Comprehensive Protein Synthesis: Transcription, Translation, and Regulation in Molecular Biology

Central Dogma of Molecular Biology

DNA makes RNA makes Protein.

Transcription

Generates a single-stranded RNA directed by the sequence of DNA.

mRNA

The 4-letter language of DNA (ATGC) is transcribed into a similar language for mRNA (AUGC).

Hydrogen bonds in Transcription

H-bonded complementary base pairs are formed (A-U, T-A, G-C, C-G).

Translation

Converts nucleotide sequence of m-RNA into the sequence of amino acids comprising a protein.

Gene

DNA section that codes for one specific protein.

Messenger RNA (mRNA)

Consists of a reverse copy of the bases transcribed off the template strand of the DNA.

Ribosome

Translator and protein assembly site that reads the base sequence off mRNA codons.

Transfer RNA (tRNA)

'Truck' used to pick up requested amino acid and bring it over to ribosome.

Transcription Steps

Transcription involves 3 steps: Initiation, Elongation, Termination.

Initiation

Special DNA sequences called Promoters direct RNA polymerase to proper site to initiate transcription.

Open Promoter Complex

RNA polymerase unwinds about 17 base pairs of ds DNA to form the open promoter complex.

Transcription Bubble

Region containing RNA polymerase, DNA, and RNA product during elongation.

Direction of RNA Synthesis

Direction of synthesis is 5' to 3'.

Phosphodiester Bond

New phosphodiester bond formed during RNA elongation.

Coding Strand

The sequence of m-RNA is exactly the same as the coding strand (except T replaced by U).

Template Strand

The strand of DNA that is used as a template for transcription.

Transcription Factors

Regulatory proteins that bind the promoters & interact with RNA polymerase.

Closed Promoter Complex

Complex formed when the promoter is initially located by polymerase, with the DNA helix not unwound.

RNA Elongation Process

Once the DNA is unwound, elongation takes place.

Transcription Problem

Write the sequence of mRNA that corresponds to the given DNA sequence.

DNA-RNA hybrid helix

An intermediate in RNA synthesis consisting of approximately 8 nucleotides.

Termination of Transcription

Elongation continues until a termination signal is detected, which is a hairpin structure followed by several uracil residues.

Stop signal

A hairpin structure followed by several uracil residues that indicates the end of transcription.

Nascent mRNA

mRNA that travels out of the nucleus through nuclear pores to find a ribosome.

Gene Expression & Regulation

The control of the process of gene expression influenced by various factors.

Regulation of Gene Expression

Influenced by regulation of transcription, RNA processing, and the nuclear membrane.

Promoter

A DNA sequence that initiates transcription of a particular gene.

TATA box

Located between positions -24 and -32 bp upstream of the initiation site, it is essential for RNA polymerase binding.

Initiator element (Inr)

Located between base pairs -3 and +5, often paired with the TATA box.

Downstream core promoter element (DPE)

Located between base pairs +28 and +35, it plays a role in transcription initiation.

CAAT box

A regulatory element located between -40 and -150 bp upstream of the gene.

GC box

Another regulatory element located between -40 and -150 bp upstream of the gene.

Steroid hormones

Powerful regulatory molecules that control gene expression, such as estradiol.

Estradiol

A hormone that controls genes involved in the development of female secondary sex characteristics.

Progesterone

A hormone involved in mammary gland development, a secondary sex characteristic.

Pre-mRNA

Messenger RNA precursors synthesized by RNA polymerase II that undergo processing.

5' cap addition

Modification of the 5' end of pre-mRNA by adding a GTP.

Poly A tail addition

A stretch of polyadenylate added to the 3' end of pre-mRNA, typically about 250 nucleotides long.

Splicing

The process of removing noncoding stretches of RNA (introns) and ligating the remaining exons to form mature mRNA.

Defects in Splicing

Can cause diseases in humans due to improper processing of mRNA.

Gene expression in prokaryotes

The primary transcript serves as mRNA and is used immediately as a template for protein synthesis.

