Histones are the chief protein components of chromatin. They act as spools around which DNA winds and they play a role in gene regulation.
Classes
Six major histone classes are known:
H1 (sometimes called the linker histone or H5.)
H2A
H2B
H3
H4
Archaeal histones
Two each of the class H2A, H2B, H3 and H4, so-called core histones, assemble to form one octameric nucleosome core particle by wrapping 146 base pairs of DNA around the protein spool in 1.65 left-handed super-helical turn. The linker histone H1 binds the nucleosome and the entry and exit sites of the DNA, thus locking the DNA into place and allowing the formation of higher order structure. The most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around nucleosomes with approximately 50 base pairs of DNA spaced between each nucleosome (also referred to as linker DNA). Higher order structures include the 30 nm fiber (forming an irregular zigzag) and 100 nm fiber, these being the structures found in normal cells. During meiosis, through the combination of nucleosome interactions with other proteins, the chromosome is assembled. The assembled histones and DNA is called chromatin.
Two each of the class H2A, H2B, H3 and H4, so-called core histones, assemble to form one octameric nucleosome core particle by wrapping 146 base pairs of DNA around the protein spool in 1.65 left-handed super-helical turn. The linker histone H1 binds the nucleosome and the entry and exit sites of the DNA, thus locking the DNA into place and allowing the formation of higher order structure. The most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around nucleosomes with approximately 50 base pairs of DNA spaced between each nucleosome (also referred to as linker DNA). Higher order structures include the 30 nm fiber (forming an irregular zigzag) and 100 nm fiber, these being the structures found in normal cells. During meiosis, through the combination of nucleosome interactions with other proteins, the chromosome is assembled. The assembled histones and DNA is called chromatin.
Structure
The nucleosome core is formed of two H2A-H2B dimers and a H3-H4 tetramer, forming two nearly symmetrical halves by tertiary structure (C2 symmetry; one macromolecule is the mirror image of the other). The H2A-H2B dimers and H3-H4 tetramer also show pseudodyad symmetry.
The 4 'core' histones (H2A, H2B, H3 and H4) are relatively similar in structure and are highly conserved through evolution, all featuring a 'helix turn helix turn helix' motif (which allows the easy dimerisation). They also share the feature of long 'tails' on one end of the amino acid structure - this being the location of post-transcriptional modification
In all, histones make five types of interactions with DNA:
Helix-dipoles from alpha-helices in H2B, H3, and H4 cause a net positive charge to accumulate at the point of interaction with negatively charged phosphate groups on DNA.
Hydrogen bonds between the DNA backbone and the amine group on the main chain of histone proteins.
Nonpolar interactions between the histone and deoxyribose sugars on DNA.
Salt links and hydrogen bonds between side chains of basic amino acids (especially lysine and arginine) and phosphate oxygens on DNA.
Non-specific minor groove insertions of the H3 and H2B N-terminal tails into two minor grooves each on the DNA molecule.
The highly basic nature of histones, aside from facilitating DNA-histone interactions, contributes to the water solubility of histones.
Histones are subject to posttranslational modification by enzymes primarily on their N-terminal tails, but also in their globular domains. Such modifications include methylation, citrullination, acetylation, phosphorylation, Sumoylation, ubiquitination, and ADP-ribosylation. This affects their function of gene regulation
In general, genes that are active have less bound histone, while inactive genes are highly associated with histones during interphase. It also appears that the structure of histones have been evolutionarily conserved, as any deleterious mutations would be severely maladaptive.
Functions
Packing proteins
Histones act as spools around which DNA winds. This enables the compaction necessary to fit the large genomes of eukaryotes inside cell nuclei: the compacted molecule is 50,000 times shorter than an unpacked molecule.
