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enzymes-
-definition,types and classification of enzymes.
-coenzymes,specificity of enzymes ,isoenzymes,enzyme kinetics including factors affecting velocity of enzymes catalysed reaction.enzyme inhibition

enzymes-
-definition,types and classification of enzymes.
-coenzymes,specificity of enzymes ,isoenzymes,enzyme kinetics including factors affecting velocity of enzymes catalysed reaction.enzyme inhibition

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unit-4 enzymes by poonam9 Pgdiploma.pptx

  1. 1. PRESENTED BY: POONAM PG Diploma in Nutrition and Dietetics BIOCHEMISTRY (ENZYMES AND NUCLEIC ACIDS) 2022-2023
  2. 2. TOPICS TO BE DISCUSSED  What is biochemistry?  Objectives,scope and importance of biochemistry and its relation to nutrition  ENZYMES-  Definition,types and classification  Coenzymes,specificity of enzymes,isoenzymes,enzyme kinetics including factors affecting velocity of enzymes catalysed reaction.Enzyme inhibition  NUCLEIC ACIDS-  Classification,composition and function of nucleic acids  Structure and properties of nucleosides,nucleotides  Genetic code.
  3. 3. BIOCHEMISTRY “Biochemistry has become the foundation for understanding all biological processes. It has provided explanations for the causes of many diseases in humans, animals and plants.” “Biochemistry is a study of the chemical substances & processes that occur in plants, animals & microorganisms & of the changes they undergo during development & life.”
  4. 4.  Biochemistry is both life science and a chemical science - it explores the chemistry of living organisms and the molecular basis for the changes occurring in living cells.  It uses the methods of chemistry, physics, molecular biology, and immunology to study the structure and behavior of the complex molecules found in biological material and the ways these molecules interact to form cells, tissues, and whole organisms
  5. 5. OBJECTIVES OF BIOCHEMISTRY  Study the structures and functions of biomolecules like carbohydrate, lipids, proteins minerals and DNA.  Focuses on techniques used to control diseases, abnormal deficiency and treatment of deficiencies.  Understand the dynamic changes of cellular systems and corresponding need of nutrients.  They act as catalyst agent.  Metabolic abnormalities can be studied by knowledge of biochemistry.  Study of the energy transformations in living cells, organisms is another objective of study of biochemistry.
  6. 6. IMPORTANCE OF BIOCHEMISTRY  Biochemistry is thriving right now. In recent years it has become the most critical area of science.  It combines the core of biology and chemistry, which opens a new door for research from the very ground up.  Biochemistry helps us understand the medical conditions such as diabetes, jaundice, rickets, etc. with its research, and scientists are now able to find a medication that can cure them or put them in control.  Biochemistry can help us find a way to decompose our waste without harming nature successfully.  This field can also do wonders in the coming years and make us live on other planets as we study the chemical changes that happen on other planets such as mars.
  7. 7. SCOPES OF BIOCHEMISTRY Biochemistry play an important role in various fields such as; in clinical medicine, pharmacology, biotechnology, agriculture, horticulture, forestry, nursing, pathology, in physiology, and also in microbiology. BIOCHEMISTRY IN MEDICINE • Physiology • Pathology • Nursing and diagnosis
  8. 8. SCOPES OF BIOCHEMISTRY BIOCHEMISTRY IN AGRICULTURE • Prevent diseases and Enhance Yield/ growth • Adulteration
  9. 9. SCOPE OF BIOCHEMISTRY BIOCHEMISTRY IN NUTRITION • Food chemistry gives an idea of what we eat. The nutrients value of food material can also be determined by biochemical tests. • Nutritional biochemical therapy saves lives, reduces morbidity, improves health outcomes, and reduces healthcare costs and patients.
