Biological Macromolecules Lecture 1

HIV proteases consist of two chains that form a dimer.

The active site is located at the interface of the dimer, and substrate binding is assisted by two flaps that sequester the substrate.

The inhibitor mimics the transition state, binds with high affinity to the active site, but cannot be cleaved.

<p>The six classes are oxidoreductases, ligases, hydrolases, transferases, isomerases, and lyases.</p> Signup and view all the answers

<p>Transferases transport chemical groups from donor molecules to acceptor molecules.</p> Signup and view all the answers

<p>Vmax is the maximum turnover rate of an enzyme when substrate concentration is infinitely high, meaning there is no free enzyme available.</p> Signup and view all the answers

<p>Km is the substrate concentration required to achieve half the maximum efficiency or turnover of the enzyme.</p> Signup and view all the answers

<p>Experiments are typically done in vitro, and the cellular environment can differ significantly from these conditions.</p> Signup and view all the answers

<p>Biological macromolecules are complex molecules composed of repeating monomers covalently bound, including nucleic acids, proteins, and carbohydrates.</p> Signup and view all the answers

<p>Carbohydrates are classes of biological molecules made of repeating sugar monomers with the general formula $C_n(H_2O)_n$.</p> Signup and view all the answers

<p>Aldoses contain an aldehyde group, while ketoses contain a ketone group, with glucose being an example of an aldose and fructose a ketose.</p> Signup and view all the answers

<p>When glucose is in excess, it is converted into glycogen for storage in the muscle, liver, and kidneys through enzymatic pathways.</p> Signup and view all the answers

<p>Upon cyclisation, glucose can form either an alpha or beta conformation based on the position of the OH group on carbon 1.</p> Signup and view all the answers

<p>The anomeric carbon in glucose is carbon 1, which is the site of the carbonyl group in its linear form and dictates the alpha or beta conformation.</p> Signup and view all the answers

<p>Beta glucose is more stable than alpha glucose due to the greater distance between the OH on carbon 2 and carbon 1, leading to lower energy structure.</p> Signup and view all the answers

<p>Condensation refers to a chemical reaction where two molecules combine, releasing water and forming a covalent bond, typically seen in the synthesis of macromolecules.</p> Signup and view all the answers

<p>This equation implies that the maximum rate of reaction (Vmax) is directly proportional to the total concentration of the enzyme and the rate constant k2 when all enzyme is bound to the substrate.</p> Signup and view all the answers

<p>Km reflects the affinity between the enzyme and substrate; a lower Km indicates higher affinity.</p> Signup and view all the answers

<p>The Lineweaver-Burk plot allows for the determination of Km and Vmax by plotting the reciprocal of reaction rates against the reciprocal of substrate concentrations.</p> Signup and view all the answers

<p>An enzyme activator increases enzyme activity by binding to the active or allosteric site, which can be either reversible or irreversible.</p> Signup and view all the answers

<p>In competitive inhibition, a molecule competes with the substrate for binding to the active site, which reversibly decreases the rate of reaction.</p> Signup and view all the answers

<p>Irreversible inhibitors form covalent bonds with active site residues, permanently preventing substrate binding and catalytic activity.</p> Signup and view all the answers

<p>For non-competitive inhibition to not affect Km, the condition k-1 must be significantly greater than k2 (k-1 &gt;&gt; k2).</p> Signup and view all the answers

<p>Penicillin initially acts as a substrate for the enzyme, but it ultimately covalently modifies the active site, leading to enzyme inactivation.</p> Signup and view all the answers

<p>The active site must bind to the substrate selectively, induce distortion of the substrate, and stabilize the transition state while allowing product release.</p> Signup and view all the answers

<p>The induced-fit model describes a flexible interaction between enzyme and substrate, where both undergo deformation upon binding; this is evidenced by the closing of a flexible loop over the substrate in hexokinase.</p> Signup and view all the answers

<p>It catalyzes the reaction CO2 + H2O to HCO3- + H+, involving a zinc ion that polarizes water and facilitates the transfer of protons and nucleophilic attack by hydroxide.</p> Signup and view all the answers