Histone modifications in chromatin regulation
Histones undergo posttranslational modifications which alter their interaction with DNA and nuclear proteins. The H3 and H4 histones have long tails protruding from the nucleosome which can be covalently modified at several places. Modifications of the tail include methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, and ADP ribosylation. The core of the histones (H2A and H3) can also be modified. Combinations of modifications are thought to constitute a code, the so-called "histone code". Histone modifications act in diverse biological processes such as gene regulation, DNA repair and chromosome condensation (mitosis)
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Showing posts with label protein. Show all posts
Showing posts with label protein. Show all posts
Wednesday, December 17, 2008
Protein Synthesis Animation
Protein biosynthesis (Synthesis) is the process in which cells build proteins. The term is sometimes used to refer only to protein translation but more often it refers to a multi-step process, beginning with amino acid synthesis and transcription which are then used for translation. Protein biosynthesis, although very similar, differs between prokaryotes and eukaryotes.
Amino acid synthesis
Amino acids are the monomers which are polymerized to produce proteins. Amino acid synthesis is the set of biochemical processes (metabolic pathways) which build the amino acids from carbon sources like glucose. Not all amino acids may be synthesised by every organism, for example adult humans have to obtain 8 of the 20 amino acids from their diet.
The amino acids are then loaded onto tRNA molecules for use in the process of translation.
Transcription is the process by which an mRNA template, carrying the sequence of the protein, is produced for the translation step from the genome. Transcription makes the template from one strand of the DNA double helix, called the template strand. Transcription takes place in 3 stages.
Transcription starts with the process of initiation. RNA polymerase, the enzyme which produces RNA from a DNA template, binds to a specific region on DNA that designates the starting point of transcription. This binding region is called the promoter. As the RNA polymerase binds on to the promoter, the DNA strands are beginning to unwind.
The second process is elongation. RNA polymerase travels along the template (noncoding) strand, synthesizing a ribonucleotide polymer. RNA polymerase does not use the coding strand as a template because a copy of any strand produces a base sequence that is complementary to the strand which is being copied. Therefore DNA from the noncoding strand is used as a template to copy the coding strand.
The third stage is termination. As the polymerase reaches the termination stage, modifications are required for the newly transcribed mRNA to be able to travel to the other parts of the cell, including cytoplasm and endoplasmic reticulum, for translation. A 5' cap is added to the mRNA to protect it from degradation. In eukaryotes, poly-A-polymerase adds a poly-A tail onto the 3’ end for stabilization, protection from cytoplasmic hydrolytic enzymes, and as a template for further processes. Also in eukaryotes (higher organisms) the vital process of splicing occurs at this stage by the spliceosome enzyme. It removes the introns (non-coding bits of genetic material) and glues together the exons (the segments that code for a specific protein).
The mRNA now exits the nuclear pore to be translated.
Translation
Protein translation involves the transfer of information from the mRNA into a peptide, composed of amino acids. This process is mediated by the ribosome, with the adaptation of the RNA sequence into amino acids mediated by transfer RNA. Numerous initation and elongation factors also play a role.
Translation requires a lot of energy, with the hydrolysis of approximately 4 NTP --> NDP per amino acid added. (This includes the aminoacylation of the tRNA. Thus, gene expression is highly regulated to ensure that only proteins that are required are translated.
Translation involves 3 processes: initiation, elongation, and termination.
Initiation in Prokaryotes
The initiation of protein translation involves the assembly of the ribosome and addition of the first amino acid, methionine.
The 30S ribosomal subunit attaches to the mRNA, mediated by IF-1 and IF-3 (initiation factors). The 30S ribosome brings with it the P and A site, but the A site is blocked by IF-1 to prevent binding of tRNA. It aligns to the Shine-Dalgarno sequence, which positions the first codon (AUG) in the P site.
Next, the specific aminoacyl-tRNA for N-formylmethionine (F-Met) is brought into the P site by IF-2. The anticodon of this tRNA will bind to the AUG codon on the mRNA. Note: this is the only tRNA brought into the P site; all successive aminoacyl-tRNAs will be brought to the A site for peptide elongation.
The 50S ribosomal subunit is then brought in to complete the ribosome, and with it, IF-1, IF-2, and IF-3 come off the complex. The A and P site are completed, and the 50S subunit also brings the E (exit) site.
Initiation in Eukaryotes
The initiation of protein translation in eukaryotes is similar to that of prokaryotes with some modifications.
A complex of proteins will connect the 5'cap and 3'PolyA tail, and this complex will recruit the ribosome subunits.
