Final Review PPT Flashcards
H-Bond Interactions
Hydrogen bound to electronegative atom
Van der Waals Interactions
Transient dipole due to optimal distance
Electrostatic Interactions
Opposite charges attract according to Coulomb’s Law
E = kq1q2/r2D
Hydrophobic Effect
Nonpolar molecules are driven together in an apparent attraction to minimize interactions with polar molecules
Importance of pH
- pH effects protonation/deprotonation state and overall charge of molecules
- Changes in pH can drastically alter important weak interactions in the Biological System
- Living systems are buffered to prevent pH changes and maintain optimal pH
Amino Acids
- Building blocks of proteins
- The central carbon is linked to an amino group, a carboxylic acid, a hydrogen atom, and a distinctive side chain called the R-group
- Have a neutral pH in solution and can exist as zwitterions (2 charges)
- Amino Group (NH3+)
- Carboxyl Group (COO-)
Primary Structure
The amino acid sequence N⇒C held together by the covalent bonds of a peptide backbone
Secondary Structure
3D structures maintained largely by noncovalent interactions of the peptide backbone
- Alpha-helices
- Beta-sheets
- Beta-turns
Tertiary Structure
Overall 3D fold of the protein maintained by weak interactions and disulfide bonds
Quarternary Structure
Interactions between multiple protein chains
How is protein folding driven?
Protein folding is driven largely by the hydrophobic effect and occurs via the progressive stabilization of intermediates
Separation and Purification Techniques
- Assay: Performed at each step to tract protein locations
- Cell Breakage
- Differential Centrifugation: gross size separation
- Salting out: characteristic surface charge separation
- Dialysis: size separation
- Chromatography
- Gel filtration: size separation
- Ion-exchange: charge separation
- Affinity: separation based on binding to a specific group
- HPLC: special format to high resolution separation
Analytical Techniques
-
Electrophoresis (size, charge, or both)
- SDS-PAGE: size separation
- Isoelectric focusing: charge separation
- 2D gels: size and charge separation
-
Immunological techniques: use antibodies for specific target detection
- Immunoprecipitation
- ELISA
- Western blotting
- Protein Structure Determination: X-ray crystallography
General Enzyme Function
- Enzymes speed up reactions by lowering the activation energy (DG‡) of reactions.
- This is achieved by the stabilization of the transition state (X‡) at the enzymes active site
- Enzymes change the rate of the reaction but not its equilibrium
Michaelis-Menten Model for Enzyme Kenetics
E + S ⇔ ES ⇒ E + P
- Vmax = fastest turnover rate
- A high Km value means that a greater amount of substrate is required to reach ½ Vmax. (lower affinity of enzyme for the substrate)
- A lower Km value means that a lesser amount of substrate is required to reach ½ Vmax. (higher affinity of enzyme for the substrate)
- KM values for enzymes vary widely and evidence suggests that the KM value is approximately the substrate concentration of the enzyme in vivo.
Competitive Inhibitors
The inhibitor is structurally similar to the substrate and can bind to the active site, preventing the actual substrate from binding.
Uncompetitive Inhibitors
The inhibitor binds only to the enzyme-substrate complex.
Noncompetitive Inhibitors
The inhibitor binds either the enzyme or enzyme-substrate complex.
Allosteric Enzymes
Enzymes with quaternary structure and multiple active sites, which do not obey Michaelis-Menten kinetics. Typically these types of enzymes are at key regulatory points in metabolic pathways.
- Concerted Model
- Sequentisl Model
Concerted Model
- T state = stable/less active
- R state = less stable/active
- Enzyme is all-T or all-R state
- NO T/R hybrid allowed
- Conversion is based on equilibrium
Sequential Model
- T state = stable/less active
- R state = less stable/active
- T/R hybrids allowed
- Conversion effects adjacent sites
Hemoglobin: Typical Allosteric Protein
- Quaternary structure with multiple active sites
- Displays sigmoidal curve for oxygen binding
- Oxygen concentration has a big influence on binding
- T-state favors oxygen release; R-state favors oxygen binding
- 2,3-Bisphosphoglycerate (2,3-BPG) stabilizes the T state of hemoglobin and thus facilitates the release of oxygen contributing to delivery capacity.
- Carbon dioxide and H+ also stabilize the T-state and enhance oxygen release by hemoglobin to ensure oxygen release at actively respiring tissues.
Membrane Proteins
- Integral membrane proteins are embedded in the hydrocarbon core of the membrane.
- Peripheral membrane proteins are bound to the polar head groups of membrane lipids or to the exposed surfaces of integral membrane proteins.
- Some proteins are associated with membranes by attachment to a hydrophobic moiety that is inserted into the membrane.
Transporters
- Active Transport
- Require ATP hydrolysis
- Pumps
- Passive Transport
- Energy comes from favorable concentration gradient
- Channels
- Secondary transporters
- Synporter
- Antiporter
Carrier Molecules in Metabolism