  10. 10. SCOPES OF BIOCHEMISTRY BIOCHEMISTRY IN PHARMACY • Drug Constitution • The half-life and Drug storage • Drug metabolism
  11. 11. OTHER SCOPES • Biotechnologist • Research Scientist • Clinical Scientist • Research Associates • Chemist Microbiologist • Biomedical Scientist • Pharmacologist Laboratory Technician • Lecturer in an Educational institution
  12. 12. RELATIONSHIP WITH NUTRITION Nutrition is the study of nutrients in food, how the body uses them, and the relationship between diet, health, and disease. Nutritional biochemistry deals with various studies in nutrients, food constituents and their function regarding humans and other mammals, nutritional biochemistry specifically focuses on nutrient chemical components, and how they function biochemically, physiologically, metabolically, as well as their impact on disease.
  13. 13. Definition “Enzymes can be defined as biological polymers that catalyze biochemical reactions.” • Enzymes are nitrogenous organic molecules produced by living organisms such as plants and animals. A long chain of one or more amino acids is connected together using amide or peptide bonds to make them. • Enzymes have a specific method of action (Lock- and-Key mechanism and Enzyme Fit Hypothesis).
  14. 14. STRUCTURE OF ENZYMES • Enzymes are proteins that are made up of several polypeptide chains, also known as amino acids, that have been folded and coiled numerous times. • They have linear chains of amino acids in three-dimensional structures. • The enzyme’s catalytic activity is determined by the amino acid sequence. Only a small portion of an enzyme’s structure participates in catalysis and is located around the binding sites. • They have separate sites; the active site of an enzyme is made up of the catalytic and binding sites.
  15. 15. CLASSIFICATION OF ENZYMES
  16. 16. 1. Oxidoreductases Catalyze oxidation/reduction reactions Oxidation is the loss of electronsor an increase in the oxidation state of an atom, an ion, or of certain atoms in a molecule.  Reduction is the gain of electrons or a decrease in the oxidation state of an atom, an ion, or of certain atoms in a molecule.  Eg. Alcohol dehydrogenase  Cytochrome oxidase  Amino acid oxidases
  17. 17. 2. Transferases • Involved in transfer of functional groups between molecules Eg. :- ➢Hexokinase ➢Transaminases ➢Phosphorylase 3. Hydrolases • Break bonds by adding H2O Eg:-  Lipase (triacylglycerol acyl hydrolase)  Choline esterase  Acid and alkaline phosphatase  Pepsin  Urease
  18. 18. 4. Lyases • Elimination reactions to form double bonds Eg.-  Aldolase  Fumarase Histidase 5. Isomerases • Intramolecularrearangements Eg:-  Triose phosphale isomerase  Phosphohexose isomerase
  19. 19. 6. Ligases • Join molecules with new bonds Eg:- Glutamine synthetase Succinate thiokinase Acetyl CoA carboxylase
  20. 20. Examples of Enzymes Beverages • Alcoholic beverages generated by fermentation vary a lot based on many factors. Based on the type of the plant’s product, which is to be used and the type of enzyme applied, the fermented product varies. • For example, grapes, honey, hops, wheat, cassava roots, and potatoes depending upon the materials available. Beer, wines and other drinks are produced from plant fermentation. Food Products • Bread can be considered as the finest example of fermentation in our everyday life. • A small proportion of yeast and sugar is mixed with the batter for making bread. Then one can observe that the bread gets puffed up as a result of fermentation of the sugar by the enzyme action in yeast, which leads to the formation of carbon dioxide gas. This process gives the texture to the bread, which would be missing in the absence of the fermentation process.
  21. 21. Drug Action Enzyme action can be inhibited or promoted by the use of drugs which tend to work around the active sites of enzymes. Mechanism of Enzyme Reaction Enzymes are said to possess an active site. The active site is a part of the molecule that has a definite shape and the functional group for the binding of reactant molecules. The molecule that binds to the enzyme is referred to as the substrate group. The substrate and the enzyme form an intermediate reaction with low activation energy without any catalysts.
