lecture 5 concepts bchm

Explain the acid and base mechanism of the Enolase reaction 

1. Lys acts as a nucleophile and grabs a proton from active site via base catalysis . Mg2+ ions stabilize leading to an enolic intermediate 

2. Glu kicks off the OH (the enzyme protonates OH, turning it to H20 so it can leave) by acid catalysis 

What is a lysozyme and what does it do generally?

It cleaves the peptidoglycan leading to bacterial cell lysis

• acts as antibacterial enzyme, key immune defense (targeting peptidoglycan easily degrades bacterial cell wall)

• cleaves the glycosidic linkage (B1-4) between NAM and NAG

Explain the SN1 peptidoglycan cleavage by a lysozyme

• SN1*LESS STABLE CARBOCATION PATH

  • 1.Glycosidic bond cleavage and carbocation formation.

    • glycosidic bond breaks —> glycosyl carbocation (high energy is not stable)

    • Glu52 (acid catalysis) protonates the leaving Glc NAC oxygen to facilitate its departure

  • 2. Water Reactivation

    • Glu35 (base catalysis deprot. H20—> stronger nuc

  • 3. Nuc attach and product form

    • activated H20 attacks carbocation making product

    • enzyme stabilizes carbocation during this step

Explain the SN2 peptidoglycan cleavage by a lysozyme

• 1. Covalent Nuc Attack

  • Asp acts as a covalent nuc, directly attackign the anomeric carbon to displace Glu NAC

  • Substrate adopts a leaving tetrahedral intermediate

• 2. Base catalysis/ H20 activation

  • Glu 35—> general base catalysis to facilitate SN2 attack of water—> displacing Asp52—→ product

List  biological functions of nucleotides

Energy currency (ATP); enzyme cofactors (e.g., NAD⁺); second messengers (cAMP, cGMP), DNA (genetic info store), mRNA (transmission of genetic info), tRNA and r RNA (protein synthesis) 

Define: gene.

A segment of DNA containing the information to synthesize a functional product (protein or RNA).

What are the Fxns of DNA vs RNA

• DNA: store biological info and transmit that to next gen

• RNA:

  • ribosomal RNAs (rRNAs) = components

of ribosomes

• messenger RNAs (mRNAs) =

intermediates in protein synthesis

• transfer RNAs (tRNAs) = adapter

molecules that translate the information in

mRNA into a specific amino acid sequence

• noncoding RNAs (ncRNAs) = wide

variety of functions

Nucleoside vs. nucleotide—what’s the difference?

• Nucleoside = nitrogenous base (purine or pyrimidine) + pentose.

• Nucleotide = nucleoside (purine or pyrimidine base, pentose) + ≥1 phosphate.