There is no Shine-Dalgarno sequence in eukaryotes. Instead, the ribosome scans along the mRNA for the first methionine codon. Similarly, there is no N-formylmethionine in eukaryotic cells.
Elongation
Elongation of protein biosynthesis is fairly similar between prokaryotes and eukaryotes. The following is a description of elongation in prokaryotes.
Elongation proceeds after initiation with the binding of an aminoacyl-tRNA to the A site, which is the next codon in the mRNA. The aminoacyl-tRNA is brought to the ribosome through a series of interactions with EF-Tu (an elongation factor). This step involves the hydrolysis of GTP: EF-Tu-GTP --> EF-Tu-GDP (The hydrolyzed GDP is switched for GTP through another series of reactions with EF-Ts.)
The next aminoacyl-tRNA binds to the codon, and the C-terminus of the F-Met undergoes nucleophilic attack by the N-terminus of the second amino acid. The F-Met is now connected to the second amino acid through a peptide bond.
The first tRNA (for F-Met) is now uncharged. The entire ribosome complex moves along the mRNA through the action of another elongation factor (EF-G) and the hydrolysis of GTP --> GDP.
The first tRNA is now in the E site and comes off from the ribosome, while the second tRNA, with the nascent peptide chain, is in the P site. Step 1-4 will repeat as successive amino acids are added.
Termination
Termination of protein biosynthesis occurs when the ribosome comes across a stop codon, for which there is no tRNA. At this point, protein biosynthesis halts and one of three release factors will bind to the stop codon. (Note: In eukaryotes, there is only one release factor that will bind to all three stop codons.) This induces a nucleophilic attack of the C-terminus of the nascent peptide by water - this hydrolysis releases the peptide from the ribosome. The ribosome, release factor, and uncharged tRNA then dissociates and translation is complete.
Events following Protein Translation
The events following biosynthesis include post-translational modification and protein folding. During and after synthesis, polypeptide chains often fold to assume, so called, native secondary and tertiary structures. This is known as protein folding.
Many proteins undergo post-translational modification. This may include the formation of disulfide bridges or attachment of any of a number of biochemical functional groups, such as acetate, phosphate, various lipids and carbohydrates. Enzymes may also remove one or more amino acids from the leading (amino) end of the polypeptide chain, leaving a protein consisting of two polypeptide chains connected by disulfide bonds.
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Amino acid synthesis
Amino acids are the monomers which are polymerized to produce proteins. Amino acid synthesis is the set of biochemical processes (metabolic pathways) which build the amino acids from carbon sources like glucose. Not all amino acids may be synthesised by every organism, for example adult humans have to obtain 8 of the 20 amino acids from their diet.
The amino acids are then loaded onto tRNA molecules for use in the process of translation.
Transcription is the process by which an mRNA template, carrying the sequence of the protein, is produced for the translation step from the genome. Transcription makes the template from one strand of the DNA double helix, called the template strand. Transcription takes place in 3 stages.
Transcription starts with the process of initiation. RNA polymerase, the enzyme which produces RNA from a DNA template, binds to a specific region on DNA that designates the starting point of transcription. This binding region is called the promoter. As the RNA polymerase binds on to the promoter, the DNA strands are beginning to unwind.
The second process is elongation. RNA polymerase travels along the template (noncoding) strand, synthesizing a ribonucleotide polymer. RNA polymerase does not use the coding strand as a template because a copy of any strand produces a base sequence that is complementary to the strand which is being copied. Therefore DNA from the noncoding strand is used as a template to copy the coding strand.
The third stage is termination. As the polymerase reaches the termination stage, modifications are required for the newly transcribed mRNA to be able to travel to the other parts of the cell, including cytoplasm and endoplasmic reticulum, for translation. A 5' cap is added to the mRNA to protect it from degradation. In eukaryotes, poly-A-polymerase adds a poly-A tail onto the 3’ end for stabilization, protection from cytoplasmic hydrolytic enzymes, and as a template for further processes. Also in eukaryotes (higher organisms) the vital process of splicing occurs at this stage by the spliceosome enzyme. It removes the introns (non-coding bits of genetic material) and glues together the exons (the segments that code for a specific protein).
