Prokaryotic Gene Expression
Whether or not Gene is transcribed depends on environment of cell: specifically, availability of metabolites.
Functioning unit of genes all controlled by the same regulatory gene or promoter, these are usually transcribed and sent into the cytoplasm together.
Bacterial Gene Organization
No tightly clustered packed coding clusters and no exons/introns-- instead genes that function together are physically located near each other in operons.
DNA sequence which overlaps with the promoter or is located "downstream" of it; signals the initiation of operon sequence transcription.
A protein which can bond to a promoter sequence to prevent transcription from occurring. These function by inhibiting RNA polymerase: either preventing it from moving, or by preventing it form binding.
Repressible v. Inducible Operons.
Repressible operons generally enzymes in anabolic pathways & are generally turned off when enough product's around. Inducible operons are used in catabolic pathways and are turned on when reactants are present in environment.
Substance that regulates (inhibits) the expression of genes though interaction with repressor proteins.
Tryptophan vs. Lactose operons
Tryptophan is a repressible operon, anabolic p.w. can be shut off when a corepressor binds to a repressor which binds to an operator and turns off the operon. Lactose operon functions catholically, the repressor is bound by allolactose, impedes repressor from binding to operator and turns on the operon.
Difference between prokaryotic and Eukaryotic Genes
Eukaryotes have far more DNA and keep it tightly packed into chromatids/to fit into the nucleus, unlike prokaryotes which have less DNA.
Very tightly packed regions of the genome. These regions contain no genes. These serve as centromeres (region where spindles bind in cell division) and telomeres (chromosome ends), though heterochromatin is also interspersed through rest of chromosomes, seems to serve structural role in mitosis.
Less tightly packed regions of chromosomes which actually contain the DNA which encodes for genes.
How RNA is stopped from transcribing/how gene expression is prevented.
1) Methylate C's at or near the promoter sequence to disguise it. 2) Remove Acetyl (-COCH3) from the histone proteins coating DNA: making them negative and causing them to very tightly wrap nucleosomes.
Unit of DNA packaging: this is what comprises a chromosome.
Initiating (low level) gene transcription
C's are demethylated and histones have acetyl groups added/replaced-- loosens histome grasp on DNA/ undoes nucleosome packaging, usually only allows for basal transcription on its own.
Transcription taking place as a result of promoter sequence not being methylated, but-even though the RNA polymerase can bind the activator, it won't do much without mediator proteins and general transcription factors present.
Initiating (strong) gene transcription
Activator proteins bind to enhancer sequences, often located far from gene, these then bind mediator proteins (bending is happening here), which then bind general transcription factors, which then actively recruit RNA Polymerase to a promoter sequence.
Eukaryotic Activator Proteins
Specific transcription factors called activators that bind to enhancer DNA sequences and to mediator proteins (coactivators that bind general transcription factors), all of which function to recruit RNA polymerase and initiate transcription.
Eukaryotic Enhancer Sequences
DNA nucleotide sequences that serve as bonding points for activator proteins, these are bespoke to specific genes and enable their transcription/expression, even though they don't need to actually be close to the genes they effect.
Coordination of "Genes that function together" in eukaryotes
Genes that function together are seldom located near one another, even if they are, each gene tends to have its own promoter and each mRNA encodes only one gene. SO- in order to fucntion, genes that fucntion together have the same DNA sequences to bind the same activator proteins.
a.k.a. a sequence specific DNA binding factor, a protein which binds specific DNA sequences & thereby controlling the transcription of given DNA information into RNA: perform this function either alone or as a part of a complex, and can either promote transcription as an activator, or block it as a repressor.
Receptor Tyrosine Kinases: plasma membrane receptors that can behave enzymatically, can catalyze the transfer of phosphate groups- & attach them to tyrosines. Has a bonding site outside of cell membrane
signal transduction pathways
Signal transduction occurs when an extracellular signaling molecule activates a cell surface receptor, this causes a second messenger to continue into the cell (released from receptor) and trigger physiological response.
how genes are able to function together in eukaryotes
So, in eukaryotic cells, genes are seldom close to each other, all have their own promoter sequences, and each mRNA sequence will only ever encode for one gene. SUCH THAT- in order to coordinate expression, Genes that function together have the same DNA sequences to bind the same activator proteins.
Short ranged signals sent between cells- preformed via one signaling cell secreting local regulators which any number of neighboring cells can then receive.
Long range cellular signals which travel through a larger organism's blood stream (or system of the like). Utilized hormones as signaling molecules.
Term for any molecule which specifically binds to another one- here refers to signaling molecules which bind to receptor proteins/complexes on cellular membranes.
a protein in the cellular membrane/ecm of a given cell which binds signaling molecules and allows them to be expressed within the cell (think key in lock)-- this is what allows for cell's "selective hearing"
receptor mediated endocytosis
when a ligand binds to a membrane-receptor and in so doing simply triggers endocytosis and is engulfed by the cell.
ligand gated channel
a type of membrane receptor containing a region that can act as a "gate" when the receptor changes shape as the result of interaction with a ligand, etc.
G-protein coupled receptors
A plasma membrane receptor, part of a signal transduction pathway, that works with the help of a 'G-protein' which becomes active whenever GTP (energy rich molecule) is bound & dephosphorylated, otherwise it just holds onto GDP and is inactive.
Guanosine Triphosphate: high energy molecule which can act as a substrate for the synthesis of RNA in transcription.
Signaling molecules which can pass through the cellular membrane because they are non-polar (hydrophobe), which is done as a means of allowing them to reach their receptor complexes within the cytoplasm: e.g. estrogena and testosterone.
Receptors for Estrogen and Testosterone- sig. of placement in cell
The Estrogen Receptor binds estrogen and the Androgen receptor binds testosterone. These are located in the cytoplasm, as opposed to the membrane, because they both act as direct transcriptional activators- necessitates being able to enter the nucleus, WHICH can only occur when their hydrophobic hormone ligand is bound.
After egg fertilized, proteins/mRNA/etc unevenly distributed such that first division of daughter cells has very uneven distribution of supplies, despite having same genome. As result of this daughter cells will communicate (why exactly??) via paracrine signaling. -One expresses receptor and the other receives signal.
Happens early early in post-fertilization development for virtually all multicellular organisms: tissues begin to differentiate, form distinct anterior, posterior, ventral, and dorsal identities.
These control what body part a cell contributes to: are actually transcriptional factors that turn on many other genes needed for organ/tissue development. e.g. "eyeless" & "pax" genes.
Cell Fate- first irreversible step in assigning cell's specific functions. e.g. muscle cells: once a myoblast determined as muscle cell, gene MyoD is expressed. It then stops the cell cycle from continuing, begins to express muscle-specific genes, and also begins to force muscle cell determination on neighboring cells. Via inductive paracrine signaling.
Uncommitted/non-determined cells. Completely versatile- totipotent: can be determined as any cell.
Totipotence vs. Pluripotence
totipotence is the ability of stem cells to divide and differentiate into all of the cells in a given organism. Whereas puripotency (see- cord blood, bone marrow, etc.) is the ability of a cell to differentiate into many different cell types.
Kinase enzymes: phosphorylate ADP to ATP by holding onto each other and working in unison to catalyze Phosphates onto Adenosines.