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MindMap Gallery Biochemistry and Molecular Biology-Protein Synthesis
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Biochemistry and Molecular Biology-Protein Synthesis
People's Medical Publishing House "Biochemistry and Molecular Biology" Ninth Edition Chapter 15 Protein Synthesis is introduced in detail and described comprehensively. I hope it will be helpful to interested friends!
Edited at 2023-11-26 11:13:38
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Biochemistry and Molecular Biology-Protein Synthesis
- bacteria
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- Plant asexual reproduction
This is a mind map about plant asexual reproduction, and its main contents include: concept, spore reproduction, vegetative reproduction, tissue culture, and buds. The summary is comprehensive and meticulous, suitable as review materials.
- Reproductive development of animals
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- Outline
protein synthesis
protein synthesis system
mRNA is the template for protein synthesis
a
definition
In the open reading frame region of mRNA, every three adjacent nucleotides form a group, encoding the start/stop information for the synthesis of an amino acid or peptide chain, called a codon, also known as the triplet code
64 codons
61 coded amino acids
special
AUG
not only represents methionine
It can also represent the initiation codon for peptide chain synthesis.
3 stop codons
UAA
UAG
UGA
5 major characteristics of the genetic code
Directionality
The reading direction of the genetic code during translation is 5'→3', that is, the reading code starts from the start codon AUG of the mRNA and is read one by one in the direction of 5'→3' until the stop codon.
Determine the order of amino acids from N-terminus to C-terminus
continuity
There are no intervening nucleotides between codons, and reading continues from the start codon to the stop codon.
frameshift mutation
frameshift
definition
Inserting or deleting nucleotides that are not multiples of 3 in the open reading frame will cause the mRNA open reading frame to shift.
definition
Frameshift causes subsequent changes in the amino acid coding sequence, causing the protein it encodes to completely lose or change its original function.
degeneracy
definition
Some amino acids can be encoded by multiple codons
Performance
61 codons code for amino acids, but there are only 20 types of amino acids
Except for tryptophan (UGG) and methionine (AUG), which only have one codon, the other amino acids have 2, 3, 4 or up to 6 triplets coding for them.
Degenerate codons (synonymous codons)
definition
Codons encoding the same amino acid
Features
In most cases, the first two bases of a degenerate codon are the same, and only the third base is different.
Codon specificity is mainly determined by the first two nucleotides
Changes in the third base often do not change the amino acid encoded by it, and the synthesized protein has the same primary structure.
significance
Degeneracy reduces biological effects of genetic mutations
Swingability
definition
The pairing between the anticodon on tRNA and the codon on mRNA sometimes does not strictly follow the common base pairing rules. This phenomenon is called wobble pairing.
site of occurrence
The first base of the anticodon
The third base of the codon
For example: hypoxanthine (I) can pair with A, C, and U in the third codon position
significance
Enables one tRNA to recognize multiple degenerate codons of mRNA
Versatility
definition
From lower organisms to humans, they all use the same genetic code
significance
Provides strong evidence to support the theory of evolution that all living things on earth come from the same origin
Special case examples
In mammalian mitochondria, UGA not only represents the termination signal, but also represents tryptophan.
tRNA is a specific linker between amino acids and codons (the "transportation tool" for specific amino acids)
Two functional parts of tRNA
amino acid binding site
Adenylate 3'-OH at the -CCA end of the amino acid arm of tRNA
mRNA binding site
Anticodon in tRNA anticodon loop
effect
Carry amino acids
An amino acid usually binds specifically to multiple tRNAs (compatible with the degeneracy of codons)
A tRNA can only transport one specific amino acid
Acts as an "adapter"
The anticodon of each tRNA determines how accurately the amino acid it carries can be positioned on the mRNA.
Ribosomes are the site of protein synthesis
The composition of ribosomes
A large ribonucleoprotein particle composed of rRNA and multiple proteins, consisting of two subunits, large and small.