  22. 22. reactant(1)+reactant(2) product reactant(1)+enzyme intermediate intermediate+reactant(2) product+enzyme
  23. 23. Action and Nature of Enzymes • The enzyme action basically happens in two steps: • Step1: Combining of enzyme and the reactant/substrate. • E+S → [ES] • Step 2: Disintegration of the complex molecule to give the product. • [ES]→E+P • Thus, the whole catalyst action of enzymes is summarized as: • E + S → [ES] → [EP] → E + P
  24. 24. ENZYME ACTION
  25. 25. Factors Affecting Enzyme Activity • The conditions of the reaction have a great impact on the activity of the enzymes. Enzymes are particular about the optimum conditions provided for the reactions such as temperature, pH, alteration in substrate concentration, etc.
  26. 26. Active site Enzymatic catalysis depends upon the activity of amino acid side chains assembled in the active centre. Enzymes bind the substrate into a region of the active site in an intermediate conformation. Temperature and pH Enzymes require an optimum temperature and pH for their action. The temperature or pH at which a compound shows its maximum activity is called optimum temperature or optimum pH, respectively. As mentioned earlier, enzymes are protein compounds. A temperature or pH more than optimum may alter the molecular structure of the enzymes. Generally, an optimum pH for enzymes is considered to be ranging between 5 and 7.
  27. 27. • Optimum T° • The greatest number of molecular collisions • human enzymes = 35°- 40°C • body temp = 37°C • Heat: increase beyond optimum T° • The increased energy level of molecule disrupts bonds in enzyme & between enzyme & substrate H, ionic = weak bonds • Denaturation = lose 3D shape (3° structure) • Cold: decrease T° • Molecules move slower decrease collisions between enzyme & substrate
  28. 28. ENZYME INHIBITION
  29. 29. ENZYME INHIBITION Enzyme inhibitor is defined as a substance which binds with the enzyme and brings about a decrease in catalyrtc activity of that enzyme. The inhibitor may be organic or inorganic in nature. There are three broad categories of enzyme inhibition • 1 . Reversible inhibition. • 2. Irreversible inhibition. • 3. Allosteric inhibition.
  30. 30. 1. Reversible inhibition The inhibiior binds non-covalently with enzyme and the enzyme inhibition can be reversed if the inhibitor is removed. The reversible inhibition is further sub-divided into l. Competitive inhibition ll. Non-competitive inhibition
  31. 31. l. Competitive inhibition
  32. 32. ll. Non-competitive inhibition
  33. 33. 2. lrreversible inhibition  Inhibitor binds covalently(strong)with the enzyme irreversibly  Soit can’t dissociate from the enzyme  Inhibitor cause conformation change at active site of the E –destroying their capacity to function as catalysts  Enzyme activity is not regained on dialysis/by increasing the conc.of S  A variety of poisons,such as iodoacetate,OP poisoning and oxidizing agents act as irreversible inhibition
  34. 34. In terms of kinetics –irreversible is similor to non competitive inhibition Vmax– Decreased Km– No change
  35. 35. Suicide Inhibition Specialized form of irreversible inhibition Also known as mechanism based inactivation I makes use of all enzyme’s own reaction mechanism to inactivate it Inhibitor(structural analog) is converted to a more effective inhibitor with the help of the E to be inhibited E literally commits suicide-they utilize normal E mechanism to inactivate the E.
  36. 36. 3. Allosteric inhibition  Some E possess additional site other than the active siete called as Allosteric sites,E –AllostericE.  They are unique site on protein molecule  Allosteric effectors–substances bind of Allosteric site & regulate E activity  Positive Allosteric effectors-E activity is increased  Negative Allostric effectors-E activity is decreased  Allostric enzyme-sigmoidal curve
  37. 37. ENZYME SPECIFICITY Enzymes are highly specific in their action when compared with the chemical catalysts. The occurrence of thousands of enzymes in the biological system might be due to the specific nature of enzymes.
