Chap 5B

Protein Synthesis

Overview of Protein Synthesis

Protein synthesis, also known as gene expression, is the process by which genetic information within a cell is read and used to create gene products, primarily proteins. This process is essential for cell survival and function, as proteins carry out most cellular activities.

• Transcription: The process of copying genetic information from DNA to RNA.

• Translation: The process by which ribosomes decode mRNA to build proteins.

• Protein synthesis occurs in the nucleus of eukaryotes and the cytoplasm of prokaryotes.

Transcription

Steps of Transcription

Transcription is the first stage of protein synthesis, where a segment of DNA is used as a template to synthesize RNA.

• Initiation: RNA polymerase binds to the promoter region of DNA.

• Unwinding: The DNA double helix is unwound to expose the template strand.

• Elongation: RNA polymerase lays down complementary ribonucleotides (A pairs with U, G pairs with C).

• Termination: Transcription continues until a termination sequence is reached, at which point RNA polymerase falls off the DNA and the newly made RNA transcript is released.

Reverse Transcription

Definition and Biological Significance

While genetic information usually flows from DNA to RNA to proteins, some cells and viruses can perform reverse transcription.

• In reverse transcription, RNA is used as a template to build complementary DNA (cDNA).

• This process requires the enzyme reverse transcriptase.

• Reverse transcription is a key step in the life cycle of retroviruses such as HIV.

Types of RNA in Protein Synthesis

Messenger RNA (mRNA), Transfer RNA (tRNA), and Ribosomal RNA (rRNA)

Three main types of RNA participate in protein synthesis, each with a distinct role:

• Messenger RNA (mRNA): Contains codons that code for either an amino acid or a stop signal.

• Transfer RNA (tRNA): Contains an anticodon loop complementary to the codon and carries the correct amino acid to the ribosome to build proteins.

• Ribosomal RNA (rRNA): Folds into 3D structures and combines with proteins to form ribosomes.

In prokaryotes, one mRNA molecule can carry codes for several different proteins (polycistronic), while in eukaryotes, mRNA is usually monocistronic (codes for one protein).

Splicing of mRNA

mRNA Processing in Eukaryotes

In eukaryotic cells, mRNA must be processed before it can be translated. This involves the removal of non-coding sequences and joining of coding sequences.

• RNA splicing: The process of clipping out certain sequences in RNA and joining the remaining parts by a spliceosome.

• Exons: Segments of mRNA that are decoded to build a protein (KEPT).

• Introns: Intervening sequences of mRNA that are not decoded to build the protein (CUT).

• Alternative splicing allows for new combinations of exons, increasing protein diversity.

Splicing occurs in many types of RNA in both prokaryotes and eukaryotes, but mRNA splicing is a key feature in eukaryotes.

Ribosomes and Translation

Structure and Function of Ribosomes

Ribosomes are the molecular machines that perform translation. They are composed of a large and a small subunit that combine to form an active ribosome.

• In eukaryotes, the ribosome is made up of a 60S large subunit and a 40S small subunit, forming an 80S ribosome.

• Ribosomes read the mRNA and facilitate the addition of amino acids to the growing polypeptide chain.

The Genetic Code and Amino Acids

Codons and the Redundancy of the Genetic Code

The genetic code is the set of rules by which information encoded in mRNA is translated into proteins. It is based on codons, which are sequences of three nucleotides.

• There are 4 nucleotides in RNA (A, U, G, C), and 3 nucleotides make up a codon, resulting in 64 unique codons ($4 \times 4 \times 4 = 64$).

• 64 codons encode:

  • 60 sense codons (code for 22 amino acids)

  • 3 nonsense codons (stop signals)

  • 1 start signal

• The codons in mRNA guide the production of all proteins.

• The genetic code exhibits redundancy: a single amino acid can be coded by multiple codons (e.g., there are six codons for leucine).

• Redundancy in the genetic code helps protect cells from genetic changes (mutations).

Table: The Genetic Code

First Base	Second Base	Third Base	Amino Acid	Codon(s)
U	U	U, C	Phenylalanine	UUU, UUC
U	U	A, G	Leucine	UUA, UUG
A	U	G	Methionine (Start)	AUG
U	A	A, G	Stop	UAA, UAG
U	G	A	Stop	UGA
G	G	Any	Glycine	GGU, GGC, GGA, GGG

Translation Process

Steps of Translation

Translation is a rapid and accurate process by which ribosomes synthesize proteins using the information encoded in mRNA.

• Initiation: The ribosome assembles around the target mRNA. The first tRNA is attached at the start codon.

• Elongation: The ribosome continues to translate each codon in turn, adding the appropriate amino acid to the growing polypeptide chain.

• Termination: When a stop codon is reached, the ribosome releases the polypeptide chain.

• In E. coli, translation can add up to 20 amino acids per second and only misreads about one in 10,000 codons.

Example: Start and Stop Codons

• Start codon: AUG (codes for methionine)

• Stop codons: UAA, UAG, UGA

Summary Table: Key Features of Protein Synthesis

Feature	Prokaryotes	Eukaryotes
Location of Transcription	Cytoplasm	Nucleus
mRNA Processing	Rare/Absent	Splicing, capping, polyadenylation
mRNA Type	Polycistronic	Monocistronic (usually)
Translation Initiation	Shine-Dalgarno sequence	5' cap recognition

Additional info: The notes above are expanded with academic context to ensure clarity and completeness for exam preparation. The genetic code table is a simplified version; students should refer to a full codon table for all 64 codons.