Three important functional parts of ribosomes
A site (aminoacyl site——aminoacyl site)
Binds aminoacyl-tRNA
P site (peptidyl site——peptidyl site)
Binds peptidyl-tRNA
E position (exit site——exit position)
Release tRNA from which amino acids have been unloaded
Protein synthesis requires a variety of enzymes and protein factors
energy supply substance
ATP or GTP
inorganic ions
Mg2, K, etc.
enzyme
Aminoacyl-tRNA synthetase, peptidyl transferase, translocase, etc.
protein factors
Eukaryote: eucaryote
initiation factor IF
prokaryotes
IF
eukaryotes
eIF
elongation factor EF
prokaryotes
EF
eukaryotes
EF
Termination factor [also known as release factor] RF (release factor)
prokaryotes
RF
eukaryotes
EF
Amino acid activation and connection to tRNA
Aminoacyl-tRNA synthetase recognizes specific amino acids and tRNA
23 aminoacyl-tRNA synthetases have been discovered so far
The main steps in the reaction catalyzed by aminoacyl-tRNA synthetase
The reaction consumes 2 high-energy phosphate bonds from ATP
① Aminoacyl-tRNA synthetase catalyzes the decomposition of ATP into PPi and AMP
② AMP, enzyme, and amino acid are combined into an intermediate complex (aminoacyl-AMP-enzyme)
The carboxyl group of the amino acid is connected to the phosphate of adenosine phosphate through an anhydride bond and is activated.
③ The activated amino acid combines with the free hydroxyl group at the 2' or 3' position of the adenylate ribose at the 3'-CCA end of the tRNA through an ester bond to form the corresponding aminoacyl-tRNA, and the AMP is released in a free form
Proofreading activity of aminoacyl-tRNA synthetase
It can hydrolyze and release incorrectly combined amino acids, and then replace them with the correct amino acids to correct mismatches that occur during the synthesis process.
The synthesis of peptide chains requires a special starting aminoacyl-tRNA
prokaryotes
The initial methionine is formylated to form N-formylmethionine (fMet-tRNAfMet), which can be in place at the start codon AUG of the mRNA and participate in the formation of the translation initiation complex
eukaryotes
The eukaryotic start code is different from the tRNA bound by Met in the subsequent reading frame: the starting tRNA is the initiator tRNA, that is, tRNAi; Met-tRNAMet can be recognized during elongation
Post-synthesis processing and targeted transport of proteins
post-translation processing
定义
新生多肽链不具备蛋白质的生物学活性，必须 经过复杂的加工过程才能转变为有活性的成熟 蛋白质，这一加工过程称为翻译后加工
包括
正确折叠成三维结构、形成二硫键、亚基 聚合形成四级结构、水解切除、侧链化学修饰 等
Folding of nascent peptide chains requires molecular chaperones
background
The unfolded peptide segments of newly synthesized proteins have many exposed hydrophobic groups, which tend to aggregate intramolecularly or intermolecularly and cannot form a correct spatial conformation.
Excessive production of disordered peptide chain aggregates can have fatal effects on cells
meaning
Most protein folding is not completed spontaneously and requires the assistance of other enzymes or proteins. These auxiliary proteins can guide the nascent peptide chain to fold correctly in a specific way, called molecular chaperones, such as heat shock proteins, chaperones, etc.
Chaperone
definition
Molecular chaperones are conserved proteins that recognize unnatural conformations of peptide chains in cells and promote the correct folding of each functional domain and the overall protein.
main effect
Block the exposed hydrophobic segments of the peptide chain to be folded
Create an isolated environment so that the folding of peptide chains does not interfere with each other
Promote peptide chain folding and deaggregation
Encountering stress stimuli, unfolding the folded protein
Example
Heat shock protein 70 (HSP 70)
Features
It is a stress-responsive protein with a molecular weight of about 70kD.
It is expressed to a certain extent at room temperature, and high temperature stress can induce a large amount of synthesis of this protein.
It can promote the folding of polypeptides that need to be folded into proteins with natural spatial conformation.
Role in post-translational processing
Binding to the hydrophobic region of unfolded proteins not only prevents protein denaturation due to high temperatures, but also prevents premature folding of nascent peptide chains.
Allows some transmembrane proteins to remain unfolded before being translocated to the membrane
Binding to unfolded polypeptide chains can unravel aggregations between polypeptide chains or prevent the formation of new aggregations.
