Transcription and Translation: The Central Dogma of Molecular Biology, Lecture notes of Biology

A comprehensive overview of transcription and translation, the fundamental processes by which genetic information encoded in dna is converted into functional proteins. It delves into the key players involved, including rna polymerase, mrna, trna, and ribosomes, and explains the intricate mechanisms of these processes in both prokaryotes and eukaryotes. The document also explores the genetic code, mutations, and the significance of splicing in eukaryotic gene expression.

Typology: Lecture notes

2023/2024

Uploaded on 02/11/2025

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15.1 Experiments Have Revealed the Nature of Genes
Nutritional mutation: a mutation affecting a synthetic pathway for a vital compound such as
amino acid or vitamin.
- Resulting from damage to genes encoding functions necessary to make important
biological molecules
- They concentrated on the ability to synthesize the amino acid arginine where the
biosynthetic pathway was known called “arg” mutants.
- Beadle and Tatum found that all the arg- could be assigned to one of four chromosomal
locations
oargE
oargF
oargG
oargH
One-gene/one-enzyme hypothesis
- To determine where each mutation was blocked in the biochemical pathway for arginine
biosynthesis, the researchers supplemented the medium with each intermediate in the
pathway to see which would support each mutant’s growth.
oIf mutation affects an enzyme in the pathway that acts prior to the supplement,
then growth should be supported
oIf not, the mutation affects a step after the intermediate used.
- Through this approach, they were ablet. Isolate a mutant strain defective for each enzyme
in the biosynthetic pathway.
oEach of the mutants they examined had a defect in a single enzyme caused by a
mutation at a single site on a chromosome.
- In conclusion they believed that genes specify the structure of enzymes, and that each
gene encodes the structure of one enzyme.
oOne-gene/one-enzyme hypothesis
- Today, because many enzymes contain multiple polypeptide subunits, each encoded by a
separate gene, the relationship is more commonly referred to one-gene/one-polypeptide
hypothesis
Crick States the Central Dogma
- How is the information stored in DNA converted to protein enzymes?
oInformation passes in one direction from the gene (DNA) to an RNA copy of the
gene, which directs the sequential assembly of a chain of amino acids into a
protein
DNA mRNA protein
Transcription: the enzyme-catalyzed assembly of an RNA molecule complementary to a strand
of DNA
- Produces an exact copy of the DNA
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15.1 Experiments Have Revealed the Nature of Genes

Nutritional mutation : a mutation affecting a synthetic pathway for a vital compound such as amino acid or vitamin.

  • Resulting from damage to genes encoding functions necessary to make important biological molecules
  • They concentrated on the ability to synthesize the amino acid arginine where the biosynthetic pathway was known called “ arg” mutants.
  • Beadle and Tatum found that all the arg- could be assigned to one of four chromosomal locations o argE o argF o argG o argH

One-gene/one-enzyme hypothesis

  • To determine where each mutation was blocked in the biochemical pathway for arginine biosynthesis, the researchers supplemented the medium with each intermediate in the pathway to see which would support each mutant’s growth. o If mutation affects an enzyme in the pathway that acts prior to the supplement, then growth should be supported o If not, the mutation affects a step after the intermediate used.
  • Through this approach, they were ablet. Isolate a mutant strain defective for each enzyme in the biosynthetic pathway. o Each of the mutants they examined had a defect in a single enzyme caused by a mutation at a single site on a chromosome.
  • In conclusion they believed that genes specify the structure of enzymes, and that each gene encodes the structure of one enzyme. o One-gene/one-enzyme hypothesis
  • Today, because many enzymes contain multiple polypeptide subunits, each encoded by a separate gene, the relationship is more commonly referred to one-gene/one-polypeptide hypothesis

Crick States the Central Dogma

  • How is the information stored in DNA converted to protein enzymes? o Information passes in one direction from the gene (DNA) to an RNA copy of the gene, which directs the sequential assembly of a chain of amino acids into a protein  DNA  mRNA  protein Transcription : the enzyme-catalyzed assembly of an RNA molecule complementary to a strand of DNA
  • Produces an exact copy of the DNA

Translation : the assembly of a protein on the ribosome using mRNA to specify the order of amino acids.

  • Requires translating from the nucleic acid to the protein “languages”

Transcription makes an RNA copy of DNA

  • Produces RNA copy of the information in DNA, the DNA-directed synthesis by using RNA polymerase o Uses the principle of complementarity to use DNA as a template to make RNA Template Strand : the DNA strand that is used as a template in transcription, this strand is copied to produce a complementary mRNA transcript Coding Strand: the strand of DNA duplex that is the same as the RNA encoded by a gene. This strand is NOT used as a template in transcription only to be complementary to the template o Same sequence as the RNA transcript except U (uracil) in the RNA is T (Thymine) in the DNA strand.

Translation uses information in RNA to synthesize proteins

  • Translation is much more complex that RNA cannot be used as a direct template for a protein because there is no complementarity o A sequence of amino acids cannot be aligned to an RNA template based on any kind of “chemical fit.”
  • Transfer RNA (tRNA) were found to be some kind of adapter molecule that can interact with both RNA and amino acids

RNA has multiple roles in gene expression

mRNA: the RNA transcribed from structural genes; RNA molecules complementary to a portion of one strand of DNA which are translated to ribosomes to form proteins. rRNA: a class of RNA molecules found in ribosomes transcribed from the DNA of the nucleolus tRNA: amino acids that are covalently attached to one end and an anticodon that can base-pair with an mRNA codon at the other.

