Protein synthesis
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- Created by: Huzaima1
- Created on: 30-12-18 23:32
Introduction
- Cells synthesise large numbers of diverse proteins which all have different functions, e.g;
- structural - such as assemble the plasma membrane, cytoskeleton and other organelles
- hormones, antibodies, contractile elements in muscular tissue, enzymes
- Proteins determine the physical and chemical characteristics of cells and therefore of the organisms formed from them
- Proteome - refers to all of an organism's proteins
- In the process called Gene Expression - a gene's DNA is used as a template for synthesis of a specific protein - through the processes transcription (the information encoded in a specific region of DNA is transcribed (copied) to produce a specific molecule of RNA) and translation (the RNA attaches to a ribosome where the information contained in RNA is translated into a corrosponding sequence of amino acids to form a new protein molecule)
- DNA and RNA - store genetic information as sets of three nucleotides - called a base triplet
- Each base triplet - transcribed as a complementary sequence of three nucleotides - a codon
- A given codon specifies a particular amino acid
- The genetic code = a set of rules that relate the base triplet sequence of DNA to the corrosponding codons for RNA and the amino acids they specify
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Transcription - occurs in the nucleus;
- the genetic information represented by the sequence of base triplets in DNA serves as a template for copying the information into a complementary sequence of codons
- RNA polymerase - catalyses the transcription of DNA
- Only one of the two DNA strands serves as a template for RNA synthesis
- Transcription begins at a special nucleotide sequence called a promoter - located near the beginning of a gene, where RNA polymerase attaches to the DNA
- During transcription, complementary bases pair - C,G,T and A in DNA pair up with G,C,A, and U in RNA (Uracil replaces Thymine in the RNA strand)
- Transcription of the DNA strand ends at another special nucleotide sequence called a terminator, which specifies the end of the gene - this is where RNA polymerase detaches from the transcribed RNA strand and the DNA strand
- Note: not all parts of the gene code for protein
- regions within a gene which do NOT code for proteins are called introns; regions which DO code for proteins are called exons
- the transcribed RNA (which contains both introns and exons) is called pre-mRNA
- Splicing occurs - a process which removes the introns using enzymes called small nuclear ribonucleoproteins which cut the introns and splice the exons together - resulting product = functional mRNA; exits through a nuclear envelope pore to reach the cytoplasm
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Translation
- occurs in the cytoplasm - carried out by ribosomes
- translation is where the nucleotide sequence in an mRNA molecule specifies the amino acid sequence of a protein
- the small subunit of a ribosome has a binding site for mRNA; the larger subunit has three binding sites for tRNA molecules; a P, A and E site
- AUG = start codon but also the codon for the amino acid methionine = always first aa in a growing polypeptide chain (tRNA anticodon = UAC)
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Lecture notes
Transcription -
- RNA polymerase breaks apart the DNA strands
- A single strand of mRNA is transcribed from the template strand using the base pair rule
- In mRNA, the nucleobase T is substituted by U
- Required nucleotides for mRNA synthesis are found freely in the nucleus
Pre mRNA capping -
- Pre mRNA needs a 5" cap
- the cap is composed of phosphorylated 7-methyl guanosine which is added to the 5" end of the mRNA by guanyltransferase
- ensures mRNA is exported out of the nucleus
- blocks degradation of mRNA by 5' exonucleases
- promotes translation
- [Eukaryotic mRNA has a structure known as a cap at the 5'' end, a sequence of adenine nucleotides at the 3'' end, and a coding region in between containing codons that dictate the sequence of amino acids in a protein or relay a signal]
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Lecture notes
Polyadenylation of pre-mRNA
- Pre mRNA needs a 3' poly A-tail:
- the pre-mRNA is cleaved by an endonuclease near a signal AAUAAA sequence at the 3' end
- Approx 200 adenosine residues are then added at the cleavage site by poly-A-polymerase
- this poly-A-tail protects the mRNA from degradation by 3'' exonucleases
- the poly-A-tail also aids in termination of transcription, ensures export from the nucleus and is important in translation
Alternative splicing - alternative splicing of a pre-mRNA sequence can produce different proteins from the same gene
Summary - mRNA consists of:
- 5' cap
- 5' UTR [untranslated region]
- coding region [to be translated into a protein] (with a start and stop codon)
- 3' UTR [untranslated region]
- poly(A) tail
Proteins consist of amino acids covalently linked with peptide bonds into a polypeptide chain
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Lecture notes - genetic code and proteins
Basic and acidic aa: Hydrophobic residues (fold on inside) + Hydrophilic residues = important for protein folding
The Genetic Code
- DNA base triplets represent each amino acid
- Base triplets in mRNA are called codons
- There are 20 amino acids and 64 (48 ) mRNA codons:
- More than one codon codes for each of the 20 amino acids (the genetic code is degenerate)
- First two bases in the codon are the most crucial: give tolerance against mutations , e.g:
