Protein Synthesis Flashcards
Protein synthesis
DNA -> RNA -> Protein
DNA holds the genetic information
RNA mediates the transfer of the genetic information
Proteins are end effectors, encoded by the DNA
This process is a cascade; one gene on the DNA gives rise to many molecules of RNA because it can be transcribed many times. Eac( of those molecules of RNA can be translated many times.
In eukaryotic cells, proteins don’t just get made- they have to be packaged and sorted and sent to the right part of the cell because the cell is compartmentalised with different organelles and regions. Proteins have to go to the right part of the cell- the part that requires that specific protein. Proteins need to be sorted, and often modified, before they can be used by the cell.
Sometimes in eukaryotic cells, after the proteins have been made, they need to be modified before being sorted out. This is called post-translational modification. An example of post-translation modification is glycolysation. This is the addition of carbohydrate group to the finished protein. Another example of PTM is phosphorylation where a phosphate group is added to the protein structure.
This process is dynamic. New proteins are constantly being made and old ones degraded. Different cells need different proteins so the ones that are not needed and are old need to be degraded to change the ratio of new to old.
How does the process flow from the nucleus
Flow of information
RNA is transcribed from DNA in the nucleus
RNA is processed into mRNA in the nucleus
RNA is exported to the cytoplasm
RNA is translated into protein by ribosomes on the ROUGH ENDOPLASMIC reticulum
Proteins are transported to the golgi body
Proteins are sorted, modified and directed to their destination
DNA encodes information
Then it is transcribed into mRNA
The mRNA holds the information to make the protein. rRNA and tRNA help mRNA be translated.
Before being exported out to the cytoplasm, the mRNA is modified. mRNA can be translated either by the ribosomes that float in the cytoplasm or the ribosomes embedded in the RER.
Some proteins, particularly those made in the RER, is send to the Golgi body. In the Golgi body, they will be post- translationally modified by the addition of a carbohydrate group (glycosylisation). From, the golgi body, they will be sorted and send to where ever they need to go.
The genetic code
Only 1.5% of the genome codes protein and the rest is other stuff.
The genetic information is held in the order of bases of a nucleic acid
Each three bases in the coding region of a gene is known as a codon
Each codon specifies one amino acid (residue)
In the correct order a series of amino acids makes a protein
The genetic code is universal
The genetic code is the same for all living things
The genetic code is degenerate i.e different codons can code for the same amino acid
E.g GGG and GGU code for glycine
Although the code is universal there are differences in USAGE
All these codons encode for the same amino acid in every living thing.
However, prokaryotes will have preferred codons over the other whilst eukaryotes will prefer to use some other codons. This preference depends on each type of group. There are differences in usage because some codons work better than the other for that group.
Transcription
Transcription is the act of making an RNA copy of a DNA template. The mRNA is sort of the disposable photocopy of the precious DNA that is stored away in the nucleus.
RNA is a nucleic acid like DNA, but is different in two ways:
1. There is no 2’ hydroxyl- chemical difference
2. Uracil replaces thymine- biological difference
The active process of transcription is helped by the enzyme, RNA polymerase. Polymerases extend new nucleic acid chains. RNA polymerase makes a RNA strand from a DNA template.
All polymerases progress in the 5’ to 3’ direction.
RNA polymerase uses the raw ingredient, ribonucleotides in triphosphate forms to extend the RNA strand (which is based on the DNA template).
The rNTP (ribonucleotide triphosphate) looks like a pentose sugar (for a RNA strand- so has an OH group on the C-2’) which is attached to a triphosphate chain. So, the rNTPs will attach themselves to the extending RNA strand. The beta and gamma phosphate groups will be cleaved off and fall away (called the pyrophosphate). However, the alpha phosphate will be incorporated into the chain along with the sugar.
The initial RNA transcript must be processed
The ‘raw’ RNA (pre-mRNA) transcript must now be processed
Non-coding intron sequences must be removed
A complicated process in which introns are cut out and exons stuck back together
Before the introns are cut off and exons stuck together, the RNA is called pre-RNA.
The transcript must be polyadenylated at the 3’ end (at the 3’ end, a long series of As (adenine) are added after the introns in the preRNA are cut out and the exons are stuck together).
The number of As added depend on the type of gene it is.
The As are added to protect the 3’ end as RNA can be quite unstable. The As stabilise the RNA at the 3’ end. The same goes for the capping at the 5’ end. The capping helps protect and stabilise the RNA.
The next thing that follows is that The 5’ end is CAPPED
A highly modified methylated guanine is added at the 5’ end by a 5’ to 5’ linkage. This is unusual because normally nucleotides are connected through a 5’ to 3’ linkage.
Untranslated regions (UTRs)
The processed mRNA still contains some non-protein coding regions even after having the introns removed. These non-coding parts are in the 5’ and 3’ ends. So, they are not internal to the gene itself but at each ends.
These are transcribed and kept in the mature RNA but are not translated.
