Gene to Protein Terms
Get down with the lingo
Alpha-sheet(or α-sheet) A secondary structural orientation of a protein (a fancy way to say how a protein is folded—think of a Yoga pose). It is recognized by the fact that the carbonyl group (a functional group containing C=O, a carbon double bonded to an oxygen) is located on one side, and the amino groups are on the opposite side. Don't confuse the α-sheet structure of a protein with the α-helix form of DNA.
Beta-sheet(β-sheet) A secondary structural orientation of a protein—as in, another fancy way to say how a protein is folded, just in a different specific way.
Alternative SplicingThe production of mRNAs (messenger RNAs) containing different exons as a result of selective splicing (cutting and pasting together). Alternative splicing allows for a variety of proteins to be produced from the same gene.
AnticodonThe three-nucleotide sequence on the tRNA that is the reverse complement (or match) to a specific codon on the mRNA.
Base-pairing RuleA matchmaking rule that states that uracil (or thymine) nucleotides can pair with adenine, and guanine nucleotides can pair with cytosine.
CappingThe process where the 5' end of mRNAs is given a guanine in reverse orientation along with several other modifications. This "cap" on the mRNA helps to stabilize the RNA, and also sometimes plays a role in its export, splicing, and translation. Go ahead and think of a baseball cap here if it helps you—this cap does go on the head of the RNA.
ChaperoneA protein that helps another protein fold into its three-dimensional structure by making certain conformations more energetically favorable. You may also find them at prom.
CodonThe three-letter RNA code (or word) that encodes for a specific amino acid during transcription. Several different codons can code for the same amino acid. In this case, many times the first two bases of the codons are the same, while the third base differs.
ElongationThe step of transcription or translation between initiation and termination. This is where the new mRNA or protein continues to be synthesized, or in other words…becomes longer.
EnhancerA region of the genome that influences (increases or decreases) the transcription of a gene. These regions can be located thousands of base pairs away from the gene. They usually result in the binding of a regulatory protein, a protein that can control the transcription of the gene. Talk about long-range influence.
ExonA region of a gene that codes for a protein and appear in the final mature RNA. Not to be confused with the oil company.
Gene ExpressionThe production of a protein or functional RNA from a gene. It is useful to think about gene expression as similar to a light on a dimming switch. You can turn the light on or off, or gradually change its intensity.
Genetic CodeThe code that describes how the nucleotide sequence of a gene is translated into an amino acid sequence through a RNA intermediary. The RNA molecule is basically the middleman that transfers the information in DNA to make a protein.
Homeodomain ProteinThe DNA-binding, helix-turn-helix protein that recognizes specific regions of DNA by
interacting with the outer edge of the DNA helix in a specific way. The
protein taking on a particular structure determines this specificity.
InitiationThe first step in transcription or translation where RNA or protein synthesis begins, or "initiates."
IntronThe region of a gene that is removed and therefore not present in the final mature RNA. These regions are not used to code for the production of a protein. Helpful hint: introns aren't in the final RNA at all. Tricky stuff.
Messenger RNA (mRNA)A type of RNA that codes for the production of a protein. It is transcribed from a gene and is often the result of post-transcriptional editing.
NucleolusA region of the nucleus where rRNAs (ribosomal RNAs) and a subset of other non-coding RNAs are produced and processed.
OperonAn operon is a group of similar genes arranged together in the genome. This arrangement allows for their translation to be jointly regulated. This most often results in the production of a single mRNA transcribed from multiple genes. The genes usually share a common function, such as involvement in the production of a specific biosynthetic or metabolic pathway (ex: the lac operon). Not to be confused with opera or Oberon, the fairy from a Midsummer's Night's Dream.
PolyadenylationThe addition of adenine residues to the end of an mRNA in eukaryotes by a poly-A polymerase. This poly-A tail assists in export, translation, and RNA stability. Remember, poly means many.
PolymerA molecule that comprises repeating units.
