Error Catastrophe Theory of Senescence

The catastrophe theory

Mistakes at the translation and transcription level

• mRNA mistakes
• Missing of repair systems
• Cytokinins in the t-RNA adjacent to the anti-codon loop
• Nonsense protein formation (faulty translation)

Post-transcriptional protein folding

Bad DNA multiplication

DNA repair potential decreases

DNA in dry tissue (seeds) more susceptible to damage

mRNA life time changes

Changes at the DNA and RNA levels

oIncreases of RNAses

oDecrease of DNA-RNA polymerase

The error catastrophe theory of aging was proposed by Leslie Orgel in 1963 and states that -
in an individual, the aging (senescence) occurs as a result of accumulation of errors committed by the molecular genetic apparatus during protein synthesis. It claims that when the amount of error product exceeds a certain threshold value; malfunction, senescence and death results. Although these mistakes can occur in any protein made by the cell, when these mistakes occur in the enzymes and other proteins responsible for synthesizing DNA and RNA, or in the protein synthesizing machinery itself, this could lead to an increasing cascade of errors, referred to as an "Error catastrophe". 
The error could be at one or more sites along the protein production line, either at a transcriptional or translational level, resulting in the  "nonsense proteins" acccumulate. These are non-functional enzymes containing mistakes in the amino acid sequence. This escalating process could turn what is initially a very low error rate in young individuals into a significant rate of accumulation of errors in older individuals, and one would predict that the rate of error accumulation might continue to increase exponentially throughout the life of the individual. 

The genetic blueprint for each biological species occurs in the Deoxyribo nucleic acid (DNA) in the nucleus of each cell. When the cell divides, an enzyme known as DNA polymerase makes a new copy of the DNA by combining the appropriate building blocks known as deoxyribonucleotides in the correct sequence in a process known as DNA replication. The genetic sequences in the DNA are then transcribed by another kind of copying enzyme, known as RNA polymerase, into a ribonucleic acid (RNA) molecule called messenger RNA. Specific messenger RNAs contain the instructions for synthesizing individual proteins of the correct amino acid sequence, corresponding to the original blueprint in the DNA. This final protein synthesizing process is called translation.

During DNA replication, many DNA polymerases possess the ability to recognize mismatched bases, then back up and correct their own mistakes. In addition, very robust DNA repair systems are present to correct mistakes made during synthesis, or afterward by chemicals able to damage DNA. Thus, the error frequency in DNA replication is usually extremely low, perhaps less than one in a million bases. Studies to demonstrate age-related changes in the copying fidelity of polymerases or DNA repair capacity have not provided convincing support for the error catastrophe theory.

In general, RNA polymerases also combine ribonucleotide building blocks to make RNA with high sequence fidelity, but lower than that exhibited by DNA polymerases. However, the overall instability and turnover of messenger RNA tends to attenuate the impact of any mistakes made during messenger RNA synthesis. Protein synthesis is also generally carried out with high fidelity, and there is little evidence to suggest that this changes with age.

Gershon 1985, however challenged this theory and claimed that-

the process most prone to ageing is post-transcriptional protein folding and the most probable candidate being proteases. Erroneously folded non-functional proteases therefore lead to erratic cell metabolism and senescence.

Proteins do become randomly altered after they are synthesized; a variety of such processes is collectively referred to as post-translational modification because it occurs after synthesis of the protein and use of the messenger RNA as a template has been completed. Although distinct from the damage hypothesized in the original error catastrophe theory, post-translational modification of proteins could functionally resemble an error catastrophe. These modifications include oxidation of amino acid sidechains, racemization of certain amino acids, and condensation of the lysine side chain amino group with aldehyde groups such as those found in glucose. This latter process is known as non-enzymatic glycation. Biochemical mechanisms exist to repair the damage caused during some of these processes, suggesting they could have biological significance with implications for aging. However, there is a dearth of evidence unequivocally indicating that damage-inducing processes, damage accumulation, or repair processes are casually related to aging in mammalian species.

In summary, although altered proteins do accumulate with increasing age in mammals, the error catastrophe theory itself is no longer regarded as a viable theory. Nevertheless, there remains a healthy research interest in determining what roles damaged proteins, and the processes that either destroy the damaged protein or repair the damage, might play as casual factors in aging.

Types of Senescence

Leopold in 1975 has proposed four kinds of senescence patterns:

Whole plant (Overall) senescence:

 The complete plant dies soon after ripening of the seeds.This is found in monocarpic plants that generate fruit and flower only once in their life cycle. The plants might be annual (example: rice, gram, mustard, wheat, and so on), biennials (example: cabbage, henbane) or perennials (example: certain bamboos and so on).

 Figure: Types of senescence

Shoot (TOP) senescence:

The above-ground plant organs die off seasonally, to be renewed by growth from sub-terranian organs. This kind of senescence is found in some perennial plants that possess underground perennating structures such as rhizomes, corm, bulbs, and so on. The ground portion of the shoot dies each year after flowering and fruiting, however the underground portion (stem and root) survives and puts out new shoots again next year. Example: banana, ginger, gladiolus, and so on.