Some Hsp70 bind to polypeptide chains and are released through the cycle process. Correct folding of the polypeptide chain. This process requires ATP hydrolysis for can, and requires the cooperation of other chaperone proteins such as Hsp40
If the polypeptide chain is not fully folded, it can be repeated until the natural conformation formation
Hsp protein family
position
Can exist in the cytoplasm, endoplasmic reticulum cavity, mitochondria, nucleus and other parts (human)
Function
Involved in multiple cell protective functions
For example, keeping mitochondrial and endoplasmic reticulum proteins in an unfolded state allows them to be transported and span membranes, and then refolded to produce work. energy conformation
Avoid or eliminate the consequences of protein denaturation Irreversible aggregation due to exposure of hydrophobic groups to facilitate removal Denatured or misfolded polypeptide intermediates, etc.
chaperone protein
Classification (eukaryotic, prokaryotic)
E. coli
GroES/GroEL system
composition
bucket
Gro EL
It consists of 14 subunits forming a barrel-shaped cavity with the cavity exit at the top.
build
GroES
Dome-shaped complex composed of 7 identical subunits
Action process
When the peptide chain to be folded enters the barrel-shaped cavity of Gro EL, Gro ES acts as a "lid" to instantly seal the Gro EL cavity outlet. The closed barrel-shaped cavity provides a microenvironment that can complete the folding of the peptide chain.
Functional characteristics
Consumes a lot of energy, which is released after folding is completed
The peptide chain that has not yet been completely folded can enter the next cycle, and the above process is repeated until the native conformation is formed.
Eukaryotic cells (chaperone protein similar to GroES/GroEL system function)
Hsp60
main effect
Provide a microenvironment for non-spontaneously folding proteins to fold into their native spatial conformations
Isomerase (folding enzyme)
background
In addition to molecular chaperones assisting in peptide chain folding, some Amino acid residues crucial for the formation of white matter spatial structure (e.g. Correct folding of cysteine, proline, etc.) also requires enzymatic reaction
Classification
protein disulfide isomerase (PDI)
effect
Disulfide isomerase is highly active in the lumen of the endoplasmic reticulum and can catalyze the cleavage of mismatched disulfide bonds in larger segments of peptide chains and form correct disulfide bond connections, ultimately allowing the protein to form the most thermodynamically stable natural conformation.
Assists in the correct formation of disulfide bonds within or between polypeptide chains
Mainly carried out in the endoplasmic reticulum
Peptide prolyl-cis-trans isomerase (PPI)
Rate-limiting enzyme for protein three-dimensional conformation formation
background
The peptide bond formed between peptidyl-proline in the polypeptide chain has two isomers, cis and trans, with obvious differences in spatial conformation.
effect
Peptidyl-prolyl cis-trans isomerase can promote the conversion between the two cis-trans isomers mentioned above.
Make the polypeptide form an accurate fold at each proline bend
Hydrolytic processing of peptide chains to produce active proteins or peptides
The N-terminal methionine residue of the nascent peptide chain
prokaryotes
About half of the methionine remains
The N-formyl group is removed by deformylase and methionine is retained.
The other part removes N-formylmethionine
Hydrolyzed by aminopeptidase to remove N-formylmethionine
eukaryotes
All eukaryotic Mets are cut off
signal peptide
definition
A signal peptide of 13-36 amino acids at the N-terminus of a secreted protein or transmembrane protein precursor
ending
cleaved during protein maturation
The C-terminal amino acid residues of some proteins are cleaved by enzymes
Make proteins perform specific functions
Hydrolysis of precursor molecules
Many proteins are inactive precursor molecules when synthesized, such as proinsulin, trypsinogen, etc., and only after partial peptide fragments are removed by hydrolysis can they become active protein molecules or functional peptides (proinsulin is hydrolyzed to insulin by enzymes; proteases Protocleavage and activation into protease)
Some polypeptide chains can produce several small molecule active peptides after hydrolysis
For example: hydrolytic modification of proopiomelanocortin (POMC) produces 9 active products
Chemical modification of amino acid residues alters protein activity
Mechanism of action
These modifications can change the protein's solubility, stability, subcellular localization, and interactions with other proteins in the cell.
thereby diversifying the functions of the protein
Table of common chemical modifications in the body
Features
There are more than 100 modified amino acids. Change solubility, stability, subcellular localization, interaction properties with other proteins, etc.
