What is the Relationship Between Dna Codons and Proteins

Organization and Function of Mitochondria

Mitochondria are surrounded past a double-membrane system, consisting of inner and outer mitochondrial membranes separated past an intermembrane space (Figure 10.ane). The inner membrane forms numerous folds (cristae), which extend into the interior (or matrix) of the organelle. Each of these components plays distinct functional roles, with the matrix and inner membrane representing the major working compartments of mitochondria.

The matrix contains the mitochondrial genetic system as well as the enzymes responsible for the central reactions of oxidative metabolism (Figure 10.2). As discussed in Chapter 2, the oxidative breakdown of glucose and fatty acids is the master source of metabolic energy in animal cells. The initial stages of glucose metabolism (glycolysis) occur in the cytosol, where glucose is converted to pyruvate (see Figure 2.32). Pyruvate is then transported into mitochondria, where its complete oxidation to CO₂
yields the bulk of usable energy (ATP) obtained from glucose metabolism. This involves the initial oxidation of pyruvate to acetyl CoA, which is and so cleaved down to CO₂
via the citric acid cycle (see Figures 2.33 and 2.34). The oxidation of fatty acids also yields acetyl CoA (see Figure two.36), which is similarly metabolized by the citric acid bicycle in mitochondria. The enzymes of the citric acrid bike (located in the matrix of mitochondria) thus are central players in the oxidative breakdown of both carbohydrates and fatty acids.

The oxidation of acetyl CoA to CO₂
is coupled to the reduction of NAD⁺
and FAD to NADH and FADH₂, respectively. Most of the energy derived from oxidative metabolism is then produced by the procedure of oxidative phosphorylation (discussed in particular in the next section), which takes place in the inner mitochondrial membrane. The high-energy electrons from NADH and FADH₂
are transferred through a serial of carriers in the membrane to molecular oxygen. The free energy derived from these electron transfer reactions is converted to potential energy stored in a proton gradient across the membrane, which is then used to bulldoze ATP synthesis. The inner mitochondrial membrane thus represents the chief site of ATP generation, and this disquisitional role is reflected in its construction. First, its surface area is substantially increased by its folding into cristae. In addition, the inner mitochondrial membrane contains an unusually loftier percentage (greater than lxx%) of proteins, which are involved in oxidative phosphorylation as well as in the send of metabolites (e.g., pyruvate and fat acids) between the cytosol and mitochondria. Otherwise, the inner membrane is impermeable to most ions and modest molecules—a holding critical to maintaining the proton gradient that drives oxidative phosphorylation.

In contrast to the inner membrane, the outer mitochondrial membrane is freely permeable to small molecules. This is because it contains proteins called
porins, which class channels that allow the free diffusion of molecules smaller than most 6000 daltons. The composition of the intermembrane space is therefore similar to the cytosol with respect to ions and small-scale molecules. Consequently, the inner mitochondrial membrane is the functional barrier to the passage of small molecules betwixt the cytosol and the matrix and maintains the proton gradient that drives oxidative phosphorylation.

The Genetic Organisation of Mitochondria

Mitochondria contain their own genetic arrangement, which is divide and singled-out from the nuclear genome of the cell. Equally reviewed in Chapter i, mitochondria are thought to accept evolved from bacteria that adult a symbiotic relationship in which they lived inside larger cells (endosymbiosis). This hypothesis has recently been substantiated by the results of Deoxyribonucleic acid sequence analysis, which revealed striking similarities between the genomes of mitochondria and of the bacterium
Rickettsia prowazekii.
Rickettsia
are intracellular parasites which, like mitochondria, are only able to reproduce within eukaryotic cells. Consistent with their similar symbiotic lifestyles, the genomic DNA sequences of
Rickettsia
and mitochondria suggest that they share a common ancestor, from which the genetic system of present-day mitochondria evolved.

