PPT 1

DNA Replication, Gene Expression, and Regulation

Overview of Bacterial Processes

• Bacteria replicate DNA through specific processes.
• The central dogma of molecular biology: DNA → RNA → Protein.
• Gene regulation is vital for both prokaryotes and eukaryotes, controlling transcription and translation.

Learning Outcomes

• Distinguish between DNA and RNA characteristics.
• Explain the significance of gene regulation in cells.
• Describe the DNA replication process.
• Detail transcription, including the roles of RNA polymerase, sigma factors, promoters, and terminators.
• Explain translation, highlighting mRNA, ribosomes, rRNAs, tRNAs, and codons.

Dental Biofilm Case Study

• Patient History: Tina, a 33-year-old, experienced gum pain and stains on her pillow.
• Examination: Swollen gums that bled upon probing, with 5 mm deep pockets and bone loss evident in X-rays.
• Diagnosis: Periodontitis, an inflammatory gum and bone disease caused by dental plaque biofilm.
• Plaque, a biofilm of mixed bacterial species, leads to tooth loss without proper oral hygiene.
• Testing: PCR test to identify bacteria in plaque by amplifying and sequencing bacterial DNA.
• Identified bacteria: Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, both Gram-negative anaerobes.
• These bacteria are sensitive to metronidazole and amoxicillin, respectively.

DNA: The Blueprint of Life

• DNA dictates the diversity of life through its encoded information.
• Composed of nucleotides, each with a nucleobase: Adenine (A), Thymine (T), Cytosine (C), Guanine (G).
• Three nucleotides encode a specific amino acid.
• Amino acids form proteins; the amino acid sequence determines the protein's structure and function.
• Proteins include structural proteins and enzymes.

Genome Overview

• Genome: The complete set of genetic information, including chromosomes and plasmids.
• All cells have a DNA genome, while viruses may have an RNA genome.
• Gene: The functional unit that encodes a gene product, typically a protein.
• Genomics: The study of nucleotide sequences of DNA.

Cell Multiplication Tasks

• Cells multiply through:
  • DNA replication.
  • Gene expression: decoding DNA to synthesize gene products.
• Transcription: Copying DNA information into RNA.
• Translation: Using RNA to synthesize the encoded protein.

Central Dogma

• Information flow: DNA → RNA → Protein.
• DNA Replication: Duplicates the DNA molecule for passing encoded information to the next generation.
• Transcription: Copies DNA information into RNA.
• Translation: Interprets RNA information to synthesize proteins.

DNA Characteristics

• DNA forms a double-stranded helix.
• Carbon atoms of the pentose sugar are numbered.
• Nucleotides are joined by phosphodiester bonds between the 5' phosphate group and the 3' hydroxyl group (3'OH).
• This forms the sugar-phosphate backbone.
• A single DNA strand has a 5' end and a 3' end.

DNA Complementarity and Antiparallel Arrangement

• Strands are complementary and held together by hydrogen bonds between nucleobases.
• Base-pairing:
  • Adenine (A) pairs with Thymine (T) via two hydrogen bonds.
  • Cytosine (C) pairs with Guanine (G) via three hydrogen bonds.
• Strands are antiparallel, oriented in opposite directions.

RNA Characteristics

• RNA (ribonucleic acid) differs from DNA:
  • Ribose replaces deoxyribose.
  • Uracil replaces thymine.
  • Usually a shorter, single strand.
• Synthesized from a DNA template strand; the RNA molecule is the transcript.
• Base-pairing rules apply, but uracil pairs with adenine.
• The transcript quickly separates from the DNA.

Types of RNA

• Three types of RNA:
  • Messenger RNA (mRNA).
  • Ribosomal RNA (rRNA).
  • Transfer RNA (tRNA).

Gene Expression Regulation

• Cells regulate the expression of certain genes.
• Rapid degradation of mRNA transcripts controls gene expression.
• Example:
  • Low levels of transcription for Gene A result in some transcripts and Protein A.
  • No transcription for Gene B means no Protein B synthesis.
  • Continuous transcription of Gene C generates many transcripts and Protein C molecules.

DNA Replication Overview

• DNA replication is typically bidirectional from the origin of replication.
• Two replication forks meet at the terminating site.
• Replication starts at the origin and proceeds in both directions, creating two advancing forks.

Semiconservative Replication

• Replication is semiconservative: each DNA molecule contains one original strand and one newly synthesized strand.

Initiation of DNA Replication

• DNA gyrase and helicases bind to the origin of replication to break and unwind the DNA helix.
• This exposes single-stranded regions that act as templates.
• Primases synthesize short RNA primers.
• The coordinated action of many enzymes forms replisomes.

DNA Polymerase Function

• DNA polymerases synthesize in the 5' to 3' direction.
• Hydrolysis of high-energy phosphate bonds powers the process.
• DNA polymerase can only add nucleotides and cannot initiate synthesis; primers are required.

Helicases and DNA Polymerases

• Helicases