Phosphorylation
Phosphorylation of Ser, Thr and Tyr residues of signaling molecules mediates cell signaling
Enzyme proteins change activity and regulate metabolic levels through phosphorylation and dephosphorylation of Tyr residues
Glycosylation
The amide nitrogen of the asparagine residue, the hydroxyl group of the serine or threonine residue can be covalently linked to the oligosaccharide chain to glycosylate the polypeptide chain.
Hydroxylation
Hydroxylation of lysine and proline residues is the basis for the formation of interchain covalent cross-linked structures in mature collagen.
Methylation
Histone arginine residues can be modified by methylation to affect chromatin structure, thereby participating in the regulation of gene expression.
Aspartate in damaged proteins can be methylated, promoting protein repair or degradation
disulfide bond formation
Some secreted proteins often form intra-chain disulfide bonds to stabilize the protein's natural conformation and avoid denaturation due to environmental influences.
lipophilic modification
Covalently link one or more hydrophobic lipid chains at specific sites on the peptide chain to enhance their binding ability to membrane systems or enhance protein-protein interactions.
All are enzymatic reactions, requiring protein kinase, sugar/methyltransferase, hydroxylase, etc.
Subunits polymerize to form active proteins with quaternary structure
sequentiality
Proteins with quaternary structure formed by non-covalent subunit polymerization: such as hemoglobin
Proteins with quaternary structure are composed of two or more peptide chains polymerized through non-covalent bonds to form oligomers.
After the prosthetic group is connected, a complete binding protein is formed
After the synthesis of binding proteins, they need to be combined with corresponding prosthetic groups to become functionally active natural proteins.
After protein synthesis, it is targeted and transported to specific parts of the cell.
definition
After proteins are synthesized on the ribosome, they must be sorted out and transported to an appropriate site in order to perform their respective biological functions.
Features
Targeted protein delivery is synchronized with post-translational modification processes
The protein targeted for delivery has a signal sequence
There is a sorting signal in the primary structure of all targeted proteins that can guide the protein to transfer to the appropriate target site in the cell. This type of sequence is called a signal sequence.
distributed
At the N-terminus, C-terminus or within the peptide chain
ending
Some are removed after the transfer is completed, and some are retained.
5 proteins have different destinations
Secreted proteins are processed and targeted for transport in the endoplasmic reticulum
Intracellular secretory protein synthesis and transport occur simultaneously. They all have a signal peptide structure at their N-terminus, which is composed of dozens of amino acid residues.
Common characteristics and structural characteristics of signal peptides
N-端含1个或多个带正电荷的碱性氨基酸残基，如赖氨酸、精氨酸
中段为疏水核心区，主要含疏水的中性氨基酸，如亮氨酸、异亮氨酸等
C-端加工区由一些极性相对较大、侧链较短的氨基酸（如甘氨酸、丙氨酸、丝氨酸）组成，紧接着是被信号肽酶(signal peptidase)裂解的位点
Synthesis and transport mechanism of secreted proteins
The signal peptide is first synthesized because it is located at the N-terminus and can be recognized and bound by the signal recognition particle (SRP) in the cytoplasm. SRP binds to ribosomes
There are SRP receptors, namely SRP docking proteins, on the endoplasmic reticulum. The SRP ribosome complex is directed to the endoplasmic reticulum
The peptide translocation complex of the endoplasmic reticulum membrane forms a channel across the endoplasmic reticulum membrane, and the peptide chain enters the endoplasmic reticulum.
SRP breaks away from the signal peptide and ribosomes, and the peptide chain continues to elongate until it is completed.
The signal peptide is cleaved by signal peptidase in the endoplasmic reticulum
The peptide chain folds into its final conformation in the endoplasmic reticulum; the vesicles formed as the endoplasmic reticulum buds are transferred to the Golgi apparatus
Packed into secretory vesicles in the Golgi, transported to the cell membrane, and then secreted outside the cell
The C-terminus of the protein localized in the endoplasmic reticulum contains a retention signal sequence
Example
Chaperone
The endoplasmic reticulum contains a variety of molecular chaperones that help nascent peptide chains fold into their natural configuration.
