Scribd Logo
Upload

Welcome to Scribd!

  • 15 views

    Lecture 28: Carbohydrates 2: Biochemistry I Fall Term, 2004

    Uploaded by

    Louis Fortunato
    This document summarizes a lecture on carbohydrates and lysozyme catalysis. The lecture covered structural polysaccharides like cellulose and chitin, storage polysaccharides like starch and glycogen, and glycoproteins. It also described the catalytic mechanism of lysozyme, a protein that hydrolyzes bacterial cell walls. Key aspects of lysozyme catalysis include transition state stabilization through substrate binding and residues that provide acid catalysis and stabilize the carbocation intermediate.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd

    Lecture 28: Carbohydrates 2: Biochemistry I Fall Term, 2004

    Uploaded by

    Louis Fortunato
    15 views3 pages
    This document summarizes a lecture on carbohydrates and lysozyme catalysis. The lecture covered structural polysaccharides like cellulose and chitin, storage polysaccharides like starch and glycogen, and glycoproteins. It also described the catalytic mechanism of lysozyme, a protein that hydrolyzes bacterial cell walls. Key aspects of lysozyme catalysis include transition state stabilization through substrate binding and residues that provide acid catalysis and stabilize the carbocation intermediate.

    Original Title

    Biochem Lec28

    Copyright

    © Attribution Non-Commercial (BY-NC)

    Available Formats

    PDF, TXT or read online from Scribd

    Did you find this document useful?

    Is this content inappropriate?

    This document summarizes a lecture on carbohydrates and lysozyme catalysis. The lecture covered structural polysaccharides like cellulose and chitin, storage polysaccharides like starch and glycogen, and glycoproteins. It also described the catalytic mechanism of lysozyme, a protein that hydrolyzes bacterial cell walls. Key aspects of lysozyme catalysis include transition state stabilization through substrate binding and residues that provide acid catalysis and stabilize the carbocation intermediate.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    15 views3 pages

    Lecture 28: Carbohydrates 2: Biochemistry I Fall Term, 2004

    Uploaded by

    Louis Fortunato
    This document summarizes a lecture on carbohydrates and lysozyme catalysis. The lecture covered structural polysaccharides like cellulose and chitin, storage polysaccharides like starch and glycogen, and glycoproteins. It also described the catalytic mechanism of lysozyme, a protein that hydrolyzes bacterial cell walls. Key aspects of lysozyme catalysis include transition state stabilization through substrate binding and residues that provide acid catalysis and stabilize the carbocation intermediate.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 3

    Biochemistry I Fall Term, 2004

    November 12, 2004

    Lecture 28: Carbohydrates 2


    Lecture by Dr. Grotzinger Assigned reading in Campbell: Chapter 13.4-13.5 Key Terms: Cellulose (14) glucose Starch (14) glucose Glycogen (16) branch points NAG (N-acetylglucosamine) Lysozyme: acid catalysis transition state stabilization oxonium ion

    Links: (I) Review Quiz on Lecture 28 concepts: (I) Lysozyme Chemical Mechanism: Handout for Lecture 28. (I) Trypsin and Lysozyme Mechanisms Compared: Handout for Lecture (S) Lysozyme Binding & Catalysis: Structure is related to function on a Chime page. Polysaccharides Structural Polysaccharides Cellulose: Structural polysaccharide of plants. Polymer of (14) glucose. Similar in structure to -sheets in proteins: cellulose forms flat sheets with multiple hydrogen bonds between strands. Digested by symbiotic microorganisms. Chitin: Structural polysaccharide in insect and shellfish exoskeletons. Contains N-acetylglucosamine (NAG).

    Storage Polysaccharides 1. Starch [plants] (amylose and amylopectin): Amylose = Polymer of (14) glucose. Similar in structure to -helix in proteins: forms a helix. Amylopectin = amylose + (16) branches. 1

    2. Glycogen [animals]: More highly branched than starch. Glucose units are released by the enzyme glycogen phosphorylase, producing glucose-1-phosphate. Glycoproteins & Glycosylated Proteins Bacterial Cell Walls: Polysaccharide chains of alternating NAG and NAM (N-acetylglucosamine + a lactic acid on O3). NAG NAM chains are crosslinked with pentaglycine bridges. Synthesis of bacterial cell walls is inhibited by penicillin.

    Eukaryotic Glycoproteins: Common form of protein modification (another is phosphorylation). Branched chain with a common core of saccharides. Attached oligosaccharide chains are usually solvent exposed. They can be removed without large effects on protein structure. They are more disordered than the polypeptide part. Play an important role in directing intracellular location of protein ("protein trafficking"). Define blood group (ABO) antigens. Two common linkages: 1. N-linked: The first residue is usually NAG (N-acetylglucosamine) attached to an Asn side chain in the sequence (Asn-X-Ser/Asn-X-Thr). 2. O-linked: The first and second residues are usually -galactosyl-(1,3)--Nacetylgalactosyl attached to the OH of Ser or Thr. Lysozyme Mechanism 14 kDa protein. Found in egg whites, tears, various other secretions.

    Disulfide bonded. Hydrolyzes the bond between NAG units in bacterial cell walls. May serve as a defence mechanism.

    The rate of enzyme catalyzed hydrolysis is approximately 108 times that of the uncatalyzed reaction. This enhancement is due to: 1. Binding of the substrate in a conformation that resembles the transition state. 2. Acid catalysis provided by a Glu residue. 3. Stabilization of the positive charge in the transition state by an ionized Asp residue. Catalytic Mechanism (Residue numbers are for human lysozyme.): 1. A total of 6 NAG units fit in the active site cleft (subsites are designated "A-F"). 2. A large number of interactions in the 'specificity pocket' define specificity for NAG. 3. Gbinding for NAG3 = -24 kJ/mol 4. Gbinding for NAG4 = +12.1 kJ/mol. 5. Therefore NAG bound in the active site is in a strained conformation - transition state stabilization. 6. This distortion is due to a hydrogen bond between the main chain of Val 110 and the O6 atom of NAGD. 7. Glu 35 (pKa = 6.3!) protonates the oxygen in the glycosidic bond (between NAGD and NAGE (acid catalysis) 8. The glycosidic bond is broken, resulting in a carbocation on the C1 of NAGD. 9. The carbocation is stabilized by formation of an oxonium ion. This requires the formation of a planar, half-chair conformation of NAGD. 10. The carbocation is stabilized by the negative charge on Asp 53 (pKa=3.5, i.e. normal), but a covalent intermediate is not formed. This is an example of transition state stabilization in enzyme catalysis. 11. The reaction is completed by attack of a water molecule (hydroxide) on the oxonium ion and the reprotonation of Glu 35.
    11.9.04

    You might also like