  38. 38. COENZYME  The non-protein, organic, Iow molecular weight and dialysable substance associated with enzyme function is known as coenzyme.  The functional enzyme is referred to as holoenzyme which is made up of a protein part (apoenzyme) and a non-protein part (coenzyme).  Coenzymes are often regarded as the second substrates or co-substrafes, since thev have affinity with the enzyme comparable with that of the substrate.  the coenzymes are the derivatives of water soluble B-complex vitamins. In fact, the biochemical functions of B-complex vitamins are exerted through their respective coenzyme.
  39. 39. LOCK- AND- KEY MODEL • In the lock and key model of enzyme action: -the active site has a rigid shap. -only substrate with the matching shape can fit. -the substrate is a key that fits the lock of the active site. -the amino acid R group of enzymes hepl to mediat interaction of active site and substrate. • This is an older model,however and does not work for all enzymes. Limitations • Generally applicable for enzymes that work on single type of substrate. • It indicates the active site as a rigid shape but it is actually flexible. • Rigid shape is insensitive to enviroment modification for substrate binding.
  40. 40. INDUCED FIT MODEL • In the induced fit model of enzyme action: -the active site is flexible,not rigid. -the shape of the enzyme,active site and substrate adjust to maximize the fit,which improves catalysis. -there is greater range of substrate specificity • This model is more consistant with a wider range of enzymes. Advantages:  Support enzymes which can act on different Substrate of different conformations.  Enhance fidelity of molecular recognition In presence of competitor via conformational Proof reading.  Much accepted as enzymes are not rigid and Different conditions promote differential interactions. If it was rigid all the actions were same att always.
  41. 41. ISOENZYMES • Isoenzymes are enzymes that catalyze identical • But they differ in their amino acid sequence.
  42. 42. HOW ARE THEY FORMED? • formed due to homologous or recombination of genepair. • i.e.during gene duplication the duplicate code is retained which leads to formation of isoenzymes.
  43. 43. Isoenzymes existence’s explanation 1.lsoenzymes synthesized from different genes e.g. malate dehydrogenase of cytosol is different from that found in mitochondria. 2. Oligomeric enzymes consisting of more than one type of subunits e.g. lactate dehydrogenase and creatine phosphokinase. 3. Isoenzyme may be active as monomer or oligomer e.g. glutamate dehydrogenase. 4. Differences in carbohydrate content may be responsible for isoenzymes e.g. alkaline phosphatase.
  44. 44. Isoenzymes of Lactate Dehydrogenase • Tetramer with foursubunits • Subunits may be either H or M polypeptide chain • Due to different combination of H & M 5 isoforms are there Isoform subunits Location LDH1 H4 Heart LDH2 H3M1 RBC LDH3 H2M2 Brain LDH4 H1M3 Liver LDH5 M4 Muscle Function:-convert locatate to pyruvate.
  45. 45. Isoenzymes of creatine phosphokinase • Dimer • Contain M and B subunits • Has 3 isoforms Isoform subunits Location CPK1 MM Muscle CPK2 MB Heart CPK3 BB Brain Function:-converts creatine phosphatase to creation.
  46. 46. Alkaline phosphatase • Has 6 isoenzymes • Monomer • Isoenzymes are due to different in carbohydrate content. 1. Alpha1 ALP -epithelial cells of biliary canaliculi 2. Alpha2 ht labile -hepatic cells 3. Alpha2 ht stable -placenta 4. Pre beta ALP -bone 5. Gamma ALP -intestinal cells 6. Leukocyte ALP
  47. 47. ENZYME PATTERN IN DISEASES • Enzymes in myocardial infarction Creatine phosphokinase Asparate transaminase Lactate dehydrogenase Cardiac troponins
  48. 48. • Enzymes in liver diseases • Enzymes in muscle diseases • Enzymes in cancers
  49. 49. ENYME KINEETICS-FACTORS • The catalytic properties of enzymes,and consequently their activity,are influenced by numerous factors. • These factors include Physical quantities(temperature,pressure) The chemical properties of the solution (pH vatue,ionic strength) The concentrations of the relevent subntrates,cofactors and inhibitors.