Sequential (Progressive) Senescence:

This is found mostly in perennial plants in which the tips of main shoot and branches remaining a meristematic state and carry on to generate new buds and leaves. The older leaves and lateral organs such as branches exhibit senescence and die and new ones gradually substitutes for them. Sequential senescence is obvious in evergreen plants. Example: Eucalyptus, Pinus and so on.

Simultaneous or Synchronous (Deciduous) senescence:

This is found in temperate deciduous trees like elm and maple. Such plants show seasonal (summer or winter) foliage senescence depending on the local stress. Pome and drupe deciduous fruit tress usually manifest winter shedding, while xerophytic species such as Zygophyllum shed foliage during the hot dry summer. Such a senescence of leaves or plant organs is termed as synchronous.

Senescence Curves

Several essentially different death curves can be observed for different plant population.
1. In the case of seasonal, annual, and monocarpic species, senescence can be dramatic. Until a certain stage, plants develop, elongate and produce grain/fruit and menifest a very low incidence of mortality. However, after the sensing of certain death signal, all individual cells die off with military parade precision. Curve E is typical of such behavior and is designated as a square wave.

Curve C is typical of human and domestic animal mortility. The more progressive the society the smaller the peak indicating infant mortality. After a period of relative stability, maximal mortality is observed in the latter period of life span.

Under certain circumstances of regulated diet and hygiene, the sygmoidal curve C, may be deflected to the square wave trend i.e. curve D, which has a definite advantage.

Curve A,B are believed to be typical to the perennial and polycarpic trees and shrubs. Also called as "an ecological mortility curve" typical of wild animals where very few individuals live to die of natural causes and not prey to younger or stronger animals, disease or natural disasters.

Protein Gelation

Gels consist of 3D networks (with junctions that can be polimer or polisacharides) of a biopolymer in which water is trapped and retained (Gelatine, pudin, boiled egg). These biopolimers are polysaccharides or proteins, or combinations of both. The junctions are neded in order to be able to build the network.

The properties of the gel are largely dominated by two types of interaction forces: protein protein interactions and water-protein interactions. In fact these two proteins are to some extend opposing each other a bit, so they should be in good balance in order to ensure a good gel network. A good gel network consists of a gel wich over the time retains its water. So the water does not leak out of the gel network, this process is known as syneresis. Typically this process is not desirable.

As mentioned, protein-protein and water-protein interactions should be balanced. It p-p interactions dominate, then proteins will form clusters, which grow bigger and finally will become insoluble in the aqueous solutions. The result is an agglomerations and coagulation of proteins, resulting in bigger protein particles which precipitate from the solution. Sometimes these coagulated proteins may still contain some water, but in general considerably lower amounts compared to those present in the original protein-water mixture. A typical example would be a casein curd which is obtained during cheese making. The curd obtained in this case though can still be considered as a gel, since sufficient protein-water water interactions are still present too. If protein water interactions are dominations then the proteins will not show a tendency to interact with each other. As a result the 3D network needed to form the 3D structure of gel will not be formed, or only to a limited extend. Possible viscosity of the protein solution can be increased because some water can be retained  and temporary a 3D network between the protein can be formed, which is however not stable and will be disturbed by the Brownian motion of all molecules present in the aqueous protein. 

These aspects are illustrated in the figures:

1: Represents  individual protein particles which are sometimes interacting with each other, but mainly interact with water, thus a 3D network is not created.

2And 3: The protein interactions increase and as it can be observed protein strings are being created which are interactions at some points thus creating juctions, it is a 3D structure so the water is entrapped into the structure.

4 the proteins interact so strongly that in fact the water is being expelled out of the protein-water system, giving rise to protein clumps which become unsoluble in the aqueous system and thus precipitate. 

Protein-protein Interation

The protein-protein interaction and water protein interaction play a major role in determining gel strength and quality. It is obvious that by changing particular parameters (both intrinsic and extrinsic) the gel properties can be changed). Therefore it could be discussed first how protein interactions originate. A part from peptide bonds linking up aminoacids, only one type of covalent bond may impact the interaction between proteins: these are the disulphide bonds between two residues (SH group). As aaminoacids and their side groups can be charged (due to protonation + charge, due to proton loss: -charge), obviously the carge intermediation are also potentially important; moreover these can be attractive or repulsive.  H-bridge formation between  a H donating (eg. OH group) and a H- acceptor (eg. C=O group) support protein protein interaction too. Temporary dipole interactions between phenyl group from an aromatic amino acid such as tryptophan, tyrosine or phenilaanine are also relevant, but already considerably weaker. So are the lipophilic interactions between the side changes of a-polar amino acids such as leucine, alanine, iso leucine, etc.

Having these interactions in mind it is clear that for instance, by changins the PH of a protein solution, protein-protein interactions may change considerably and thus conduce to gel formation. A typical example can be found in the fresh cheese (cottage cheese) production of yogurt. In fact a combination of other charge interactions and an increased lipophilic interaction between the casein proteins are at the origin of this gelation.

