P Proline in proteins Pair-rule genes Developmental genes that establish the basic segmentation
pattern of the Drosophila embryo palindromic sequence A DNA or RNA sequence that reads the same on the
complementary strand (e.g., AATGCATT). A DNA or RNA sequence
that shows symmetry about a central axis point. pan-editing The extensive insertion of nucleotides into an
abbreviated RNA, resulting in a functional molecule. PAM Percent Acceptable Mutations - 1 PAM means there has been
one mutation per 100 residues, 250 PAM would be 2.5
mutations per residue. If you use a molecular clock of 1
mutation every million years, you would use a PAM 250
scoring matrix for species that diverged around 250 million
years ago. parallel substitutions The independent occurrence of the same mutation at the
same nucleotide site in two or more lineages. paralogs Homologous sequences in two organisms that are
descendants of two different copies of a sequence that was
created by a duplication event in the genome of the common
ancestor paralogy sequence similarity between the descendants of a
duplicated ancestral gene paranemic Refers to a helix whose strands can be separated without
unwinding pararetrovirus A virus that contains a gene for reverse transcriptase
but cannot insert itself into the host chromosome parse to resolve (as a sentence) into component parts of speech
and describe them grammatically. Flat file data often have
to be parsed into separate files prior to analysis. parsimony The use of a minimum number of means to achieve an
end partial linkage The type of linkage usually displayed by a pair of
genetic andor physical markers on the same chromosome, the
markers not always being inherited together because of the
possibility of recombination between them. partial restriction Digestion of DNA with a restriction endonuclease under
limiting conditions so that not all restriction sites are
cut. path graph A figure showing the locations of the pointers in a
dynamic programming alignment pattern of mutation The relative frequency with which a nucleotide or an
amino acid changes into another during evolution. pattern of substitution The relative frequency with which a nucleotide or an
amino acid changes into another during evolution. PCR Polymerase chain reaction. A method of amplification of a
chosen DNA sequence from unpurified mixtures. pedigree A chart showing the genetic relationships between the
members of a human family pedigree analysis The use of pedigree charts to analyze the inheritance of
a genetic or DNA marker in a human family P element A DNA transposon of Drosophila pentose A sugar comprising 5 carbon atoms peptide bond The chemical link between adjacent amino acids in a
polypeptide. peptide nucleic acids A polynucleotide analog in which the sugar-phosphate
backbone is replaced by amide bonds. P-site The site in the ribosome occupied by the tRNA attached to
the growing polypeptide during translation peptidyl transferase The enzymatic activity that synthesizes peptide bonds
during translation an interpreted computer language for easily manipulating
text, files and processes. Popular in bioinformatics. permissive conditions Conditions under which a conditional-lethal mutant is
able to survive PEST sequences Amino acid sequences that influence the degratation of
proteins in which they are found. permutations all the possible arrangements of a particular set of
characters phage bacteriophage. A virus that infects bacteria phage display A technique for identifying proteins that interact with
one another. pharmacophore A specific arrangement of chemical groups in a ligand
that are essential for recognition by a receptor. phase phase class The position of an intron relative to the reading frame
of the two adjacent protein-coding exons phase-0 intron An intron that lies between two codons phase-1 intron An intron that lies between the first and second
nucleotides of a codon phase-2 intron An intron that lies between the second and third
nucleotides of a codon phenogram A graphic representation that portrays or attempts to
portray the taxonomic relationships among a number o
findividuals, species, or higher taxa on the basis of
overall similarities between them phenotype The observable characteristics of a genetically
controlled trait phylogenetic tree the graphic representation of the phylogeny of a group of
taxa or genes phylogenetics The reconstruction of the evolutionary history of a group
of taxa or genes phylogeny The evolutionary history of a group of taxa or genes and
their ancestors pilus A structure involved in bringing a pair of bacteria
together during conjugation; possibly the tube through which
DNA is transferred pi-pi interactions The hydrophobic interactions that occur between adjacent
base pairs in a double-stranded DNA molecule. plaque A zone of clearing on a lawn of bacteria caused by lysis
of the cells by infecting bacteriophages plasmid An autonomous, self-replicating extrachromosomal circular
DNA. Typically found in bacteria. Often used as a cloning
vector. platform The operating system running software on a computer. More