Targeted delivery process
ribosome → endoplasmic reticulum
Proteins that need to stay in the endoplasmic reticulum to perform functions are first synthesized by ribosomes on the rough endoplasmic reticulum and enter the endoplasmic reticulum lumen.
Endoplasmic reticulum→Golgi complex
Then transported with vesicles to the Golgi complex
Golgi complex → endoplasmic reticulum
Since the C-terminus of the protein peptide chain located in the endoplasmic reticulum contains a retention signal sequence, the endoplasmic reticulum proteins in the Golgi complex bind to the corresponding receptors on the endoplasmic reticulum through this retention signal sequence and are transported back to the endoplasm along with the vesicles. net
Most mitochondrial proteins are targeted to the mitochondria after synthesis in the cytosol
mitochondrial proteins
The vast majority of mitochondrial proteins (95%, approximately 1100 species) are encoded by the nuclear genome
Released after synthesis by cytosolic ribosomes and targeted for transport to mitochondria
signal sequence
position
mitochondrial matrix
The N-terminus of the protein precursor is a signal sequence leader peptide composed of 20-35 amino acid residues, which is rich in serine, threonine and basic amino acids.
Targeted transport process
Newly synthesized mitochondrial proteins bind to HSP or mitochondrial import stimulating factor and are transported to the outer mitochondrial membrane
Receptor complex that recognizes and binds to mitochondrial outer membrane through leader peptide sequence
Under the combined action of HSP hydrolyzing ATP and the electrochemical gradient across the inner membrane, it passes through the transmembrane channel composed of the outer membrane transporter and the inner membrane transporter and enters the mitochondrial matrix.
Excise the signal sequence and fold into a functional protein
inner mitochondrial membrane
mitochondrial intermembrane space
In addition to the above-mentioned leader peptide, there is another signal sequence
Its role is to guide protein transport from the matrix to the inner mitochondrial membrane or across the inner membrane into the intermembrane space
Targeted transport of plasma membrane proteins from vesicles to the cell membrane
Features
Anchored
The transmembrane mechanism in the rough endoplasmic reticulum during plasma membrane protein synthesis is similar to that of secreted proteins.
However, the peptide chains of plasma membrane proteins do not completely enter the lumen of the endoplasmic reticulum, but are anchored on the endoplasmic reticulum membrane. Vesicles are formed through budding and reach the Golgi apparatus. After processing, they are transported to the cell membrane with the vesicles to function.
Different ways of anchoring
Different types of transmembrane proteins are anchored to the membrane in different ways
single transmembrane protein
There is an N-terminal signal peptide and a transmembrane sequence that is a stop transfer sequence. This sequence can bind to the lipid bilayer of the endoplasmic reticulum membrane, preventing the imported peptide chain from moving into the endoplasmic reticulum lumen.
multiple transmembrane proteins
There are multiple signal sequences and multiple stop transfer sequences that can form multiple transmembranes in the endoplasmic reticulum membrane.
Nuclear proteins are transported into the nucleus through nuclear pores by nuclear import factors
nuclear protein
Example
Enzymes, histones and transcription factors involved in DNA replication and transcription
Features
The peptide chain contains a specific nuclear localization signal (NLS), 4-8 amino acid residues, mainly basic amino acids, the position is not fixed, and it will not be removed after the positioning is completed.
Targeted delivery of nuclear proteins
process
Nuclear proteins synthesized in the cytoplasm form complexes with nuclear import factors and are directed to nuclear pores
RAN protease with GTPase activity hydrolyzes GTP to release energy, and nuclear proteins and nuclear import factor complexes enter the nucleus through the nuclear pore through an energy-consuming mechanism.
