Lakhasly

This lecture by Prof. Dr. Samir Ali El-Masry covers enzyme chemistry, emphasizing their crucial role in life ("No enzyme…No Life"). Enzymes are defined as biological catalysts accelerating biochemical reactions without being consumed. Most are proteins; some are RNA-based ribozymes. They lower activation energy and exhibit specificity. Biomedically, enzymes are vital for metabolism, diagnosis (e.g., myocardial infarction detection via blood enzyme levels), and therapeutics (e.g., digestive enzymes). Enzyme characteristics include high efficiency at low concentrations, an active site for substrate binding, and dependence on primary to quaternary structures for activity. Molecular weight ranges from 12,000 to over one million Daltons; some require cofactors (inorganic ions or organic coenzymes) or both. Enzyme action involves an enzyme-substrate complex formation, often explained by the lock-and-key or induced-fit models. The active site, a cleft with functional groups and cofactors, facilitates substrate transformation into products. Enzymes are classified as simple (protein only) or complex (holoenzymes, comprising apoenzyme and cofactor – either coenzyme or prosthetic group). Zymogens are inactive enzyme precursors activated by pH changes or kinases. Isoenzymes, like lactate dehydrogenase (LDH), catalyze the same reaction but differ structurally and in properties. Finally, enzyme specificity varies, ranging from single substrate to bond type recognition.

Prof Dr/ Samir Ali El-Masry
Prof of Biochemistry and Molecular Biology
Lecture (7) Biochemistry 1
Enzymes Chemistry
Molecular Biology Dept. Genetic Engineering and Biotechnology Institute, Sadat City University

Enzymes are key to life
No enzyme ..... No Life
Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

1. 
   

   Biomedical Importance of Enzymes
   • Enzymes are biological substance that catalyze the chemical reactions which make life as we know it possible.
   • The presence and maintenance of a complete and balanced set of enzymes is essential for the breakdown of nutrients to supply energy and chemical building blocks.
   • The assembly of those building blocks into proteins, DNA, membranes, cells, and tissues; and the harnessing of energy to power cell motility and muscle contraction.
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   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

   
   


2. 
   

   Biomedical Importance of Enzymes (cont.)
   • Enzymes play an important role in Metabolism, Diagnosis, and Therapeutics.
   • All biochemical reactions are enzyme catalyzed in the living organism.
   • Level of enzyme in blood are of diagnostic importance e.g. it is a good indicator in disease such as myocardial infarction.
   • Enzyme can be used therapeutically such as digestive enzymes.
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   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

   
   
   
   
   2. Enzymes Definition
      • Enzymes are organic substance that act as catalysts or accelerate the rate of the biochemical reactions without being consumed or produced from the reaction.
      Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology
   
   
   
   

    Most of enzymes are proteins in nature, but small groups 0f enzymes are non-protein called ribozymes which made from RNA.
    Enzymes increase the rate of chemical reactions by lowering the energy of activation.
    All enzymes show a degree of specificity
    Enzymes is produced inside the body cells but can act inside and outside the body cells

   
   


3. 
   

   Characteristics of Enzymes
   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

   
   

 Enzyme catalysts bind with the reactants (substrates), convert them to the products, and release the products.
Although enzymes may be modified during their participation in this reaction sequence, they return to their original form at the end.
 In addition to increasing the speed of reactions, enzymes provide a means for regulating the rate of metabolic pathways in the body
3. Characteristics of Enzymes (Cont.)
Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

 If an enzyme is denatured or dissociated into its subunits, catalytic activity is usually lost.
 If an enzyme is broken down into its component amino acids, its catalytic activity is always destroyed. Thus the primary, secondary, tertiary, and quaternary structures of protein enzymes are essential to their catalytic activity
3. Characteristics of Enzymes (Cont.)
Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

 Enzymes, like other proteins, have molecular weights ranging from about 12,000 to more than one million Dalton.
 Some enzymes require no chemical groups for activity other than their amino acid residues.
 Others require an additional chemical component called a cofactor either one or more inorganic ions, such as Fe2, Mg2, Mn2, or Zn2, or a complex organic or metalloorganic molecule called a coenzyme.
 Some enzymes require both a coenzyme and one or more ions for their activity.
3. Characteristics of Enzymes (Cont.)
Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

3. 
   

   Characteristics of Enzymes (Cont.) Characteristics of Enzymes
   • They are effective at extremely small concentrations.
   • Each enzyme has an active site in which the substance binds.
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   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

   
   


4. 
   

   Activation energy
   All chemical reactions require some amount of energy to get them started.
   It is First push to start reaction. This energy is called activation energy.
   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

   
   

Enzymes Lower a Reaction’s Activation Energy
Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

5. The Enzyme Active Site

• To catalyze a chemical reaction, the enzyme forms an enzyme - substrate complex in its active catalytic site.
• The active site is usually a cleft in the enzyme formed by one or more regions of the polypeptide chain.
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Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology
Active Site

5. 
   