By denaturing proteins, new disulphide bonds can be produced between proteins, ot disulphide bonds I proteins can be broken, thus facilitating the interaction with other proteins (because the protein chain has increased its flexibility, it can move freely in the 3D space). Tus gels can be induces. A typical example is boiled egg, resulting from gelation of ovoalbumin.

As the concentration of ions (salts) impacts protein protein interactions (the higher the salt  concentration the higher the protein-protein interaction) the concentration of salt can have an impact on gel formation.

Upon protein degradation (during cheese fermentation) in which part of the proteins ae hydrolised, shorter peptide chains are produced, thus lowering protein protein interactions. These results in gel losing its strength: the interior of the cheese becomes liquid.

Another example of Gel is gelatin: it is a special case because it is produced by parcial hydrolisis of collagen, increasing its solubility in water and therefore decreasing protein-protein interaction in binding tissue.

Protein-protein interactions can also be influenced by adding crosslinking agents, thus influencing gel formatin potential. 

Protein-Water Interaction

Solubility of proteins depends on the Ph. Caseins precipitates at ph of 4, caseins then are unsoluble. Why? Because At 4.5 the caseins reach the isoelectric point (ph at which the proteins have a neutral charge zero). The results is that phosphate groups are neutralized, and calcium bridges fall out of  each other, and the caseins  micelle fall out of each other, and the prteins will start to act differently until they precipitate.

It is possible to enhance the protein solubility by decreasing the ph. Why? Because we give them strong charge. When we protonate, by giving acid, we get positive charge. For casein it is not possible because when the micelles are disintegrated, then it is irreversible.

Water binding capacity: amount of water that can be bound in an amount of protein. Very important for meat products (weight is money). If you cook ham (pink or purple in color), during boiling we lose water binding capacity of the product because of protein denaturation. The apolar group is exposed so the water goes away. If I boil a pig leg the water will be evaporated, so we need to reduce this water loses. For this we need to increase the water binding capacities. It depends on the ph, at high ph we will have more water binding capacity (more water, but less quality)

Interfacial Properties of Protein: Emulsion and Foam

Emulsion: Mix of water and oil. Water and oil normally cannot be mixed. 2 kinds

a. Mixtures Were water is the continuous phase: oil in water emulsion (eg. simple sauce, mayonnaise )

b. Mixtures were oil is the continuous phase: water in oil emulsion (eg. margarine)

Why is it not stable? In milk for example there is cream at the top, the fat separates from the milk. What happens here? Small droplets on surface. In milk there are small casein micelles. In raw milk what happens is that the fat droplets are bigger and because there is a density difference between fat and water the droplets go upwards. The bigger the droplets the higher the density difference and the faster the speed at which the droplets go up.  The higher the density difference, the faster the droplet goes up. When we have creaming or a layer of oil on the top it means that it is unstable.

The important is what happens in the interphase between the water and the oil. The interphase must be stable. To make the interphase between the water and oil stable, we need to the polar and apolar part of the molecule together (anphiphilic part). The apolar par will be in the fat phase and polar par in the water phase. The oil droplet will be covered by water, the polar head will be attracted water, and it means that the water won’t feel the oil. Same with the oil, it will be only attracted by oil phase. In this way the interphase will be stabilized. To let this stable interphase happen we need an emulsifier. So for this we can use either a random coil protein (casein, don’t have tertiary structure) or globular.

When we have casein (random coil), some parts will be in the polar phase, others in the apolar phase, and other right on the interphase. This happens because the R group (leucine, phenil alanine are apolar), (cerine, aspartic acid, glutamic acid, this group is polar group). When we see at the primary structure we will se that there are parts were there is polar concentration, other apolar concentration , and in other a mix of polar and apolar. This is because the protein doesnt have a tertiary structure, it is a random coil, it is extremely flexible. In the primary structure there are this local zones of apolar, polar amino acids, then the caseins are good emulsifiers.

Globular protein is normally present in an aqueous environment and is not normally good emulsifier. So the surphase of the protein is in majority oil, because it is soluble in water.  If we bring this protein in an interphase between water and oil,  we will have a problem because they won’t like to be in the oil (if whoe surface is polar). The protein be defolded, it can undergo denaturation. When It is denatured, then it can enter in the interphase an d act as emulcifier. So normally globular proteins (with 3 rd structure) must to undergo denaturation (or partial denaturation). Before they become good emulsifiers. It can be done when we have the interphase and we mix water and oil, by adding mechanical energy, the protein can go out of each other , the dimer will be lost. The apolar and poalr zone will be separated and the emulsifier will be stabilized. Also in the globular protein there can be some more apolar zones and some more polar zones. It can act as an emulsifier depending on the distribution of the apolar zones, so sometimes we need denaturation and sometimes not.

Foams: Mixture of water and air. Composed of air bubles and they are surrounded by water. There is an interphase between air and water, the air is the apolar matrix and water is the polar matrix. It is chemicallya problem in protein solutions because they are foeaming when they have surface active properties (casein solutions, ovalbumine).