Gene Regulation Part 1 Flashcards
Chromatin is a combination of
DNA and protein (histones)
Histones are
any group of basic proteins found in chromatin
Define nucleosome
a structural unit of a eukaryotic chromosome
What is a eukaryotic chromosome?
A length of DNA coiled around a core histone
How are genes regulated?
Chromatin structure and the control of transcription factors (MAIN WAYS) but also mRNA processing, and control of translation
Chromosome structure goes what to what
DNA double helix, to supercoiling around histones, which make nucleosomes, which make up chromatin the spaghetti noodles to make up a chromosome
General transcription factors are also known as
basal transcription factors
What are basal transcription factors?
A class of protein transcription factors that bind to specific sites (promoters) on DNA to activate transcription of genetic information from DNA to mRNA
How does chromatin structure affect transcription?….and thus how genes are regulated
DNA packing (the shape of the DNA) can alter the level of transcription because when DNA is is tightly wound into nucleosomes it is not available for transcription. (LITERALLY you can’t go through transcription because it’s all wound up)
How can chromatin structure be altered in order to undergo transcription?
There are remodeling proteins that can change the DNA packing in specific areas to remove nucleosomes, in order for transcription factors to bind and allow transcription take place.
Define epigenetics
Changes in gene sequence or phenotype that don’t involve changes to the DNA sequence. These are also defined as heritable changes in gene activity and expression that occur without alteration in DNA sequence
Euchromatin
Regions with highly transcriptional activity who are loosely packed
Heterochromatin
Regions with low or no transcriptional activity who are tightly, densely packed
Difference between chromatin and a nucleosome go
Chromatin is the whole spaghetti structure to make up a chromosome. A nucleosome is one singular thing of the pictures you always used to draw. The coiled DNA with four histones
What is a cytosine?
The letter C. LITERALLY.IT’S THE LETTER C
What is methylation?
DNA methylation is an epigenetic mechanism used by cells to control gene expression. A number of mechanisms exist to control gene expression in eukaryotes, but DNA methylation is a commonly used epigenetic signaling tool that can fix genes in the “off” position
what does acetylated mean?
Adding an acetyl group
how can genes be switched on and off?
It depends on how tightly packed they are but this happens through methylation, which makes euchromatin or heterochromatin
What are the three different types of motifs you need to know for this test?
helix loop helix(HLH), helix turn helix(HTH), and zinc finger
What is the TATA box?
A DNA sequence that indicates where a genetic sequence can be read and decoded. It is a type of promoter sequence, which specifies to other molecules where transcription begins.
What is transcription?
The process by which an RNA molecule is produced from a DNA sequence
Affinity
the pull towards something
What are the three different types of protein domains that can interact with DNA?
HLH, HTH, and zinc finger
Difference between motif and domain
A domain can function by itself. It is independently stable. If a motif has a biological function, it can be called a domain. ex. zinc-finger motifs are also related to DNA , are also related to DNA binding, so they are also called zinc-finger domains. This means motifs are structural characteristics and domains are functional regions of a protein.
How do transcription factors search for specific binding sequences?
They slide along the DNA segment, ON THE INTERIOR OF THE HELIX, until it finds its specific binding sites
How can transcription factors become dislodged from the DNA strand when searching for specific binding sequences? And how do they overcome this?
It can encounter other proteins that are in the way, compacted sections of DNA, or movement of the DNA itself.
Scientists suggest the TF make short hops to bypass other proteins and compacted sections of DNA.
Transcription factors are?
DNA binding proteins that control transcription
What are three examples of transcription factors?
Basal, activator, repressor
the same transcription factor can influence ______ genes
many
What do transcription factors modulate transcription?
These regulatory proteins modulate transcription by determining when, where, and how much transcription occurs in a particular type of cell
Why is gene expression regulated?
So genes can be turned on and off at the appropriate time. This occurs during development, when responding to the environment, maintaining homeostasis,
How does the cell know it needs to maintain homeostasis?
Through cellular signaling
Cellular signaling
Cellular communication process that governs basic activities of cells and coordinates all cells in action
What are two common types of cellular signaling?
The kinase cascade and second messenger pathway
what is a kinase cascade?
A kinase enzyme that modifies other proteins by chemically adding phosphate groups to them (phosphorylation). This, (phosphorylation), usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins
Second messenger pathway
Molecules that relay information received at the receptors on the cell surface-such as the arrival of protein hormones, or growth hormones-to target molecules in the nucleus and/or cytosol
Cytosol
an aqueous component of the cytoplasm of the cell
Short term processes of cellular signaling
Cellular movement, etc.
What are the long term effects of cellular signaling
The activation of transcription factors
Which in turn causes movement of TFs from cytoplasm to the nucleolus (where it can act),
and phosphorylation on the transcription factor itself to initiate dimerization. It does this to become active and thus DNA binding can occur because it IS active
Dimerization
two transcription factors coming together so it can act