   The Enzyme Active Site (cont.)
   Substrate
   • Within the active site, cofactors and functional groups from the polypeptide chain participate in transforming the bound substrate molecules into products.
   • Initially, the substrate molecules bind to their substrate binding sites, also called the substrate recognition sites.
   • The three-dimensional arrangement of binding sites in a cleft of the enzyme allows the reacting portions of the substrates to approach each other from the appropriate angles.
   • The proximity of the bound substrate molecules and their precise orientation toward each other contribute to the catalytic power of the enzyme.
   Active Site
   cofactor
   Enzyme
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   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

   
   


6. 
   

   The Enzyme Active Site (Cont.)
   • The active site also contains functional groups that directly participate in the reaction.
   • The functional groups are donated by the polypeptide chain, or by bound cofactors (metals as Fe2, Mg2, Mn2, or Zn2) or complex organic molecules (metalloorganic molecule as vitamins or compound derived from vitamins) called a coenzyme.
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   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology
   Cofactors and coenzymes

   
   


7. 
   

   The Enzyme Active Site (Cont.)
   • As the substrate binds, it induces conformational changes in the enzyme that promote further interactions between the substrate molecules and the enzyme functional groups. (For example, a coenzyme might form a covalent intermediate with the substrate, or an amino acid side chain might abstract a proton from the reacting substrate.)
   • The activated substrates and the enzyme form a transition state complex, that is intermediate between substrate and product.
   • The transition state complex decomposes to products, which dissociate from the enzyme. The enzyme generally returns to its original form. The free enzyme then binds another set of substrates, and repeats the process.
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   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

   
   

• Enzymes increase reaction rates by decreasing the activation energy
• Enzyme-SubstrateInteractions: Formation of Enzyme substrate complex by: 1. Lock-and-Key Model 2. Induced Fit Model
6. Mechanisms of Enzymes Action
Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

1. 
   

   Lock-and-Key Model
   • In the lock-and-key model of enzyme action: - The active site has a rigid shape - Only substrates with the matching shape can fit - The substrate is a key that fits the lock of the active site
   • This explains enzyme specificity
   • This explain the loss of activity when enzymes denatur
   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

   
   


2. 
   

   Induced Fit Model
   In the induced-fit model of enzyme action:

   
   


3. 
   

   Theactivesiteisflexible,notrigid

   
   


4. 
   

   Theshapesoftheenzyme,activesite,andsubstrate adjust to maximize the fit, which improves catalysis

   
   


5. 
   

   Thereisagreaterrangeofsubstratespecificity
   This model is more consistent with a wider range of enzymes
   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

   
   
   
   
   7. Chemical Structure of enzymes
      Simple (only protein)
      Coenzyme
       Large organic molecule
       Loosely bound to apoenzyme
      Enzymes
      Cofactor
      Complex or holoenzymes (protein part and nonprotein part – cofactor)
      Prosthetic groups
       Usually small inorganic molecule or atom;
       Usually tightly bound to
      apoenzyme
      Apoenzyme (protein part)
      Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology
   
   
   
   


6. 
   

   Chemical Structure of enzymes (Cont.)
   Enzymes are protein in nature; they are divided chemically into two groups:
   (a) Simple protein enzymes:
   Consisting wholly of proteins, e.g. pepsin, maltase, ........ etc (b) Conjugated protein enzymes (holoenzmes) Consisting of protein part and non-protein part. 1) The protein part of the enzymes is known as apoenzyme 2) The non-protein part of the enzymes (cofactor) may be: A. Organic Part: is loosely attached to the protein part and called Coenzymes, e.g. Vitamin B, Nicotinamide adanine dinucleotides (e.g. NAD+ and NADP+) for transfer of hydrogen.
   B. Inorganic metal Part: is firmly attached to the protein part and called prosthetic group. e.g.: ascorbic acid oxidase contains copper and cytochrome oxidase contains iron
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   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

   
   

Apoenzyme and Holoenzyme
• The enzyme without its non protein moiety is termed as apoenzyme and it is inactive.
• Holoenzyme is an active enzyme with its non protein component.
Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

• Enzymes secreted in inactive forms especially proteolytic enzymes to prevent destruction of the proteins of the cells that synthesize them.
• Activation of zymogen takes place either by: 1. pH change: e.g. pepsinogen formed pepsin in the presence of HCL 2. Kinase: e.g. trypsinogen formed trypsin by enterokinase enzyme
• The mechanism of activation may involve unmasking of a polypeptide chain that may be blocking or masking the active center of the apoenzyme
Zymogen (pro-enzyme or pre-enzyme)
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Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

Isoenzymes
• Enzymes that catalyze the same reaction but differ in their structure, properties and activity
• Best example is lactate dehydrogenase (LDH) in plasma which is separated into 5 isoenzymes by electrophoresis
• LDH molecules consists of 4 polypeptides chains, each may be H or M types
• Thus the five isoenzymes are present of this structure called LDH 1. 2. 3. 4. and 5
• LDH1 (HHHH) is produced by heart and LDH5 (MMMM)by muscle and liver
Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

8. Enzyme Specificity
   • Enzymes have varying degrees of specificity for substrates
   • Enzymes may recognize and catalyze: 1. A single substrate 2. A group of similar substrates 3. A particular type of bond
   Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology

Enzyme Specificity (Cont.)

Prof Dr/ Samir Ali El-Masry , Professor of Biochemistry and Molecular Biology