Eukaryotic Gene Regulation and Chromatin Structure

Flashcards covering introductory gene expression, DNA structure, histone packaging, chromatin states, and transcription factor regulation based on the lecture transcript.

What complex must assemble at the plus one site (+1) of a gene to initiate transcription?

The transcription initiation complex.

How do transcription factors acting as activators or repressors regulate gene expression?

Activators function to expose the promoter region so the transcription initiation complex can assemble, whereas repressors cause DNA to condense and cover the promoter region.

Why is the 'dimmer switch' analogy used to describe gene regulation?

Because cells rarely use binary on/off control; instead, simultaneous actions of strong/weak activators and repressors precisely tune the specific level of transcription.

What chemical group is exposed on the 3' end of a DNA strand?

A hydroxyl group on carbon number 3 of the deoxyribose sugar.

What chemical group is exposed on the 5' end of a DNA strand?

A phosphate group on carbon number 5 of the deoxyribose sugar.

Why is the DNA backbone negatively charged?

Because it is composed of acidic phosphate groups that donate protons, resulting in a negative charge on the phosphodiester backbone.

Where on the DNA double helix do transcription factors typically bind?

In the major grooves of the alpha-helical structure.

What is the total nucleotide count of the complete human genome, and what length of DNA does a single nucleus contain?

The genome consists of $3.2 \times 10^9$ nucleotides (or $6.2 \times 10^9$ nucleotide pairs in a diploid cell), which measures approximately $2\text{ meters}$ long when laid end to end.

What is the diameter of a typical human nucleus relative to the diameter of a human hair?

A nucleus is approximately $6\text{ microns}$ in diameter, whereas a typical human hair is about $30\text{ to }110\text{ microns}$ in diameter.

What is chromatin, and what is its composition by mass?

Chromatin is a fibrous nuclear protein complex that is approximately one-third DNA and two-thirds protein by mass.

During which phase of the cell cycle does gene transcription take place?

Interphase, because during mitosis the chromatin is too highly condensed for transcription factors and machinery to access transcription start sites.

What are the diameters of naked double-stranded DNA and the 'beads on a string' chromatin fiber?

Naked double-stranded DNA is $2\text{ nm}$ in diameter, and the 'beads on a string' nucleosome fiber is $11\text{ nm}$ in diameter.

How far must chromatin decondense to allow promoter exposure for transcription?

Down to the $11\text{ nm}$ fiber, at which point specific mechanisms can slide histones out of the way without needing to completely disassemble them.

What is the diameter of a single chromosome arm compared to a full chromosome?

A single chromosome arm attached to a scaffold is $700\text{ nm}$ in diameter, making a full chromosome $1400\text{ nm}$ in diameter.

What components constitute a single nucleosome?

Approximately 147 nucleotide pairs of DNA wrapped around a histone octamer core, plus a linker DNA region of about 50 nucleotides.

How many times does DNA wrap around a single histone octamer core?

Approximately 1.7 times.

Which histone proteins make up the core octamer, and which histone functions as the linker?

The core octamer consists of two copies each of H2A, H2B, H3, and H4. Histone H1 functions as the linker histone.

Which two basic amino acids make up about 20% of the histone core proteins, and why are they important?

Lysine and arginine; their positive charges create electrostatic attraction with the negatively charged phosphodiester backbone of DNA.

What secondary structural elements compose the 'histone fold' motif?

An alpha helix, random coil, alpha helix, random coil, and alpha helix.

How do histone proteins H2A and H2B associate within the nucleosome core?

They form a heterodimer through interactions between their histone fold motifs in a mechanism called the 'handshake model'.

What structural role do N-terminal histone tails play in forming the 30 nm chromatin fiber?

The eight histone tails extend outward from the core octamer and facilitate physical interactions between adjacent histones to form the $30\text{ nm}$ fiber.

What are nuclear neighborhoods?

Specialized spatial locations within the nucleus where extended loops of actively transcribed DNA gather alongside concentrated transcription machinery and RNA polymerases.

What is the primary difference between euchromatin and heterochromatin?

Euchromatin is less condensed, lightly staining, and transcriptionally active, whereas heterochromatin is highly condensed, darkly staining, and transcriptionally inactive.

What distinguishes facultative heterochromatin from constitutive heterochromatin?

Facultative heterochromatin can reversibly transition between euchromatin and heterochromatin states, whereas constitutive heterochromatin remains permanently condensed and inactive.

How does a reader-writer complex spread heterochromatin across a chromosome region?

A reader protein binds a specific histone tail modification, and its associated writer protein applies the exact same modification to an adjacent histone core, repeating this process sequentially until reaching a barrier sequence.

How are transcription factors primarily regulated within the cell?

They are regulated at the levels of protein activation and nuclear localization/translocation, rather than at the level of their own gene transcription.

What is meant by the dynamic nature of nucleosomes?

Nucleosomes naturally and spontaneously unwrap for about $10\text{ to }50\text{ ms}$ and re-wrap for about $250\text{ ms}$, briefly exposing DNA sequences to allow active transcription factors to bind.