Nuclear import factors β and α are dissociated from the complex one after another, moved out of the nuclear pore and reused; nuclear protein localization is completed
Features
Requires nuclear input factor (nuclear protein) α/β (recognition binding NLS) heterodimer and low molecular weight G protein RAN
The synthesis process of peptide chain
Assembly of the translation initiation complex initiates peptide chain synthesis
Formation of the translation initiation complex in prokaryotes
① Separation of large and small subunits of ribosomes
30S small subunit, 50S large subunit
process
IF3 and IF1 bind to the small subunit, separate the large and small subunits, and prepare mRNA and fMet-tRNAfMet binds to the small subunit
Intact ribosomes dissociate their large and small subunits with the help of IF
The role of IF
Stabilizes the separation of large and small subunits. Without IF, large and small subunits can easily repolymerize.
②mRNA binds to ribosome small subunit
process
The P position binds to the start codon AUG
There are multiple AUGs on an mRNA chain, and the small ribosome subunit binds to the mRNA. The initial AUG must be identified in order to form a specific ORF; while Does not recognize the AUG inside the ORF, thus accurately translating the target protein
How is prokaryotic mRNA accurately positioned (binding with the P position) on the small subunit of the ribosome?
① Ribosome-binding site RBS - about 10 nucleotides upstream of AUG is usually -AGGAGG-, also known as Shine-Dalgaron sequence, S-D sequence
② The 16S-rRNA in the small subunit has a complementary sequence -UCCUCC-
The complementary sequence of 16S-RNA in the small subunit is complementary to the S-D sequence base pairing, so that the small subunit is determined to be located in the mRNA
③ fMet-tRNAfMet binds at the P position
process
fMet-tRNAfMet, together with GTP-bound IF2, recognizes and binds to corresponding The start codon AUG on the P position of the small subunit mRNA sequence
Features
At this time, the translation initiation A position is occupied by IF1 and does not bind to any aminoacyl-tRNA.
④ Formation of translation initiation complex
(1) Hydrolysis of GTP bound to IF2, and the energy released promotes the release of three types of IF (1, 2, 3)
(2) Formation of translation initiation complex
The small subunit that combines mRNA and fMet-tRNAfMet combines with the large subunit to form Translation initiation complex composed of intact ribosomes, mRNA, fMet-tRNAfMet compound.
Formation of the eukaryotic translation initiation complex
Comparison with prokaryotic translation initiation complex
More and more complex types of initiation factors are required
The 5’ cap structure and 3’ poly A tail of the mRNA are both correctly necessary to begin with
The initiating aminoacyl-tRNA binds to the small subunit before the mRNA, and Prokaryotes are different
process
① Formation of pre-43S initiation complex
Initiation factors eIF1A, eIF3 (with IF1 and IF3 have similar functions) combined In the small subunit, the large and small subunits are separated
eIF1A (similar to IF1) occupies the A position to prevent tRNA binding and prevent premature binding of the large and small subunits
eIF1 binds to the E position
GTP-eIF2 binds to Met-tRNAiMet (initiating aminoacyl-tRNA)
Subsequently eIF5 and eIF5B join to form the 43S pre-initiation complex
②mRNA binds to ribosome small subunit
The mRNA binds to the 43S pre-initiation complex, mediated by the eIF4F complex, to form the 48S initiation complex
eIF4F complex
eIF4E
结合 mRNA 的 5’ 帽
eIF4A
具有ATPase和RNA 解旋酶活性
eIF4G
结合eIF3、eIF4E和PABP(多聚腺苷酸结合蛋白)
③ Binding of ribosome large subunit
The 48S initiation complex scans from 5' to 3' of the mRNA and locates the initiation codon. The initiation factor dissociates, and then the large subunit joins, and the translation initiation complex is formed.
Requires eIF5 and eIF5B to participate
Prompts eIF2 to hydrolyze GTP, thereby indirectly promoting the dissociation of initiation factors
eIF5 prompts eIF2 to exert GTPase activity and hydrolyze the GTP bound to eIF2. The generated eIF2-GDP has a weakened affinity with the starting tRNA and dissociates, and other starting factors are also dissociated.
Some mRNA translations do not depend on the 5'-cap structure
During translation initiation, ribosomes can be directly recruited to the translation start site by the internal ribosome entry site (IRES) on the mRNA.
This process requires the assistance of multiple proteins (such as IRES trans-acting factors, eIF4GI, etc.)
