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Glossary |
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Unit Cladogram |
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mRNA: RNA species which are used as templates to produce proteins (in the process known as translation). Prokaryotic mRNA consists of an unbroken series of nucleotide bases in the triplet genetic code for amino acids.
murein: the cell wall material of Eubacteria, a/k/a peptidoglycan. The structure of murein is discussed here.
N-formyl
methionine: usually abbreviated fmet, an amino acid derivative
used, together with a special tRNAf, to initiate translation.
tRNAf bears the same anticodon as the tRNA for methionine.
However, tRNAf has unique structural features, such as the sequence
GCGCGC on the anticodon stem. See Protein Synthesis: The Ingredients,
also the source of the image. fmet is formed from methionine by a specific
formyl transferase, using formyl
tetrahydrofolate as the formyl group donor. fmet is used only in protein
initiation. When the polypeptide translation is complete, fmet is cleaved
off. Our understanding is that this occurs in two steps, with the formyl
group removed first, then the methionine.
Ozaki fragment: see lagging strand
peptide bond: an amide linkage between two amino acids. See, amino acid.
peptidoglycan: the cell wall material of Eubacteria, a/k/a murein. The structure of murein is discussed here.
photosynthesis: a process by which an organism uses energy from light and an (usually) inorganic electron source to reduce organic compounds. There are three major groups of photosynthetic bacteria: cyanobacteria, purple bacteria, and green bacteria. The cyanobacteria carry out oxygenic photosynthesis, that is, they use water as an electron donor and generate oxygen during photosynthesis.The photosynthetic system is located in an extensive thylakoid membrane system that is lined with particles called phycobilisomes. The green and purple bacteria carry out anoxygenic photosynthesis. They use reduced molecules such as H2, H2S, S, and organic molecules as an electron source and generate NADH and NADPH. In green bacteria, the photosynthetic system is located in ellipoidal vesicles called chlorosomes that are independent of the cytoplasmic membrane. In purple bacteria, the photosynthetic system is located in spherical or lamellar membrane systems that are continuous with the cytoplasmic membrane. Introduction to Photosynthesis.
polypeptide: any relatively long chain of amino acids linked by peptide bonds. Usually treated as synonymous with "protein," however the term polypeptide is not restricted to structures similar to those produced by organisms.
protease: an enzyme evolved to digest other proteins into their component amino acids.
proteasome:
a proteasome is the evil twin of a chaperonin.
Like a chaperonin, it is a longitudinally symmetrical series of 7-member rings
(but four rings, not two) with a hole through the middle and an affinity for
improperly-folded polypeptides. Unlike a
chaperonin, a proteasome does not restore proteins to conformational health and
send them on their way. Instead, the proteasome slashes the doomed
polypeptide into little 7-13 amino acid
oligopeptides so that they may be completely degraded by other proteases.
Since its function is reclamation, not rehabilitation, a proteasome lacks any of
the bells and whistles of a chaperonin and possesses a much narrower
aperture. Thus, only proteins which are more or less completely unfolded
can pass into the destructive core of the complex. The basic 20S
proteasome is found in Actinobacteria and Archea. In eukaryotes, the 20S
structure forms the core of a 26S proteasome. Image from the Max-Planck-Institut
für Biochemie, Abteilung für Strukturforschung.
ribosomal RNA: ribosomes are the small, but incredibly complex nucleoprotein complexes responsible for protein synthesis. They bind to mRNA molecules from the nucleus and physically move along the molecule, "reading" the code on the mRNA and attaching amino acids to the growing peptide (protein) chain. In eukaryotes there are three, quite distinctive RNA species bound up in the ribosome. These are known by their "Svedberg" numbers, a possibly obsolete measure of relative movement in centrifugation through a density gradient. The three species in prokaryotes are the 5S, 16S and 23S RNAs, vide infra.
ribosomal RNA, 16S or ssu RNA: the RNA molecule associated with the small ribosomal subunit. The secondary structure of typical 16S rRNA is extremely complex. An exhaustive set of maps and sequences can be found at rRNA secondary structure models.
ribosome: the cellular organelle responsible for translating mRNA into protein. Ribosomes are complexes of specialized RNA species and numerous proteins. A really outstanding short explanation of the ribosome can be found at Ribosome Structure and Function.
