Eukaryotic Gene Regulation

what is the central dogma of molecular biology

6 mechanisms where regulation of any given gene could occur

what are the mechanisms of central dogma

1) chromatin remodeling

2) transcriptional regulation

3) mRNA processing

4) mRNA stability

5) translational regulation

6) post-translational modification

what steps of the central dogma occur in the nucleus/transcription

1) chromatin remodeling

2) transcriptional regulation

3) mRNA processing

what steps of the central dogma occur in the cytoplasm/translation

4) mRNA stability

5) translational regulation

6) post-translational modification

chromatin remodeling

regulating certain parts of the DNA to make it more or less accessible when it needs to because typically DNA is hard to find since it is tightly packed into chromatin

chromatin

DNA and protein

is chromatin remodeling heritable

yes, through mitosis from one cell to the next

open chromatin

allows transcription because the transcription factors are able to find the specific sequences to then initiate RNA polymerase

closed chromatin

prevents transcription because it is difficult for the transcription machinery to find the unique sequences

is chromatin dynamic

yes, it can change over time

• occurs locally (one or a few genes, not the entire chromosome) in the cell

histone tail modification

enzymes come in and make slight chemical changes to the amino acids that make up the histone tails, they are signals to bring in other chromosomes that tell the cell to open/close

DNA methylation

• part of chromatin remodeling

• example of epigenetic regulation

epigentic regulation

something that is inherited through mitosis, but NOT the DNA sequence

methylation

• adding methyl groups to cytosine to chemically change the bases so it no longer looks like a C to the cell, and the transcription factor cannot bind (preventing transcription)

• form of dynamic regulation

• heritable

CpG

cytosine, phosphodiester bond, guanine

• the C is always followed by a G

• palindrome

CpG island

places (usually promoters) with a lot of CpGs next to each other

transcriptional regulation

specific (or necessary and regulatory) transcription factor

enhancer

takes promotion to the next level to make it more complex since eukaryotes are more complex organisms

specific transcription factor

holds assembling complex and everything together, if it did not exist the looping mechanism and complex would fall apart

• combos of cell specific factors that allows eukaryotes to have very precise and specific gene expressions for specific environments and actions

• always binds to sequence in specific way

general transcription factors

necessary, but not sufficient

mRNA processing

mRNA alternative splicing and editing as regulatory

mRNA alternative splicing

splices introns in a specific way so it results in versions of the same receptor with high or low affinity for specific functions

mRNA editing

gene cranks out a bunch of mRNAs in different ways by alternatively splicing them in different ways so phosphates are functional in different environments

different environments proteins can function in from mRNA editing

• secreted so protein functions in bloodstream

• transmembrane so protein functions in membrane

• cytoplasmic so protein stays in cytoplasm

altenative splicing vs polycistronic transcripts

alternative splicing occurs in eukaryotes so molecules of mRNAs can be spliced in different ways to result in slightly different variations of proteins and polycistronic transcripts are in prokaryotes so mRNA can start translation at different genes

mRNA stability

inherently unstable because meant for transcription/lation and then goes away

mRNA stability as regulation

cell will want to increase/decrease mRNA stability at any point to make more/less protein and at only certain parts of the gene, not the whole gene

• does this with RNA binding proteins

RNA binding proteins

bind sequence specifically in 5’ and 3’ untranslated regions to prevent degradation of mRNA and avoid getting in the way of protein coding region

untranslated areas

in between 5’ and start codon as well as between stop codon and 3’

things that prevent degradation of mRNA

• 5’ cap and 3’ PolyAtail

• RNA binding proteins

mRNA destruction

mRNA is actively destroyed by cell at specific moments when cell wants to stop translation because enough protein has been made

microRNA

• binds sequence specifically to mRNA and the proteins attached to the microRNA destroys the mRNA

• usually targets untranslated regions

• short, not translated, does not code for proteins

translational regulation

regulation after transcription has been made during the initiation of translation

initiation of translation in eukaryotes

1) initiation factors bind to 3’ cap

2) initiation factors bring up charged tRNA-Met

3) small subunit recruited

4) complex scans for AUG codon

initiation of translation regulation

RNA binding proteins prevent initiation from occurring because mRNA will produce a protein that the cell wants, just not yet, so translation needs to be stopped

RNA binding proteins

• negative regulators

• default of initiation without them is on

• bind sequence specifically

post translational modification

modification to a protein after it is made

ways to activate a protein

1) enzyme snips off the end of an inactive protein

2) kinase phosphorylates a protein

phosphorylation

• reversible

• kinase adds a phosphate group to activate a protein

dephosphorylation

• deactivates a protein

• done by phosphotase

why regulate gene expression early vs late

every gene does not use every regulator

why regulate gene expression early

efficient because not wasting resources or energy to transcribe and translate a protein that will not be used

why regulate gene expression late

making something/activating proteins quickly when needed

proteins involved in transcription and translation

1) transcription factor

2) initiation factor'

3) repressor

DNA involved in transcription and translation

1) enhancer

2) promoter

3) operator

4) -10 and -35 sites

5) CpG islands

6) TATA box

RNA involved in transcription and translation

1) tRNA

2) start codon

3) Shine-Delgarno sequence