Final Review PPT

Question 1

H-Bond Interactions

Answer 1

Hydrogen bound to electronegative atom

Question 2

Van der Waals Interactions

Answer 2

Transient dipole due to optimal distance

Question 3

Electrostatic Interactions

Answer 3

Opposite charges attract according to Coulomb’s Law

E = kq₁q₂/r²D

Question 4

Hydrophobic Effect

Answer 4

Nonpolar molecules are driven together in an apparent attraction to minimize interactions with polar molecules

Question 5

Importance of pH

Answer 5

• 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

Question 6

Amino Acids

Answer 6

• 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-)

Question 7

Primary Structure

Answer 7

The amino acid sequence N⇒C held together by the covalent bonds of a peptide backbone

Question 8

Secondary Structure

Answer 8

3D structures maintained largely by noncovalent interactions of the peptide backbone

• Alpha-helices
• Beta-sheets
• Beta-turns

Question 9

Tertiary Structure

Answer 9

Overall 3D fold of the protein maintained by weak interactions and disulfide bonds

Question 10

Quarternary Structure

Answer 10

Interactions between multiple protein chains

Question 11

How is protein folding driven?

Answer 11

Protein folding is driven largely by the hydrophobic effect and occurs via the progressive stabilization of intermediates

Question 12

Separation and Purification Techniques

Answer 12

• 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

Question 13

Analytical Techniques

Answer 13

• 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

Question 14

General Enzyme Function

Answer 14

• 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

Question 15

Michaelis-Menten Model for Enzyme Kenetics

Answer 15

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.

Question 16

Competitive Inhibitors

Answer 16

The inhibitor is structurally similar to the substrate and can bind to the active site, preventing the actual substrate from binding.

Question 17

Uncompetitive Inhibitors

Answer 17

The inhibitor binds only to the enzyme-substrate complex.

Question 18

Noncompetitive Inhibitors

Answer 18

The inhibitor binds either the enzyme or enzyme-substrate complex.

Question 19

Allosteric Enzymes

Answer 19

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

Question 20

Concerted Model

Answer 20

• 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

Question 21

Sequential Model

Answer 21

• T state = stable/less active
• R state = less stable/active
• T/R hybrids allowed
• Conversion effects adjacent sites

Question 22

Hemoglobin: Typical Allosteric Protein

Answer 22

• 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.

Question 23

Membrane Proteins

Answer 23

• 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.

Question 24

Transporters

Answer 24

• Active Transport
  
  • Require ATP hydrolysis
  • Pumps
• Passive Transport
  
  • Energy comes from favorable concentration gradient
  • Channels
  • Secondary transporters
    
    • Synporter
    • Antiporter

Question 25

Carrier Molecules in Metabolism

Answer 25