Post-translational ModificationThe chemical alteration of amino acids in a protein. These modifications are often reversible. They influence the structure and function of a protein. For example, the phosphorylation of growth factor receptors results in their activation.
PromoterThe specific DNA sequence recognized by transcription factors. RNA polymerase binds to the promoter. This sequence also determines which of the two DNA strands will be transcribed. Has absolutely nothing to do with prom.
Protein FoldingThe term that describes how an amino acid chain folds into a three-dimensional structure. Think yoga.
Protein SynthesisThe production of a protein from an RNA intermediate. Proteins are synthesized (produced) by the translation process.
Reading FrameThe term that explains how an RNA can be translated into 3 different amino acid sequences depending on where translation begins. Take a deep breath, we have an example to illustrate.
RepressionThe inhibition of transcription of a gene, often due to the binding of a regulatory factor, or a protein that controls transcription either positively or negatively.
RepressorA term used most often to describe a protein that inhibits the transcription of a gene.
RibosomeThe protein-making machine that is composed of rRNA (ribosomal RNA) and many proteins. It catalyzes the synthesis of the amino acid chain. Not to be confused with ribose, the sugar that comprises RNA.
RibozymeAn RNA that has the ability to act as an enzyme and catalyze (or jump start) chemical reactions.
RNA PolymeraseThe polymerase that catalyzes the formation of the phosphodiester bonds between ribonucleic acids bases during transcription. It uses a DNA strand as a template to generate the RNA strand.
Ribosomal RNA (rRNA)A special type of RNA that is not translated into a protein. Instead it assembles with several proteins to create the ribosome. The rRNA (ribosomal RNA) works within the ribosome to catalyze the creation of a new polypeptide chain.
SplicingThe process whereby introns are removed from an RNA, leaving a complete mature RNA that comprises entirely exons. Think cutting and pasting.
SpliceosomeThe enzymatic complex responsible for the splicing reaction. It consists of several RNAs and over 50 proteins.
Start CodonThe codon AUG, which signals the start of translation and results in the insertion of the amino acid methionine.
Stop CodonThe three-letter codon that signals for a stop of translation. Important to remember: it does not result in the insertion of an amino acid.
TerminationThe completion of a metabolic process, such as DNA replication, RNA transcription, or translation. There are different cues for each: DNA replication terminates by replication forks running into each other or reaching the end of DNA, RNA transcription terminates with either the formation of a 3´ hairpin loop or the arrival at a polyadenylation signal, and translation terminates with the stop codon.
TerminatorThe particular sequence of a DNA template that results in the RNA polymerase falling off of the nascent RNA. Terminators signal the end of transcription.
TATA BoxA specified sequence that is the part of a eukaryotic RNA polymerase II promoter. It has a high amount of thymine and adenine bases in its sequence, which is how it got its name. This sequence signals the beginning of a gene that will be transcribed, and it is bound by a transcription factor.
TranscriptionThe process where the information in a DNA strand is expressed. The DNA code is used to produce an RNA, which in turn can be used to make a protein. Think about transcription like a copy machine…or a copycat.
Transcription FactorThe protein that recognize the promoter and are responsible for recruiting RNA polymerase during transcription.
TranslationThe process of using an RNA template to create a polypeptide (or protein) made of amino acids. Think of translation as translating one language into another.
Transfer RNA (tRNA)A key player in translation. The tRNA (transfer RNA) recognizes a specific codon and carries the corresponding amino acid to the codon site at the same time. Together this process insures that the correct amino acid is inserted into the growing polypeptide chain.
UracilThe nucleotide base that replaces thymine in RNA. It has the capacity to base pair with adenine.
WobbleThe mismatched pairing on the third nucleotide of the anticodon/codon that allows some tRNAs to base pair to a codon that is not a perfect match. Has nothing to do with the sound a turkey makes.
Zinc FingerA protein motif (think structure) that uses zinc molecule(s) to stabilize the structural motif. Zinc finger motifs are common in DNA transcription factors, but are also found in other functional protein groups.
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