P

o-o items o-o are in brief format
o-o PCD
o-o phylogenetics
o-o plasmid
o-o plastid
o-o pleiotropic
o-o polyphenic gene
o-o proto-oncogene
o-o pseudogenes

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p53 PA ф pattern-recognition receptors PD: PDGF receptor ◊ PDK1 ◊ PDK1 PE ~ peptide סּ peroxisome »» Persistence of functional gene duplicates PH ф phagocyte סּ phagocytosis ◊ phosphatases : phosphatidic acid, PA : phosphatidylinositol : phosphatidylinositol phosphates, PIPs ◊ phosphodiesterases ¨ phospholipases : phospholipase A2 : phospholipase C family : phospolipase C-γ סּ phosphotransfer-mediated signaling pathways ◊ phosphorylases ››› phosphorylation ~ phospolipid סּ photosynthesis »» Phyletic gradualism ^ Phylogenetics סּ physiological function PI ◊ PIKK ◊ PI3K : PI3K ARF : PI3K cancer : PI3K Kit : PI3K signaling ~ PIPs PL סּ plant cell PK ◊ PKA ◊ PKB ◊ PKCs PO »» point mutation : polar amino acids ~ polyadenylation ~ polypeptide : polyphosphoinositides »» Population Genetics and Formulae PR~ preinitiation complex ~ pre-mRNA ~ pre-mRNA splicing ~ promoters ~ proteome »» proteome and genome סּ prokaryotes, prokaryotic ¤ proliferation : prostaglandins סּ protein degradation סּ proteasome ◊ protein kinases סּ Protein Kinase Signaling Networks ~ proteins ~ protein tyrosine kinases ¤ proto-oncogenes PT ◊ PTEN ~ PTKs PU »» Punctuated equilibria סּ pumps סּ

Molecules and Pathways φ phenylalanine ☼ Photosynthesis Overview ☼ Photophosphorylation φ proline φ purine pyrimidine φ pyruvate ››› pyruvate dehydrogenase reaction

Microbiology • Phosphorylation switches • Photosynthetic bacteria • Prokaryote Genetics & Biochemistry • Prokaryote Physiology & Communication

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PCD

Programmed cell death (PCD) or cellular death-by-suicide is part of normal development, and is termed apoptosis. PCD is a part of normal cell turnover and tissue homeostasis, and it plays a significant role in embryogenesis, induction and maintenance of immune tolerance, development of the nervous system, and atrophy of endocrine-dependent tissue.

Signals from tumor suppressors such as APC, CBFA2T3, FAS gene, Hsp90, MDM2, p53, PTEN, TP53, Wnt prevent the uncontrolled proliferation characteristic of cancers by inducing apoptosis.

PCD is initiated via the death receptor pathway or the mitochondrial pathway, which lead to the activation of an initiator caspase, which in turn initiates a proteolytic cascade, ultimately leading to apoptotic cell death. Death receptors include the TNF-R (tumour necrosis factor receptors) and Fas receptor families (FADD). Activation of death receptors by binding of ligands such as TNF-α and CD-95L (FasL) leads to caspase-8 activity. Players in the mitochondrial pathway include members of the Bcl-2 family, which regulate the release, through the mitochondrial PT pore, of pro-apoptotic substances such as AIF, Endonuclease G, Smac/DIABLO and cytochrome C. Mitochondrial efflux of cytochrome-c drives generation of the apoptosome (apoptotic body) in the cytoplasm, which in turn leads to caspase-9 activity.

Apoptosis (PCD) exhibits characteristic morphological changes, and is distinct from necrosis.

Џ Flash animation Џ ICAD-CAD animation Џ

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plasmid

Plasmids are small circular, extrachromosomal, mobile genetic elements that can be transmitted from one bacterium to another through the pili during conjugation.

Plasmids are not to be confused with plastids, which are chloroplasts – cellular, membrane- bounded organelles containing photosynthetic and/or acessory pigments in their internal (thylakoid) membranes. The plastid is the site of photosynthesis in eukaryotic cells, and is the site of the Calvin cycle just as the mitochondrion is the site of oxidative phosphorylation.

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pleiotropic

In pleiotropy a single gene is associated with more than one phenotype for an organism. A pleiotropic gene is also termed polyphenic gene.

Pleiotropic effects result from environmental, regulatory, and epigenetic phenomena that result in complex transcriptional responses involving multiple genes and regulons. (A regulon is defined as a group of transcriptional units or operons that are coordinately controlled by a regulator. Bacteria have operons, which are protein-encoding gene clusters.)

Examples of pleiotropic mechanisms:
● the cyclic-AMP concentration in a cell can produce a variety of effects because the cAMP second messenger controls protein kinases that affect a variety of proteins.
● TNFR cluster of differentiation, CD30 binding by CD30L mediates pleiotropic effects, including cellular proliferation, activation, differentiation, and apoptosis..

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phylogenetics

Phylogenetic system: groups organisms based on shared evolutionary heritage. DNA and RNA sequencing techniques are considered to give the most meaningful phylogenies.

Phylogenetic separation into evolutionary relationships (clades), based on comparison of genomes is likely to supplant phenotypical (phenetic) taxonomies of the prokaryotes.

Monophyletic taxon or clade: an accurate grouping of only (opp. polyphyletic) and all (opp. paraphyletic) descendents of a shared common ancestor. A monopyletic group is genetically homogeneous and reflects evolutionary relationships.

Paraphyletic taxon or clade: a monophyletic group that excludes one or more discrete groups descended from the most recent common ancestral species of the entire group. Other descendent species of the most recent common ancestor have been excluded from the paraphyletic taxon, usually because of morphologic distinctiveness.

Polyphyletic taxon: opposite to monophyletic taxon: A polyphyletic group is mistakenly or improperly erected on the basis of homoplasy—characteristics that have arisen despite not sharing a common ancestor. Homoplasy arises because of convergent evolution, parallelism, evolutionary reversals, horizontal gene transfer, or gene duplications. Polyphyletic taxa are genetically heterogeneous because members do not share a common ancestor.

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proto-oncogene

Proto-oncogenes participate in a variety of normal cellular functions, but have the potential to tranform into cellular oncogenes when damaged.

Proto-oncogenes normally function in the various signal transduction cascades that regulate cell growth, proliferation and differentiation. Cellular proto-oncogenes resident in transforming retroviruses are designated as c- (cellular origin) as opposed to v- (retroviral origin). Oncogenes are malignantly transformed proto-oncogenes. Table  Oncogenes Proto-oncogenes.

¤ c-Fos ¤ c-Jun ¤ c-Myc ¤ c-Sis ¤ c-Src ¤ Ras ¤ Rb ¤ Src ¤ v-Src ¤

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pseudogenes

Pseudogenes are non-functional relatives of known functional genes, which have lost protein-coding ability or are no longer expressed in the cell.

Pseudogenes may have some gene-like features, such as promoters, CpG islands, and splice sites, yet are nonfunctional in that they lack protein-coding ability. This loss of gene function results from stop codons, frameshifts, lack of transcriptional capacity, or from an inability to function as an RNA (as with rRNA pseudogenes).

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