Textbook reading class 3

General Transcription Factors

A set of proteins required for the initiation of transcription by eukaryotic RNA polymerase II. They help position the polymerase, unwind DNA, and initiate transcription. Examples include TFIID, TFIIB, TFIIH.

TFIID

A general transcription factor that initiates assembly at the promoter by binding to the TATA box via its TBP subunit. It contains ~11 TAF subunits that recognize other promoter elements and regulate TBP binding.

TBP (TATA-Binding Protein)

The subunit of TFIID that recognizes and binds to the TATA box sequence (TATAAA), causing a significant distortion and bend in the DNA, which serves as a landmark for assembling other transcription factors.

TAFs (TBP-Associated Factors)

The approximately 11 additional subunits of the TFIID complex. They recognize other DNA sequences near the transcription start point (like INR or DPE) and help regulate the DNA-binding activity of TBP.

TFIIB

A general transcription factor (1 subunit) that recognizes the BRE element in promoters. It accurately positions RNA polymerase II at the correct start site of transcription.

TFIIF

A general transcription factor (3 subunits) that stabilizes the interaction of RNA polymerase II with TBP and TFIIB. It also helps attract TFIIE and TFIIH to the growing initiation complex.

TFIIE

A general transcription factor (2 subunits) that attracts and helps regulate the activity of the multi-subunit TFIIH complex.

TFIIH

A large, complex general transcription factor (9 subunits). It contains DNA helicase activity to unwind DNA at the start point and a protein kinase activity that phosphorylates Ser5 on the RNA polymerase II CTD. This phosphorylation releases the polymerase from the general factors to begin elongation.

CTD (C-Terminal Domain)

The long tail of RNA polymerase II, consisting of multiple tandem repeats of a 7-amino acid sequence. Phosphorylation of serines (e.g., Ser5 by TFIIH) in the CTD helps release the polymerase into elongation and recruits RNA processing machinery.

TATA Box

A common promoter element with the consensus sequence TATAAA, located about 25 nucleotides upstream of the transcription start site. It is recognized by TBP.

BRE Element

A promoter element with the consensus sequence G/C G/C G/A C G C C. It is recognized by the general transcription factor TFIIB.

INR (Initiator) Element

A promoter element that overlaps the transcription start point, with the consensus sequence C/T C/T A N T/A C/T C/T. It is recognized by subunits of TFIID (TAFs).

DPE (Downstream Promoter Element)

A promoter element located in the transcribed region, around +30, with the consensus sequence A/G G A/T C G T G. It is recognized by subunits of TFIID (TAFs).

Mediator

A large protein complex that acts as a bridge between transcription activator proteins (bound to enhancers) and RNA polymerase II with the general transcription factors at the promoter. It is essential for proper communication and coordination of transcription initiation in vivo.

Transcriptional Activators

Gene regulatory proteins that bind to specific DNA sequences called enhancers. They help attract RNA polymerase II, the general transcription factors, Mediator, chromatin remodeling complexes, and histone-modifying enzymes to the promoter.

Chromatin Remodeling Complexes

ATP-dependent enzyme complexes that alter the structure of nucleosomes to make DNA more accessible for transcription. They are recruited to promoters by activator proteins.

Histone-Modifying Enzymes

Enzymes that add or remove chemical groups (e.g., acetyl, methyl) from histones. These modifications can make chromatin more open and accessible, facilitating the assembly of the transcription initiation machinery.

Elongation Factors

Proteins that associate with RNA polymerase during the elongation phase of transcription. They increase the polymerase's processivity, helping it move through various DNA sequences and past nucleosomes without dissociating prematurely.

Restriction Nucleases (Restriction Enzymes)

Enzymes that cut DNA at specific nucleotide sequences. They are used by bacteria as a defense mechanism and are fundamental tools in molecular biology for DNA manipulation and cloning.

Sticky Ends

The short, single-stranded overhangs generated when a restriction enzyme makes staggered cuts in the two strands of DNA. These ends can base-pair with complementary sticky ends on other DNA fragments, facilitating the joining of DNA pieces.

Blunt Ends

The even ends generated when a restriction enzyme cuts straight across both strands of the DNA double helix. These ends are more difficult to join together ligate than sticky ends.

Gel Electrophoresis

A technique used to separate DNA molecules based on their size. DNA fragments are loaded into a gel matrix and an electric field is applied, causing smaller fragments to migrate faster than larger ones.

Agarose Gel Electrophoresis

A type of gel electrophoresis used to separate DNA fragments ranging from a few hundred to about 20,000 nucleotide pairs. The gel is made from agarose, a polysaccharide derived from seaweed.

Polyacrylamide Gel Electrophoresis

A type of gel electrophoresis with a tighter matrix than agarose, used to separate very small DNA fragments (less than 500 nucleotides) that differ in length by as little as a single nucleotide.

Pulsed-Field Gel Electrophoresis

A variation of agarose gel electrophoresis where the direction of the electric field is periodically changed. This allows for the separation of extremely long DNA molecules, like entire chromosomes from yeast or bacteria.

Ethidium Bromide

A fluorescent dye that intercalates between DNA bases. It is used to stain DNA in gels, making the bands visible under ultraviolet light.

Polymerase Chain Reaction (PCR)

A powerful technique used to amplify specific DNA sequences in vitro. It involves repeated cycles of DNA denaturation, primer annealing, and DNA synthesis by a heat-stable DNA polymerase.