  50. 50. pH dependency of enzyme activity • Eeffect of enzymes is strongly dependent on the Ph • A ctivity is plotted against pH,a bell-shapped curve is usually obtained • Bell shape of the activity-pH profile results from the fact that amino acid residues with ionizable groups in the side chain are essential for catalysis. pH dependency of enzyme activity • A basic group B(pKa=8)which has to be protonated in order to become active. • A second acidic amino acid AH(pKa=6),which is only active in a dissociated state. • At the optimum pH of 7,around 90%of both groups are present in the active form. • At higher and lower values,one or the other of the groups
  51. 51. Temperature dependency of enzyme activity • The pemperature dependency of enzymatic activity is usually asymmetric. • With increasing temperature,the increased thermal movement of the molecules initially leads to a rate acceleration. • At a certain temperature the enzyme then becomes unstable and its activity is lost within a narrow temperature difference as a result of denaturation.
  52. 52. HISTORIC RESUME FRIEDRICH MIESCHER IN 1869 • Isolated what he called nuclein from the nuclei of pus cells. • Nuclein was shown to have acidic properties,hemce it became called nucleic acid. NUCLEIC ACID • Nucleicc asid aree polymers that consist of nucleotide residues. • Located in nuclei of cell. • Hereditary determinants of living organisms • Elemental composition- carbon,hydrogen,oxygen,nitrogen and phosphorus.
  53. 53. TYPES OF NUCLEIC ACID • Deoxyribonucleic acid(DNA) • Ribonucleic acid(RNA)
  54. 54. The Distribution of nucleic acids in the eukaryotic cell • DNA is found in the nucleus with small amounts in mitochondria and chloroplasts • RNA is found throughtout the cell NUCLEIC ACID STRUCTURE • Nucleic acids are polynucleotides • Their building blocks are nucleotides
  55. 55. NUCLEOTIDES • Energy rich compounds that drive meta bolic process in cell • Serve as chemical signals,key links in cellilar systems that respond to hormones and other extracellular stimuli • Structural component of an of enzyme cofactor and metabollic intermediate • Each nucleotide is formed by 3 units- PHOSPHATE,SUGAR,NITROGENUOS BASE
  56. 56. NUCLEOSIDES When ribose or 2-deoxyribose is combinedwith purine and pyramidine base Nucleoside is formed.
  57. 57. Properties of Nucleotides Properties of purine bases • Sparingly soluble in water • Absorb light in UV region at 260 nm. (detection & quantitation of nucleotides) • Capable of forming hydrogen bond • Aromatic base atoms numbered 1 to 9 • Purine ring is formed by fusion of pyrimidine ring with imidazole ring. • Numbering is anticlockwise. Adenine : Chemically it is 6-aminopurine Guanine : Chemically it is 2-amino,6-oxy purine Can be present as lactam & lactim form
  58. 58. Properties of pyrimidine bases • Sparingly soluble in water • Absorb light in UV region at 260 nm. (detection & quantitation of nucleotides) • Capable of forming hydrogen bond • Aromatic base atoms numbered 1 to 9 • Purine ring is formed by fusion of pyrimidine ring with imidazole ring. • Numbering is anticlockwise. • Adenine : Chemically it is 6-aminopurine • Guanine : Chemically it is 2-amino,6-oxy purine Can be present as lactam & lactim form
  59. 59. Properties of pyrimidine bases • Soluble at body pH • Also absorb UV light at 260 nm • Capable of forming hydrogen bond • Aromatic base atoms are numbered 1 to 6 for pyrimidine. • Atoms or group attached to base atoms have same number as the ring atom to which they are bonded. • Cytosine: Chemically is 2-oxy ,4-amino pyrimidine Exist both lactam or lactim form • Thymine: Chemically is 2,4 dioxy ,5-methyl pyrimidine • Occurs only in DNA • Uracil: Chemically is 2,4 dioxy pyrimidine Found only in RNA
  60. 60. Properties of Pentose Sugars • A pentose is a monosaccharide with five carbon atoms. • Ribose is the most common pentose with one oxygen atom attached to each carbon atom. • Deoxyribose sugar is derived from the sugar ribose by loss of an oxygen atom. • The aldehyde functional group in the carbohydrates react with neighbouring hydroxyl functional groups to form intramolecular hemiacetals. • The resulting ring structure is related to furan, and is termed a furanose. • The ring spontaneously opens and closes, allowing rotation to occur about the bond between the carbonyl group and the neighboring carbon atom yielding two distinct configurations (α and β). This process is termed mutarotation.
