Chapter 7.2 Flashcards
What is the purpose of the 5’ Cap?
The 5’ cap is a methylated GTP molecule that is added during transcription. This molecule protects the mRNA from degredation in the cytoplasm. It is also recognized by the ribosome as a binding site.
What is meant by alternative splicing?
Depending on how a single transcript of hRNA is spliced, you can get different proteins. This is hypothesized to make it so we can fit more potential proteins into a smaller amount of DNA/RNA. For example, the same segment of DNA and the hnRNA transcript that goes with it could be spliced 5 different ways to make 5 completely different proteins.
What is the purpose of the 3’ Poly- A tail?
The 3’ Poly A Tail is a long chain of Adenines. The Poly A tail is a shield for the mRNA transcript in the cytoplasm. As soon as the mRNA transcript hits the cytoplasm, the poly A tail starts to get destroyed. The longer the Poly A tail, the more time the mRNA transcript has to get translated. Also asists with export from the nucleus
What is a UTR?
UTR stands for untranslated region. It refers to small portions at the ends of the RNA transcript that do not get translated. Remember, Translation always starts at AUG and ends at stop codons, so UTR’s are just the mRNA before the start codon and after the stop codon.
What is the ribosome?
The ribosome is a structure made of proteins and RNA that associates with mRNA in the cytoplasm and constructs chains of amino acids using tRNA’s.
What are the three binding sites for tRNA’s in ribosomes?
- A - AminoAcyl Site
- P - Peptidyl Site
- E - Exit Site
What are the three main steps of translation?
- Initiation
- Elongation
- Termination
What are the necessary requirements for each step of translation?
- Initiation - Initiation Factors and GTP
- Elongation- Elongation Factors and GTP
- Termination - Releases Factors and GTP
What is the Shine-Dalgarno sequence?
The Shine-Dalgarno sequence is seen in prokaryotes. It is a piece of RNA in the 5’ UTR that allows the small sub unit of the ribosome to bind.
If prokaryotes use the Shine-Dalgarno sequence to recruit the small sub unit of the ribosome, how do eukaryotes do it?
Eukaryotes use the 5’ cap to recruit the small sub unit of the ribosome.
Describe Initiation of translation
First, the small ribosomal sub unit binds to the mRNA (using shine-dalgarno in prokaryotes or the 5-cap in eukaryotes) and scans for start codon.
Second, the activated initiator tRNA (fMet in prokaryotes and Met in eukaryotes) binds to the start codon through base pairing at the P site of the small ribosome.
Third, the large sub unit binds to the small sub unit with the help of initiation factors, forming the completed initiation complex.
Describe the role of the A site
The A site holds the incoming aminoacyl-tRNA. This is the next amino acid that is being added to the growing chain.
Describe the role of the P site?
The P site holds the tRNA that carries the growing polypeptide chain. It is also where methionine (starting AA) binds during initiation. In this part of the ribosome, an enzyme called peptidyl transferase uses GTP to transfer the peptide chain from the tRNA in the P site to the tRNA A site.
Describe the role of the E site.
After a tRNA in the P site loses its peptide chain, it is transferred to the E site where it pauses for just a second before dissociating back into solution so it can be recharged.
What are Elongation Factors?
Elongation Factors are proteins that speed up elongation by bringing in tRNAs and GTP. Elongation Factors also get rid of GDP (used up GTP) so that fresh GTP’s can take their place.
What is a signal sequence?
A signal sequence is a part of the new peptide chain that directs the ribosome to move to the rough ER and finish translation there. Signal sequences are meant for proteins that won’t be in the cytoplasm, which includes secretory proteins (like hormones and digestive enzymes), membrane proteins, and lysosome proteins.
Describe Elongation in translation.
First, the appropriate tRNA will enter the A-site of the complete ribosome.
Second, GTP is used to transfer the polypeptide from the tRNA in the P site to the tRNA in the A site.
Third, GTP is used to move the tRNA from the P site into the E site, and the tRNA in the A site to the P site. This also moves the ribosome one codon down the mRNA.
Elongation factors are responsible for moving it down a a codon
Fourth/First, the tRNA leaves the E site and the next appropriate tRNA binds the A site.
Describe Termination of translation?
When a stop codon moves into the A site, a protein called Release Factor binds to the codon and causes a water to be added to the chain. Next, termination factors and peptidyl transferase hydrolyze the peptide chain from tRNA. The ribosome will dissociate shortly after.
What is post-translational processing and what are the commom types?
Post-Translational processing refers to any modifications made to a protein after it has already been translated.
A. Folding by chaperones
-bonus: signal pepties
B. Cleavage events (signal sequence needs to be cleaved for function)
C. Adding biomolecules
1. Phosphorylation
2. Carboxylation
3. Glycosylation
4. Prenylation
Generally speaking, how does phosphorylation affect proteins?
Addition of phosphate groups. Phosphorylation is used to activate or deactivate proteins, especially enzymes.
