MV

Chapter 7

Chapter 7: From DNA to Protein - How Cells Read the Genome

7.1 Introduction to DNA and the Central Dogma

  • Discovery of DNA Structure:

    • The double helix structure was discovered in the 1950s by Watson, Crick, Wilkins, and Franklin.

    • Heredity is encoded in the linear sequence of four distinct nucleotides.

  • 4 Nucleotides:

    • They are responsible for coding the sequence that dictates protein synthesis.

    • Central question: How can a simple alphabet of 4 letters produce such a diverse array of proteins?

7.2 Flow of Genetic Information

  • Overview of the Flow:

    • DNA contains the instructions necessary to synthesize proteins.

    • The flow of genetic information is: DNA → RNA → Protein.

      • Central Dogma of Molecular Biology

  • Nucleotide Sequence:

    • Holds the genetic code for amino acids (aa's) that constitute proteins.

    • This sequence is transcribed into RNA, which is subsequently translated into proteins within ribosomes.

7.3 Transcription and RNA Processing

  • Universal Processes:

    • Transcription, RNA processing, and translation are processes that occur across all species (both prokaryotes and eukaryotes), albeit with some differences.

    • DNA → RNA: transcription

      • RNA chain synthesized = transcript

      • Primary RNA is directly used in the cytoplasm

      • transcript processed into a final mature RNA transcript that exist the nucleus to the cytoplasm. Then in the cytosol, the final RNA transcript associated with a ribosome either in the cytoplam or the rough ER

      • RNA → Protein: translation

From DNA to RNA

  • Different parts of the genome can be “used” by a different cell

  • Some genes transcribed in large/small/no quantities

    • Proteins are needed in large/small quantity or not needed

  • Different parts of the genome can be used in the same cell but at different times

  • RNA is a nucleic acid polymer that is similar to DNA in components and chemistry, has the same backbone structure linking nucleotides by phosphodiester bonds, and in polarity

    • It only looks different because it is single stranded

  • RNA is different than DNA because its sugar is ribose (instead of deoxyribose) and has ribonucleotides, it uses U instead of T, and is single stranded that has intra-molecular basepairing that can fold into many shapes to code into proteins and for structural, catalytic, and regulatory functions, and has no hydrogen bonds like DNA

  • RNA transcript identical to DNA’s NON-template strand

    • All T’s in DNA are Us in transcript

    • Substrate: DNA (template strand) + ribonucleotide triphosphates (NTPS)

    • Enzyme: RNA Polymerase

      • Catalyzes info of phosphodiester bonds between nucleotides (sugar to phosphate) which is the same as the DNA polymerase during replication

      • It uncoils the DNA

      • Adds the nucleotides one at a time in the 5’3 → 3’ direction

        • DNA polymerase: yes

        • DNA template not read same as replication: 3’ → 5’

        • Releases RNA strand almost immediately

        • Reads DNA template 3’ → 5’

        • Adds the RNA nucleotides 5’ → 3’

          • 5’ phosphate to 3’ hydroxyl

          • 5’ phosphate of incoming nucleoside triphosphate attacks 3’ OH

        • Orientation: Antiparallel replicating leading strand strand of DNA (without a primer)

      • It uses the energy trapped in the phosphoanhydride bonds to form new bonds

    • Product: Transcript or RNA transcript

    • New RNA released from duplex

      • Many copies of a gene can be made simultaneously; many cards (RNA Pols) of a train (DNA template)

      • Often many RNA copies begun before first is completely transcribed

    • Can have multiple RNA polymerase molecules catalyzing reactions on a gene at the same time

  • RNA Synthesis:

    • RNA polymerase reads the DNA template in a 3’ to 5’ direction and synthesizes RNA in a 5’ to 3’ direction.

    • In eukaryotes, primary RNA transcripts undergo processing (capping, polyadenylation, splicing)

Compare and Contrast: DNA Replication and RNA Transcription

Differences in RNA Transcription

  • RNa strand product does not stayed paired with DNA template vs replication

    • RNA dissociates and DNA recoils

    • Single stranded RNA free to cytoplasm in prokaryotes and nucleus in eukaryotes

  • 1 DNA strand (template) read in transcription is asymmetric while both DNA strands read in replication is semiconservative

  • Only a portion of DNA is transcribed; all DNA is replicated

RNA Pol is different from DNA Pol

  • Nucleotide building blocks

    • Ribonucleotides vs. Deoxyribonucleotides

  • Starting nucleic acid synthesis (polymerization)?

    • RNA pol can work without a primer

  • Correcting mistakes?

    • No proofreading what it transcribes

    • DNA pol error rate is 1 in 107 nucleotides

    • RNA pol have about 1 in 104 nucleotides

  • This error is acceptable is the only part of it is being used, so many genes are being made

7.4 Differences Between Prokaryotic and Eukaryotic Transcription

  • Prokaryotic Transcription:

    • Involves a single RNA Polymerase.

    • Transcription occurs within the cytoplasm.

  • Eukaryotic Transcription:

    • Involves multiple RNA Polymerases (primarily RNA Polymerase II).

    • Transcription takes place in the nucleus and requires transcription factors for initiation.

    • mRNA is processed prior to export into the cytoplasm.

7.5 RNA Processing in Eukaryotes

  • 3 Key Modifications:

    • 5’ Capping: Addition of a unique nucleotide that protects the RNA.

    • Polyadenylation: The addition of a poly-A tail to the 3’ end.

    • RNA Splicing: The removal of introns and the joining of exons to produce mature mRNA.

    • Small nuclear RNAs (snRNAs) and spliceosomes are crucial for the splicing process.

7.6 Translation: From RNA to Protein

  • Translation Steps:

    • Initiation: Involves the assembly of ribosomal subunits and the initiator tRNA, supported by initiation factors in eukaryotes.

    • Elongation: tRNAs deliver amino acids to the ribosome according to mRNA codons. Finished polypeptides elongate as the ribosomal subunits advance along the mRNA.

    • Termination: Translation concludes at stop codons (UAG, UAA, UGA); no tRNAs correspond to these codons, prompting release factors to bind and free the completed polypeptide.

7.7 The Role of Ribosomes

  • Functionality:

    • Ribosomes serve as the machinery for protein synthesis, composed of rRNA and proteins.

    • They contain multiple active sites for mRNA and tRNA binding, as well as for peptide bond formation.

7.8 Genetic Code and Codons

  • Defining Codons:

    • Codons are sequences of three nucleotides that specify particular amino acids during translation.

    • There are 64 potential codons, but only a subset corresponds to amino acids due to redundancy.

7.9 Polyribosomes and Efficiency

  • Efficiency in Translation:

    • Multiple ribosomes can simultaneously translate a single mRNA, thereby enhancing the efficiency of protein synthesis.

7.10 Summary of Key Concepts

  • Eukaryotes vs. Prokaryotes:

    • Differences in transcription initiation, processing of pre-mRNA, translation processes, and modifications of proteins.

  • Review: Recognizing the importance of understanding both transcription and translation processes is essential for a comprehensive grasp of gene expression.

Understanding the Central Dogma (DNA → RNA → Protein) is fundamental to advancing knowledge in cellular biology, genetics, and molecular biology.