Molecular Biology and Biochemistry

Computer-Assisted Note Taking

• Computers balance note-taking speed with real-time organization.

• AI transcripts can serve as a backup.

Accommodating Different Learning Styles

• Some students may effectively use AI, while others benefit from traditional methods.

• Instructors may be incoherent, rendering AI transcripts less effective.

Course Logistics

• The Google Drive has been reorganized.

• The course will continue with the remaining material, and a research paper will be uploaded.

Recursive Material: Amino Acid Qualities

• The course will cover material that builds on the qualities of amino acids.

• The exam will focus on extrapolations: changes to amino acids, codons, proteins, and cells.

• Genetic code is both practicable and recursive.

Exam Question: Sequence to Peptide

• A question will involve converting a given sequence into its corresponding peptide.

Codon Mutations and Their Impact

• Codons:

  • Mutations can occur at any of the three base pairs.

  • Third base pair (wobbly base pair):

    • Often leads to silent mutations with negligible downstream impacts.

    • Sometimes have silent mutations.

  • First base pair:

    • Changes can result in conservative substitutions of amino acids with similar properties.

Upstream vs. Downstream Analogy

• Upstream (DNA):

  • Changes have pervasive impacts.

  • Every protein printed may be altered.

• Downstream (aminoacyl tRNA synthetase grabbing the wrong amino acid):

  • Impacts are localized.

  • Only the specific protein may be affected.

Protein Synthesis Steps

• PrEP step: Aminoacylation of tRNA (activation).

• Initiation: Assembly of mRNA with small ribosomal subunits, addition of aminoacylated tRNA, and assembly of the large ribosomal subunit.

• Elongation: Repetitive formation of peptide linkages and codon movement.

Biochemistry vs. Molecular Biology

• Molecular biology:

  • Focuses on genetics and molecular influences on genes.

  • Popularized in the 1980s-2000s.

• Biochemistry:

  • Explosion of growth in the last 20 years.

  • Focuses on the chemistry and physics of biological processes.

Omitted Step: mRNA Processing

• Molecular biology perspective: Preparation and alternative splicing of mRNA before translation.

Importance of Basic Sciences

• The course emphasizes the importance of chemistry, organic chemistry, and physics for understanding biological phenomena.

• Biology is becoming more quantitative and chemistry-focused.

Termination and Processing

• Termination: mRNA and ribosome separate; small and large ribosomal subunits may be recycled or broken down via the ubiquitination pathway.

• Processing: Post-translational processing and folding (most diverse step).

Post-Translational Modification of Ribosomes

• Emerging research: Post-translational modification of ribosomes with TCA cycle intermediates.

Aminoacyl tRNA Synthetases

• Esterify 20 different amino acids to their corresponding tRNAs.

• Terminology:

  • Esterification: Process.

  • Ester linkage: Bond.

  • Aminoacylated tRNA: tRNA attached to the amino acid.

  • Aminoacyl linkage: Ester bond.

Specificity vs. Reusability

• A central problem in biology is balancing specificity with reusability.

• Aminoacyl tRNA synthetases act on specific amino acids but varying tRNA molecules.

• Ubiquitination pathway addresses protein degradation.

Charging Amino Acids

• ATP molecule + amino acid → aminoacyl adenylate (charged amino acid).

• Requires significant energy; organic chemistry allows for usable energy release to attach to the CCA motif at the tRNA's three prime end.

Class 1 and Class 2 Aminoacyl Synthetases

• Both classes:

  • Goal: Attach amino acids to the same position in the tRNA molecule; both have nucleophiles and electrophiles.

• Class one:

  • Attacks with the two prime hydroxide in that CCA motif. Specifically that A.

• Class two:

  • Attacks with the three prime hydroxide.

• Class one requires a transesterification reaction due to attacking with the wrong hydroxide.

Protein Demands and Cell Fate

• Protein demands of a given cell might dictate cell fate.

• Example: Pyrroline-5-carboxylate synthase in proline synthesis affects mitochondrial creation based on ATP demand.

• Cells with fewer aminoacyl tRNA synthetases express other enzymes to convert amino acids.

Aminoacyl Group

• The aminoacyl group is attached via an ester linkage at the three prime end of the tRNA molecule.

Class Specificity

• There need to be two different classes to work on the different amino acids.

Second Genetic Code

• Matching amino acids with the correct tRNA codon is referred to as a second genetic code.

• Less critical than the first genetic code.

Specificity of tRNA Molecules

• Only a few nucleotides in tRNA confer specificity.

• Example: Alanine tRNA requires a single GU pairing for recognition.

Start Codon: Methionine

• The first codon will be a methionine with asterisks.

• In prokaryotes: Formal Methionine

• In eukaryotes: Methionine.

• Different tRNA molecules are used for the star codon vs. internal methionine.

Initiation Factors and Ribosomal Subunits

• Components necessary for initation.

• I will note that the structure of the rest of this PowerPoint is that it will have the image explanation, image explanation. I will kind of jump through the explanations and focus on the images, and we'll do that verbally.

Shine-Dalgarno Sequence

• The Shine-Dalgarno sequence is a region in mRNA that signals the start codon is coming.

• It is complementary to ribosomal RNA and prevents initiation at incorrect AUG codons.

30s Subunit Assembly

• The 30s subunit assembles with IF1 and IF3.

• IF1 lodges at the A site to prevent early starts.

• IF3 lodges at the rim of the E site to prevent premature assembly of the large subunit.

tRNA Molecule Movement

• EPA (left to right).

• APE (order that tRNA moves through it).

• A: Accepting the next tRNA molecule.

• P: Protein Synthesis.

• E: Exit.

Ribosomal RNA

• That Chine Del Garneau sequence is complementary to that ribosomal RNA.

IF2 and GTPase Activity

• IF2 is a GTPase that recruits the tRNA molecule attached to formal methionine.

• The GTPase cleaves energy to dissociate initiation factors and allow the large subunit to attach.

Varying Sequences

• It can vary based on the story itself, iterating two different points.

• Occured early in evolution.

Beaks of Two Different tRNA Molecule.

• Imagine two different peaks, like, facing each other.

• Protein Synthesis:

  • PEEps are the site of that.

• Nucleophillic Attack:

  • A is going to attack the carboxlic in the c terminus.

Terminolgy

• The site of protein synthesis is the b site.

• The bond forms across the a and b p site.

• When that bond fully forms, the peptide will let go of one of the two things it's holding.

EF & Printer Analogy

• Our Efs here will is another GTPase.

• You are essentially pressing enter on the typewriter and starting at the beginning of the line again.