lecture cycle 3

• What are the 4 levels of protein structure - what is the change that indicates each new level?

  1. primary: amino acid sequence

  2. secondary: conformation of polypeptide backbone

  3. tertiary: 3D arrangement of the protein molecule

  4. quaternary: spatial arrangements of subunits within a protein
• Why do we need to eat?

  we need to fight entropy to maintain energy
• How do enzymes lower activation energy?

  the active site forces molecules into transition state (percise orientation, charge interactions, conformational strain)
• What are the most reduced carbon compounds and the most oxidized?

  - most reduced: molecules that have more CH bonds (methane)

  - most oxidized: molecules that have more CO bonds (carbon dioxide)
• Do heterotrophs take in reduced or oxidized molecules?

  reduced
• Do autotrophs take in reduced or oxidized molecules?

  oxidized
• How does the second law of thermodynamics apply to living systems?

  living organisms increase the entropy of the surroundings
• What is the definition of free energy?

  energy available to do work
• What is entropy? enthalpy?


  Entropy- The measure disorder

  
  

  Enthalpy- the amount of heat content used or released in a system
• What is the definition of an exothermic reaction?

  reaction that gives off energy
• What is the definition of an endothermic reaction?

  A reaction that takes in energy
• What is the definition of an exergonic reaction?


  spontaneous
• What is the definition of an endergonic reaction?

  not spontaneous
• How do enzymes participate in spontaneous and nonspontaneous reactions?

  - enzymes increase the rate of spontaneous reactions

  - enzymes cannot catalyse nonspontaneous reactions
• What are the features of the 'exergonic reaction energy profile'?

  - graph of free energy vs progress of the reaction

  - activation energy

  - transition state
• How does an enzyme impact the 'exergonic reaction energy profile'?


  lowers the action potential so that more molecules can get to the transition state
• Why are enzymes important to the evolution of life?

  speed up slow reactions, lower activation energy, can operate at various temperatures
• What is required for a protein to fold correctly?

  correct amino acid sequence
• What is Anfinsen's Dogma?


  primary structure of a protein determines native conformation of the protein.
• How does urea denature proteins?

  by disrupting hydrogen bonding, losing tertiary structure
• What do chaperones do?

  use energy to unfold and refold misfolded proteins
• What are the basic parts of an enzyme structure?


  - big

  - flexible

  - active site
• What is the structure of the catalytic cycle?


  enzyme + substrate, enzyme substrate complex, enzyme + product, repeat
• What is the link between the active site, protein folding, and the primary structure?

  you cannot find the active site from the primary sequence, you need to see the folded protein
• What processes explain the shape of a Growth vs Temperature curve in E. coli

  - as the temperature increases growth increases

  - at the optimal growth temp, the catalytic cycle is at its fastest

  - on the decline enzyme activity is low
• How is the tertiary structure of the enzyme Hexokinase different between organisms adapted to extreme cold versus extreme heat


  - at low temperatures: the tertiary structure is built around weak bonds that denature at room temperature

  - at high temperatures: stronger bonding
• What is the basic structure of a phospholipid? What parts are hydrophobic and hydrophilic?

  - hydrophillic head containing ohosphate and glycerol

  - hydrophobic tails, saturated or unsaturated fatty acids
• What are the consequences of introducing a carbon double bond to a phospholipid?

  unsaturated hydrocarbon tails, increasing the fluidity because it is harder to pack
• What are the characteristics of molecules that can easily diffuse across a membrane and those that cannot?

  - can diffuse: non-polar molecules, small uncharged polar molecules

  - not as easilly: large uncharged polar molecules, ions
• What are the steps and purpose of the secretory pathway?

  - ER, vesicles, golgi, vesicles, membrane

  - carries proteins to the plasma membrane that will function or be secreted
• What is the role of the SRP? What does it detect?

  recognizes and binds to the signal sequence and brings it to the ER
• What is simple diffusion? What molecules do this?

  no membrane protein required, molecules easily diffuse in and out (O2, CO2)
• What is facilitated diffusion?


  The diffusion of molecules across a membrane through transport proteins that shield from the hydrophobic core
• What is active transport?


  movement of ions or molecules against concentration gradient
• What is an ABC transporter? What are the functions of each part?

  - ATP dependent pumps that pump substrate in and out of cell, decreasing entropy

  - transmembrane domain: interacts with hydrophobic core and confers specifity

  - ATP-binding domain: breaks apart ATP, has free energy
• What drives transport? Does this relate to free energy?

  concentration gradient, which uses ATP and a change in free energy
• What causes a channel to be specific for a certain molecule?

  specific sequence of amino acids that will interact with molecules
• How can you determine if a protein is an integral membrane protein given the primary sequence?

  using a hydropathy plot, and looking at the hydrophopic peaks, indicating that the amino acids interact with the membrane
• What is cystic fibrosis and the function of CFTR?

  - cystic fibrosis: mutation to CFTR, causing dry lungs, poor gas exchange

  - CFTR: ABC transporter which pumps Cl
• What is the end result of the deltaF508 form of CFTR?

  does not make it to the cell membrane, degraded by protosome