Molecular Biology: Chromatin Structure and Function

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Questions and Answers

What is the approximate distance between two consecutive nucleosomes?

400 bp

200 bp (correct)

100 bp

300 bp

Which structure directly forms from the 30 nm chromatin fiber during further packaging?

11 nm fibers

600-700 nm fibers

300 nm fibers (correct)

Double-stranded DNA

What role does histone acetylation play in chromatin structure?

Relax chromatin to facilitate transcription (correct)

Stabilizes nucleosomes without modification

Condenses chromatin for transcription

Inhibits gene expression

Which of the following fiber structures arises first in the DNA packaging process?

11 nm fiber Signup and view all the answers

What do SAR and MAR sequences in chromatin do?

Link chromatin loops to a protein scaffold Signup and view all the answers

How much does the final DNA packaging reduce its length during mitosis?

Which amino acid modification is associated with transcriptional repression?

Methylation of Lys Signup and view all the answers

The 300 nm chromatin fiber is characterized by which structural feature?

Loops linked to a protein scaffold Signup and view all the answers

What role do miRNAs play in cellular processes?

They direct RISC to target and regulate mRNAs. Signup and view all the answers

How many mRNAs can a single miRNA potentially target?

100 Signup and view all the answers

What is the main function of long non-coding RNAs (lncRNAs)?

They regulate gene expression in eukaryotes. Signup and view all the answers

Which of the following correctly describes the nuclear pore complex?

It constitutes the only communication channels between the nucleus and cytoplasm. Signup and view all the answers

What is the approximate representation of repetitive DNA sequences in human genomic DNA?

10% Signup and view all the answers

Which structure underlies the inner nuclear membrane?

Nuclear lamina Signup and view all the answers

What type of sequences are described as non-transcribed and important for chromosome structure?

Repetitive DNA sequences Signup and view all the answers

What is a function of the nuclear envelope beyond providing a barrier?

Regulates transport of transcription factors to the nucleus. Signup and view all the answers

Which DNA polymerase is responsible for the replication of mitochondrial DNA in eukaryotes?

DNA polymerase γ Signup and view all the answers

In what direction do DNA polymerases synthesize DNA?

5' to 3' Signup and view all the answers

What is the role of initiator proteins in the process of DNA replication?

To bind to specific nucleotide sequences and facilitate strand separation Signup and view all the answers

Why do eukaryotes need multiple origins of replication?

To replicate long chromosomes in a reasonable time Signup and view all the answers

During DNA replication in prokaryotes, how many replication forks are formed?

Two replication forks Signup and view all the answers

Which of the following statements about DNA polymerases is incorrect?

They synthesize DNA in the 3' to 5' direction. Signup and view all the answers

What is the result of the DNA molecule opening at the origins of replication?

Separation of DNA strands into two replication forks Signup and view all the answers

What is a primary function of helicase during DNA replication?

Unwinding the DNA double helix Signup and view all the answers

What role do helicases play during DNA replication?

They catalyze the unwinding of parental DNA. Signup and view all the answers

How do topoisomerases aid in DNA replication?

By catalyzing the breaking and rejoining of DNA strands. Signup and view all the answers

What is the error frequency during DNA replication?

Less than one incorrect base for every 1 billion nucleotides. Signup and view all the answers

What is a unique function of telomerase?

It synthesizes only oligonucleotides with the telomeric sequence. Signup and view all the answers

What mechanism allows DNA polymerase to maintain fidelity during replication?

It uses a proofreading mechanism to remove incorrect bases. Signup and view all the answers

What is a function of single-stranded DNA-binding proteins during DNA replication?

They stabilize the uncoiled DNA template strand. Signup and view all the answers

What occurs at the head of the replication fork during DNA replication?

Helicases unwind DNA and topoisomerases manage stress. Signup and view all the answers

What is the role of the clamp-loading protein during DNA replication?

It holds DNA polymerase in place at the replication fork. Signup and view all the answers

What is the primary function of housekeeping genes?

Expressed in all cells of the body. Signup and view all the answers

Which feature is characteristic of enhancers?

They can act from long distances due to DNA looping. Signup and view all the answers

Which statement about transcription factors and enhancers is accurate?

Multiple transcription factors can bind to enhancers simultaneously. Signup and view all the answers

What role do enhancer elements play in gene expression?

They regulate gene expression during development and in response to external signals. Signup and view all the answers

Which sequence is NOT considered a common binding site for transcription factors in eukaryotic promoters?

ACTG Signup and view all the answers

Which best describes the relationship between enhancers and gene mutations?

Many mutations related to human diseases affect enhancer regions. Signup and view all the answers

What does DNA looping facilitate in relation to transcription?

It brings distant enhancers into proximity with the promoter. Signup and view all the answers

Why are enhancers considered to represent a significant portion of human genomic DNA?

Because many enhancers exist, often outnumbering genes. Signup and view all the answers

What type of RNA polymerase transcribes the 5.8S, 18S, and 28S rRNA?

RNApolI Signup and view all the answers

How many copies of the gene encoding 5S rRNA are present in the human genome?

2000 Signup and view all the answers

Which component of the nucleolus is primarily involved in ribosomal subunit assembly?

Granular component (G) Signup and view all the answers

What is the significance of the high density of RNA polymerase molecules during transcription?

It results in a high number of RNA molecules synthesized. Signup and view all the answers

Which chromosomal regions contain the genes for 5.8S, 18S, and 28S rRNAs in humans?

