biochemistry of alzheimer's disease biochemistry of alzheimer's disease the biochemistry of alzheimer's disease, the most common cause of dementia, is not yet very well understood. alzheimer's disease (ad) has been identified as a proteopathy: a protein misfolding disease due to the accumulation of abnormally folded amyloid beta (aβ) protein in the brain. amyloid beta is a short peptide that is an abnormal proteolytic byproduct of the transmembrane protein amyloid-beta precursor protein (app), whose function is unclear but thought to be involved in neuronal development. the presenilins are components of proteolytic complex involved in app processing and degradation. amyloid beta monomers are soluble and contain short regions of beta sheet and polyproline ii helix secondary structures in solution, though they are largely alpha helical in membranes; however, at sufficiently high concentration, they undergo a dramatic conformational change to form a beta sheet-rich tertiary structure that aggregates to form amyloid fibrils. these fibrils and oligomeric forms of aβ deposit outside neurons in formations known as senile plaques. there are different types of plaques, including the diffuse, compact, cored or neuritic plaque types, as well as aβ deposits in the walls of small blood vessel walls in the brain called cerebral amyloid angiopathy. ad is also considered a tauopathy due to abnormal aggregation of the tau protein, a microtubule-associated protein expressed in neurons that normally acts to stabilize microtubules in the cell cytoskeleton. like most microtubule-associated proteins, tau is normally regulated by phosphorylation; however, in alzheimer's disease, hyperphosphorylated tau accumulates as paired helical filaments that in turn aggregate into masses inside nerve cell bodies known as neurofibrillary tangles and as dystrophic neurites associated with amyloid plaques. although little is known about the process of filament assembly, depletion of a prolyl isomerase protein in the parvulin family has been shown to accelerate the accumulation of abnormal tau. neuroinflammation is also involved in the complex cascade leading to ad pathology and symptoms. considerable pathological and clinical evidence documents immunological changes associated with ad, including increased pro-inflammatory cytokine concentrations in the blood and cerebrospinal fluid. whether these changes may be a cause or consequence of ad remains to be fully understood, but inflammation within the brain, including increased reactivity of the resident microglia towards amyloid deposits, has been implicated in the pathogenesis and progression of ad. much of the known biochemistry of alzheimer's disease has been deciphered through research using experimental models of alzheimer's disease. neuropathology at a macroscopic level, ad is characterized by loss of neurons and synapses in the cerebral cortex and certain subcortical regions. this results in gross atrophy of the affected regions, including degeneration in the temporal lobe and parietal lobe, and parts of the frontal cortex and cingulate gyrus. both amyloid plaques and neurofibrillary tangles are clearly visible by microscopy in ad brains. plaques are dense, mostly insoluble deposits of protein and cellular material outside and around neurons. tangles are insoluble twisted fibers that build up inside the nerve cell. though many older people develop some plaques and tangles, the brains of ad patients have them to a much greater extent and in different brain locations. biochemical characteristics fundamental to the understanding of alzheimer's disease is the biochemical events that leads to accumulation of the amyloid-beta plaques and tau-protein tangles. a delicate balance of the enzymes secretases regulate the amyloid-beta accumulation. alpha secretase can render a non-pathological (non-amyloidogenic) amyloid beta (doi: 10.2174/156720512799361655). recently, a link between cholinergic neuronal activity and the activity of alpha-secretase has been highlighted, which can discourage amyloid-beta proteins deposition in brain of patients with alzheimer's disease. alzheimer's disease has been identified as a protein misfolding disease, or proteopathy, due to the accumulation of abnormally folded amyloid-beta proteins in the brains of ad patients. abnormal amyloid-beta accumulation can first be detected using cerebrospinal fluid analysis and later using positron emission tomography (pet). although ad shares pathophysiological mechanisms with prion diseases, it is not transmissible like prion diseases. amyloid-beta, also written aβ, is a short peptide that is a proteolytic byproduct of the transmembrane protein amyloid precursor protein (app), whose function is unclear but thought to be involved in neuronal development. the presenilins are components of a proteolytic complex involved in app processing and degradation. although amyloid beta monomers are harmless, they undergo a dramatic conformational change at sufficiently high concentration to form a beta sheet-rich tertiary structure that aggregates to form amyloid fibrils that deposit outside neurons in dense formations known as senile plaques or neuritic plaques, in less dense aggregates as diffuse plaques, and sometimes in the walls of small blood vessels in the brain in a process called amyloid angiopathy or congophilic angiopathy. ad is also considered a tauopathy due to abnormal aggregation of the tau protein, a microtubule-associated protein expressed in neurons that normally acts to stabilize microtubules in the cell cytoskeleton. like most microtubule-associated proteins, tau is normally regulated by phosphorylation; however, in ad patients, hyperphosphorylated tau accumulates as paired helical filaments that in turn aggregate into masses inside nerve cell bodies known as neurofibrillary tangles and as dystrophic neurites associated with amyloid plaques. levels of the neurotransmitter acetylcholine (ach) are reduced. levels of other neurotransmitters serotonin, norepinephrine, and somatostatin are also often reduced. replenishing the ach by anti-cholinesterases is an approved mode of treatment by fda. an alternative method of stimulating ach receptors of m1-m3 types by synthetic agonists that have a slower rate of dissociation from the receptor has been proposed as next generation cholinomimetic in alzheimer's disease. potential disease mechanisms while the gross histological features of ad in the brain have been well characterized, several different hypotheses have been advanced regarding the primary cause. among the oldest hypotheses is the cholinergic hypothesis, which suggests that deficiency in cholinergic signaling initiates the progression of the disease. other hypotheses suggest that either misfolding tau protein inside the cell or aggregation of amyloid beta outside the cell initiates the cascade leading to ad pathology. still other hypotheses propose metabolic factors, vascular disturbance, or chronically elevated inflammation in the brain as the primary cause for ad. while researchers have not identified a clear causative pathway originating from any of the molecular hypothesis that explains the gross anatomical changes observed in advanced ad, variants of the amyloid beta hypothesis of molecular initiation have become dominant among many researchers to date cholinergic hypothesis the cholinergic hypothesis of ad development was first proposed in 1976 by peter davies and a.j.f maloney. it states that alzheimer's begins as a deficiency in the production of acetylcholine, a vital neurotransmitter. much early therapeutic research was based on this hypothesis, including restoration of the "cholinergic nuclei". the possibility of cell-replacement therapy was investigated on the basis of this hypothesis. all of the first-generation anti-alzheimer's medications are based on this hypothesis and work to preserve acetylcholine by inhibiting acetylcholinesterases (enzymes that break down acetylcholine). these medications, though sometimes beneficial, have not led to a cure. in all cases, they have served to only treat symptoms of the disease and have neither halted nor reversed it. these results and other research have led to the conclusion that acetylcholine deficiencies may not be directly causal, but are a result of widespread brain tissue damage, damage so widespread that cell-replacement therapies are likely to be impractical. more recent hypotheses center on the effects of the misfolded and aggregated proteins, amyloid beta and tau. the two positions are lightheartedly described as "ba-ptist" and "tau-ist" viewpoints in one scientific publication. therein, it is suggested that "tau-ists" believe that the tau protein abnormalities initiate the disease cascade, while "ba-ptists" believe that beta amyloid deposits are the causative factor in the disease. tau hypothesis the hypothesis that tau is the primary causative factor has long been grounded in the observation that deposition of amyloid plaques does not correlate well with neuron loss. a mechanism for neurotoxicity has been proposed based on the loss of microtubule-stabilizing tau protein that leads to the degradation of the cytoskeleton. however, consensus has not been reached on whether tau hyperphosphorylation precedes or is caused by the formation of the abnormal helical filament aggregates. support for the tau hypothesis also derives from the existence