ABI Bioinformatics Guide 2024
  • INTRODUCTION
    • How to use the guide
  • MOLECULAR BIOLOGY
    • The Cell
      • Cells and Their Organelles
      • Cell Specialisation
      • Quiz 1
    • Biological Molecules
      • Carbohydrates
      • Lipids
      • Nucleic Acids (DNA and RNA)
      • Quiz 2
      • Proteins
      • Catalysis of Biological Reactions
      • Quiz 3
    • Information Flow in the Cell
      • DNA Replication
      • Gene Expression: Transcription
      • Gene Expression: RNA Processing
      • Quiz 4
      • Chromatin and Chromosomes
      • Regulation of Gene Expression
      • Quiz 5
      • The Genetic Code
      • Gene Expression: Translation
    • Cell Cycle and Cell Division
      • Quiz 6
    • Mutations and Variations
      • Point mutations
      • Genotype-Phenotype Interactions
      • Quiz 7
  • PROGRAMMING
    • Python for Genomics
    • R programming (optional)
  • STATISTICS: THEORY
    • Introduction to Probability
      • Conditional Probability
      • Independent Events
    • Random Variables
      • Independent, Dependent and Controlled Variables
    • Data distribution PMF, PDF, CDF
    • Mean, Variance of a Random Variable
    • Some Common Distributions
    • Exploratory Statistics: Mean, Median, Quantiles, Variance/SD
    • Data Visualization
    • Confidence Intervals
    • Comparison tests, p-value, z-score
    • Multiple test correction: Bonferroni, FDR
    • Regression & Correlation
    • Dimentionality Reduction
      • PCA (Principal Component Analysis)
      • t-SNE (t-Distributed Stochastic Neighbor Embedding)
      • UMAP (Uniform Manifold Approximation and Projection)
    • QUIZ
  • STATISTICS & PROGRAMMING
  • BIOINFORMATICS ALGORITHMS
    • Introduction
    • DNA strings and sequencing file formats
    • Read alignment: exact matching
    • Indexing before alignment
    • Read alignment: approximate matching
    • Global and local alignment
  • NGS DATA ANALYSIS & FUNCTIONAL GENOMICS
    • Experimental Techniques
      • Polymerase Chain Reaction
      • Sanger (first generation) Sequencing Technologies
      • Next (second) Generation Sequencing technologies
      • The third generation of sequencing technologies
    • The Linux Command-line
      • Connecting to the Server
      • The Linux Command-Line For Beginners
      • The Bash Terminal
    • File formats, alignment, and genomic features
      • FASTA & FASTQ file formats
      • Basic Unix Commands for Genomics
      • Sequences and Genomic Features Part 1
      • Sequences and Genomic Features Part 2: SAMtools
      • Sequences and Genomic Features Part 3: BEDtools
    • Genetic variations & variant calling
      • Genomic Variations
      • Alignment and variant detection: Practical
      • Integrative Genomics Viewer
      • Variant Calling with GATK
    • RNA Sequencing & Gene expression
      • Gene expression and how we measure it
      • Gene expression quantification and normalization
      • Explorative analysis of gene expression
      • Differential expression analysis with DESeq2
      • Functional enrichment analysis
    • Single-cell Sequencing and Data Analysis
      • scRNA-seq Data Analysis Workflow
      • scRNA-seq Data Visualization Methods
  • FINAL REMARKS
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  1. MOLECULAR BIOLOGY
  2. Biological Molecules

Catalysis of Biological Reactions

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Last updated 11 months ago

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Numerous chemical reactions within cells would proceed at unfeasibly slow rates under the conditions in which biological organisms exist. This sluggishness arises from the fundamental nature of chemical reactions, entailing breaking and forming bonds, which requires reactant molecules to convert to unstable transition states. The energy that needs to be absorbed from the environment to reach the transition state is termed activation energy.

Catalysts are substances that accelerate reactions without being consumed and without altering the reaction equilibrium. In biological systems, these catalysts are primarily proteins known as enzymes. Enzymes facilitate chemical reactions by lowering the activation energy required for the reaction to occur.

In enzyme-catalyzed reactions, the molecules undergoing transformation are referred to as substrates. The substrate binds to a specific region on the enzyme known as the active site, forming an enzyme-substrate complex. The active site's shape and physical properties are tailored to accommodate only particular substrates, which explains the specificity of enzymes to their substrates.

During catalysis, the substrate remains bound to the active site, undergoing conversion into products. This interaction is characterised by an induced fit model, where the active site's shape is not rigid but rather adjusts upon substrate binding. Weak interactions between chemical groups on the enzyme and substrate cause the active site to conform around the substrate.

Enzymes employ diverse mechanisms to reduce activation energy in chemical reactions. One approach involves properly orienting substrate molecules within the active site, facilitating bond formation. Alternatively, enzymes may distort substrate molecules, promoting bond-breaking. Some enzymes create a microenvironment within their active sites that favours specific reactions. For instance, the presence of acidic amino acid residues can lower pH, increasing the likelihood of hydrogen ion transfer to the substrate. Additionally, certain enzymes utilise amino acid residues in their active sites to form transient covalent bonds with substrates as part of the reaction process.

Activation energy of a reaction with and without enzyme Image source: Microbialmatt - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=126786827
The induced fit model. Substrate binding makes the enzyme undergo a conformational change