<p>Proteases are enzymes that hydrolyze peptide bonds in proteins, and they contain a catalytic triad composed of serine, histidine, and aspartate in their active site.</p> Signup and view all the answers

<p>Chymotrypsin selects substrates using a selectivity pocket that accommodates bulky hydrophobic residues in the R1 position, such as phenylalanine, tryptophan, or tyrosine.</p> Signup and view all the answers

<p>Trypsin preferentially selects positively charged residues, specifically lysine or arginine, in the R1 position.</p> Signup and view all the answers

<p>Elastase selects small residues like glycine, alanine, or valine in the R1 position due to its ability to accommodate smaller side chains in its active site.</p> Signup and view all the answers

<p>Vitamin C maintains Fe2+ in its reduced state, essential for hydroxylating proline to form hydroxyproline in collagen. Its deficiency leads to insufficient collagen production, resulting in symptoms like bleeding gums and poor wound healing.</p> Signup and view all the answers

<p>The mechanism involves Ser195 performing a nucleophilic attack on the carbonyl carbon of the substrate, while His57 and Asp102 stabilize the positive charge on His57, leading to a tetrahedral intermediate.</p> Signup and view all the answers

<p>A motif is a collection of structural elements within a protein. Three classical examples are the beta-alpha-beta, alpha helical, and Greek key motifs, held together by hydrogen and hydrophobic interactions.</p> Signup and view all the answers

<p>Motifs are not structurally independent and only form in the context of the whole protein, while domains are several motifs assembled together, are structurally independent, and possess a hydrophobic core.</p> Signup and view all the answers

<p>Antibodies are tetrameric proteins comprising two identical heavy and two identical light chains with 12 domains. The variable domains are located at the N terminus of each chain, facilitating specific binding to antigens.</p> Signup and view all the answers

<p>The immunoglobulin domain provides a structural framework that allows antibodies to bind specifically to the antigen's epitope.</p> Signup and view all the answers

<p>Quaternary structure refers to the interactions between multiple polypeptide subunits to form a multimeric protein.</p> Signup and view all the answers

<p>The stability of a beta-alpha-beta motif is primarily maintained by hydrogen bonds and hydrophobic interactions.</p> Signup and view all the answers

<p>The variable domain of antibodies can adapt to various shapes and structures of different antigens, allowing for specific binding to diverse epitopes.</p> Signup and view all the answers

<p>Peptide bonds are covalent bonds formed between two amino acids through the elimination of water. Specifically, the O from the COO group and the H from the amino group are removed.</p> Signup and view all the answers

<p>The primary structure of a protein is the linear sequence of amino acid residues linked by peptide bonds. It is critical for the protein's overall structure and function.</p> Signup and view all the answers

<p>Denaturing agents such as mercaptoethanol break covalent bonds, while urea disrupts non-covalent bonds, leading to the loss of protein structure and function. Removing these agents allows proteins to refold back into their native state.</p> Signup and view all the answers

<p>The two main types of secondary structure in proteins are the alpha helix and the beta pleated sheet. These structures are stabilized by hydrogen bonds between the backbone residues.</p> Signup and view all the answers

<p>Alpha helices are stabilized by hydrogen bonds between the carbonyl group on residue (i) and the amino group on residue (i+4) in the same polypeptide chain. This arrangement leads to a right-handed helical structure.</p> Signup and view all the answers

<p>The beta pleated sheet consists of hydrogen bonds between carbonyl and amino groups of neighboring strands, which can be either parallel or anti-parallel arrangements. This conformation provides structural stability and strength to proteins.</p> Signup and view all the answers

<p>The five types of interactions in tertiary structure, ordered by strength, are disulfide bridges, ionic bonds, hydrogen bonds, hydrophobic interactions, and van der Waals forces. Each type contributes differently to protein folding.</p> Signup and view all the answers

<p>Loop regions in proteins connect secondary structure elements and do not have a defined structure themselves. They provide flexibility and can play critical functional roles.</p> Signup and view all the answers