A three-step reaction repeated on the ribosome to extend the peptide chain
definition
Refers to the process in which amino acids sequentially enter the ribosome and polymerize into polypeptide chains under the guidance of the mRNA template.
direction
5' end → 3' end of mRNA
Polypeptide chain N-terminal→C-terminal
three steps
Carry (registration)
definition
Refers to the process in which aminoacyl-tRNA enters and binds to the A site of the ribosome according to the codon instructions of the mRNA template.
Features
After the initiation factor is released, position A becomes vacant, corresponding to the second codon of the ORF (open reading frame).
Aminoacyl-tRNA first forms a complex with GTP-EF-Tu and then enters the A site
During carry, aminoacyl-tRNA first forms a complex with GTP-EF-Tu and then enters the A position; GTP is then hydrolyzed to GDP, and GDP-EF-Tu is released for recycling.
Ribosomes have a corrective effect on aminoacyl-tRNA carry
The correct one can quickly match the codon Enter the A position
Wrong ones cannot pair and dissociate.
One of the mechanisms of high fidelity in peptide chain synthesis
EF-Tu related introduction
https://baike.baidu.com/item/EF-Tu/15285411
into peptides
definition
The process in which the amino acids carried by tRNA at the A and P positions of the ribosome are condensed into peptides
Features
enzyme
peptidyltransferase
Belongs to a ribozyme
chemical nature
RNA
prokaryotes
23SRNA
eukaryotes
28SRNA
in the starting complex
The formylmethionine carried by the tRNA at the P position is the same as the newly carried one at the A position. Amino acids carried by aminoacyl tRNA condense into peptides
After peptide formation, the dipeptidyl tRNA occupies the A position, and the tRNA with methionine unloaded remains at the P position.
Transposition
definition
After the peptide formation reaction, the ribosome needs to move one codon distance to the 3'-end of the mRNA before it can read the next codon. This process is called translocation.
Features
Requires elongation factor EF-G (i.e. translocase)
Requires GTP hydrolysis for energy
The result of transposition
amino acid or peptide
P to A
The amino acid or peptide carried by the tRNA at the P position is handed over to the amino acid at the A position after peptide formation.
tRNA
A to P
After translocation, the peptidyl tRNA in the A position moves to the P position through translocation
P to E
The tRNA unloaded from the P position is translocated into the E position and then falls off the ribosome.
Seat A is vacated
The A position is vacated and positioned exactly at the next codon to accept the next Aminoacyl-tRNA
The difference between eukaryotes and prokaryotes
The peptide chain elongation mechanism of eukaryotes is basically the same as that of prokaryotes
The extension factors required for the two are different
Eukaryotes require eEF1α, eEF1βγ and eEF2
The above three elongation factors of eukaryotes correspond to EF-Tu, EF-Ts, and EF-G of prokaryotes respectively.
In eukaryotes, when a new aminoacyl-tRNA enters the A position, it will produce an allosteric effect, causing the empty tRNA to be expelled from the E position.
significance
Repeat carry-to-peptide-translocation, adding one amino acid at a time in each cycle, reading from 5' to 3', and the peptide chain extends from the N-terminus to the C-terminus.
energy consumption
For every peptide bond formed, at least 4 high-energy phosphate bonds are consumed
Without making any mistakes, for every peptide bond produced, 4 high-energy phosphate bonds are consumed.
During the peptide chain elongation stage, each time a peptide bond is formed, 2 molecules of GTP (one molecule each for carry and translocation) must be hydrolyzed to obtain energy.
When an amino acid is activated into aminoacyl-tRNA, 2 high-energy phosphate bonds are consumed
If there is an incorrect connection, energy will also be consumed for hydrolysis; this energy is used to maintain a high degree of fidelity in protein translation, with an error rate of less than 1 in 10,000
Stop codons and release factors lead to the termination of peptide chain synthesis
stop codon
The elongation of the peptide chain continues until the A position of the ribosome corresponds to the stop codon of the mRNA
Not recognized by any aminoacyl-tRNA
Only the release factor RF can recognize the stop codon and enter the A position
The recognition process consumes GTP
release factor RF
binding site
Only RF can recognize the stop codon and enter the A position
Mechanism of action
The binding of RF to the A site changes the conformation of the ribosome, Convert peptidyl transferase activity to esterase, hydrolyze The ester bond between the peptide chain and tRNA at the P position makes the peptide Strand release, mRNA, tRNA, ribosomes Separation of large/small subunits etc.