Mitochondrial genomes are usually circular DNA molecules, like those of bacteria, which are present in multiple copies per organelle. They vary considerably in size betwixt dissimilar species. The genomes of human and nigh other fauna mitochondria are only nearly 16 kb, only essentially larger mitochondrial genomes are plant in yeasts (approximately 80 kb) and plants (more than 200 kb). However, these larger mitochondrial genomes are composed predominantly of noncoding sequences and practice not appear to contain significantly more genetic information. For example, the largest sequenced mitochondrial genome is that of the institute
Arabidopsis thaliana. Although
Arabidopsis
mitochondrial Deoxyribonucleic acid is approximately 367 kb, it encodes simply 32 proteins: only more than twice the number encoded by human mitochondrial DNA. The largest number of mitochondrial genes has been found in mitochondrial DNA of the protozoan
Reclinomonas americana, which is 69 kb and contains 97 genes. The mitochondrial genome of
Reclinomonas
appears to more closely resemble the bacterial genome from which mitochondria evolved than almost present-day mitochondrial genomes, which encode but a small number of proteins that are essential components of the oxidative phosphorylation system. In addition, mitochondrial genomes encode all of the ribosomal RNAs and nigh of the transfer RNAs needed for translation of these protein-coding sequences within mitochondria. Other mitochondrial proteins are encoded past nuclear genes, which are thought to accept been transferred to the nucleus from the ancestral mitochondrial genome.

The human mitochondrial genome encodes 13 proteins involved in electron ship and oxidative phosphorylation (Figure ten.3). In addition, human mitochondrial Dna encodes 16S and 12S rRNAs and 22 tRNAs, which are required for translation of the proteins encoded by the organelle genome. The two rRNAs are the only RNA components of animal and yeast mitochondrial ribosomes, in contrast to the three rRNAs of bacterial ribosomes (23S, 16S, and 5S). Plant mitochondrial DNAs, however, also encode a 3rd rRNA of 5S. The mitochondria of plants and protozoans also differ in importing and utilizing tRNAs encoded by the nuclear equally well every bit the mitochondrial genome, whereas in animal mitochondria, all the tRNAs are encoded by the organelle.

The modest number of tRNAs encoded by the mitochondrial genome highlights an important feature of the mitochondrial genetic organization—the use of a slightly different genetic code, which is distinct from the “universal” genetic lawmaking used by both prokaryotic and eukaryotic cells (Table 10.i). As discussed in Chapter iii, there are 64 possible triplet codons, of which 61 encode the 20 unlike amino acids incorporated into proteins (see Table 3.1). Many tRNAs in both prokaryotic and eukaryotic cells are able to recognize more a unmarried codon in mRNA because of “wobble,” which allows some mispairing between the tRNA anticodon and the third position of certain complementary codons (run across Effigy 7.three). However, at least 30 different tRNAs are required to translate the universal code according to the wobble rules. Withal human mitochondrial Dna encodes only 22 tRNA species, and these are the just tRNAs used for translation of mitochondrial mRNAs. This is achieved past an extreme form of wobble in which U in the anticodon of the tRNA tin pair with any of the 4 bases in the third codon position of mRNA, assuasive four codons to exist recognized by a single tRNA. In add-on, some codons specify different amino acids in mitochondria than in the universal code.

Like the DNA of nuclear genomes, mitochondrial DNA can be contradistinct by mutations, which are oft deleterious to the organelle. Since virtually all the mitochondria of fertilized eggs are contributed by the oocyte rather than past the sperm, germ-line mutations in mitochondrial DNA are transmitted to the next generation by the female parent. Such mutations take been associated with a number of diseases. For example, Leber’s hereditary optic neuropathy, a disease that leads to blindness, can be acquired past mutations in mitochondrial genes that encode components of the electron ship concatenation. In improver, the progressive accumulation of mutations in mitochondrial DNA during the lifetime of individuals has been suggested to contribute to the process of crumbling.

Protein Import and Mitochondrial Assembly

In contrast to the RNA components of the mitochondrial translation apparatus (rRNAs and tRNAs), most mitochondrial genomes practice not encode the proteins required for Deoxyribonucleic acid replication, transcription, or translation. Instead, the genes that encode proteins required for the replication and expression of mitochondrial DNA are contained in the nucleus. In addition, the nucleus contains the genes that encode most of the mitochondrial proteins required for oxidative phosphorylation and all of the enzymes involved in mitochondrial metabolism (due east.g., enzymes of the citric acid cycle). The proteins encoded by these genes (more than than 95% of mitochondrial proteins) are synthesized on free cytosolic ribosomes and imported into mitochondria as completed polypeptide chains. Considering of the double-membrane structure of mitochondria, the import of proteins is considerably more complicated than the transfer of a polypeptide beyond a single phospholipid bilayer. Proteins targeted to the matrix have to cantankerous both the inner and outer mitochondrial membranes, while other proteins demand to be sorted to singled-out compartments inside the organelle (due east.k., the intermembrane space).