RNA polymerase: any of the enzyme complexes directly responsible for transcription -- the manufacture of RNA from the DNA template.
rRNA: ribosomal RNA, q.v.
Sliding
clamp: the usual toroidal form of the DNA replication complex,
including (in Eubacteria) two copies of DNA
polymerase III, DNA topoisomerases, and
associated proteins. Image from the von
Hippel Lab at the University of Oregon.
snapping division: a mode of cell division characterized by rapid horizontal division of an elongated cell with the two daughters finishing at an angle to each other. The daughter cells frequently remain in contact for a period of time. The image shows two rounds of snapping division in Thermoproteus, an archean, in time lapse photography. From Horn et al. (1999).
sphingolipid:
"All sphingolipids contain a sphingoid long-chain base (e.g.
sphingosine) that is linked to a fatty acid molecule through an amide bond,
thereby forming the ceramide unit. Addition of phosphocholine or carbohydrates
to ceramide leads to sphingomyelin or glycosphingolipids,
respectively." General
sphingolipid structure.
SSU rRNA: RNA associated with the small ribosomal subunit. "16S" RNA.
teichoic
acid: anionic, phosphate-rich polymers linked to the
peptidoglycan of gram-positive bacteria. "They are made up primarily
of repeating units of either glycerophosphate or ribitol phosphate molecules
that have sugars and D-alanine attached to the glycerol or ribitol backbone.
Some teichoic acids are attached to membrane lipids and these are called
lipoteichoic acids. All gram-positive organisms contain lipoteichoic acids but
some may lack the peptidoglycan bound form." Dr. Stuart Hill's Bios 213 Lecture notes, Lecture 9.
thylakoid: a unit of a stacked, lamellar membrane system in most cyanobacteria on which photosynthesis is carried out.
topoisomerase: see DNA topoisomerase.
transfer RNA: see tRNA.
translation:
the process whereby the genetic
code carried by
mRNA
is read and used to construct proteins. This process is carried out by ribosomes.
The ribosomes recruit appropriate 4S or transfer RNAs (tRNAs) which are
(conceptually) molecules with an amino acid at one end and an
"anticodon" at the other. The anticodon consists of three
nucleotide bases which are the complement of the codon which codes for the
tRNA's amino acid. Thus, for example, proline is coded by the sequence
CCA. The corresponding tRNApro would then bear a proline amino
acid at one end, and the complementary sequence, i.e. GGU, at the other.
The ribosome sits on the mRNA molecule. If the ribosome detects that the
tRNA bases form complementary base pairs with the next mRNA triplet in line, it
clips the amino acid off the tRNA and ads it to the growing protein. It
then moves up three bases on the mRNA and looks for the next matching
tRNA. See also image at tRNA.
tRNA: 4S RNA. This is the RNA species which actually makes the connection between genetic code and amino acid. There are 61 different tRNA species -- one for each of the 64 possible codons except the termination signals. Each tRNA has an anticodon segment, with three exposed bases complementary to a particular codon. Each tRNA can be "charged" with a particular amino acid by a specific amino acyl-tRNA transferase. During translation, the tRNA which bears the appropriate anticodon base pairs with the mRNA which is being translated. The tRNA is then bound to the A-site on the small ribosomal subunit by elongation factor Tu. The ribosome then catalyzes the formation of a peptide bond between the tRNA-bound amino acid and the growing protein chain. Elongation factor G then moves the peptidyl-tRNA complex to the P-site of the ribosome. The tRNA-peptide link is cleaved on arrival of the next tRNA at the A site. The uncharged tRNA then moves to the E site and is released. Specific tRNAs are usually abbreviated with the 3-letter amino acid designation in subscript. Thus the tRNAs for alanine are abbreviated tRNAala. See also, aminoacyl-tRNA.
V-ATPase: This is the eukaryotic version of the F-ATPase, q.v. V-ATPase is constructed slightly differently so that the "forward" reaction is favored. That is, it functions as an ATP-dependent ion pump. It is used, for example, to pump protons into digestive vacuoles to maintain very low pH inside the vacuole. V-ATPases are also found in various Archaea and in some Eubacteria which seem to have acquired the archaean species by lateral gene transfer. The archaean version is sometimes referred to as "A-ATPase." Finbow & Harrison (1997),
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