- UCA,UCC,UCG,UCU - all code for Serine
- Some mRNA codons have special roles:
- START codon = AUG (methionine)
- STOP codons = UAG, UAA,UGA
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Lecture notes - genetic code, proteins and mutatio
- the order of bases in the genetic code in DNA codes for the appropriate sequence of amino acids in the proteins
- Transcription (DNA to mRNA) and translation (mRNA to protein) are important processes for protein synthesis
- Substitutions of bases changing the codon can change the corrosponding amino acid
- this can change protein structure significantly and may even result in the creation of stop codons in the wrong places
Mutations in Sickle Cell Anaemia:
- single point mutation - more common in countries with high rates of malaria as it prevents contraction of the disease in the victim
- where glutamic acid in the normal amino acid sequence [ valine-histadine-leucine-threonine-proline-glutamic acid-glutamic acid] mutates to valine
- the change in amino acid sequence causes haemoglobin to crystallise when oxygen levels are low, causing the sickle shape which gets stuck in small blood vessels
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Lecture notes - clinical consequence of mutations
- Accumulation of sickled cells in small blood vessels leads to;
- downstream tissue ischaemia (not enough oxygen reaches the tissues) - causing pain and infarction
- in severe cases, organ damage and ischaemic stroke
- inherited and chronic disease with periodic painful attacks
- common in sub-saharan Africa where sickled red blood cells provide protection against the malarial parasite, thus giving individuals with the mutation a selective advantage
- in the US where malaria is not endemic, the sickle cell trait is slowly dissappearing from the african-american population
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Lecture notes - protein synthesis
- DNA code is transcribed into mRNA in the nucleus
- Protein synthesis takes place outside the nucleus
- DNA is too big to leave the nucleus
- mRNA small and mobile
- mRNA leaves the nucleoplasm via nuclear pores in the nuclear envelope and enters the cytoplasm
- mRNA can then travel to ribosomes for translation of the DNA code into proteins
- Ribosomes -
- are composed of ribosomal RNA and ribosomal proteins
- consist of a 60S and a smaller 40S subunit
- can be free or attached to the RER
tRNAs link mRNA with amino acid assembly - so they are assembled in the correct sequence
- tRNA molecules have complementary base triplets that match up to the mRNA code
- there is a tRNA for each codon;tRNA molecules have amino acids attached
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Lecture notes - tRNA structure and translation
- a tRNA bound to an amino acid (ester bond) = aminoacyl tRNA (also known as a charged tRNA)
- a tRNA molecule which has had its amino acid removed = a deacylated or uncharged tRNA
- a tRNA molecule bound to growing polypeptide chain = peptidyl tRNA
Translation
- during translation, the amino acid sequence is determined by the 3 base sequence making up the codon
- the process in the ribosome builds the polypeptide chains that will make up the protein
- tRNA from the cytosol carries the amino acid and anticodon
- complementary base pairing occurs with the anticodon and codon
- two amino acids join using a peptide bond
- tRNA is released after the amino acid is removed
- THERE IS ALWAYS 3 TRNA BOUND AT ANY TIME
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Lecture notes - definitions
- Initiation - binding of ribosomes to the 5' end of mRNA and hydrogen binding of the anticodon of an aminoactylated tRNA carrying methionine on the AUG start codon
- Elongation - the addition of further amino acids to the growing polypeptide chain brought by corrosponding aminoacylated tRNAs. Peptidyl transferase creates covalent peptide bonds between the amino acids
- Termination - when the stop codon (UAA,UAG,UGA) is reached and the peptide and ribosomal subunits are released
Fate of synthesised polypeptide
- has to acquire a secondary structure; alpha helices and beta pleated sheets
- has to fold into a tertiary structure
- has to assemble into a quaternary structure if appropriate
- proteins have to reach their destinations
- proteins destined for use within the cytoplasm are synthesised on free ribosomes
- proteins destined for secretion out of the cell are synthesised on ribosomes attached to the rough ER (exocytosis - out of the cell)
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Lecture notes - secreted proteins
- synthesised on ribosomes attached to the RER
- RER is a system of flattened cavities
- lined by thin membrane running from nuclear envelope and into the cytoplasm and with many ribosomes on its surface
- provides compartment for protein synthesis
- secreted proteins have special signal sequences which interact with the RER membrane
- these proteins are incorporated into vesicles (small spherical compartments made from RER membrane) for transport to the golgi apparatus
- vesicles move to the golgi complex/apparatus
- GA is a system of flattened plate-like cavities
- lined by a thin membrane
- post-translational modification of proteins occurs in the GA cavities. E.g. glycosylation of membrane spanning proteins
- the now modified proteins traverses the GA and is packaged into secretory vesicles
- protein containing secretory vesicles move to the cell membrane, fuse with it and expel their contents into the extracellular space (exocytosis)
- some specialised GA vesicles called lysosomes contain enzymes which can digest old organelles
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