Gene Expression/Regulation
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71 Terms
What is the genome?
The whole genetic information of an organism
What is the transcriptome?
All the RNA in an organism
What is the proteome?
All the proteins in an organism
What percent of the human genome is actually genes (coding)?
2%
What are the 3 stages of transcription?
Initiation, Elongation, Termination
What region of the DNA signals the start of a gene?
The promoter region
What part of the promoter region do transcription factors bind to?
The TATA Box
What is the DNA sequence of a TATA box?
TATAAAA
What binds to the promoter region?
Transcription factors
What macromolecule are transcription factors?
Proteins
What is the role of transcription factors?
To bind to promoter regions of genes that code for needed proteins and to flag down RNA Polymerase II
The initiator complex is made of what?
Transcription factors, RNA Polymerase II, Repressors, Activators
What protein/enzyme transcribes DNA to mRNA?
RNA Polymerase II
RNA Polymerase II copies which strand of DNA?
3’→5’
What happens in the elongation step of transcription?
DNA is rewound behind RNA Polymerase II, mRNA is copied off the 3’ to 5’ DNA strand at the unzipped part, and DNA is unzipped in front of RNA Polymerase II.
What is a transcription unit?
The stretch of DNA that is transcribed.
What causes RNA Polymerase II to stop transcribing?
It hits a terminator sequence
In what kinds of organisms is mRNA translated right after or while it is being transcribed?
Prokaryotes
What is a polyribosome?
A group of ribosomes on translating an mRNA sequence
Which comes first transcription or translation?
Transcription (c before l in the alphabet so same here)
In Eukaryotes what happens between transcription and translation?
mRNA Processing
What are introns?
INTerruptions of the gene (need to be removed)
What are exons?
Need to be EXpressed
What cuts out the introns?
snRNPs
What does snRNP stand for?
Small Nuclear RNA
How do snRNPs cut out introns?
snRNPs attach at each of the boundaries between the intron and exon, and come together into a spliceosome loop, then cutting the intron.
What is alternative splicing?
Exons from one gene can be combined in different ways to make different proteins
How is mRNA protected before it leaves the nucleus on the 5’ end?
A guanine/GTP cap and a Kozak Sequence is added
How is mRNA protected before it leaves the nucleus on the 3’ end?
With a poly-A tail
What is the poly-A tail made up of?
100-250 adenine nucleotides
What is a codon?
3-base sequence of nucleotides
What is mRNA?
Messenger RNA, codes for protiens
What is rRNA?
Ribosomal RNA, makes ribosomes
What is tRNA?
Transfer RNA, brings amino acids to the ribosome for protein assembly
What end (5’ or 3’) does the amino acid attach to in tRNA?
3’
What part of the tRNA is checked against the mRNA codon in a ribosome?
The anti-codon
What enzyme adds amino acids back onto tRNA?
Aminoacyl-tRNA Synthetase
Aminoacyl-tRNA Synthase accepts what as its substrates?
tRNA
Corresponding Amino Acid
ATP
Ribosomes in eukaryotes are what size?
80S
Ribosomes are made of what two parts (in Eukaryotes)?
50S subunit and 30S subunit
What are the three sites for tRNA on the 50s subunit?
A site, P site, E site
What does the A site stand for?
Aminoacyl-tRNA site
What does the P site stand for?
Peptidyl-tRNA site
What does the E site stand for?
Exit site
What are the three steps in translation?
Initiation, Elongation, Termination
What happens in initiation of tranlsation?
The 30s subunit identifies the G-cap and the Kozak sequence and attaches to the mRNA, and moves to the ‘Start’ Sequence, where a tRNA for met attaches. The 50s subunit is then attached on top of that (requires GTP)
In initiation, the 50s subunit attaches so that the met-tRNA is in which site?
The A site
What happens in elongation of translation?
The next amino acid tRNA enters at the P site, and GTP is used to bond the polypeptide chain to the new amino acid. The ribosome then translocates.
What is translocation?
The movement of the ribosome by one codon, thereby ejecting what was in the A site, and moving what was in the P site to the A site.
What happens in termination of translation?
A release factor binds to the stop codon, and blows apart the ribosome. Some adenines are also cut off the poly-A tail.
What is an enhancer?
A section of DNA before the promoter that improves transcription of a gene.
What is a silencer?
A section of DNA before the promoter that decreases transcription of a gene.
What attaches to enhancers?
Activators
What attaches to silencers?
Repressors
Activators and repressors are what kind of macromolecule?
Proteins
How to activators and silencers affect transcription?
They attach to the initiation complex through a hairpin loop
What is the initiation complex?
All the transcription factors, activators, silencers, and RNA Polymerase II combined into a complex
Histones control DNA transcription how?
They tighten or loosen their ‘grip’ on DNA, allowing it to either by read (lose) or not be read (tight)
What is acetylation of a histone?
Acetyl groups attach to histone tails in DNA creating a looser hold allowing DNA to be read
What is methylation of a histone?
Methyl groups attach to histone tails, causing them to grab on tighter and stopping DNA from being read.
What are the epigenetics of an individual?
The methylation or acetylation of genes affecting the phenotype of the individual.
Can epigenetics be inherited?
Yes, but usually epigenetic markers are removed from sex cells.
What causes changes to the epigenome?
Environmental factors (smoking, sun exposure, air pollution, etc)
What is post-translational regulation?
Regulation of a protein after it has been created
What are some mechanisms of controlling proteins?
Phosphorylation, Methylation, Glycosylation, Ubiquitination, or the creation/lack of creation of cofactors/coenzymes
What is ubiquitination and why is it important?
Ubiquitination is the adding of ubiquitin to mark proteins for breakdown by enzymes so that they can be reused
How do most methods of controlling proteins work?
By changing the active site/shape of the protein