Chapter 17: From Gene to Protein

Transcription binding

RNA polymerase binds a precise location and orientation on the promoter, therefore determining where transcription starts.

5' cap

A modified form of guanine nucleotide added onto the nucleotide at the 5' end of a pre-mRNA molecule.

Transcription initiation

After RNA polymerase binds to the promoter, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand.

What is mRNA splicing? What does the splicing, what is spliced, where does it occur, and why is this necessary?

After synthesis of a eukaryotic primary RNA transcript, the removal of introns that will not be included in the mRNA and the joining together of exons. snRNAs (small nuclear RNAs) catalyzes these processes

What is the name of the units that compose a protein?

Amino acids are the units that compose a protein.

What is the difference between different amino acids?

Amino acids differ in their R groups. There are 20 different kinds of amino acids.

What are the advantages of RNA splicing?

An advantage of RNA splicing is that a single primary transcript can be spliced into different mRNA by the inclusion of different exons. In other words, one gene can code for several versions of a polypeptide.

What is the general formula of an amino acid? How many different amino acids are commonly present in proteins?

An amino acid contains a carboxyl group (-COOH) and an amino group (-NH2 or -NH3).

RNA polymerase

An enzyme that links ribonucleotides into a growing RNA chain during transcription, based on complementary binding to nucleotides on a DNA template strand.

TATA box

A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.

What is a ribosome, what are its components?

A complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm; consists of a large and a small subunit.

How does a segment of mRNA code for an amino acid and the sequence of amino acids in a protein?

As a molecule of mRNA is moved through a ribosome, codons are translated into amino acids. A tRNA adds its amino acid cargo to a growing polypeptide chain.

Polyadenylation signal

Signals the addition of a poly-A tail to a messenger RNA.

Transcription termination

The RNA transcript is released and the polymerase detaches from the DNA.

What enzyme attaches amino acids to tRNA?

The aminoacyl-tRNA synthetase is the enzyme.

What part of tRNA is complementary to the codons of mRNA?

The anticodon is complementary to the codons of mRNA.

What is the "central dogma of molecular biology"?

The central dogma of molecular biology is that information is transferred from DNA to RNA to protein.

What are start and stop codons?

The codon AUG stands for both Met (methionine) and functions as a start signal for ribosomes to begin translating the mRNA at that point. Three of the 64 codons function as "stop" signals, marking where ribosomes end translation.

Why is the genetic code redundant but not ambiguous?

The genetic code is redundant but not ambiguous because, for example, codons GAA and GAG both specify glutamic acid (redundancy), neither of them ever specifies any other amino acid (no ambiguity).

What is the name of the bond that is formed between two amino acids by a dehydration reaction?

The peptide bond is formed between two amino acids by a dehydration reaction.

Transcription elongation

The polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5' to 3'. In the wake of transcription, the DNA strands re-form a double helix.

Describe how ribosomes and various forms of RNA cooperate to translate mRNA into protein.

A molecule of mRNA is moved through a ribosome, codons are translated into amino acids. The interpreters are tRNA molecules with a specific anticodon on the end and a corresponding amino acid on the other end. tRNA adds its growing amino acids to a polypeptide chain.

Extensive missense mutation

A mutation in which there are insertions and deletions not in a multiple of three. All nucleotides that are downstream will be improperly grouped. This usually involves 1 nucleotide-pair deletion.

Frameshift mutation

A mutation occurring when nucleotides are inserted in or deleted from a gene and the number inserted or deleted is not a multiple of three, resulting in the improper grouping of the subsequent nucleotides into codons.

Nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein; can be a substitution or insertion/deletion via frameshift. When a frameshift occurs, 1 nucleotide-pair is inserted.

Intron

A noncoding, intervening sequence within a primary transcript that is removed from the transcript during RNA processing; also refers to the region of DNA from which this sequence was transcribed.

Silent point mutation

A nucleotide-pair substitution that has no observable effect on the phenotype; for example, within a gene, a mutation that results in a codon that codes for the same amino acid.

Missense point mutation

A nucleotide-pair substitution that results in a codon that codes for a different amino acid.

What is a protein? What are some of the functions of proteins?

A protein is a biologically functional molecule consisting of one or more polypeptides folded and coiled in a specific three-dimensional structure. Proteins can serve as enzymes or aid in structure, storage, and transport.

Transcription factor

A regulatory protein that binds to DNA and affects the transcription of specific genes.

Poly-A tail

A sequence of 50-250 adenine nucleotides added onto the 3′ end of a pre-mRNA molecule.

Exon

A sequence within a primary transcript that remains in the RNA after RNA processing; also refers to the region of DNA from which this sequence was transcribed.

Promoter

A specific nucleotide sequence in the DNA of a gene that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place.

What are codons?

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

How can four nucleotides code for twenty amino acids?