of other diseases known as tauopathies in which the same protein is identifiably misfolded. however, a majority of researchers support the alternative hypothesis that amyloid is the primary causative agent. amyloid hypothesis the amyloid hypothesis is initially compelling because the gene for the amyloid beta precursor app is located on chromosome 21, and patients with trisomy 21 – better known as down syndrome – who have an extra gene copy exhibit ad-like disorders by 40 years of age. the amyloid hypothesis points to the cytotoxicity of mature aggregated amyloid fibrils, which are believed to be the toxic form of the protein responsible for disrupting the cell's calcium ion homeostasis and thus inducing apoptosis. this hypothesis is supported by the observation that higher levels of a variant of the beta amyloid protein known to form fibrils faster in vitro correlate with earlier onset and greater cognitive impairment in mouse models and with ad diagnosis in humans. however, mechanisms for the induced calcium influx, or proposals for alternative cytotoxic mechanisms, by mature fibrils are not obvious. flow chart depicting the role of apomorphine in alzheimer's disease. a more recent variation of the amyloid hypothesis identifies the cytotoxic species as an intermediate misfolded form of amyloid beta, neither a soluble monomer nor a mature aggregated polymer but an oligomeric species, possibly toroidal or star-shaped with a central channel that may induce apoptosis by physically piercing the cell membrane. this ion channel hypothesis postulates that oligomers of soluble, non-fibrillar aβ form membrane ion channels allowing unregulated calcium influx into neurons. a related alternative suggests that a globular oligomer localized to dendritic processes and axons in neurons is the cytotoxic species. the prefibrillar aggregates were shown to be able to disrupt the membrane. the cytotoxic-fibril hypothesis presents a clear target for drug development: inhibit the fibrillization process. much early development work on lead compounds has focused on this inhibition; most are also reported to reduce neurotoxicity, but the toxic-oligomer theory would imply that prevention of oligomeric assembly is the more important process or that a better target lies upstream, for example in the inhibition of app processing to amyloid beta. for example, apomorphine was seen to significantly improve memory function through the increased successful completion of the morris water maze. soluble intracellular (o)aβ42 two papers have shown that oligomeric (o)aβ42 (a species of aβ), in soluble intracellular form, acutely inhibits synaptic transmission, a pathophysiology that characterizes ad (in its early stages), by activating casein kinase 2. inflammatory hypothesis converging evidence suggests/supports that a sustained inflammatory response in the brain is a core feature of ad pathology and may be a key factor in ad pathogenesis. the brains of ad patients exhibit several markers of increased inflammatory signaling. the inflammatory hypothesis proposes that chronically elevated inflammation in the brain is a crucial component to the amyloid cascade in the early phases of ad and magnifies disease severity in later stages of ad. aβ is present in healthy brains and serves a vital physiological function in recovery from neuronal injury, protection from infection, and repair of the blood-brain barrier, however it is unknown how aβ production starts to exceed the clearance capacity of the brain and initiates ad progression. a possible explanation is that aβ causes microglia, the resident immune cell of the brain, to become activated and secrete pro-inflammatory signaling molecules, called cytokines, which recruit other local microglia. while acute microglial activation, as in response to injury, is beneficial and allows microglia to clear aβ and other cellular debris via phagocytosis, chronically activated microglia exhibit decreased efficiency in aβ clearance. despite this reduced ab clearance capacity, activated microglia continue to secrete pro-inflammatory cytokines like interleukins 1β and 6 (il-6, il-1β) and tumor necrosis factor-alpha (tnf-a), as well as reactive oxygen species which disrupt healthy synaptic functioning and eventually cause neuronal death. the loss of synaptic functioning and later neuronal death is responsible for the cognitive impairments and loss of volume in key brain regions which are associated with ad. il-1b, il-6, and tnf-a cause further production of aβ oligomers, as well as tau hyperphosphorylation, leading to continued microglia activation and creating a feed forward mechanism in which aβ production is increased and aβ clearance is decreased