Learning goal 1 (case3) Flashcards
where translation occures in eukaryotic cell
cytoplasma
which organel do the translation
ribosomes
codons
sets of thre nucleotides, on the MRna strand, codes for protein amino acids synthesizing
how many amino acids are in the human body
20
how many codons can code for a specific amino acids
one or more codons can code for one amino acid
imagine the General tRNA structure, descripe it, descripe its function briefly
base pairing on the same streng, with loops, a 3’ ACC 5’ end here the amino acid attaches, anticodon 5’ GAA 3’ where MRna binds its start codon 5’-AUG-3’
which molecule binds amino acids to tRNA’s
aminoacyl-tRNA synthase
how many sorts are out there for this Molecule that bind tRNA’s to Amino acids
20
what is the process of binding tRNA to amino acid, and its energy source
Aminoacylation, ATP
CCA, and Amino acid
carboxyl group from amino, attached to the 3’-OH or 2’-OH of ribose of the Adenine nucleotide, ester bond (Adenine-O-C=O (carboxyl group))
initiation translation pro
tRNA-fMet (formylated methinone) + (if-2) attached to the 30S body + initiation factors (If-3 IF-1) = pre-initiation complex
pre initiation complex binds to the mRNA the ribosome Aligned with mRNA base by recognizing Shine-dalgarno sequence
3’ UAC 5’ tRNA
5’ AUG 3’ mRNA
forming the full ribosomal complex: 50S+30S=70S
now it has A P E sites
P site here peptide chain grows
A (acceptor) tRNA binds
E (end) dittached tRNA
full initiation complex is completed, the initition factors dissociate and the GTP is hydrolzed to GDP
initation facors prokaryotes
IF1, IF2, IF3
translation elongation prokaryotation and eukaryote
(Aminocyl-tRNA) Alanine binds on A with help of EF-Tu(or IF1)-Ts (pro) (eEF1a1, eEF1a) (euk) complex binding Ts requires GTP> GDP+P
At A site Ala forms and is linked to fMet with a peptide bond (o=c-n-h) with help of Peptidyl transferase, with fMET on p site
eFE2(euk) (EF-G pro) helps with the translocation of ribosomal bodies towards 3 end the peptide chain that was on A is on P site now, this requires a GTP and H2O is formed
E site is emptied of its empty tRNA
the cycle occurs again
peptidyl transferase
binds aminoacids formed from translation in euk and pro
elongation factors pro
eEF1A, eEF1B, eEF2
translation termination prokaryotation
stopation (5’ UAA, UGA, UAG 3’)
releasing factors (3D structure similar to tRNA)
releasing factors pro
RF1 UAA UAG
RF2 UAA UGA
RF3 releases the RF1 and RF2 from stop codon
releasing factors euk
eRF1 recognises all stop codons
eRF3 stimulate termination events
termenation
eleasing factors then cleave the polypeptide chain from the last tRNA via a GTP requiring mechanism (active research area not fully understood yet)
1-stop codon Lys
2-RF-1 binds to stop codon on A site
3- the peptide chain is released
4- RF3-GDP binds causing RF-1 releases
5- GTP replaces the GDP and hydrolisis causing the releases of RF3
6-recycling factor binds to A site (RRF)
7- EF-G-GTP binds ribosome> hydrolysis> EF-G-GDP in A relocation of ribosome is (RRF) in the P and the tRNA in E
8-RRF releases tRNA> EF-G> RRF it self and the ribosomal bodies disbond at the same time
from the MRNA.
RRF only in eukaryotes
Transcription Factor
regulate gene expression, which regulates protein synthesis
binds to promotor DNA
Can work alone to regulate or together with a rotein complexes, activators, repressors influences transcription factors
Micro-RNA’s (miRNA)
non-coding, post- transcriptional regulation of gene expression
can degrade mRNA, speeding up the breakdown of the poly-A tail (deadenylation)
prevent mRNA from being translated
protein secondery, with mos common ones
Secondary structure: the folding pattern of the protein, mostly caused by hydrogen bonds between N-H and C = O groups in the polypeptide backbone.
Two different, most common ones alpha-helix: right handed helix form. The H-bonds are between N-H group and a C = O group of four amino acids away.
beta-sheet: the strands are parallel or antiparallel bonded with H-bonds (this one is a antiparallel one).
teritary structure protein
the folding of the protein altogether.(Hydrophobic interactions between non-polar side chains.(Van der Waals interactions.
electronatic attractions.
ion-bonds (salt bridges).
Di-sulphide bridges between cysteines, these are covalent.
Metal-bridges between two side chains with similar charge
H-bridges between polar groups of backbone and side chains
more than one polypeptide chain folded into each other and forming bonds between those chains.
determine protein destination
After the proteins got their total structure, they are scanned just outside the endoplasmic reticulum (ER) and then modified inside of the ER. Here a short amino acid sequence is added to show where the protein should go in the body.
The proteins are sorted out in the Golgi apparatus and then sent oû to the correct part of the human body.
protein lifetime
After a protein is released from the ribosome, a cell can control its activity and longevity in various ways. Proteins vary enormously in their life-span.!For example:!-Structural proteins (bone and muscle tissue) lasts for months/years.!-Metabolic enzymes/regulation proteins for cell growth and division lasts for days/hours/secondsÉ
protein degrade, proteolysis
There are diûerent pathways to ezymatically break proteins down into amino acids, this is called proteolysis. The enzymes who do this are generally known as proteases. They cut the peptide bonds between amino acids (hydrolyzing).!
Functions of proteases:!-Rapidly degrade proteins whose lifetimes must be kept short.!-Recognize and remove proteins that are damaged/misfolded.
Long lasting proteins are eventually being damaged, so they have to be degraded by proteolysis.!
poteasomes
The proteolysis in eukaryotes is done by large protein machines called proteasomes, which are present in the nucleus and cytosol.!1. First a small protein called ubiquitin is attached by ubiquitin-ligase with a covalent bond to proteins that have to be degraded.!2. Specialized enzymes recognize these proteins which have a short polyubiquitin chain.!3. This complex goes to the proteasomes, where the protein is unfolded in the stopper.!4. When itÕs unfolded, the chain goes to the central cylinder (made out of proteases). Here the proteases chop the protein into amino acids.
How does ubiquitin know where to bond?
Short-lived proteins contain a short amino acid sequence that identifies the protein as on to be ubiquitylated and then degraded
Healthy proteins contain an amino acid sequence or conformational motifs that are buried deep in the 3D structure.!When a protein is damaged or misfolded, this amino acid sequence or conformational motif is no longer buried and then sends out a signal.!Special enzymes recognize this signal and adds a polyubiquitin chain to the protein. The protein is now ready to be degraded
