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Gene to Protein

Gene to Protein

Gene to Protein Terms

Get down with the lingo

Zinc Finger

A 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.

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 Splicing

The 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.

Anticodon

The three-nucleotide sequence on the tRNA that is the reverse complement (or match) to a specific codon on the mRNA.

Base-pairing Rule

A matchmaking rule that states that uracil (or thymine) nucleotides can pair with adenine, and guanine nucleotides can pair with cytosine.

Capping

The 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.

Chaperone

A 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.

Codon

The 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.

Elongation

The 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.

Enhancer

A 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.

Exon

A 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 Expression

The 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 Code

The 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 Protein

The 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.

Initiation

The first step in transcription or translation where RNA or protein synthesis begins, or "initiates."

Intron

The 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.

Nucleolus

A region of the nucleus where rRNAs (ribosomal RNAs) and a subset of other non-coding RNAs are produced and processed.

Operon

An 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.

Polyadenylation

The 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.

Polymer

A molecule that comprises repeating units.

Post-translational Modification

The 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.

Promoter

The 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 Folding

The term that describes how an amino acid chain folds into a three-dimensional structure. Think yoga.

Protein Synthesis

The production of a protein from an RNA intermediate. Proteins are synthesized (produced) by the translation process.

Reading Frame

The 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.

Repression

The 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.

Repressor

A term used most often to describe a protein that inhibits the transcription of a gene.

Ribosome

The 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.

Ribozyme

An RNA that has the ability to act as an enzyme and catalyze (or jump start) chemical reactions.

RNA Polymerase

The 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.

Splicing

The process whereby introns are removed from an RNA, leaving a complete mature RNA that comprises entirely exons. Think cutting and pasting.

Spliceosome

The enzymatic complex responsible for the splicing reaction. It consists of several RNAs and over 50 proteins.

Start Codon

The codon AUG, which signals the start of translation and results in the insertion of the amino acid methionine.

Stop Codon

The three-letter codon that signals for a stop of translation. Important to remember: it does not result in the insertion of an amino acid.

Termination

The 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.

Terminator

The 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 Box

A 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.

Transcription

The 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 Factor

The protein that recognize the promoter and are responsible for recruiting RNA polymerase during transcription.

Translation

The 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.

Uracil

The nucleotide base that replaces thymine in RNA. It has the capacity to base pair with adenine.

Wobble

The 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 Finger

A 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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