Genome and Chromosome Structure Quiz

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Questions and Answers

What characterizes highly repetitive sequences in the genome?

They include functional sequences like rRNA genes.

They have a single copy in the genome.

They are involved in gene regulation.

They contain multiple copies, such as satellite DNA. (correct)

Which type of supercoiling aids in DNA replication and transcription?

Looped domain organization

Positive supercoiling

Negative supercoiling (correct)

Nucleosome formation

What defines constitutive heterochromatin?

It is located in actively transcribed regions of the genome.

It is always condensed and found in centromeres. (correct)

It can change locations within the genome.

It is less condensed and transcriptionally active.

Which process organizes bacterial chromosomes into microdomains?

NAP-mediated folding Signup and view all the answers

In the context of eukaryotic chromosomes, what is euchromatin?

It is less condensed and transcriptionally active. Signup and view all the answers

What structure is formed by DNA wrapped around histone proteins?

Nucleosome Signup and view all the answers

Which type of chromatin can vary in its state of condensation?

Facultative heterochromatin Signup and view all the answers

What is the role of Topoisomerase I in DNA compaction?

To relax positive supercoiling. Signup and view all the answers

What is the primary function of Alu elements within the genome?

They act as tandem repeats in moderately repetitive sequences. Signup and view all the answers

What is the final level of chromatin structure in the compaction hierarchy?

Heterochromatin Signup and view all the answers

Which model of DNA replication allows both parental and daughter strands to be mixed together?

Dispersive model Signup and view all the answers

What initiates the DNA replication process in E. coli?

DnaA proteins binding to DnaA box sequences Signup and view all the answers

In eukaryotic transcription, which factor is primarily involved in recognizing the TATA box during initiation?

Transcription factors like TFIID Signup and view all the answers

What mechanism does telomerase perform to address the chromosome end problem in eukaryotes?

Adds repetitive sequences to telomeres Signup and view all the answers

Which RNA polymerase is responsible for synthesizing mRNA in eukaryotes?

RNA Polymerase II Signup and view all the answers

What occurs during the splicing of hnRNA to form mature mRNA?

Introns are removed and exons are joined Signup and view all the answers

What is the role of the Shine-Dalgarno sequence in bacterial translation?

It helps in ribosomal binding to mRNA Signup and view all the answers

Which step in DNA replication is specifically performed by DNA Polymerase I?

Filling in gaps after RNA primers are removed Signup and view all the answers

Which hypothesis regarding genes was initially proposed by Garrod?

Inborn error of metabolism Signup and view all the answers

What does the Wobble Hypothesis imply about tRNAs?

Fewer tRNAs are needed due to base-pairing flexibility Signup and view all the answers

What characteristic of the C-Value Paradox highlights a discrepancy in organism genetics?

Genome size does not correlate with organism complexity. Signup and view all the answers

Which type of supercoiling is induced by DNA gyrase during the process of DNA replication?

Negative supercoiling Signup and view all the answers

Which feature distinguishes facultative heterochromatin from constitutive heterochromatin?

It can change its state of compaction under certain conditions. Signup and view all the answers

In the context of bacterial chromosomes, what is the primary function of looped domains?

To compact the chromosome and organize its structure. Signup and view all the answers

What level of chromatin structure is described by the term '30 nm Fiber'?

The arrangement of nucleosomes into a compact form. Signup and view all the answers

Which type of repetitive sequence is characterized by short DNA sequences that can move within the genome?

Alu elements Signup and view all the answers

What role do NAPs play in the structure of bacterial chromosomes?

They are involved in organizing the DNA into microdomains. Signup and view all the answers

Which of the following accurately depicts the state of euchromatin compared to heterochromatin?

Euchromatin is less condensed and transcriptionally active. Signup and view all the answers

Which subunit of chromatin structure is primarily associated with the formation of nucleosomes?

Histones Signup and view all the answers

What is the main difference between negative and positive supercoiling in DNA?

Negative supercoiling unwinds the DNA, while positive induces tension in the strands. Signup and view all the answers

What occurs during the elongation phase of eukaryotic transcription?

The RNA molecule produced contains both introns and exons. Signup and view all the answers

In the context of DNA replication, what is the function of DNA ligase?

Joins Okazaki fragments on the lagging strand. Signup and view all the answers

During RNA processing, what modification occurs at the 5' end of mature mRNA?

Addition of a 5' cap for stability. Signup and view all the answers

How do chromosomes in eukaryotic cells manage the large DNA volume during replication?

Through multiple replication origins across different chromosomes. Signup and view all the answers

What is the reason for having a degenerate code in protein synthesis?

To allow for multiple codons for a single amino acid. Signup and view all the answers

What is the role of helicase during DNA replication?

To unwind the DNA double helix ahead of the replication fork. Signup and view all the answers

What distinguishes the 'one gene-one polypeptide' hypothesis from earlier theories about genes?

It emphasizes the unique contribution of each gene to a single protein product. Signup and view all the answers

Which statement accurately describes the function of the rho protein during transcription?

It leads to the termination of transcription by binding to the rut site. Signup and view all the answers

What is the significance of the Shine-Dalgarno sequence in bacterial translation?

It aids in the initiation of translation by aligning the ribosome with mRNA. Signup and view all the answers

What triggers the end of eukaryotic transcription?

