LC 01: Introduction to Cell and Molecular Biology

• Cell theory states that the cell is the basic organizational unit of life, all organisms are comprised of one or more cells, and cells arise from pre-existing cells
• Prokaryotic cells lack nuclei, while eukaryotic cells have nuclei; prokaryotic cells are typically single-celled, while eukaryotic cells can be single-celled or multicellular
• Plant cells have unique features like cell walls, chloroplasts, and vacuoles, which are not present in animal cells
• Mitochondria were originally free-living aerobic prokaryotes that could use oxygen to generate ATP; they formed through ectosymbiosis, a form of symbiotic behavior
• Ectosymbiosis is when an organism lives on the body surface of another organism, including internal surfaces; early archaean cells could not use oxygen to generate ATP
• The process of forming mitochondria involved enclosure of the ectosymbiont by archal membrane fusion, escape of the endosymbiont into the cytosol, and the formation of new intracellular compartments
• Common features of models explaining mitochondria origin include an ancient anaerobic archal cell, an ancient aerobic bacterium, and a symbiotic relationship between the two over evolutionary time
• Endosymbiont hypothesis defines a cell that lives inside another cell with mutual benefit, like mitochondria and chloroplasts in cells
• Evidence supporting the endosymbiont hypothesis includes mitochondria and chloroplasts retaining remnants of their own genomes and genetic systems resembling modern-day prokaryotes
• Membranes in mitochondria and chloroplasts often resemble those in prokaryotes and appear to have been derived from engulfed bacterial ancestors
• The Tree of Life diagram in the textbook shows the ancestral prokaryote diverging into bacteria and archaea, with the later addition of mitochondria and the nucleus
• Recent discoveries in biology include a new supergroup of eukaryotes found in December 2022, indicating ongoing exploration and discoveries in the field
• Model organism definition:

  • A living thing selected for intensive study as a representative of a large group of species
• Characteristics of model organisms:

  • Rapid development with short life cycles
  • Small adult reproductive size
  • Readily available in collections or widespread
  • Tractable, meaning easy to manipulate or modify
• Examples of characteristics of model organisms:

  • Elephants are not suitable as model organisms due to slow development, long life cycles, large adult size, and lack of tractability
• Central Dogma of Molecular Biology:

  • Original concept: DNA transcribed to RNA, RNA translated to Protein
  • Refined concept includes different types of RNA: mRNA, tRNA, rRNA
• Elaborated Central Dogma:

  • Genome: all DNA sequences in a cell or organism
  • Transcriptome: all RNA sequences in a cell or organism
  • Proteome: all protein sequences in a cell or organism
  • Interactome: all protein-protein interactions in a cell or organism
  • Metabolome: all small molecule metabolites in a cell or organism
  • Phenome: all phenotypes in a cell or organism
• Review of Information Flow for Prokaryotes and Eukaryotes:

  • DNA, RNA, and proteins are synthesized as linear chains of information with definite polarity
  • DNA has a 3' and 5' end, RNA has a 3' end, and proteins have an N-terminus and C-terminus
  • RNA sequences are translated into amino acid sequences via a universal genetic code
• Introduction to Nucleic Acids:

  • Parts of a nucleic acid, RNA and DNA
  • Nucleic acid nomenclature
• Structure and function are intertwined in nature, where understanding the structure of an organism leads to insights about its function
• Nucleic acids, the genetic material in cells, include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
• In nucleotides, the basic units of nucleic acids, the three parts are a phosphate group (can be one, two, or three), a pentose sugar, and a nitrogenous base
• The difference between DNA and RNA lies in their sugars: DNA has deoxyribose (missing an oxygen on the 2' carbon), while RNA has ribose
• Bases in nucleotides can be purines (two rings, adenine and guanine) or pyrimidines (one ring, cytosine, thymine in DNA, uracil in RNA)
• Remembering the structures of bases is not necessary, but knowing purines have two rings and pyrimidines have one ring is important
• A key difference between DNA and RNA bases is that RNA uses uracil (U) instead of thymine (T) found in DNA
• Thymine in DNA has an extra methyl group compared to uracil in RNA, a distinction relevant in understanding mutations
• Nucleoside: base + sugar.

  Nucleotide: base + sugar + at least one phosphate group (could be one, two, or three)
• Nucleoside monophosphate: nucleoside + one phosphate group.

  Nucleoside diphosphate: nucleoside + two phosphate groups.

  Nucleoside triphosphate: nucleoside + three phosphate groups
• DNA is synthesized from deoxyribonucleoside triphosphates (dNTPs) and bases (G, C, T).

  RNA is synthesized from ribonucleoside triphosphates (NTPs) and bases (A, G, C, U)
• Nucleotides are linked by phosphodiester bonds.

  DNA strands are anti-parallel, with bases pairing (A-T, G-C) held by hydrogen bonds (2 between A-T, 3 between G-C)
• Base pairing in DNA holds the double helix together:

  • Between A and T there are two hydrogen bonds
  • Between G and C there are three hydrogen bonds
• DNA strands are anti-parallel: one strand is 5' to 3' while its partner goes 3' to 5'
• The three forces that keep DNA strands together are:

  • Hydrogen bonds (2 between A-T, 3 between G-C)
  • Hydrophobic interactions due to the hydrophobic nature of base ring structures
  • Vander Waals attractions between base stacking
• Incorrectly drawn DNA double helices lack major and minor grooves, which are essential for protein-DNA interactions
• Denaturation of DNA occurs when non-covalent bonds are broken by heating, leading to the destruction of the normal structure; renaturation happens when the strands slowly cool and reanneal
• DNA strands can be unzipped like a zipper due to their complementary sequences, crucial for DNA replication and RNA synthesis
• In DNA, G always pairs with C and A with T in base pairing interactions
• Proteins can recognize and make specific contact with DNA sequences in the major or minor grooves, offering selectivity in altering DNA
• The DNA double helix structure has major and minor grooves, allowing proteins to interact selectively with DNA sequences