Chapt 5 notes

SPL

• Genetically engineered E. coli produce human insulin.

Chapter 5: Genetics

1. Overview of Genetics

• Genetics: Study of heredity.

• Explores:

  • Transmission of traits from parent to offspring (heritability)

  • Expression and variation of traits

  • Structure and function of genetic material

  • Changes in genetic material.

2. Genome

• Genome: Complete set of genetic material in a cell or virus (includes chromosomes, mitochondria, chloroplasts, and/or plasmids).

• Prokaryotes: One circular chromosome (DNA).

• Eukaryotes: Multiple linear chromosomes (DNA).

• Viral Genomes: Can be DNA or RNA; single or double-stranded.

• DNA Organization: DNA organized into complexes with protein to form chromosomes.

3. Genes and Chromosomes

• Chromosome: Subdivided into genes (fundamental units of heredity).

  • A gene is a DNA segment coding for a protein or RNA molecule.

• Gene Types:

  • Structural genes (code for proteins)

  • Genes coding for RNA

  • Genes that control gene expression.

• Genotype: The genetic makeup.

• Phenotype: The observable traits from the genotype.

4. Nucleotide Structure

• Nucleic acids: DNA and RNA composed of nucleotide monomers.

• Nucleotide Components:

  • 5-carbon sugar

  • Phosphate group

  • Nitrogen base (adenine, guanine, thymine, cytosine, or uracil).

• Covalent bonds form a sugar-phosphate backbone:

  • Each sugar attaches to two phosphates (5' carbon and 3' carbon).

5. DNA Structure

• DNA: Two strands twisted into a double helix.

• Sugar in DNA: Deoxyribose

• Nitrogen bases: A, T, C, G.

  • Single strands held by covalent phosphodiester bonds.

  • Base pairing: Adenine-Thymine (2 hydrogen bonds), Guanine-Cytosine (3 hydrogen bonds).

• Antiparallel arrangement: Strands run 3' to 5' and 5' to 3'.

6. RNA Structure

• RNA: Often single-stranded; made of ribonucleotides.

• Composition:

  • Ribose sugar

  • Nitrogen bases: Adenine, Uracil, Guanine, Cytosine.

• Directionality: 5’ to 3’.

7. Flow of Genetic Information

• Central Dogma: DNA -> RNA -> Protein.

• Recent understanding indicates flows of information may not be strictly unidirectional.

8. DNA Replication Process

• Eukaryotic vs Prokaryotic:

  • Similar processes; eukaryotic involves more factors and takes longer.

• Key Points:

  • Replication occurs on both strands simultaneously.

  • Complementary daughter strands are made from parental strands.

  • Semiconservative replication: Each new helix has one original strand.

9. Prokaryotic DNA Replication

• Starts at the origin of replication.

• Replication fork: Point of unwinding in a circular chromosome, bidirectional.

• Completed copies separate at the end of replication.

10. Key Steps in Bacterial DNA Replication

• DNA polymerase: Cannot start new strand; requires a primer, builds in a 5' to 3' direction.

• Leading strand: Continuously copied in the same direction as unwinding.

• Lagging strand: Copied in the opposite direction, with Okazaki fragments.

11. Applications of the DNA Code

• DNA transcription to RNA, followed by translation into proteins.

• RNA types in transcription:

  • mRNA, tRNA, rRNA

  • Regulatory RNAs (miRNA, interfering RNA, riboswitches).

12. Gene-Protein Connection

• RNA triplets specify amino acids.

• Proteins influence phenotype; the primary structure determines function.

13. Types of RNA in Translation

• mRNA: carries genetic message in codons.

• rRNA: forms ribosomes, combines with proteins.

• tRNA: adapter molecule delivering amino acids to ribosomes.

14. Overview of Transcription

• Transcription: The first stage of protein synthesis.

• Enzyme: RNA polymerase; uses DNA as a template.

• Process occurs differently in prokaryotes (cytoplasm) and eukaryotes (nucleus).

  • Energy-intensive and tightly regulated.

• Steps:

  1. RNA polymerase binds promoter; DNA unwinds.

  2. RNA is synthesized 5' to 3'; complementary ribonucleotides added.

  3. Termination sequence signals RNA polymerase to detach.

15. Splicing of Eukaryotic mRNA

• Prior splicing modifies mRNA before translation.

• Exons: Coding sequences.

• Introns: Non-coding sequences removed during splicing.

• Splicing can influence protein expression.

16. The Genetic Code

• Code: mRNA codons specify amino acids; universal among organisms.

• Redundancy from the wobble hypothesis; two nonstandard amino acids involved.

17. Interpreting the DNA Code

• Complementary mRNA produced during transcription.

• tRNAs interpret mRNA codons, delivering corresponding amino acids.

• First two codon positions show Watson-Crick pairing; third can wobble.

18. Overview of Translation

• After ribosome release, proteins undergo post-translational modifications for functionality.

19. Polysome Formation

• Polyribosomal complex allows for efficient protein production in prokaryotes and eukaryotes.

20. Control of Protein Synthesis

• Operons, quorum sensing, and riboswitches.

21. Operons

• Operons: Collections of genes controlled by shared regulatory elements.

  • Found primarily in prokaryotes and some eukaryotes.

  • Components: promoter, genes, repressor, operator.

  • Types: Inducible (off by default) & Repressible (on by default).

22. Lactose Operon: An Inducible Operon

• Operon is off when lactose is absent; on when lactose is present and glucose is absent.

23. Arginine Operon: A Repressible Operon

• Operon is on when arginine is low; off when arginine is abundant.

24. Quorum Sensing

• Bacteria communicate via quorum sensing, altering gene expression based on population density.

• Secretion of signaling molecules (e.g. AHL lactone) drives these changes.

25. Riboswitches

• Built-in switches in mRNA that regulate protein synthesis without translation.

• Common regulatory elements among bacteria.

26. Causes of Mutations

• Induced mutations: Result from mutagens.

• Spontaneous mutations: Random changes during replication.

27. The Ames Test

• Identifies mutagens that may cause cancer by exposing histidine-deficient bacteria to suspected agents.

28. Categories of Mutations

• Classes: Substitution, Insertion, Deletion.

• Effects vary: Missense, Nonsense, Silent, Reversion, and Frameshift mutations.

29. Repair of Mutations

• Enzymatic mechanisms to repair damaged DNA:

  • DNA polymerase (proofreading)

  • Mismatch repair

  • Direct repair

  • Nucleotide excision repair.

30. DNA Recombination Events

• Horizontal gene transfer: Passes genetic information independently of cell division.

• Methods: Conjugation, Transformation, Transduction.

31. Conjugation

• Plasmid or chromosomal fragment transfer between living, related cells via a pilus.

32. Transformation

• Uptake of DNA from the environment into cells, can be natural or induced.

33. Transduction

• DNA transfer via bacteriophages, which can involve generalized or specialized transduction.

34. Transposons

• Jumping genes that can alter genomes by moving within DNA; implicated in mutations.

• Classes: Retrotransposons (RNA intermediate) and DNA transposons.

35. Q&A Recap

• Q1: Transformation vs Conjugation (Answer: Transformation takes DNA from environment).

• Q2: Enzyme unwinding DNA (Answer: Helicase).

• Q3: RNA bringing amino acids (Answer: tRNA).

• Q4: Eukaryotic transcription/translation occur simultaneously (Answer: False).

• Q5: Mutation changing normal codon to stop codon (Answer: Nonsense mutation).

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