The mRNA now exits the nuclear pore to be translated.
Translation
Protein translation involves the transfer of information from the mRNA into a peptide, composed of amino acids. This process is mediated by the ribosome, with the adaptation of the RNA sequence into amino acids mediated by transfer RNA. Numerous initation and elongation factors also play a role.
Translation requires a lot of energy, with the hydrolysis of approximately 4 NTP --> NDP per amino acid added. (This includes the aminoacylation of the tRNA. Thus, gene expression is highly regulated to ensure that only proteins that are required are translated.
Translation involves 3 processes: initiation, elongation, and termination.
Initiation in Prokaryotes
The initiation of protein translation involves the assembly of the ribosome and addition of the first amino acid, methionine.
The 30S ribosomal subunit attaches to the mRNA, mediated by IF-1 and IF-3 (initiation factors). The 30S ribosome brings with it the P and A site, but the A site is blocked by IF-1 to prevent binding of tRNA. It aligns to the Shine-Dalgarno sequence, which positions the first codon (AUG) in the P site.
Next, the specific aminoacyl-tRNA for N-formylmethionine (F-Met) is brought into the P site by IF-2. The anticodon of this tRNA will bind to the AUG codon on the mRNA. Note: this is the only tRNA brought into the P site; all successive aminoacyl-tRNAs will be brought to the A site for peptide elongation.
The 50S ribosomal subunit is then brought in to complete the ribosome, and with it, IF-1, IF-2, and IF-3 come off the complex. The A and P site are completed, and the 50S subunit also brings the E (exit) site.
Initiation in Eukaryotes
The initiation of protein translation in eukaryotes is similar to that of prokaryotes with some modifications.
A complex of proteins will connect the 5'cap and 3'PolyA tail, and this complex will recruit the ribosome subunits.
There is no Shine-Dalgarno sequence in eukaryotes. Instead, the ribosome scans along the mRNA for the first methionine codon. Similarly, there is no N-formylmethionine in eukaryotic cells.
Elongation
Elongation of protein biosynthesis is fairly similar between prokaryotes and eukaryotes. The following is a description of elongation in prokaryotes.
Elongation proceeds after initiation with the binding of an aminoacyl-tRNA to the A site, which is the next codon in the mRNA. The aminoacyl-tRNA is brought to the ribosome through a series of interactions with EF-Tu (an elongation factor). This step involves the hydrolysis of GTP: EF-Tu-GTP --> EF-Tu-GDP (The hydrolyzed GDP is switched for GTP through another series of reactions with EF-Ts.)
The next aminoacyl-tRNA binds to the codon, and the C-terminus of the F-Met undergoes nucleophilic attack by the N-terminus of the second amino acid. The F-Met is now connected to the second amino acid through a peptide bond.
The first tRNA (for F-Met) is now uncharged. The entire ribosome complex moves along the mRNA through the action of another elongation factor (EF-G) and the hydrolysis of GTP --> GDP.
The first tRNA is now in the E site and comes off from the ribosome, while the second tRNA, with the nascent peptide chain, is in the P site. Step 1-4 will repeat as successive amino acids are added.
Termination
Termination of protein biosynthesis occurs when the ribosome comes across a stop codon, for which there is no tRNA. At this point, protein biosynthesis halts and one of three release factors will bind to the stop codon. (Note: In eukaryotes, there is only one release factor that will bind to all three stop codons.) This induces a nucleophilic attack of the C-terminus of the nascent peptide by water - this hydrolysis releases the peptide from the ribosome. The ribosome, release factor, and uncharged tRNA then dissociates and translation is complete.
Events following Protein Translation
The events following biosynthesis include post-translational modification and protein folding. During and after synthesis, polypeptide chains often fold to assume, so called, native secondary and tertiary structures. This is known as protein folding.
Many proteins undergo post-translational modification. This may include the formation of disulfide bridges or attachment of any of a number of biochemical functional groups, such as acetate, phosphate, various lipids and carbohydrates. Enzymes may also remove one or more amino acids from the leading (amino) end of the polypeptide chain, leaving a protein consisting of two polypeptide chains connected by disulfide bonds.
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