Chromosomes 13, 14, 15, 21, and 22 Signup and view all the answers

What is the role of spacer DNA in the context of rRNA genes?

It separates different rRNA genes. Signup and view all the answers

What factor primarily determines the size of the nucleolus?

The metabolic activity of the cell Signup and view all the answers

What does the presence of multiple copies of rRNA genes in cells allow for?

Higher transcription rates of rRNA Signup and view all the answers

Study Notes

Unit 3: The Nucleus

The nucleus is a compartment within eukaryotic cells.
It houses the cell's genetic information (DNA).
DNA replication, transcription, and processing occur within the nucleus.
Gene expression is regulated by controlling the transport of transcription factors from the cytoplasm to the nucleus.

3.1. The Cell Nucleus and DNA

The nucleus serves as a storehouse for genetic information.
DNA replication takes place within the nucleus.
RNA transcription and processing occur within the nucleus.
Gene expression is regulated by controlling the transport of transcription factors between the cytoplasm and the nucleus.

Chromosomes and Chromatin

Eukaryotic genomes are more complex than prokaryotic genomes because DNA is organized on multiple chromosomes.
DNA binds to histone proteins to condense into an orderly structure (chromatin) so that it fits within the cell nucleus.
Chromatin exists in different condensed states, depending on the phase of the cell cycle.

Chromosomes

Tightly packaged DNA only found during cell division.
DNA is not being used for macromolecule synthesis.

Chromatin

Unwound DNA found throughout interphase.
DNA is being used for macromolecule synthesis.

Heterochromatin and Euchromatin

Heterochromatin has a condensed structure and is inactive for transcription.
Euchromatin has a loose structure and is active for transcription.

Levels of DNA Packaging

Level 1: DNA double helix coils around histone proteins to form nucleosomes ("beads on a string").
Level 2: Nucleosomes coil into a 30-nm chromatin fiber.
Level 3: 30-nm chromatin fibers form loops attached to a protein scaffold, creating a 300-nm fiber.
Level 4 (mitosis): 300-nm fibers condense further into chromatids.
The degree of condensation varies over the cell cycle.

3.3. DNA Replication

DNA replicates through a semi-conservative mechanism.
Each new double helix contains one original and one new strand that were copied from the original strands.
Complementary base pairing is fundamental to accurate replication.
DNA polymerases are enzymes that synthesize new DNA strands.

DNA Polymerase

DNA polymerase III is the main polymerase responsible for replication in bacteria.
In eukaryotes, different DNA polymerases (α, δ, ε, and γ) replicate nuclear and mitochondrial DNA, respectively.
DNA polymerases synthesize DNA in the 5' to 3' direction. They require a primer to start synthesis.
DNA can't be synthesized from a free nucleotide—it needs a pre-existing strand.
Replication begins at defined origins of replication.

Origin of Replication

The origins of replication are specific sequences in the DNA molecule where replication starts.
The initiator proteins recognize these sequences and facilitate the attachment of proteins for two replication forks.
Eukaryotic chromosomes have multiple origins of replication to complete replication in a reasonable time.
Replication forks move in opposite directions along the DNA.
Okazaki fragments are short DNA segments synthesized on the lagging strand of a replication fork and then joined.

DNA Maintenance

High fidelity of DNA replication is essential.
Errors are minimized through double-reading activity and exonuclease proofreading.

Telomerase

Telomerase is a DNA polymerase with an RNA component.
It replicates telomeric DNA sequences at the ends of chromosomes to prevent shortening during replication.
During replication, the 3′ end of the lagging strand is not fully replicated, creating a gap that must be filled by telomerase.

3.4. DNA Transcription

DNA strands have different functions in transcription; the antisense strand acts as a template for RNA synthesis.
RNA polymerase is the main enzyme responsible for RNA synthesis.
RNA polymerase synthesizes RNA in the 5' to 3' direction complementary to the antisense DNA strand.
The RNA transcript (mRNA) is identical to the sense DNA strand, except uracil replaces thymine.

RNA Polymerase in Eukaryotes

Eukaryotes have three RNA polymerases (I, II, and III) which transcribe different classes of genes.

Transcription Initiation

Transcription begins with RNA polymerase binding to the promoter.
The promoter region is upstream of the gene.

Transcription Elongation

Transcription factors are released at the beginning of elongation
RNA polymerase synthesizes RNA in the 5' to 3' direction by adding ribonucleotides to the 3' end.

Transcription Termination

RNA synthesis ends when RNA polymerase recognizes sequences at the end of genes.
The details are less understood in eukaryotes compared to prokaryotes.

3.5. Traffic Between the Nucleus and Cytoplasm

Selective transport of proteins and RNA between the nucleus and the cytoplasm.
Passive diffusion for small molecules.
Selective transport for large molecules (RNA and proteins).
Proteins are marked with sequences (NLS or NES) recognized by transport receptors (importins or exportins).
Other proteins (Ran proteins; GTP, GDP cycles) are necessary and work with the receptors to mediate the transport through the nuclear envelope.

3.6. Nuclear Bodies

Organelles in the nucleus that concentrate RNA and proteins for different processes.
Examples include nucleolus, Cajal bodies, speckles, and histone locus bodies.
Important in ribosome assembly, mRNA splicing, and other nuclear functions.

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Description

This quiz covers key concepts related to chromatin structure, including nucleosome spacing, histone modifications, and the role of non-coding RNAs. Test your understanding of DNA packaging during mitosis and the functions of different chromatin components. Ideal for students studying molecular biology or genetics.