The formation of a polyadenylation signal. Signup and view all the answers

Study Notes

Genome Structure and Function

Genome: The complete genetic material of an organism, composed of nucleotides.
Transposable Elements: DNA sequences that can move within a genome ("jumping genes").
C-Value Paradox: Genome size does not directly correlate with organismal complexity.
Repetitive Sequences: Occur in various forms:
- Highly Repetitive: Multiple copies (e.g., satellite DNA).
- Moderately Repetitive: Functional sequences (e.g., rRNA genes).
- Tandem Repeats: Short sequences repeated in a row (e.g., Alu elements).

Chromosome Structure and Compaction

Bacterial Chromosome:
- Compacted by supercoiling.
- Negative Supercoiling: DNA unwound (left-handed twist), aiding replication and transcription. Achieved by DNA gyrase.
- Positive Supercoiling: DNA overwound (right-handed twist) relaxed by topoisomerase I.
- Looped Domains: Organized by nucleoid-associated proteins (NAPs) into micro and macrodomains.
Eukaryotic Chromosome:
- Chromatin: DNA-protein complex.
  - Euchromatin: Less condensed; transcriptionally active.
  - Heterochromatin: Highly condensed; inactive.
    - Constitutive Heterochromatin: Always condensed; found at centromeres.
    - Facultative Heterochromatin: Variable condensation; location can change.

Chromosome Compaction Steps

DNA Double Helix: Basic structure.
Nucleosome: DNA wrapped around histone proteins.
Zigzag/30 nm Fiber: Nucleosomes further compacted.
Looped Domains: Formed by CTCF and SMC proteins.
Heterochromatin: Compaction of loops.
Metaphase Chromosome: Highest compaction during cell division.

DNA Replication Models

Conservative: Parental DNA stays together; daughter strands are entirely new.
Semi-Conservative: Each new DNA molecule has one original strand and one new strand (confirmed by Meselson-Stahl experiment).
Dispersive: Original and new DNA segments are interspersed within both strands.

DNA Replication Process

Initiation: Begins at oriC in E.coli; DnaA proteins bind to DnaA box sequences. AT-rich regions unwind easily.
Unwinding: Helicase unwinds DNA; SSBPs stabilize separated strands; Topoisomerase relieves tension.
Primer Synthesis: Primase synthesizes short RNA primers to start DNA synthesis.
Elongation: DNA polymerase III extends strands, proofreading; Leading strand synthesized continuously; Lagging strand synthesized discontinuously as Okazaki fragments.
Primer Removal and Gap Filling: DNA polymerase I removes primers, fills gaps; DNA ligase joins Okazaki fragments.

Challenges in Eukaryotic Replication

Large DNA Volume: Multiple replication origins manage the task (pulse-chase experiment).
Chromosome End Problem: Telomerase adds repetitive sequences to telomeres to prevent loss.

Transcription (RNA Synthesis)

Overview of RNA Types:
- mRNA: Carries genetic instructions.
- tRNA: Transfers amino acids.
- rRNA: Forms ribosomes.
- snRNA: Involved in splicing.
Prokaryotic Transcription:
- Initiation: RNA polymerase holoenzyme binds to promoter region (Pribnow box).
- Elongation: Core RNA polymerase adds rNMPs.
- Termination:
  - Rho-Independent: GC hairpin loop and U-rich sequence cause detachment.
  - Rho-Dependent: Rho protein binds, stopping transcription.
Eukaryotic Transcription:
- Initiation: Transcription factors like TFIID bind promoter elements (TATA box) recruiting RNA Polymerase II.
- Elongation: Produces hnRNA (pre-mRNA), including introns.
- Termination: Polyadenylation signal (AAUAAA) sequence signals end; cleavage occurs downstream.
RNA Polymerases in Eukaryotes:
- Polymerase I: rRNA synthesis
- Polymerase II: mRNA synthesis
- Polymerase III: tRNA and 5S rRNA synthesis

hnRNA Processing (Eukaryotes)

Capping: 5' cap added for stability and ribosome recognition.
Polyadenylation: Poly-A tail added to 3' end for stability.
Splicing: Introns removed; exons joined by snRNPs (lariat formed).

Gene Function and Hypotheses

Genes: Segments of DNA encoding instructions for making proteins.
Theories and Experiments:
- Garrod: Inborn errors of metabolism link genes to enzymes.
- Beadle and Tatum: "One gene-one enzyme" hypothesis (refined to "one gene-one polypeptide").

Degenerate Code and Triplet Codons

Degenerate Code: Most amino acids have more than one codon.
Triplet Codons: Three nucleotides per codon; 64 combinations, enough for 20 amino acids.

tRNA and the Wobble Hypothesis

tRNA: Carries amino acids to ribosomes (matching anticodons to mRNA codons).
Wobble Hypothesis: Flexible base pairing at the third codon position reduces the number of tRNA molecules needed.

Translation

Initiation: Small ribosomal subunit binds mRNA and initiator tRNA.
- Prokaryotes: Initiator tRNA carries N-formylmethionine; Shine-Dalgarno sequence.
- Eukaryotes: Initiator tRNA uses 5' cap and poly-A tail.
Elongation: Charged tRNA enters A site; peptide bonds form (catalyzed by peptidyl transferase).
Termination: Release factors recognize stop codons; ribosome complex disassembles.

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Description

Test your knowledge on genome structure and chromosome compaction. This quiz covers essential concepts such as transposable elements, the C-value paradox, and various forms of repetitive sequences. Dive into the intricacies of bacterial and eukaryotic chromosome organization and compaction methods.