The import of proteins to the matrix is the best-understood aspect of mitochondrial poly peptide sorting (Effigy 10.iv). Most proteins are targeted to mitochondria by amino-last sequences of 20 to 35 amino acids (chosen
presequences) that are removed by proteolytic cleavage post-obit their import into the organelle. The presequences of mitochondrial proteins, first characterized by Gottfried Schatz, contain multiple positively charged amino acid residues, normally in an amphipathic α helix. The beginning step in protein import is the binding of these presequences to receptors on the surface of mitochondria. The polypeptide bondage are then inserted into a protein complex that directs translocation across the outer membrane (the translocase of the outer membrane or Tom complex). The proteins are then transferred to a second protein circuitous in the inner membrane (the translocase of the inner membrane or Tim circuitous). Continuing protein translocation requires the electrochemical potential established across the inner mitochondrial membrane during electron ship. Equally discussed in the adjacent section of this chapter, the transfer of loftier-energy electrons from NADH and FADH_ii
to molecular oxygen is coupled to the transfer of protons from the mitochondrial matrix to the intermembrane space. Since protons are charged particles, this transfer establishes an electrical potential across the inner membrane, with the matrix being negative. During poly peptide import, this electrical potential drives translocation of the positively charged presequence.

To be translocated across the mitochondrial membrane, proteins must be at least partially unfolded. Consequently, protein import into mitochondria requires molecular chaperones in add-on to the membrane proteins involved in translocation (run across Figure 10.4). On the cytosolic side, members of the Hsp70 family of chaperones maintain proteins in a partially unfolded country then that they can be inserted into the mitochondrial membrane. Equally they cross the inner membrane, the unfolded polypeptide chains bind to some other member of the Hsp70 family, which is associated with the Tim complex and acts as a motor that drives poly peptide import. The polypeptide is so transferred to a chaperone of the Hsp60 family unit (a chaperonin), within which protein folding takes place. Since these interactions of polypeptide chains with molecular chaperones depend on ATP, protein import requires ATP both exterior and within the mitochondria, in addition to the electric potential across the inner membrane.

As noted to a higher place, some mitochondrial proteins are targeted to the outer membrane, inner membrane, or intermembrane space rather than to the matrix, so additional mechanisms are needed to direct these proteins to the correct submitochondrial compartment. These proteins are targeted to their destinations by a second sorting indicate post-obit the positively charged presequence that directs mitochondrial import. The targeting of proteins to the mitochondrial membranes appears to be mediated past hydrophobic finish-transfer sequences that halt translocation of the polypeptide chains through the Tim or Tom complexes, leading to their insertion into the inner or outer mitochondrial membranes, respectively (Figure 10.five). Proteins may be targeted to the intermembrane space by several unlike mechanisms (Figure 10.vi). Some proteins are transferred across the outer membrane through the Tom complex just are then released inside the intermembrane space instead of being transferred to the Tim complex. Other proteins are transferred to the Tim circuitous but are then released into the intermembrane space as a result of cleavage of hydrophobic stop-transfer sequences. Still other proteins may be completely imported into the mitochondrial matrix so exported back across the inner membrane to the intermembrane space.

Not just the proteins, but as well the phospholipids of mitochondrial membranes are imported from the cytosol. In animal cells, phosphatidylcholine and phosphatidylethanolamine are synthesized in the ER and carried to mitochondria by phospholipid transfer proteins, which extract single phospholipid molecules from the membrane of the ER. The lipid can then be transported through the aqueous environment of the cytosol, buried in a hydrophobic binding site of the poly peptide, and released when the circuitous reaches a new membrane, such as that of mitochondria. The mitochondria so synthesize phosphatidylserine from phosphatidylethanolamine, in add-on to catalyzing the synthesis of the unusual phospholipid cardiolipin, which contains four fat acid chains (Effigy ten.7).