often used to refer to the type of computer. plectonemic Refers to a helix whose strands cannot be separated
without unwinding plesiomorphic character state A character state possessed by a remote common ancestor
of a group of organisms point mutation A mutation affecting only one nucleotide site. Usually,
in reference to a nucleotide substitution. pointer In a dynamic programming alignment, a pointer that
devines the position of the best "prevous" alignment is set
for each position in the score matrix.best previous
alignment must lie in either the previous row or column. In the C programming language, it is the internal machine
address of a value indie the computer's memory. polar A hydrophilic (water-loving) chemical group. polarity The property of nucleic acids to be read only one way
from 5' to 3' and differently in the opposite direction. polyadenylation signal A sequence region on most eukaryotic mRNA molecules that
specifies the location of the polyadenylation site. polyadenylation site (poly(A) site) The 3' end of most mRNA molecules in eukaryotes. The site
at which a poly-A tail is added poly-A tail A series of adenine nucleotides attached to the 3'-end of
a eukaryotic mRNA. This poly-A tail increases the stability
of the message, and also makes it easy to isolate the
message using an poly dT affinity column. polyclonal a colony of cells made up of more than one clone. In
immunology, a group of cells expressing a variety of
different antibodies. The opposite of monoclonal. polygamy A mating system in which a male mates with more than one
female (polygyny) or a female mates with more male
(polyandry) polygenic disorder Genetic disorders resulting from the combined action of
alleles of more than one gene. Although such disorders are
inherited, they depend on the simultaneous presence of
several alleles, thus the heriditary patterns are usually
more complex than those of single-gene disorders. polymer A long linear molecule made up of identical or similar
subunits. polymerase An enzyme that synthesizes a nucleic acid molecule
complementary to an existing single-stranded nucleic acid
moleucle. polymerase chain reaction (PCR) Polymerase chain reaction. A method of amplification of a
chosen DNA sequence from unpurified mixtures. polymorphism Differnece in DNA sequence of a specific gene among
individuals. Genetic variations occuring in more than 1% of
a population would be considered useful polymorphisms for
genetic linkage analysis. polypeptide A molecule made of amino acids covalently linked to each
other by peptide bonds. Often a term used to denote the
amino acid chain of a protein before it assumes a functional
three-dimensional configuration. polyphyletic Descended from different ancestors. polyploidy polyprotein A polypeptide that is cleaved after translation to give
rise to two or more functional proteins. polysome A mRNA molecule that is being translated by more than one
ribosome at the same time. population A group of individuals in a species that share a common
gene pool positional cloning A method for identifying disease-related genes. The
technique is to sequence parts of the genome where the gene
is expected to be in both disease afflicted individuals and
unaffected relatives to find systematic differences that
indicate the gene has been found. positive selection Selection for an advantageous mutant allele post-replication complex A complex of proteins, derived from a pre-replication
complex, that forms at a eukaryotic origin of replication
during the replication process and ensures that the genome
is copied just once per cell cycle. POU domain A DNA-binding motif found in a variety of proteins preinitiation complex The structure comprising the small subunit of the
ribosome. the initiator tRNA plus ancillary factors that
forms the initial association with teh mRNA during protein
synthesis. pre-messenger RNA (pr-MRNA) The primary transcript of a protein-coding gene before
maturation preproprotein The primary product of translation before any
posttranslational changes have been made pre-RNA The initial product of transcription of a gene or group
of genes, subsequently processed to give the mature
transcript(s). pre-rRNA The primary transcript of a gene or group of genes
specifying rRNA molecules pretermination codon A codon that requires only one mutation to become a
termination codon Pribnow box A component of the bacterial promoter primary amino acid One of the 20 amino acids specified by the universal
genetic code primary structure The sequence of amino acids in a polypeptide chain. The
sequence of nucleotides in a DNA or RNA molecule. primary transcript The initial product of transcription of a gene or group
of genes, subsequently processed to give the mature
transcript(s). primase The RNA polymerase enzyme that synthesizes RNA primers
during bacterial DNA replication primer A short oligonucleotide that is attached to a
single-stranded DNA molecule in order to provide a start
point for strand synthesis. Used in PCR, site-specific