A triplet code includes the genetic instructions for a polypeptide chain that are written in DNA as a series of non-overlapping, three-nucleotide words. mRNA nucleotide triplets are called codons and are customarily written in the 5' to 3' direction.

How were Beadle and Tatum able to support Garrod's hypothesis through scientific research? What does "one gene-one protein" mean?

Beadle and Tatum did an experiment with bread mold, Neurospora crassa, exposing its cells to X-rays, inducing mutations. Then, they screened mutants that had new nutritional requirements. The results showed that the mutant cells grew only on minimum medium + arginine, indicating that the mutant was missing the enzyme for the synthesis of arginine. This research supported the "one gene-one protein hypothesis," which states that a gene dictates the production of a specific enzyme.

What did Garrod hypothesize, but was unable to provide proof through scientific experimentation?

Garrod was the first to suggest that genes dictate phenotypes through enzymes. He postulated that the symptoms of an inherited disease reflect an inability to make a particular enzyme, which he referred to as "inborn errors of metabolism".

How does transcription termination differ in prokaryotes and eukaryotes?

In prokaryotes, transcription proceeds through a terminator sequence in the DNA, which causes the polymerase to detach from the DNA and release the transcript. In eukaryotes, RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence, which codes for AAUAAA in the pre-mRNA; at a certain point, proteins cut the RNA transcript free from the polymerase.

What is mRNA processing?

Modification of RNA primary transcripts, including splicing out of introns, joining together of exons, and alteration of the 5' and 3' ends.

What types of chemical bonds are responsible for the primary, secondary, tertiary and quaternary structure of proteins?

The primary structure is made of peptide bonds. The secondary structure includes hydrogen bonds. The tertiary structure contains a combination of hydrophobic interactions (Van der Waals) and covalent bonds (disulfide bridge), as well as hydrogen bonds and ionic bonds. The quaternary structure has bonds in the tertiary structure that are on the surface of the polypeptides.

Describe the reading frame for the genetic code. How does a frame shift affect the reading frame?

The reading frame for the genetic code is the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis. A frame shift affects the molecular language of cells. It would convey a different message, one that was not needed at the time, if a frame shift occurs.

What are the "sites" within a ribosome?

The ribosome consists of an E site (exit site), P site (peptidyl-tRNA binding site), and an A site (aminoacyl-tRNA binding site).

What is the difference between the template and non-template strand of DNA? Describe the direction of a template strand of DNA relative to a mRNA transcript.

The template strand is the DNA strand the provides the pattern for ordering by complementary base pairing, the sequence of nucleotides in an RNA transcript. The non-template strand of DNA protects the template strand. The template strand is 3' to 5', and the mRNA transcript is 5' to 3'.

Describe how the translation process is terminated.

The translation process is terminated by the use of base triplets that act as signals to stop translation. A release factor binds directly to the stop codon on the A site. The release factor causes the addition of a water molecule instead of an amino acid to the polypeptide chain.

How many polypeptide chains are there in a protein?

There are 2 or more polypeptide chains in a protein.

How many levels of structure are present in a protein?

There are four levels of structure present in a protein: primary, secondary, tertiary, and quaternary. The primary structure is the unique structure of amino acids in a polypeptide. The secondary structure is the folding or coiling of the polypeptide into a repeating pattern, including the α helix and the β pleated sheet. The tertiary structure is the three-dimensional shape of a polypeptide, resulting from interactions between amino, carboxylic, and R groups. The quaternary structure is the overall protein structure that results from the aggregation of two or more polypeptide subunits.

What is transcription? Where does it take place, and why is it necessary? What enzyme transcribes mRNA?

Transcription is the DNA-directed synthesis of mRNA. It takes place in the nucleus of the cell and is necessary for the synthesis of proteins, which occurs in translation.

Compare and contrast transcription in prokaryotes and eukaryotes.

Transcription occurs in the nucleus of a cell in eukaryotes. In prokaryotes, transcription occurs in the cytoplasm. This allows for the translation of mRNA when transcription is still in progress.

Generally speaking, what is translation? Where does it occur?

Translation is the synthesis of a polypeptide (protein) using the information in the mRNA. It occurs in the cytoplasm of the cell.

Where does translation occur? What types of RNA are involved? Describe the origin of each type of RNA.

Translation occurs in the cytoplasm of the cell. tRNA (transfer RNA), mRNA (messenger RNA) and rRNA (ribosomal RNA) are involved. tRNA and mRNA are transcribed from DNA templates, while rRNA is transcribed and assembled with proteins imported from the cytoplasm.

Why do we say that the genetic code is universal?

We say that the genetic code is universal because they contain all the same amino acids.

Describe how tRNA moves through a ribosome during protein synthesis.

tRNA moves through a ribosome with the help of an aminoacyl-tRNA synthetase. The active site fits only a certain combination of amino acids and tRNA.