Primers (PCR)

Short, single-stranded DNA sequences that are chemically synthesized to be complementary to the sequences flanking the target DNA region. They provide the 3' end from which DNA polymerase begins synthesis.

Quantitative RT-PCR (qRT-PCR)

A highly sensitive method used to quantify the amount of a specific mRNA in a sample. It involves reverse transcribing the mRNA into cDNA and then using PCR to amplify it, tracking the amplification in real time with a fluorescent dye.

DNA Microarray

A glass slide containing hundreds of thousands of spotted DNA fragments, each representing a specific gene. It is used to analyze the expression levels of thousands of genes simultaneously by hybridizing fluorescently labeled cDNA from a sample.

RNA-seq (Deep RNA Sequencing)

A method that uses high-throughput sequencing technologies to determine the sequence and abundance of all RNAs in a sample. It provides a comprehensive snapshot of gene expression and can detect alternative splicing and novel transcripts.

Cluster Analysis

A computational method used to group genes based on similar patterns of expression across different conditions. Genes that are coordinately regulated are often functionally related. "Guilt by association" is a principle where an unknown gene's function is inferred from the known functions of genes in its cluster.

Chromatin Immunoprecipitation (ChIP)

A technique used to identify the genomic locations bound by a specific protein (e.g., a transcription regulator or a modified histone) in vivo. It involves cross-linking proteins to DNA, fragmenting the DNA, immunoprecipitating the protein of interest, and sequencing the associated DNA fragments.

Ribosome Profiling

A technique that provides a snapshot of all the mRNAs being actively translated in a cell at a given moment. It involves sequencing the fragments of mRNA that are protected from nuclease digestion by being bound to ribosomes.

Ion Channel

A transmembrane protein that forms a pore, allowing the selective passage of specific inorganic ions (e.g., K+, Na+, Ca2+, Cl-) down their electrochemical gradients.

Selectivity Filter

The narrowest part of an ion channel's pore, which determines its ion selectivity by forcing permeating ions to shed their water molecules and interact directly with atoms lining the filter.

Gating

The process by which an ion channel transitions between open and closed states. Gating can be controlled by changes in membrane voltage (voltage-gated), mechanical stress (mechanically-gated), or the binding of a ligand (ligand-gated).

Resting Membrane Potential

The electrical potential difference across the plasma membrane of a non-stimulated ("resting") cell. In animal cells, it is primarily generated and maintained by K+ leak channels and the K+ concentration gradient established by the Na+-K+ pump.

K+ Leak Channels

A subset of K+ channels that are open in an unstimulated cell. They make the membrane much more permeable to K+ than to other ions, playing a crucial role in establishing the negative resting membrane potential.

Nernst Equation

A formula that calculates the equilibrium potential for a specific ion across a membrane. It is given by

Equilibrium Potential

The membrane potential at which the net flow of a particular ion through an open channel is zero, meaning the electrical and chemical driving forces for that ion are balanced.

Electrochemical Gradient

The combined influence of a solute's concentration gradient and the electrical gradient (membrane potential) across a membrane. It determines the direction and force of passive ion movement.

Aquaporin

A channel protein that facilitates the rapid passage of water molecules across the membrane. It is impermeable to ions, including H+ (hydronium ions, H3O+).

Voltage-Gated Channel

An ion channel whose opening is controlled by changes in the membrane potential.

Mechanically-Gated Channel

An ion channel whose opening is controlled by mechanical stress or strain on the membrane.

Ligand-Gated Channel

An ion channel whose opening is controlled by the binding of a specific ligand (a neurotransmitter, ion, or nucleotide).

Na+-K+ Pump (Na+/K+ ATPase)

An ATP-driven antiporter that actively transports 3 Na+ ions out of the cell and 2 K+ ions into the cell for each ATP hydrolyzed. It is electrogenic and is primarily responsible for maintaining the Na+ and K+ concentration gradients across the plasma membrane.

Action Potential

A rapid, temporary reversal of the membrane potential (depolarization) that propagates along the axon of a neuron or muscle cell. It is initiated by the opening of voltage-gated Na+ channels.

Myelin Sheath

An insulating layer formed by glial cells (Schwann cells in the PNS, oligodendrocytes in the CNS) around axons. It increases the speed of action potential propagation by saltatory conduction.

Node of Ranvier

A gap in the myelin sheath along an axon. Voltage-gated Na+ channels are highly concentrated here, allowing the action potential to be regenerated rapidly at these points.

Saltatory Conduction

The "jumping" propagation of an action potential from one Node of Ranvier to the next in a myelinated axon. This is significantly faster than continuous conduction in unmyelinated axons.

Synapse

A specialized junction where a neuron communicates with a target cell (another neuron, muscle cell, or gland cell).

Neurotransmitter

A signaling molecule released from the presynaptic neuron into the synaptic cleft. It binds to receptors on the postsynaptic cell to transmit a signal.

Synaptic Cleft

The narrow extracellular space that separates the presynaptic and postsynaptic membranes.

Postsynaptic Potential

A change in the membrane potential of the postsynaptic cell caused by the binding of neurotransmitter to ligand-gated ion channels. It can be excitatory (depolarizing, EPSP) or inhibitory (hyperpolarizing, IPSP).

Temporal Summation

The integration of multiple postsynaptic potentials that occur in rapid succession at the same synapse.

Spatial Summation

The integration of postsynaptic potentials from different synapses located close to each other on the postsynaptic cell.