type
prokaryotes
There are 3 release factors
RF-1
Specific recognition of UAA, UAG
RF-2
Specific recognition of UAA and UGA
RF-3
Binds GTP and has GTPase activity
Mediates the interaction between RF-1, RF-2 and ribosomes
eukaryotes
There is only one release factor eRF
polyribosome
definition
In prokaryotes or eukaryotes, one mRNA template strand can be attached to 10 to 100 ribosomes. These ribosomes sequentially bind the start codon and read the code in the 5-→3-direction, and simultaneously synthesize the peptide chain. The polymer formed by this kind of mRNA and multiple ribosomes is called a polysome.
significance
Enable protein biosynthesis to proceed at high speed and efficiency
Interference and inhibition of protein synthesis
Many antibiotics act by inhibiting protein synthesis
Antibiotics that inhibit translation initiation
Ibremicin
Affects initiating aminoacyl-tRNA positioning and IF3 function
mitracycline
Causes the mislocation of mRNA in ribosomes and blocks the formation of the translation initiation complex
It has inhibitory effects on both eukaryotic and prokaryotic
latemycin
Binds to specific sites on prokaryotic 23S rRNA to inhibit the translocation of prokaryotic initiating aminoacyl tRNA (fMet-tRNAfMet)
Antibiotics that inhibit translation elongation
Antibiotics that interfere with carry
tetracycline
Specifically binds to the A position of the 30S subunit and inhibits aminoacyl tRNA carry
Powdermycin
Reduce the GTPase activity of EF-Tu and inhibit the binding of EF-Tu to aminoacyl tRNA
Xanthomycin
Prevents EF-Tu release from ribosomes
Antibiotics causing code reading errors
Aminoglycosides (e.g. streptomycin)
Streptomycin
低浓度
引起读码错误
高浓度
抑制蛋白质合成的起始
Binds to 30S subunit, affecting translation accuracy
Hygromycin B and neomycin
Binds to 16S rRNA and rpS12 (ribosomal protein S12), interfering with the decoding site of the 30S subunit, causing reading errors
Antibiotics that affect peptide formation
Chloramphenicol
Binds to the 50S subunit of the ribosome, preventing peptidyl transfer and inhibiting peptide bond formation
Lincomycin
Acts on the A and P positions to prevent tRNA from being in place
Macrolide antibiotics (eg: erythromycin)
Binds to the peptide chain egress channel of the 50S subunit to prevent egress and further formation of peptide bonds.
Puromycin (structure similar to tyrosyl-tRNA)
Displaces tyrosyl-tRNA into the A position
cycloheximide
Specifically inhibits the activity of eukaryotic ribosomal peptidyltransferase
Antibiotics that affect translocation
Fusidic acid, micrococcin, thiostrepton
Inhibits EF-G translocase activity
Spectinomycin
Binds to the small subunit (30S small subunit) to inhibit its allostery and inhibit the translocation reaction
Certain toxins inhibit eukaryotic protein synthesis
diphtheria toxin
Inhibitors of eukaryotic protein synthesis
chemical nature
Modifying enzyme
Mechanism of action
Make eEF-2 undergo ADP glycosylation covalent modification, generate eEF-2 adenosine diphosphate ribose derivatives, and inactivate eEF-2
eEF-2 is involved in the carry of the initiating aminoacyl-tRNA
Castor (bi with four sounds) hemp protein
chemical components
A chain (polypeptide chain)
Nature
a protease
Mechanism of action
Acts on the 28S rRNA of the large subunit of eukaryotes, catalyzes the depurination reaction of specific adenylate, degrades the 28S rRNA, and inactivates the large subunit.
B chain (polypeptide chain)
effect
The B chain plays an important role in promoting the toxicity of the A chain.
The galactose binding site on the B chain also plays a toxic role in the toxin active site
central theme