Their function is regulatory; they control when and where translation occurs. So, they are needed in the translation stage.
These 5’ and 3’ sequences are known as UNTRANSLATED REGIONS (UTRs)
They perform a range of functions such as stabilising the mRNA and modulating translation
mRNA is transported out of the nucleus
The mRNA becomes associated with the nuclear proteins to form a MESSENGER RIBONUCLEOPROTEIN PARTICLE (mRNP)
The mRNP particle is then exported out of the nucleus through the nuclear pores
Between the 5’ and 3’ end, a continuous coding sequence exists in the mature mRNA. This part is called open reading frame and thats going to make the protein. This mRNA gets bundled up in a ribonuclear protein particle
Translation
Translation is the act of turning mRNA into protein
Translation occurs out in the cytosol
A single mRNA molecule can give rise to many proteins
There are three main components of the translation machinery
- The messenger RNA template (mRNA)
- The ribosome (big molecular structure largely composed of rRNA which is going to act as a factory that is going to convert the mRNA, using it as a template, to make protein).
- Transfer RNA (tRNA)- shuttle in the raw amino acids that is going to help build up the polypeptide protein chain.
The ribosome
The ribosome translates the mRNA into protein
The ribosome is a multi-component complex
The ribosome is composed of rRNA and proteins
Ribosome are found actively translating in two regions: free in the cytosol and also attached to the ENDOPLASMIC RETICULUM.
There are different rRNAs in a ribosome structure: 28S, 5.8S, 5S and 18S
The S stands for Svedburg (an unit named after a scientist who used a technique called hydrodynamics) this technique uses centrifuges to measure, analyse and purify things.
The unit relates to how things pellet in the centrifuge.
In the cytoplasm, there are 28S, 5.8S, 5S and 18S rRNAs in a large ribosomal fragment and small ribosomal fragment free floating around. The large ribosomal fragment/ subunit p, 60S, is made of 28S, 5.8S and 5S. One thing about svedburgs is that they don’t add up.
There is smaller 40S subunit that is made up of 18S.
These subunits float around in the cytoplasm. When they encounter a mRNA, these subunits come together- so the 60S and the 40S come together and form around the mRNA. These subunits form the 80S subunit.
These measurements will be different for prokaryotic subunits.
The full 80S ribosome subunit forms at the capped 5’ end where a methylated guanine forms 5’ to 5’ linkage (protecting the 5’ end of the mRNA).
The capping of the 5’ end of the mRNA also has another purpose and that is the spot where the whole ribosome 80S subunit comes together
tRNA
Specific tRNAs exist for each amino acid
An enzyme couples the an amino acid to its appropriate tRNA. There is a specific enzyme synthase for each tRNA and for each amino acid. Once the enzyme has selected the right amino acid for the right tRNA and the amino acid and the tRNA is attached, the tRNA is charged (ready to be used).
A given tRNA is coupled to its appropriate amino acid
A specific tRNA has three bases known as an ANTICODON (complementary sequence to the codon) corresponding to the codon encoding the amino acid on the mRNA.
So the base pairing between the anticodon on the tRNA and the codon on the mRNA allows proximity between the specific amino acid attached to the tRNA to the growing polypeptide chain and thus be attached to the chain.
Base-pairing of the tRNA anticodon to the mRNA codon
Brings the amino acid into proximity of the growing polypeptide chain
tRNA
tRNA (like rRNA) is highly structured- are single stranded but fold up on itself so can form intra regions of double strandedness (hairpin structure).
A tRNA has three hairpin structures- the one facing downwards in the anticodon loop and two coming off, one in each side. All these three hairpin structures are connected by a large stem. The stem is also double stranded. This is sort of a secondary structure of a tRNA. Primary structure is the order of the bases.
The tertiary structure of a tRNA is an upside down L and this forms after the hairpin structures fold up onto themselves again.
They are often drawn as three loops and one stem
In three dimensions these loops fold up to give an ‘L’ shape
Protein sorting
Some of the proteins need to go to a very specific location and some of them need to be imported into an organelle.
Happens at the very beginning of translation.
When the ribosome is at the AUG of the mRNA ready to start translating- it has to make a decision. Either the ribosome will continue translating the mRNA floating free in the cytoplasm and the protein will be made floating free in the cytoplasm.
Alternatively, after it started translating, the mRNA and the polypeptide chain being made is taken to RER and enters the lumen of the RER- it has entered the endomembrane system.
The growing polypeptide chain elongates as the ribosome adds new amino acids to the nascent chain.
Several polypeptide chains can be synthesised from a single mRNA chain at the same time
Protein sorting starts before the polypeptide chain leaves the ribosome
There are two pathways the growing polypeptide chain may take
1. Cytoplasm
2. Endomembrane system
Protein sorting
Elongating polypeptide chains may be attached to ribosomes which are either associated with the endoplasmic reticulum or free in the cytosol
Active ribosomes attached to the endoplasmic reticulum are together known as the ROUGH ENDOPLASMIC RETICULUM
