Protein Synthesis

• Secondary structure—this is the structure component related to the protein’s three-dimensional shape. There are two major protein structures. The alpha helix is a coiled string structure mad by hydrogen bonding in the protein’s polypeptide chain. The beta pleated sheet is a folded or pleated structure made by hydrogen bonding lined up so that there are parts of the chain lying side-byside with one another.

• The tertiary structure of the protein molecule is also three-dimensional but it is determined by specific interactions of the R side chains. The R group can be hydrophobic or hydrophilic, which determines how the peptide is folded.

Hydrophobic groups will fold themselves to keep these groups away from water.

There can be hydrogen bonding, ionic bonding, and disulfide bridges between R groups that specifically determine the peptide’s shape. Van der Waals forces also help the polypeptide have a particular shape.

• The quaternary structure is the structure made of the protein by the interaction of more than one peptide unit. It is the type of structure formed by molecules like hemoglobin, which actually consists of two pairs of globular subunit chains.

PROTEIN SYNTHESIS

Protein synthesis is actually a drawn-out process that starts with the DNA blueprint in the nucleus of the cell. The basic function of DNA is to encode for proteins that are made in the ribosomes of the cell. DNA in the cell only codes for proteins; it does not code for other cellular structures.

The genome of the cell is the full complement of DNA for the cell, while the proteome is the entirety of the proteins made by the cell. Genes are discrete sections of DNA that encode for specific proteins. There are about 20,000 genes in the human genome. Most of the DNA, however, is not made into genes and is considered noncoding DNA.

Proteins are made from amino acids and are made by “reading” the DNA in the genome. Remember that, for DNA, there are four different bases (adenine, thymine, guanine, and cytosine). In order for there to be enough sections of DNA to encode for all the possible twenty amino acids plus sections for starting and stopping protein synthesis, the DNA

segments must be read in “triplets” or groups of three bases. An example is the DNA code for valine, which is CAC for cytosine, adenine, and cytosine).

One of the important things in reading these sequences is not to be off by even one base pair. Because they are read in triplets, a missing or added base pair will throw off the entire sequence read from the point onward after the mutation is found. Sometimes, the base will be replaced by another base, leading to misreading of the triplet but with less of an impact than if a base was added or subtracted.

Transcription involves the reading of a segment of DNA in a gene in order to make messenger RNA or mRNA. This happens through the action of an enzyme called RNA polymerase. The DNA, which is normally tightly wound, gets unwound and read frame by frame in triplet code by this enzyme, leading to a single strand of messenger RNA that goes on to make proteins.

There are different types of RNA that have different functions. Most RNA is singlestranded, while DNA is almost always double-stranded. The different types of RNA include ribosomal RNA, which makes up the structure of ribosomes, messenger RNA, which is what gets transcribed into the RNA message in the nucleus, and transfer RNA, which adds the amino acids to the growing peptide chain one amino acid at a time.

Transcription occurs in the nucleus. Messenger RNA gets transcribed from the DNA template, making the single strand of RNA that ultimately exits the nucleus to go to the ribosomes in order to make protein. The RNA molecule is organized into codons, which are the triplet sequences that “code” for amino acids. There are three stages to the transcription process: initiation, elongation, and termination. Figure 31 shows the process of transcription and subsequent translation:

Figure 31.

There is a promotor region that is associated with the initiation process. This is the part of the gene that gets read first. Elongation happens when RNA polymerase unwinds the segments of DNA, reading fragments of the gene from one end to the other, creating a length of messenger RNA. Termination happens with a “stop” signal. This involves the reading of one of three specific triplets that indicate the release of the completed messenger RNA transcript.

In actuality, messenger RNA is not what comes off the transcription process. Instead, it is called pre-mRNA, which needs splicing in order to get rid of noncoding regions of RNA, leaving behind mature messenger RNA. There is a complex called a “spliceosome” that helps this process happen. The intron is the removed section of messenger RNA, while the exon is the section of RNA that remains to be translated into protein.

Translation is the process of making protein out of messenger RNA and transfer RNA. It requires the messenger RNA molecule that comes from the nucleus after being transcribed from DNA. Transfer RNA is necessary to add one amino acid at a time to the growing polypeptide chain. This takes place in the ribosomes.

The ribosomes are what makes rough endoplasmic reticulum “rough” in appearance. The ribosome is made out of ribosomal RNA and proteins. There are two components to the ribosome: a small subunit and a large subunit. The two subunits come together in order to attach to the messenger RNA. This aligns the messenger RNA so that it can

interact with transfer RNA. It is the transfer RNA that contains a specific amino acid on each molecule in order to add to the polypeptide. Figure 32 shows what ribosomes look like:

Figure 32.

The transfer RNA molecule is made up of an anticodon that matches with the triplet codon on the messenger RNA. As in the case of transcription, there is initiation, elongation, and termination. The polypeptide chain gets added on one amino acid at a time until there is a stop codon read. This stops the process so that the protein synthesis stops.