nfs 3083 exam 2

Protein Dynamics

Enzymatic Function

• Enzymes act as catalysts in biochemical reactions.

  • Most catalysts are proteins.

  • Lower activation energy to accelerate reactions.

  • Activation energy= energy difference between ground and transition states.

  • Transition state involves breaking/forming bonds.

• Enzymes are highly specific and regulate reaction rates under mild conditions.

Substrate Binding Models

• Substrates are reactants in enzyme-catalyzed reactions.

• Specificity: Enzymes selectively recognize substrates.

  • Fit between substrate and enzyme controls product formation.

Functions of Enzymes

• Enzymes mediate virtually all cellular reactions.

• Catalytic power is the ratio of enzyme-catalyzed to uncatalyzed rates.

• Regulation ensures appropriate reaction rates based on cellular needs.

• Cofactors: inorganic ions essential for enzyme function.

• Coenzymes: organic molecules that carry functional groups, often derived from vitamins.

Enzyme Kinetics

• Kinetics examines reaction rates and factors affecting them (enzymes, substrates, temperature).

• Vmax: maximum reaction velocity, theoretically asymptotic as substrate increases.

• Km: Michaelis constant; a low Km indicates high affinity for substrates.

Effects of pH and Temperature

• pH affects enzyme structure and activity; enzymes have various ionizable side chains.

Non-Protein Enzymes

• Coenzymes and cofactors act as non-protein enzymes.

Transition State Importance

• Transition state formation is crucial for enzymes to facilitate reactions.

Enzyme Inhibition Types

• Reversible inhibitors (non-covalently bound):

  • Competitive: binds the active site.

  • Uncompetitive: inhibits function without affecting substrate binding.

  • Mixed: affects both functions.

• Irreversible inhibitors (covalently bound): often transition state analogs.

Regulation of Enzyme Activity

• Regulation ensures metabolic reactions are suitable for cellular requirements.

• Involves genetic regulation, allosteric modulation, and covalent modification.

Allosteric Regulation

• Enzymes at key metabolic pathway steps are modulated by effectors.

  • Can be activators or inhibitors.

Isozymes

• Isozymes are enzymes differing in subunits but performing similar functions.

Zymogens

• Inactive enzyme precursors activated by proteolytic cleavage.

Blood Clotting Cascade Key Points

• Fibrinogen (zymogen) converts to fibrin via thrombin.

Carbohydrates Overview

• Monosaccharides, disaccharides, polysaccharides defined.

  • Monosaccharides: simplest sugars.

  • Oligosaccharides: 2-10 sugar residues.

  • Polysaccharides: polymers of sugars.

Monosaccharide Cyclization

• Cyclization forms chiral centers (anomeric carbon).

Stereochemistry Definitions

• Stereoisomers: same molecular formula, different spatial orientation.

• Diastereomers: non-mirror image stereoisomers.

• Epimers: differ at one chiral center.

Glycation vs. Glycosylation

• Glycation: non-enzymatic glucose attachment.

• Glycosylation: enzymatic glucose attachment.

Glycosidic Bonds

• Formed via dehydration reactions; various types exist (O, N, S, C).

  • Reversible under certain conditions (acidic/enzymatic hydrolysis).

Reducing vs. Nonreducing Sugars

• Nonreducing sugars lack free OH on anomeric carbons.

• Common nonreducing examples include sucrose.

Polysaccharide Functions

• Starch (amylose, amylopectin), glycogen, cellulose, chitin, hyaluronic acid, heparin defined.

  • Structural and energy storage roles.

Glycogen Storage

• Glycogen: linear a1→4 and branched a1→6 linkages.

Starch Differentiation

• Amylose has a1→4, amylopectin has a1→4 and a1→6 linkages.

Glycosaminoglycans Examples

• Heparin (anticoagulant), hyaluronates (joint lub), chondroitins, dermatan sulfate.

Lipids Overview

• Basic structure and classifications of fatty acids.

  • Saturated, mono-, polyunsaturated: natural state.

Structural and Nomenclature of Fatty Acids

• Identification via delta (Δ) and omega (ω) nomenclature.

Physical Properties Relation

• Hydrocarbon chain length and saturation affect solubility/melting points.

Trans Fatty Acids

• Form through dehydrogenation; impact on health.

Essential Fatty Acids

• EFAs required through diet; n-6:n-3 ratio relevance in health.

Triacylglycerol Storage

• TAGs as long-term energy sources, storage forms.

Cholesterol Roles

• Cholesterol modulates membrane fluidity; physiological roles.

Membrane Functions

• Barrier, transport, energy transduction functions detailed.

Lipid Aggregation

• Amphipathic nature of lipids leads to formation of micelles, vesicles, and bilayers.

Membrane Components

• Structure and importance of phospholipids and sphingolipids.

Membrane Asymmetry

• Role in protein/lipid distribution across leaflets.

Fluid Mosaic Model Summary

• Membrane proteins and lipid motion dynamics explained.