Synthetic

• Two basic concepts needed to engineer biological systems:

  • How information flows in biological systems
  • How information flow is controlled
• Biology is highly complex and differs from other engineering disciplines:

  • Interactions in biology are based on molecules, not physical position
  • Biology is subject to natural selection, leading to new definitions of robustness
  • Concepts like complexity and emergent behaviour must be understood in biology
• DNA structure:

  • DNA stores information in biological systems
  • Composed of two separate strands made of nucleotides (phosphate, deoxyribose sugar, and base)
  • Bases (A, G, C, T) provide variability and code for information
  • Complementarity between bases (A-T, G-C) leads to double-helix structure
  • DNA replication allows for reproduction by synthesising new daughter DNA helices
• PCR (Polymerase Chain Reaction):

  • Method for exponential amplification of DNA
  • Relies on DNA polymerases isolated from extremophile organisms
  • Specificity achieved through oligonucleotide primers
  • Temperature cycling used for denaturation, annealing, and synthesis
  • New DNA polymerases with proofreading domains increase accuracy in amplification
• Information flow in biology:

  • DNA stores information, proteins perform functions in the cell
  • Central dogma: DNA transcribed into RNA, then translated into protein
  • Genes code for proteins or functional RNA molecules
  • Messenger RNA (mRNA) carries message to ribosome for translation
• Genetic code:

  • Triplet code: three nucleotides code for one amino acid
  • Redundancy in the code, except for tryptophan and methionine
  • Methionine is the initiating amino acid in bacterial proteins
  • Codon usage varies between organisms, affecting translation efficiency
• Proteins:

  • Majority of functional and structural roles in organisms carried out by proteins
  • Form structural materials, act as motors, enzymes, and regulatory proteins
  • Diversity of proteins from 20 amino acids
  • Amino acids join to form peptide bonds, leading to the formation of polypeptides or proteins
• Proteins' functional properties do not come directly from their linear sequence of amino acids, but from the three-dimensional form they adopt
• It is not currently possible to computationally predict the three-dimensional structure of a given protein sequence
• 1. ray crystallography has enabled atomic resolution structures of proteins to be determined
• There are over 60,000 protein X-ray structures that have been solved
• Nuclear magnetic resonance (NMR) and electron microscopy also contribute to understanding protein structure and function
• RNA polymerase is responsible for the transcription of DNA into mRNA
• Prokaryotes have simpler transcription systems compared to eukaryotes
• A gene consists of the open reading frame (ORF) that codes for a protein and regulatory elements that control its expression
• Promoters are the genetic switches that control gene expression
• Sigma factors are essential for prokaryotic RNA polymerase activity and global gene regulation
• Transcription factors like activators and repressors control gene transcription
• Ribosome binding sites (RBS) on mRNA molecules determine the level of protein synthesis
• RNA can act as a catalyst (ribozymes) and regulate gene expression
• Small RNA molecules can modulate translation and regulate gene expression
• Riboswitches are sequences in mRNA that modulate translation through binding small metabolite molecules
• Las enzimas son las proteínas que catalizan reacciones químicas y biológicas.
• La proteína es un polipéptido, que está formado por una o más cadenas de aminoácidos.
• Los aminoácidos se unen mediante puentes peptídicos para formar polipéptidos, los cuales pueden ser cortados por enzimas para liberar nuevos aminoácidos.
• Enzimas específicas reconocen y unen con sus sustratos, lo que permite el proceso de catálisis.
• La secuencia de aminoácidos determina la estructura tridimensional y función de una proteína.
• En algunas proteínas, existen regiones donde dos o más cadenas de aminoácidos se unen para formar una única molécula.
• El sitio activo es la parte del enzima donde tiene lugar la reacción química.
• Algunas enzimas tienen cofactores, moléculas no proteicas necesarias para su actividad.
• Existen diferentes tipos de enzimas según su función, como hidrolasa (que rompe enlaces), transferasa (que transfiere grupos funcionales) y oxidorreductasa (que interviene en reacciones redox).
• El pH y temperatura también influyen en la actividad de las enzimas.
• Cada tipo de anticuerpo reconoce un solo antígeno específico.