Topic 1 Notes:

Key Concepts in Enzyme Function and Properties

Enzyme Specificity

• Each enzyme catalyzes only one type of reaction, specifically due to the shape and structure of its active site.

  • The active site is uniquely shaped to fit a specific substrate, allowing only certain reactions to occur.

  • Example: Glucose isomerase converts glucose to fructose.

Substrates and Products

• Ameloglucosidase:

  • Substrate: Maltodextrin.

  • Product: Glucose.

• Glucose Isomerase:

  • Substrate: Glucose.

  • Product: Fructose.

Induced Fit Model

• The Induced Fit Hypothesis:

  • Suggests that the binding of a substrate to the active site changes the shape of the active site to fit the substrate tightly.

  • This enhances the reaction:

    • Glucose binds to glucose isomerase, altering the enzyme's shape, facilitating the conversion of glucose to fructose.

Enzyme Reaction Mechanism

• When an enzyme binds with a substrate, an enzyme-substrate complex is formed, leading to a reaction that produces the product.

• Each enzyme's specific structure allows it to interact specifically with its substrate for efficient catalysis.

Factors Influencing Enzyme Activity

Temperature

• Enzymes have optimal temperature ranges where their activity is maximized.

  • Example: Certain proteases have specific optimum temperatures that affect their efficiency in breaking down proteins.

• High Temperatures:

  • Stability of enzymes at higher temperatures increases reaction rates.

  • Increased kinetic energy at higher temperatures promotes more frequent collisions between enzymes and substrates.

Denaturation

• High temperatures beyond the optimal range can lead to denaturation, where the enzyme loses its functional shape, making it inactive.

• Denatured enzymes cannot form enzyme-substrate complexes, leading to a cessation of the catalytic activity.

Types of Enzymes and Applications

Proteases

• Protease Enzymes: Break down proteins into amino acids.

  • Different proteases can target specific substrates (e.g., blood stains, egg stains, etc.).

  • Example Products:

    • Proteins are converted into amino acids.

    • Fats are broken down into fatty acids and glycerin.

Benefits of Enzymatic Reactions in Industry

• Utilizing enzymes that function efficiently at high temperatures can enhance production yields in industries such as food processing (e.g., production of high fructose corn syrup) by:

  • Increasing the rate of reaction at elevated temperatures.

  • Reducing reaction times leading to higher productivity and profitability.

Summary of Enzyme Structure and Function

• Enzymes compose of uniquely arranged amino acids resulting in specific active sites that determine the substrate specificity.

• Enzyme action depends on the dynamic interaction between the active site and substrates, influenced by factors like temperature and pH.

• Understanding these principles is essential for effectively applying enzymes in biochemical and industrial processes.

Enzymes as Proteins

• Definition: Enzymes are biological catalysts that are primarily composed of proteins.

Structure of Proteins

• Levels of Structure:

  • Primary Structure:

    • Linear arrangement of amino acids linked by peptide bonds.

  • Secondary Structure:

    • Formation of alpha helices and beta-pleated sheets stabilized by hydrogen bonds.

  • Tertiary Structure:

    • Three-dimensional folding of a single polypeptide chain into a functional configuration.

  • Quaternary Structure:

    • Complex formation of multiple polypeptide chains (subunits) to form a functional enzyme.

Active Site and Catalysis

• Active Site:

  • Specific region of the enzyme where substrate binding occurs and catalysis takes place.

  • Enzymes lower the activation energy needed for reaction, enabling substrates to be converted into products efficiently.

Enzyme Characteristics

• Activation Energy:

  • All reactions require a certain amount of input energy to commence, known as activation energy.

  • Enzymes reduce the activation energy needed, allowing reactions to occur more readily and at lower energy levels.

• Substrates and Examples:

  • The specific reactants that enzymes act upon; e.g., amylase acts on starch, where starch is the substrate.

Induced Fit Hypothesis

• Induced Fit vs. Lock and Key:

  • Lock and Key Model: Substrate fits perfectly into the active site without modification.

  • Induced Fit Model: When the substrate enters the active site, it causes a change in shape to allow a tighter fit, facilitating the conversion to product.

Temperature Effects on Enzyme Activity

• Temperature Influence:

  • Low temperatures render enzymes inactive.

  • Optimal temperature (e.g., 37°C for human enzymes) increases enzyme activity.

  • Beyond optimal temperature, enzymes denature, losing their functional shape and thereby their activity.

pH Effects on Enzyme Activity

• pH Influence:

  • Each enzyme has its optimal pH for activity (e.g., pepsin operates best at pH 2 in the stomach, while others require alkaline conditions).

  • Deviation from optimal pH can lead to denaturation, ceasing their activity.

  • Bile neutralizes stomach acidity for enzyme function in the small intestine.

Inhibition of Enzyme Activity

• Competitive Inhibition:

  • A competitor substance binds to the active site, preventing substrate from accessing it, thus hindering reaction.

  • Increasing substrate concentration can overcome this inhibition.

• Noncompetitive Inhibition:

  • An inhibitor binds to a site other than the active site, altering the shape of the enzyme and its active site, preventing substrate binding.

  • This type of inhibition cannot be overcome by increasing substrate concentration.

Conclusion

• Understanding enzymes is crucial in biochemistry, as they play vital roles in facilitating biological reactions by lowering activation energy and exhibiting specific structural adaptations that determine their function.

RNA Induced Silencing Complex (RISC)

• RISC: RNA Induced Silencing Complex

• Function: Can lead to the destruction of mRNA or inhibit protein synthesis, resulting in a halt in function.

Chromatin Modification

• Chromatin can be modified to influence gene expression.

• Acetylation of Histones:

  • Addition of acetyl groups to histones

  • Converts chromatin into euchromatin, making genes accessible for transcription and translation.

