Amino acids and Proteins- Biochemistry
What is Translation
The process of turning RNA to proteins within the cytoplasm
Why are proteins needed
For metabolism , organsiation , structures and development
How are amino acids joined together
By a condensation reaction to form a peptide bond between the amine group and the carboxylm group of 2 amino acids
What is the direction of translation
Proteins are synthesized in the 5 primer to 3 primer direction by the ribosome in the cytoplasm and then also in the N to C terminus direction
What are Ribosomes
A complex enzyme made up of rRNA and a protein sub-unit
They are able to reads the mRNA and translate to the primary protein sequence
Theuy have 3 sites for tRNA to Occupy which are the E,Pand A site
mRNA is able to slide through a channel on the smaller sub-unit
What are Eukaryotic ribosomes
They are 80S made up a 60S large unit and a 40S small unit
Prokaryoric ribosome size
They are 70S with a 50S large sub-unit and a 30S sub-unit
What are the roles of the 3 RNA used in translation
mRNA= Codes for the primary protein sequence made during translation
rRNA= Make up part of the ribosome
tRNA= Is able to bring an active from of an amino acid to the ribosome to be added to the protein chain,
It is folded so develop hydrogen bonding between complimentary pairs but is single stranded
Has a complimentarty anti-codon site that bind to the mRNA codon to0 bring the A.A. Keep doing this till stop codon that it cant read
What is the genetic code characteristics
It is degenerate and made up of a triplet code that is non-overlapping so one nucleotude can't be in 2 codons
Some amino acids have several codons that code for it so is degernate
Is universal excpet in human mitochondria
What is the inititation step of translation
Ribosome bind to mRNA at the start codon which is always UAG
Translation always start at the 5 primer end
The tRNA has a complimentary anticodon the codon of the mRNA
The added amino acid is determined by the attachemnet to the correct tRNA anticodon
There is the possibility for base pair wobbling due to 64 codons and only 45 anticodons, this stops mutation due to change in thiord codon postion unlikely to change the amino acid added
Transaltion elongation step
The movement from triplet to triplet is called translocaction
Ribosome has piptidyl- transferase activity
This tranfers the next amino acid onto the growing peptide chain
What is the termination step of translation
Reach a stop codon and translation stop = UAA, UAG or UGA
The A site has release factor causing termination due to polypeptide released as completed
The ribosomal sub-unit dissembles
The stop codon doesnt code for any amino acids
The peptide is cleaved at the P site by peptidyly transferase
Why are secondary protein important
Due to define the relaitionship between amino acids that have a close prozimity in the primary protein structure
What is the Linus and Corey experiemnt
Wokred out using a-keratin the structure of fibrous proteins bu x-ray differentiation
What was rule 1 of the Pauling and Corey experiment
There can be no rotation around the peptide bond due to the resonance create a partial double bond
Hydrogen bonding in the amide linkage of the N-H and C=O
What is Rule 2 of the Pauling Corey experiment
Other part of the peptide must be flexible due to other bonds present between the amino group and the central carbon and the central carbon to the carboxyl
The bons rotation angle depend on the R groups
What is the 3rd rule of the Paukling Corey experiement
Polypeprdie must have max numbver of stabilising forces between residues and are independent of the primary structure made up of hydrogen bonds
What are the 2 type of secondary protein structures
Alpha helix and Beta pleated sheets
What is the alpha helix chain
The NH of 1 resiude can H bond to the C=O on an amino acid that is 4 residues away
In the N-C terminus ther helix turns clockwise
Side chains are able to point outwards rather than in like the DNA helix structure
How to disrupt the alpha helix chain - Glycene
Glycene due to no chiral carbon so more flexible and is called a helix breaker, is usually found at the very end of the alpha helix chain so no more binding on
How can proline disrupt the alpha helix
It caues bonds to bend
The amine to C angle needs to be 45 and the C- carboxyl needs to be 60 bond angle
Proloine lower rotation so that the amine -C angle is 50 so less folding in the backbone
Tend to be at the start pof chain due to act as protection due to form capping box
How do amphipathic helixes form