  • They act to interpret information in mRNA and to help position the amino acids on the ribosome snRNA: in eukaryotes, a small RNA sequence that facilitates recognition and excision of introns by base-pairing with the 5’ end of an intron or at the branch site of the same intron SRP RNA : in eukaryotes, a complex of proteins that recognizes and binds to the signal sequence of a polypeptide then docks with a receptor that forms a channel in the ER membrane and the polypeptide is released into the lumen of the ER.

15.3 Prokaryotes Exhibit All the Basic Features of Transcription

Stages of Prokaryotic Transcription

  • The single RNA polymerase of prokaryotes exists in two forms o Core Polymerase: can synthesize RNA using DNA template but cannot initiate synthesis accurately composed of four subunits  α subunits, a β subunit, and a β’ subunit o Holoenzyme: can accurately initiate synthesis Initiated at the Promotor Region (-35 to -10 nucleotides) and terminated at the Rho terminator site.
  1. In order to initiate transcription in bacteria, core RNA polymerase and sigma factor form a holoenzyme
  2. Sigma factor recognizes the sequence of DNA at the promotor region
  3. This holoenzyme then binds to the promotor region of the DNA molecule forming the closed complex between RNA polymerase and the DNA molecule
  4. By breaking hydrogen bonds of bases in the double helix the closed complex is converted into the open complex
  5. The formation of the RNA transcript from nucleotide triphosphates then takes place as RNA polymerase is forming the new transcript starting at the 5’ end of the transcript
  6. New nucleotides are added onto the free 3’ end
  7. The initiation of transcription is completed when the sigma factor is released

Initiation

  • The action of the polymerase moving along the DNA can be thought of as analogous to water flowing in a stream o Sites on the DNA can be seen as “upstream” or “downstream” of the start site
  • The first base transcribed is called +1 and this numbering continues downstream until the last base is transcribed.
  • Any bases upstream of the start site receive negative numbers, starting at -

Elongation

  • The transcription of the RNA chain usually starts with ATP or GTP
  • One of these forms the 5’ end of the chain which grows 5’ to 3’ as ribonucleotides are added to the 3’ end.
  • As the RNA polymerase molecule leaves the promoter region, the σ factor is no longer needed o This process of leaving the promoter is called clearance or escape Transcription Bubble: The region containing the RNA polymerase, the DNA template and the growing RNA transcript because it contains a locally unwound “bubble” of DNA.

Termination

  • The end of transcription unit is marked by terminator sequences that signal “stop” to the polymerase.
  • Reaching these sequences causes the formation of phosphodiester bonds to cease and the RNA-DNA hybrid within the transcription bubble to dissociate, and the RNA polymerase to release the DNA, and the DNA within the transcription bubble to rewind.
  • The formation of the hairpin causes the RNA polymerase to pause, placing it directly over the run of four uracils.
  • The pairing of U with the DNA’s A is the weakest of the four hybrid base pairs and isn’t strong enough to hold the hybrid strands when the polymerase pauses.
  • Instead the RNA strand dissociates from the DNA within the transcription bubble and stops

Coupling Transcription to Translation

  • The mRNA produced by transcription begins to be translated before transcription is finished, they are coupled.
  • As soon as the 5’ end of the mRNA becomes available, ribosomes are loaded onto this to begin translation. o This only occurs in prokaryotes not eukaryotes because transcription occurs in the nucleus and translation occurs in the cytoplasm Operon: a cluster of adjacent structural genes transcribed as a unit into a single mRNA molecule

The 3’ Poly-A Tail

  • Unlike in prokaryotes, in eukaryotes the end of the transcript is not the end of the mRNA.
  • The eukaryotic transcript is cleaved downstream of a specific site prior to the termination site called the polyadenylation signal sequence (AAUAAA).
  • A series of adenine (A) residues, called the 3’ poly-a trail is added after this cleavage by the enzyme poly-A polymerase. o 3’ poly-A tail: a series of 1-200 adenine residues added to the 3’ end of an mRNA, the tail appears to enhance the stability of the mRNA by protecting it from degradation

15.5 Eukaryotic Genes May Contain Noncoding Sequences

Introns: portion of mRNA as transcribed from eukaryotic DNA that is removed by enzymes before the mature mRNA is translated into protein Exons: a segment of DNA that is both transcribed into RNA and translated into protein.

RNA Splicing is Carried Out by the Spliceosome

pre-mRNA splicing: in eukaryotes, the process by which introns are removed from the primary transcript to produce mature mRNA that occurs in the nucleus prior to the export of the mRNA to the cytoplasm. snRNPs: complexes composed of snRNA and protein cluster together with other associated proteins to form a larger complex called the spliceosome o Spliceosome: responsible for the splicing/removal/excision of introns and joining exons to convert the primary transcript into the mature mRNA.

  • For splicing to occur accurately, the spliceosome must be able to recognize intron-exon junction
  1. A spliceosome is composed of several small molecules called snRNPs that are made up of proteins and small RNA molecules
  2. Formation of the spliceosome begins when one kind of the snurp binds to the 5’ end of an intron and another snurp binding to the 3’ end of the intron (exon)
  3. Additional snurps then interact with the complex bringing the two ends of the intron together and causing the intron to form a loop. a. This also gathers all the snurps together as the completed spliceosome
  • Duplication
  • Insertion
  • The amount of DNA that can be deleted without drastic consequences is dependent on the region of the genome, but large deletions are usually lethal