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Glossary
Amino Acids
- The building blocks of proteins. They all have the same
carbon backbone structure but differ from one another according to the
individual side chain. Only 20 of the naturally occurring amino acids are
commonly found in proteins.
Ascospore (Spore)
- A specialized haploid cell produced during meiosis.
Ascus
- A sac-like structure containing four spores in S.
cerevisiae Plural: asci.
Autonomous Replication Sequence (ARS)
- A DNA consensus sequence which usually functions as an
origin of DNA replication. There are various consensus sequences. We used the
conservative 5'-(A/T)TTTAT(A/G)TTT(A/T)-3' consensus for our analysis (Stinchcomb
et al. 1981; Broach et al. 1983).
Bases
- The variable part of DNA. The nitrogenous bases of DNA
are divided into two groups: purines [adenine (A) and guanine (G)] and
pyrimidines [thymine (T) and cytosine (C)]. In RNA, thymine is replaced by
uracil (U). Modified and unusual bases, such as pseudouridine, are found in
tRNA molecules.
Base pair (bp)
- Two bases, linked by noncovalent forces, that pair in
double-stranded DNA or RNA molecules.
cDNA (complementary DNA)
- A DNA molecule usually obtained by a reverse
transcription of an mRNA molecule.
cds
Centromere
The attachment site of chromosomes to the mitotic or
meiotic spindle.
Chromosomes
- Discrete physical units carrying genetic information.
Each chromosome contains a long duplex DNA molecule and associated proteins.
Usually, chromosomes are visible only during cell division. The number of
chromosomes varies widely among different species.
Codon
- A sequence of three nucleotides (in a DNA or mRNA),
that encodes a specific amino acid to be incorporated into a protein.
Codon Adaptation Index (CAI)
- The CAI is used to estimate the expression level of a
protein. To calculate the CAI value of a protein, a reference set of highly
expressed genes is used. For each codon in this set of reference genes the
frequency of usage is calculated. A CAI score for a gene is calculated from
the frequency of use of all codons in that gene. [P.M. Sharp and W.H. Li
Nucleic Acids Res.15, 1281-1295 (1987)]
Diploid
- A term used to describe an organism having two sets of
identical chromosomes. S. cerevisae is chimeric, in that haploid and diploid
forms exist.
DNA (deoxyribonucleic acid)
- The primary genetic material of all cellular organisms.
It is a polymeric macromolecule composed of a repeating backbone of phosphate
and sugar subunits to which different bases are attached. DNA is arranged in
two opposing strands (the Watson-Crick double helix) in which the
complementary bases form hydrogen-bonded basepairs across the two strands. The
sugar backbone of DNA is composed of deoxyribose subunits.
DNA-Replication
- Process of synthesis of a new DNA strand by a mechanism
in which a preexisting strand (parental strand) is used as a template. Each
new strand is complementary to the parent strand.
EST (Expressed sequence tag)
- cDNA sequence of a few hundred bases used to identify
the corresponding gene.
Eukaryote
- An organism whose genetic information is, in contrast
to prokaryotes (such as bacteria), contained in a separate cellular
compartment: the nucleus. Besides algae, fungi and protozoa, all multicellular,
cell-differentiating organisms including plants and animals are eukaryotes. In
addition to their nuclear genome, all eukaryotic cells contain small
additional, extranuclear genomes, which are contained in mitochondria (in all
eukaryotes) and in plastids (only in eukaryotes that can perform
photosynthesis).
Exons
- Segments of a eukaryotic gene that encodes mRNA. In
DNA, exons are adjacent to non-coding DNA segments, called introns.
FASTA
- A computer program based on the method of W. Pearson
and D. Lipman [Proc. Natl. Acad. Sci. U.S.A. 85, 2444-2448 (1988)] to search
for similarities between one sequence (the query) and any group of sequences (the
database).
Gene
- A section of DNA coding for a single polypeptide chain;
a particular species of tRNA, snRNA or rRNA; or a sequence that is recognized
by and interacts with regulator proteins.
Haploid
- The state of having only one set of chromosomes. See
diploid.
Introns
- Noncoding regions of eukaryotic genes, which are
transcribed into mRNA but are then excised by a process called RNA-splicing.
See exon.