Detail: most commonly seen with serine, threonine, and tyorsine
Generally speaking, how does carboxylation affect proteins?
Addition of carboxylic acids. Carboxylating proteins is usually done so that the protein can have calcium binding sites.
Generally speaking, how does glycosylation affect proteins?
Addition of oligosaccharides. Glycosylation is usually conducted in the ER and the golgi apparatus. Glycosylation is most often used as a signal for where the protein is supposed to end up in the cell. For example, a certain type of glycosylation might make a protein go to the lysosome while other glycosylations might make the protein go to the mitochondria.
Generally speaking, how does prenylation affect proteins?
Prenylation (addition of lipid groups) is usually conducted on membrane bound enzymes so that they can associate with the membrane well.
What is the main way that prokaryotes regulate how much of their genome they are expressing?
Operons
What are the 5 main ways that Eukaryotes regulate how much of their genome they are expressing?
- Transcription Factors
- Enhancers
- Gene duplication
- Histone Acetylation
- DNA methylation
Describe the structure of an operon according to the Jacob-Monod model?
An operon is a cluster of genes transcribed as a single mRNA.
The main pieces of an operon from left to right are the Regulator gene, the Promotor site, The Operator site, and The Structural gene
Regulator gene- Codes for repressor
Promoter site- Provides place for RNA pol to bind
Operator site- Non transcribable region of DNA that can bind repressor
Structural gene- codes for protein of interest
What is an operon and what are the two types?
An inducible/ repressible cluster of genestranscribed as a single mRNA
- Inducible Systems
- Repressible Systems
Describe an Inducible System operon?
In an inducible system, an ever-present repressor protein (coded for by the regulator) binds to the operator and stops RNA polymerase from transcribing it.
However, if an inducer is present, then it will bind to the repressor and stop it from repressing the gene. This allows the operon to be transcribed.
This is useful because it ties transcription of these genes to the presence of a specific molecule, which means that the gene is only on when the cell feels like it is needed.
The classic inducible system is the lac operon, an operon that allows bacteria to digest lactose when it is in high enough concentrations. (they prefer glucose and thus don’t need to produce lactase regularly) Negative inducible system
What is a negative control mechanism?
Negative control mechanisms are systems in which the binding of a molecule reduces transcriptional activity. E.g. Repressor proteins
What is a positive control mechanism?
A positive control mechanism is a system in which the binding of a molecule increases transcriptional activity. Example: CAP
What is an inducer?
An inducer is a molecule that binds to a repressor to remove it from the operon.
Describe a Repressible System operon
In a repressible system, an ever-present repressor protein (coded for by the regulator) cannot bind to the operator on its own, so RNA polymerase can transcribe it.
However, if a co-repressor is present, then it will bind the repressor and allow it to repress the gene. This stops the operon from being transcribed. (Often negative feedback mechanisms, meaning product is co-repressor)
This is useful because it ties transcription of these genes to the presence of a specific molecule, which means that the gene gets turned off when the cell feels its no longer needed.
The classic repressible system is the trp operon, an operon that allows bacteria to synthesize trp when it is low in the cell. Negative repressible system
What is an enhancer?
An enhancer is a group of reponse elements that bind elements (signal molecules bind to receptors which then act as transcription factors that bind to response element on DNA) far away from the gene in question in order to enhance the transcription of said gene. The large distance between the enhancer and the genes it enhances almost always lead to the DNA bending to bring them close together. Can be located within an intron. One enhancer for one gene (we don’t have one enhancer helping multiple different promoters)
What is Gene Duplication?
Gene duplication is when certain cells modify their genome by adding more copies of a gene (can be duplicated in sseries on the same chromosome and also in parallel by letting DNA pol replicate only that gene many times) As is expected, the more copies you have of a gene, the more you express the protein associated with the protein. For example, a skin cell might have many many copies of the keratin expressing gene because of its primary importance there.
How exactly do histones get DNA to wrap so tightly?
Histones are studded with positively charged lysine residues, which bind tightly to the negative phosphate backbone of DNA.
What is Histone Acetylation?
Histone acetylation is when the positively charged lysine residues are acetylated, which reduces their positive charge and weakens the binding of the histone with DNA. This results in loose DNA that can be more easily transcribed.
What is DNA methylation?
DNA Methylation is when C and A Nucleotides are methylated. Methyl groups carry electron density in their bonds, which increases the negative charge of the DNA, which strengthens the interaction between histones and DNA. This results in tight DNA that is harder/unable to transcribe.
What are chaperones?
Chaperones are a special protein that wraps around newly synthesized proteins in order to protect them and change the microenvironment in which the protein folds.
What are the main three differences between DNA and RNA?
- RNA has Ribose, DNA has Deoxyribose
- RNA has Uracil, DNA has Thymine
- RNA is single stranded, DNA is double stranded. (except in viruses!)
What is the main difference between enhancers and promoters?
Enhancers are more than 25 base pairs away from the transcription site.
Promoters are within 25 base pairs of the transcription site.