mutagenesis and other techniques. primosome A protein complex involved in DNA replication principal component analysis A procedure that attempts to identify patterns in a large
dataset of variable character states prion An infectious agent that consists purely of protein probe Single-stranded DNA or RNA molecules of specific base
sequence, labeled either radioactively or immunologically,
that are used to detect the complementary base seuqence by
hybridization. processed gene retrogene processed pseudogene A pseudogene that results from integration into the
genome of a reverse-transcribed copy of an mRNA. processivity Refers to the length of polynucleotide that is
synthesized by a DNA polymerase before it dissociates from
the template. profile A position specific scoring table that represents the
information from a family of related sequences. A profile
can be used much like a sequence for alignment and database
searching, in effect aligning to the consensus of an entire
family. a profile is a special kind of weight matrix. programmed mutation The possibility that under some circumstances, an
organism can increase the rate at which mutations occur in a
specific gene progressive alignment A multiple alignment algorighm in which the sequences are
first clustered and then added one by one, in order of
decreasing similarity, to the growing multiple
alignment. prokaryote An organism whose cells lack a distinct nucleus promiscuous DNA DNA that has been transferred from one organelle genome
to another. promoter A region of DNA upstream of a gene, where the RNA
polymerase binds to the DNA. promoter clearance The completion of successful initiation of transcription
that occurs when the RNA polymerase moves away from the
promoter sequence. propensity In the Chou and Fasman secondary structure prediction,
the measure of a residue's tendency to assume a given
structure. proofreading The 3'->5' exonuclease activity possessed by some DNA
polymerases which enables the enzyme to replace a
misincorporated nucleotide. prophase The integrated form of the genome of a lysogenic
bacteriophage. proprotein A product of translation after the signal peptide has
been removed and before additional posttranslational
modifications have been made. PROSITE A database of "patterns" (regular expressions) specific
for various protein motifs. prosthetic group A nonprotein molecule attached to an apoprotein that is
required for functionality (e.g., heme in hemoglobin) protease An enzyme that cuts (digests) proteins. proteasome A multisubunit protein structure that is involved in the
degradation of other proteins protein A molecule composed of one or more polypeptide
chains. protein-coding gene A gene that contains a reading frame, the mRNA of which
is translated. protein engineering Various techniques for making directed alterations in
protein molecules, often to improve the properties of
enzymes ussed in industrial processes protein folding The adoption of a folded structure by a polypeptide protein-protein crosslinking A technique that links together adjacent proteins in
order to identify proteins that are positioned close to one
another in a structure such as a ribosome. Protein
crosslinking can occur naturally (especially in collagen) in
the aging process. proteome The complete protein content of a cell protogenome An RNA genome that existed during the RNA world proto-oncogene A normal gene that can be converted to an oncogene by one
of several mechanisms. prototroph An organism that has no nutritional requirements beyond
those of the wild type and which can grow on minimal
medium provirus A viral genome integrated into the genome of the host
cell pseudogene A functionless segment of DNA exhibiting sequence
homology to a functional gene. A nonfunctional member of a
gene family. pseudoknot a RNA 3D structure where the RNA folds back on a hairpin
to form a structure where three strands are held together by
hydrogen bonds. 5'-P terminus The end of a polynucleotide that terminates with a mono-,
di- or triphosphate attached to the 5'-carbon of the
sugar. punctuation codon A codon that specifies either the start or the end of a
gene Punnett square A tabular analysis for predictin the genotypes of the
progeny resulting from a genetic cross. purifying selection A selection regime resulting in the removal of an allele
from the population. purine A type of nitrogen base present in nucleotides and
composed of two joined ring structures, one five-membered
and one six-membered. The purine bases in DNA and RNA are
adenine and guanine. putative Commonly accepted or supposed pyrimidine A type of nitrogen base present in nucleotides and
composed one six-membered ring. The pyrimidine bases in DNA
are cytosine and thymine. In RNA,
the pyrimidines are cytosine and
uracil. pyrosequencing A DNA sequencing method in which addition of a nucleotide
to the end of a growing polynucleotide is detected by
conversion of the released pyrophosphate into a flash of
chemiluminescence. a computer language, similar to Perl, used for easily
manipulating text, files and processes. Popular in
bioinformatics.