Long terminal repeats (LTRs)
- Identical DNA sequences, several hundred nucleotides
long, found at both ends of transposons. They are thought to have a role in
integrating the transposons into the host DNA. Solo LTRs and remnant LTRs
indicate former integration sites of transposable elements.
Meiosis
- A special process of nuclear division during which
spores are produced. Meiosis involves a diminution (by half) in the amount of
genetic material; it consists of two successive nuclear divisions with only
one round of DNA replication producing four haploid daughter cells (the spores)
from an initial diploid cell.
Mitochondria
- Semi-autonomous, self-reproducing organelles within the
cytoplasm of eukaryotic cells that are bounded by two membranes. These
organelles are responsible for the energy conversion of most of the cellular
energy metabolites into adenosine triphosphate (ATP) by oxidative
phosphorylation.
Mitosis
- The process of nuclear division in eukaryotic cells.
mRNA (messenger RNA)
- A single-stranded RNA that acts as the template for the
amino acid sequence of proteins.
Open reading frames (ORFs)
- DNA stretches that potentially encode proteins. They
always have a start codon (ATG) at one end and a translation-terminating stop
codon at the other end.
Proteins
- Polymers composed of a linear string of amino acids.
Remnant LTR
- A solitary and degenerated LTR sequence lacking a TY
element. As the remaining LTR has no function anymore, and on the other hand
its sequence is degenerated, the transposition must have occured long time ago.
RNA (ribonucleic acid)
- Polymer composed of a repeating backbone of phosphate
and sugar subunits to which different bases are attached: adenine (A),
cytosine (C), guanine (G), and uracil (U). The sugar backbone of RNA is
composed of ribose subunits. RNAs can be distinguished by their different
properties:mRNA, tRNA, scRNA, snRNA, and rRNA.
rRNA (ribosomal RNA)
- A structural and functional component of ribosomes.
Ribosomes are the cellular machinery responsible for the translation of the
genetic information into proteins. They are composed of rRNA and ribosomal
proteins.
scRNA (small cytoplasmic RNA)
- A set of RNAs that are typically smaller than 300
nucleotides and can be part of signal recognition particles (SRPs).
Signal recognition particles (SRPs)
- Ribonucleoproteins that are part of the
protein-translocating machinery in the ER (endoplasmic reticulum) membrane.
snRNA
- A set of RNAs that are typically smaller than 300
nucleotides and function in the nucleus in the form of small nuclear
ribonucleoprotein particles (snRNPs). The function of snRNPs is to mediate and
regulate post-translational RNA processing events.
Solo LTR
- A solitary LTR sequence lacking a TY element. This
indicates that a TY was located in this region. As the remaining LTR has no
function anymore, and on the other hand its sequence is well conserved the
transposition must have occured in the near past.
Spindle
- A network of fibrous microtubules and associated
molecules formed during mitosis between the opposite poles (centromeres) of
eukaryotic cells. It mediates the movement of the duplicated chromosomes to
opposite poles.
Spore
Sporulation
- The process of spore development. Sporulation can be
induced by external signals, such as absence of nitrogen.
Telomere
- The terminal part of a eukaryotic chromosome,
consisting of a few hundred base pairs with a defined structure. Telomeres are
important for maintaining chromosomal structure and stability, as they permit
replication of the ends of the linear DNA molecule.
Transcription
- The process by which DNA is used as a template for the
synthesis of an RNA molecule.
Translation
- The process of protein synthesis from a mRNA template,
occurring at the ribosome.
Transposable element (transposon)
- A mobile DNA sequence that can move from one site in a
chromosome to another, or between different chromosomes.
tRNA (transfer RNA)
- A set of RNAs that act during protein synthesis as
adaptor molecules, matching individual amino acids to their corresponding
codon on a mRNA. For each amino acid there is at least one tRNA.
TY elements
- The retro-transposons of yeast. TYs are members of a
widely distributed family of eukaryotic elements called LTR- containing
retrotransposons. They have the same sequence organization as retroviruses.
The complete retrotransposons are 5 to 6 kilobases long. They are bracketed by
long terminal repeats (LTR), which are 300 to 400 basepairs long.
Y' element
- Y' elements normally consist of two ORFs with all
splicing signals that are located in the telomeric regions. Their function is
unknown.
Zygote
- The diploid cell resulting from the union of two
haploid cells of complementary mating types.
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