hydrophobic amino acids anjd polar oens that are mixed together so get 2 side chains of the alpha helix
Useful for generation of proteins that are soluble in the lipid bilayer due to is hyrophobic and hydrophillic side chains
What are Beta Pleated Sheets
They can be antiparrallel or parallel with the anti being more stable due to contain more H bonds that are more directly alogned so are stronger
Parallel need longer connecting loops to hold the structure together
Normal B-sheets
They have stereoisomerim and are formed in the outer membrane of the mitochondria
What are B-turns
A tyoe of non-regular secondary structure in proteins that cause a directional chnage in the polypeptide
What are random coils
When there is no secondary stucture form a random loops that are disporderd
Disorder is important due to allow ligand binding and connect 2 domains to aloow flexible linkages
What are structural motifs
Coiled coild from amphipathic proteins that are used for DNA binding, Ca2+ binding and helix turns
What are the 2 super secondary proteimn structures
Helix tunr helix that is used for DNA binding
Helix loop helix for Ca2+ binding
How does disulphide bidges between 2x cysteine effetc the protein
2 Cysteine join via sulphur in the R group due to oxidation reaction
It uses 2 e- exchange to form and 2 proton as well
Important for holding slight and heavy chain together in antibodies for their structure
What is the tertiary protein structure
A 3d polypeptide structure and is conglomeration of the 1o and 2o protein structures, this can happen due to being kinetically and thermodynamically stable in its structure
The folding of the polypeptide happens due to
R group interaaction via hydrophobic interaction, H bonding, Disulphide bridges and VDW forces
What is the Anfinsen Ribonuclease experiment
Hows that Folded active form of the protein has the lowest free emergy
All the infomation needed for a protein coded by the primary protein structure and the tertiary is coded for by the primary
Not all proteins easily fold and some need help by disulphide isomerases that are able to make and break disulphide bridges unit correct folding orientation is found
What us Levinthals paradox
Protein folding has a strong driving force that causes this to happen and is spontaenous due to negative delta G
Worked this out with 100 polypeptides and and 99 peptide bonds made lead to 198 bond angles and 3 rotameric positions
What happens to hydrophobic residfues during folding
They move to the centre of the protein to be protected from water
Factors that drive protein folding
Hydrophobic intercation + Electrostatic bonds + Hydrogen bonding + Van der waals forces
What does changing electrostatic bonds do
Protein charge determined by pH and number/type of amino acids
Used for enzymes to activate lysoszymes
At neutral pH the amino acid form zwitterions
What is protein modifications
Proteins can be further modified after synthesis to then form larger protein complexes
Use strong forces of attraction in tertiary structure to form these complexes and modifications
How is a protein modified
Conformationla change to allow a function
Act as a scaffold for other proteins to bind to
Prosthetic group additons
44% of proteins have a form different to their genetic sequence = Proteoform
What is Phosphorylation
The process of + or - a negatove charged moietry
Catalysed by Ptoein Kinase that can add phosphate group or by phosphatase that remove phosphate group
Is uded as on/off siwtch for cellualr signalling and drive protein intercation
What is methylation
The adding or removal of a methyl group
What is glycoslyation
The adding or removal of a carbohyrdate group
Will be N linked to asparagine and O linked to serine or threonine
Why is glycoosylation important
Cellular pathways, Protein trafficking, cell adhesion, pathogen intercation and protein folding
What is palmitoylation
Long lipid memrbanes that anchor proteins within the membrane due to modification of cysteine, glycine or lyscine
Proteins can also be added to other proteins to form isopeptide bond with the carboxyl end
What is ubuquiination and degradation
Ubiquitin modifies lsysene and then the polyubiquitin tails to target other proteins for degradation
Why are protein modification irreversable
Proteolytic cleavage and the chaging of amino acids make it irreversable
How to break peptide bonds
A hydrolysis reaction at boiling 6m acid or base with proteases enzymes
What are prosthetic groups
Non protein molecules that are added to the quatrernary structure E.G Haem group of haemoglobin
What is a quaternary protein
The arrangement of more than 1 polypeptide in a large protein complex