatin-remodeling complexes?

They act like molecular motors that slide DNA along histones, dynamically regulating gene accessibility and expression.

How do histone modifications affect gene expression?

Different combinations of modifications can either promote gene expression by opening chromatin or lead to gene silencing by compacting it.

What is the significance of looped chromatin domains?

They balance DNA compaction with functional accessibility, allowing for organized transcription, replication, and repair.

What happens during the propagation of heterochromatin modifications?

Bound proteins modify adjacent histones, extending the heterochromatin domain along the DNA strand.

What is the outcome of acetylation at Lysine 9 (K9)?

It promotes gene expression by opening the chromatin structure.

What is the role of chromatin in cellular function?

Chromatin structure allows cells to protect DNA while controlling gene accessibility for normal cellular functions.