Chapters 12, 13, 16, and 17: Chromosome Structure, Rearrangements, and Gene Regulation

Comprehensive practice flashcards covering chromosome packaging, structural rearrangements, prokaryotic transcription, and operon regulatory systems.

What is the difference between chromatin and chromosomes?

Chromatin is any complex of DNA and protein found within the nucleus of a cell, whereas chromosomes are the distinct, separate pieces of chromatin that behave as a unit during cell division.

What is the ratio of DNA, histones, and non-histone proteins in eukaryotic chromatin?

Chromatin is composed of approximately $\sim 1/3$ DNA, $1/3$ histones, and $1/3$ non-histone proteins.

What are the core histones and the linker histone found in chromatin?

The core histones are H2A, H2B, H3, and H4. The linker histone is H1, which dictates which histone the DNA links with.

What roles do nonhistone scaffold and nonscaffold proteins play in the radial-loop scaffold model?

Nonhistone scaffold proteins hold loop chromatin by allowing chromatin to loop through them, while nonscaffold proteins prevent the chromatin loops from overlapping.

What is the function of condensins in the radial-loop scaffold model?

Condensins further condense chromosomes into a compact bundle for mitosis by acting as the 'stem of the daisy' that goes in the middle and pulls chromatin loop rosettes together.

How does in situ hybridization detect specific nucleic acid sequences?

A labeled, single-stranded nucleic acid probe (a DNA, RNA, or synthetic oligonucleotide complementary to the target gene or mRNA) is introduced to the sample, where it searches out and spontaneously base-pairs with its exact matching sequence.

What is the key difference between Fluorescent In Situ Hybridization (FISH) and Spectral Karyotyping (SKY)?

FISH pinpoints the location of a specific known gene sequence on a chromosome using fluorescently labeled primers, whereas SKY labels entire chromosomes with distinct fluorescent dyes to identify large-scale chromosomal abnormalities such as aneuploidy.

How do heterochromatin and euchromatin differ in staining, compaction, and gene expression?

Heterochromatin is highly condensed, darkly stained, and difficult to transcribe. Euchromatin is lightly condensed, lightly stained, and readily transcribed.

How do histone acetyltransferases and histone deacetylases influence chromatin structure and transcription?

Histone acetyltransferases add acetyl groups to histone tails to open chromatin for active transcription, whereas histone deacetylases remove acetyl groups to close chromatin.

What is a telomere and what is its role at chromosome ends?

A telomere is a protective, gene-free cap composed of repetitive DNA sequences and proteins located at the ends of linear chromosomes that prevents chromosomes from fraying, tangling, or fusing with one another.

How does telomerase rebuild and maintain telomeres during successive cell divisions?

Telomerase is a ribonucleoprotein enzyme carrying an internal RNA component complementary to telomeric repeats that acts as a template for adding new DNA repeat sequences to linear chromosome ends.

What are the two primary functions of centromeres?

Centromeres serve as an attachment site for chromosome segregation machinery via kinetochore assembly (binding CENP-A nucleosomes) and hold sister chromatids together via cohesion.

What is the specific role of the protein Shugoshin?

Shugoshin protects centromeric cohesion from degradation during mitosis and meiosis.

What are the four major types of chromosomal rearrangements?

Deletions (loss of a chromosomal region), duplications (gain of a chromosomal region), inversions (a $180^\circ$ flip of a chromosomal region), and translocations (movement of a chromosomal segment to a non-homologous chromosome).

What are the two general cellular mechanisms that cause chromosomal rearrangements?

1) Double-stranded breaks (DSBs) followed by non-homologous end joining (NHEJ), and 2) homologous recombination between repetitive DNA sequences such as simple sequence repeats (SSRs) or copy number variants (CNVs).

How does the relative orientation of simple sequence repeats (SSRs) dictate whether recombination yields a deletion or an inversion?

A recombination event between SSRs oriented in the same direction results in a deletion, whereas recombination between SSRs oriented in different (opposite) directions causes an inversion.

Why are chromosomal deletions typically homozygous lethal?

Homozygous deletions completely eliminate both functional alleles of essential genes within the deleted segment, causing absolute gene loss and lethality.

What is haploinsufficiency and how does it generate a mutant phenotype in heterozygotes?

Haploinsufficiency occurs when a diploid organism has only a single functional copy of a gene due to deletion, and that single copy produces insufficient gene product to maintain the normal wild-type phenotype.

What is the structural difference between tandem and dispersive duplications?

Tandem duplications feature copied segments positioned directly adjacent to one another, while dispersive duplications have copied segments located non-sequentially in different regions.

What is the difference between paracentric and pericentric inversions?

Paracentric inversions do not include the centromere, whereas pericentric inversions do include the centromere.

What meiotic products result from crossing over within an inversion loop in a paracentric inversion heterozygote?

Recombination produces one acentric chromatid (lacking a centromere) and one dicentric chromatid (having two centromeres), both of which break during anaphase and yield nonviable zygotes.

What occurs during a Robertsonian translocation?

The long arms of two non-homologous acrocentric chromosomes fuse together while their short arms are lost, reducing the total diploid chromosome count from $46$ to $45$.

What distinguishes retrotransposons from DNA transposons?

Retrotransposons transpose via an RNA intermediate, whereas DNA transposons move directly without an RNA intermediate.

What is the difference between intrinsic and extrinsic transcription termination in prokaryotes?

Extrinsic termination requires the protein rho factor to dislodge RNA polymerase, whereas intrinsic termination uses a GC-rich stem-loop (hairpin) followed by an RNA structural shift that releases the transcript without helper proteins.

What are the structural genes of the prokaryotic lac operon and what enzymes do they encode?

The structural genes are lacZ, which encodes $\beta$-galactosidase; lacY, which encodes permease; and lacA, which encodes transacetylase.

What are the enzymatic activities of permease, $\beta$-galactosidase, and transacetylase in lactose metabolism?

Permease transports lactose across the bacterial cell membrane, $\beta$-galactosidase cleaves lactose into glucose and galactose, and transacetylase transfers an acetyl group from acetyl-CoA to galactosides, lactosides, and glucosides.

How does glucose abundance regulate cAMP and the CRP-cAMP activator complex in the lac operon?

Glucose levels are inversely correlated with cAMP levels: high glucose leads to low cAMP, preventing CRP-cAMP formation; low glucose leads to high cAMP, allowing CRP-cAMP to bind DNA and stimulate high-level transcription.

How does ribosome stalling at the trp leader sequence control attenuation in the trp operon?

When tryptophan is low, the ribosome stalls at tryptophan codons in region 1, freeing region 2 to base-pair with region 3 (forming a 2-3 antiterminator loop) and allowing transcription to proceed. When tryptophan is abundant, the ribosome translates smoothly, forcing regions 3 and 4 to form a 3-4 transcription terminator loop.

What is the operational distinction between a cis-acting element and a trans-acting element?

A cis-acting element is a physical DNA sequence contiguous with the gene it modulates (such as a promoter or enhancer), whereas a trans-acting factor is a diffusible product (such as a protein transcription factor or repressor) encoded elsewhere that migrates to interact with target DNA.