Gene expression in eukaryotes

mRNA precursors are processed and spliced in the nucleus before being transported to the cytoplasm for translation.

Genetic Code

Protein synthesis is a process of translation. Nucleic acid sequence information in DNA is translated into amino acid sequence information.

Codon

Three nucleotides, called a codon, encode an amino acid.

Nonoverlapping Code

The genetic code is nonoverlapping.

No Punctuation Code

The genetic code has no punctuation.

Direction of Code Reading

The genetic code is read in the 5' to 3' direction.

Degenerate Code

The genetic code is degenerate.

Universal Code

The genetic code is universal.

Start Codon

AUG codon signals the start of translation.

Stop Codon

UAA, UGA, UAG signals termination.

Reading Frame

It is one of the 3 possible ways to read off the bases of mRNA in triplets.

Open Reading Frame (ORF)

Sequence of mRNA (or corresponding DNA) that can be translated to a protein.

Transfer RNA (t-RNA)

Transfer RNA (tRNA) molecules function as an adaptor molecule between a codon and an amino acid.

Cloverleaf Shape of tRNA

All tRNA molecules have a cloverleaf shape.

Acceptor Stem

AA-accepting region is called acceptor stem.

Amino Acid Attachment

Amino Acid is attached to a -OH group of A in the CCA region of the acceptor stem.

Phosphorylated 5' End

The 5' end is phosphorylated and the 5' terminal residue is G.

Anticodon

The anticodon is in a loop near the center of the sequence.

Codon-Anticodon Interactions

The code is read off m-RNA base sequence H-bonding between codon (mRNA) and anti-codon of specific t-RNA.

t-RNA Synthetase

Each aminoacyl-tRNA synthetase is specific for a particular amino acid.

Loading-Up Reaction

Analogy: Twenty different colored trucks = 20 specific t-RNAs.

Ribosome Size

70S in size and is composed of two subunits, a large 50S subunit and a smaller 30S subunit.

Polyribosomes

Several ribosomes can translate an mRNA molecule at the same time, forming polyribosomes or polysomes.

Wobble Hypothesis

Some tRNA molecules can recognize more than one codon.

Ribosomes

Cellular structures where protein synthesis occurs, containing three tRNA binding sites: A, P, and E.

A site

The aminoacyl site on the ribosome that binds the incoming tRNA.

P site

The peptidyl site on the ribosome that binds the tRNA with the growing peptide chain.

E site

The exit site on the ribosome that binds the uncharged tRNA before it leaves the ribosome.

30S initiation complex

The initial complex formed during the initiation phase of translation.

70S initiation complex

The complex formed at the end of the initiation phase of translation.

Elongation

The second step of translation where the polypeptide chain is extended.

Elongation factor Tu (EF-Tu)

A protein that delivers the appropriate aminoacyl-tRNA to the A site.

Elongation factor Ts (EF-Ts)

A protein that induces the release of GDP from EF-Tu, allowing another cycle to begin.

Peptide bond formation

An exergonic process catalyzed by the enzyme Peptidyl transferase.

Translocation

The process where the mRNA moves through the ribosome by a distance corresponding to one codon.

Elongation factor G (EF-G)

Also called the translocase, it uses GTP hydrolysis energy to translocate the mRNA.

Termination

The final step of translation where the polypeptide chain is released upon encountering a stop codon.

Release factors (RF)

Proteins that recognize stop codons and facilitate the release of the complete protein.

Stop codons

Codons (UAA, UGA, UAG) that signal the termination of protein synthesis.

GTP hydrolysis

The process that provides energy for translocation and other steps in translation.

Polypeptide chain growth

The process of synthesizing a protein chain by the successive addition of amino acids.

N-terminal

The end of a polypeptide chain that has a free amino group.

C-terminal

The end of a polypeptide chain that has a free carboxyl group.

Genetic code problem

An exercise involving transcription and translation of a given DNA sequence.