  61. 61. Classification of Nucleotides 1. Ribonucleotides if the sugar is ribose. 2. Deoxyribonucleotides if the sugar is deoxyribose.
  62. 62. Classification of Nucleosides 1. Adenosine nucleotides: ATP, ADP, AMP, Cyclic AMP 2. Guanosine nucleotides: GTP, GDP, GMP, Cyclic GMP 3. Cytidine nucleotides: CTP, CDP, CMP and certain deoxy CDP derivatives of glucose, choline and ethanolamine 4. Uridine nucleotides: UDP 5. Miscellaneous : PAPS (active sulphate), SAM (active methionine), certain coenzymes like NAD+, FAD, FMN, Cobamide coenzyme, CoA
  63. 63. GENETIC CODE The genetic code can be defined as the set of certain rules using which the living cells translate the information encoded within genetic material (DNA or mRNA sequences). The ribosomes are responsible to accomplish the process of translation. They link the amino acids in an mRNA-specified (messenger RNA) order using tRNA (transfer RNA ) molecules to carry amino acids and to read the mRNA three nucleotides at a time.
  64. 64. GENETIC CODE TABLE
  65. 65. A key point of the genetic code is its universal nature. This indicates that virtually all species with minor exceptions use the genetic code for protein synthesis. In other words, genetic code is defined as the nucleotide sequence of the base on DNA which is translated into a sequence of amino acids of the protein to be synthesized. Properties of Genetic Code • Triplet code • Non-ambiguous and Universal • Degenerate code • Nonoverlapping code • Commaless • Start and Stop Codons • Polarity
  66. 66. Triplet code The four bases of nucleotide i.e, (A, G, C, and U) are used to produce three-base codons. The 64 codons involve sense codons (that specify amino acids). Hence, there are 64 codons for 20 amino acids since every codon for one amino acid means that there exist more than code for the same amino acid. Commaless code No room for punctuation in between which indicates that every codon is adjacent to the previous one without any nucleotides between them. Nonoverlapping code The code is read sequentially in a group of three and a nucleotide which becomes a part of triplet never becomes part of the next triplet. • For example • 5’-UCU-3’ codes for Serine • 5’-AUG-3’ codes for methionine
  67. 67. Polarity Each triplet is read from 5’ → 3’ direction and the beginning base is 5’ followed by the base in the middle then the last base which is 3’. This implies that the codons have a fixed polarity and if the codon is read in the reverse direction, the base sequence of the codon would reverse and would specify two different proteins. Degenerate code • Every amino acid except tryptophan (UGG) and methionine (AUG) is coded by various codons, i.e, a few codons are synonyms and this aspect is known as the degeneracy of genetic code. For instance, UGA codes for tryptophan in yeast mitochondria. • Start and Stop Codons • Generally, AUG codon is the initiating or start codon. The polypeptide chain starts either with eukaryotes (methionine) or prokaryotes (N- formylmethionine). • On the other hand, UAG, UAA and UGA are called as termination codons or stop codons. These are not read by any tRNA molecules and they never code for any amino acids.
  68. 68. Non-ambiguous and Universal The genetic code is non-ambiguous which means a specificcodon will only code for a particular amino acid. Also, the same genetic code is seen valid for all the organisms i.e. they are universal.

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