  • Promotes gene expression.

• DNA Methylation:

  • Addition of methyl groups, primarily to cytosine in DNA.

  • Highly methylated genes are turned off.

  • Removal of methyl groups can reactivate genes.

Gene Expression and Methylation Signals

• Signaling for methylation can be affected by environmental conditions and protein levels.

• Example: High protein levels can switch off genes to prevent wasteful protein synthesis.

Understanding Mutation

• Definition of Mutation:

  • Change in the base sequence of DNA or alteration in chromosome number.

  • e.g., Down syndrome: Presence of 47 chromosomes due to nondisjunction during meiosis.

Types of Mutations

• Base Substitution Mutation:

  • One base is swapped for another, potentially altering amino acid coding.

  • Can be silent (no change in amino acid) or affect protein function.

• Deletion Mutation:

  • Base is removed, causing a shift in the reading frame (frameshift mutation) which can change all codons downstream.

• Addition Mutation:

  • An extra base is added, also leading to reading frame shifts.

Codon and Amino Acids

• mRNA codons consist of three bases coding for specific amino acids.

• Changes in the DNA sequence lead to changes in codons, thus altering the resulting protein form.

Silent Mutations

• Occurs when a substitution does not change the amino acid sequence, maintaining protein function (e.g., GCA codes for alanine and GCU also codes for alanine).

Nonsense Mutations

• Results in the creation of a stop codon, terminating protein synthesis prematurely, which can lead to nonfunctional proteins.

DNA Methylation

• Definition: Addition of a methyl group (CH3) to DNA, affecting gene expression.

• Function:

  • Methyl groups added to cytosine nucleotide result in gene silencing, inhibiting transcription.

  • Conversely, removing methyl groups "activates" the genes, allowing transcription to occur.

• Significance:

  • Regulates gene expression, preventing unnecessary protein synthesis and conserving energy.

  • Example: E. coli activates or deactivates genes related to trypsin based on intestinal needs.

Chromatin Modification

• Definition: Structural changes to chromatin (DNA + proteins) that impact gene accessibility.

• Role of Acetyl Groups:

  • Presence of acetyl groups added to histones exposes DNA, permitting transcription.

  • Absence of acetyl groups tightens histone-DNA interaction, restricting gene expression.

• Mechanism: Acetylation vs. Methylation

  • Acetylation: Increases accessibility, allows transcription.

  • Methylation: Decreases accessibility, prevents transcription.

RNA Interference (RNAi)

• Definition: Regulatory mechanism controlling gene expression post-transcriptionally.

• Key Components:

  • MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are involved with enzymes forming silencing complexes.

• Mechanism:

  • RISC (RNA-induced silencing complex) degrades target mRNA or inhibits translation, silencing the gene.

  • Prevents the production of proteins from specific genes when not needed.

Importance in Gene Regulation

• Both DNA methylation and chromatin modification are vital for adaptive responses to cellular needs.

• They ensure that proteins are synthesized only when required, maintaining metabolic efficiency.

• Understanding these processes is fundamental for advancements in genetic research, biotechnology, and medicine.

Enzymes as Proteins

• Definition: Enzymes are biological catalysts that are primarily composed of proteins.

Structure of Proteins

• Levels of Structure:

  • Primary Structure:

    • Linear arrangement of amino acids linked by peptide bonds.

  • Secondary Structure:

    • Formation of alpha helices and beta-pleated sheets stabilized by hydrogen bonds.

  • Tertiary Structure:

    • Three-dimensional folding of a single polypeptide chain into a functional configuration.

  • Quaternary Structure:

    • Complex formation of multiple polypeptide chains (subunits) to form a functional enzyme.

Active Site and Catalysis

• Active Site:

  • Specific region of the enzyme where substrate binding occurs and catalysis takes place.

  • Enzymes lower the activation energy needed for reaction, enabling substrates to be converted into products efficiently.

Enzyme Characteristics

• Activation Energy:

  • All reactions require a certain amount of input energy to commence, known as activation energy.

  • Enzymes reduce the activation energy needed, allowing reactions to occur more readily and at lower energy levels.

• Substrates and Examples:

  • The specific reactants that enzymes act upon; e.g., amylase acts on starch, where starch is the substrate.

Induced Fit Hypothesis

• Induced Fit vs. Lock and Key:

  • Lock and Key Model: Substrate fits perfectly into the active site without modification.

  • Induced Fit Model: When the substrate enters the active site, it causes a change in shape to allow a tighter fit, facilitating the conversion to product.

Temperature Effects on Enzyme Activity

• Temperature Influence:

  • Low temperatures render enzymes inactive.

  • Optimal temperature (e.g., 37°C for human enzymes) increases enzyme activity.

  • Beyond optimal temperature, enzymes denature, losing their functional shape and thereby their activity.

pH Effects on Enzyme Activity

• pH Influence:

  • Each enzyme has its optimal pH for activity (e.g., pepsin operates best at pH 2 in the stomach, while others require alkaline conditions).

  • Deviation from optimal pH can lead to denaturation, ceasing their activity.

  • Bile neutralizes stomach acidity for enzyme function in the small intestine.

Inhibition of Enzyme Activity

• Competitive Inhibition:

  • A competitor substance binds to the active site, preventing substrate from accessing it, thus hindering reaction.

  • Increasing substrate concentration can overcome this inhibition.

• Non-competitive Inhibition:

  • An inhibitor binds to a site other than the active site, altering the shape of the enzyme and its active site, preventing substrate binding.

  • This type of inhibition cannot be overcome by increasing substrate concentration.

Conclusion

• Understanding enzymes is crucial in biochemistry, as they play vital roles in facilitating biological reactions by lowering activation energy and exhibiting specific structural adaptations that determine their function.