Cycle 3 BMP Workshop Flashcards
List and Describe:
Types of energy
- Kinetic: From moving particles
- Potential: “Stored” by position or chemical structure
- Chemical: From chemical reactions
List and explain:
Types of systems
- Open: Exchange matter AND energy (e.g. cells)
- Closed: Exchange energy only
- Isolated: Neither
List and explain:
The first two laws of thermodynamics
Law 1: Energy CANNOT be made or destroyed, it can only be converted
Law 2: Entropy (“disorder”) of the universe ALWAYS INCREASES
How do cells fight the 2nd Law of Thermodynamics?
Cells use energy to build “ordered” molecules
They are “islands” of low entropy (energy taken in to replace other things broken down)
State:
The levels of protein structure
- Primary (denatured)
- Secondary
- Tertiary (functional proteins)
- Quaternary (functional proteins)
Describe the structure and bonding of:
Primary structure protein
- Unfolded, 1 linear chain of amino acids
- Peptide bonds joining amino acids
Describe the structure and bonding of:
Secondary structure protein
- 1 chain of amino acids (alpha-helix form or beta-barrel form)
- Peptide + Hydrogen bonds
What are hydrogen bonds disturbed by?
Urea
Describe the structure and bonding of:
Tertiary structure protein
- 1 fully folded 3D chain
- Peptide, Hydrogen + any other bond (dipole-dipole, disulfide bridges etc.)
Describe the structure and bonding of:
Quaternary structure protein
- Multiple fully folded 3D chains
- Peptide, Hydrogen + any other bond (dipole-dipole, disulfide bridges etc.)
Describe:
Most reduced molecules
- More C-H bonds
- HIGH free energy
- Electrons are easy to remove
Describe:
Most oxidized molecules
- More C-O bonds
- LOW free energy
- Electrons are more tightly bound to oxygen
Explain:
Heterotrophs
- “We like, we want”
- Consume: Matter and energy combine through our carbs + fats
Explain:
Autotrophs
- “We hate, we expel”
- Consume matter (CO2) and energy (light)
State the type of equation and explain:
The values in the equation:
ΔG = ΔH - TΔS
Thermodynamic Equation
* ΔG: Free energy, = Products - Reactants
* ΔH: Enthalpy
* ΔS: Entropy
State the meaning of:
ΔG > 0
ΔG < 0
Free Energy
* ΔG > 0: Endergonic, requires energy
* ΔG < 0: Exergonic, spontaneous
State the meaning of:
ΔH > 0
ΔH < 0
Enthalpy
* ΔH > 0: Endothermic
* ΔH < 0: Exothermic
State the meaning of:
ΔS > 0
ΔS < 0
Entropy
* ΔS > 0: More spread out (less order)
* ΔS < 0: Less spread out (more order)
What do enzymes do?
Enzymes LOWER ACTIVATION ENERGY to speed up the reaction
True or False:
Enzymes change ΔG
False
True or False:
Enzymes do not give energy
True
What is required for endergonic reactions to occur?
Energy providers (e.g. ATP)
True or False:
Unfolded protein (primary structure) is very stable
False, unfolded proteins have high ΔG, making it very unstable
Explain:
The Energy Funneling Process
- Multiple ways to fold a protein from primary structure
- There may be transitional/misfolded proteins along the way
- Chaperones use energy to get proteins to unfold and refold correctly
- The final active protein has low ΔG, making it most stable
Define:
Active site
Area on an enzyme that binds the substrate
How is the active site found?
Discovered by looking at enzyme’s 3D shape, not primary structure
True or False:
The active site of an enzyme is only functional as tertiary structure
True
Describe:
The Catalytic Cycle
- The enzyme and substrate bind to form the ES complex
- The complex becomes enzyme and product
- The enzyme continues binding with substrate
What does extreme temperature do to enzymes? How is this dealt with?
Extreme cold causes enzyme to become too rigid
* “Weaker” tertiary structure bonds or arrangements to allow enzyme to be fluid
Extreme heat causes enzyme to become too fluid (denatures)
* “Stronger” tertiary structure bonds or arrangements to allow for more rigid enzyme
What dictates an enzyme’s optimum temperature?
The organism’s environment
What are the types of membrane-bound proteins and how are they different?
- Integral vs. Peripheral membrane proteins
- Differences in mobility
State and describe:
Types of membrane transport
- Passive: Follow their concentration gradients, spontaneous, increase in entropy
- Active: Move against concentration gradients
Explain:
Passive transporter
- The passive transporter acts as a hole in the membrane for the particle to pass through
- The membrane prevents movement of the particle; if there was no membrane, the particle would move in this way
Explain:
Active transporter
- Using ATP (energy) to move the particle, as without ATP, the reaction would be endergonic and non-spontaneous
- If there was no membrane, the particle would move in a manner opposite to this
What does normal lung physiology involve?
A delicate balance of ions and water
What maintains the correct concentration gradient of chloride within the lungs
Chloride pump (CFTR), an ABC
Why does the lung require a concentration gradient of chloride?
Ensures correct osmosis of water, as water is needed to keep cilia wet and mobile to prevent lung infections
What prevents misfolded CFTR from reaching the membrane?
HSP90
True or False:
HSP90 is useful
Conditional.
HSP90 is useful in health people, but it causes problems in cystic fibrosis (infections, thick mucus, troubles breathing)
What does the degree of lipid saturation affect?
The fluidity of the membrane
* Increased stauration = decreased fluidity
* Decreased saturation = increased fluidity
Define:
Desaturases
Enzymes that can adjust membrane fluidity by increasing the degree of unsaturation in membrane fatty acids
True or False:
Organisms cannot alter membrane fluidity
False, organisms can alter their membrane fluidity at different temperatures by changing the level of desaturase expression
State:
Components of phospholipids
- Glycerol head (hydrophilic)
- Fatty acid tails (hydrophobic
State the term for hydrophilic and hydrophobic domain together
Amphipathic
State:
Membrane permeability for different molecules
- Passive diffusion: Nonpolar molecules (lipids), small polar molecules (water)
- Facilitated diffusion: Big polar molecules (glucose), ions (Cl-, Na+…)
Define:
Facilitated diffusion
Requires membrane proteins specific to the molecule
What are integral proteins?
Proteins that act as channels spanning the phospholipid bilayer
Define:
Hydropathy Plot
A graph where:
* X-axis: Amino acid number
* Y-axis: Relative hydrophobicity index
* (Positive Y is hydrophobic, negative y is hydrophilic)
True or False:
Integral membranes have hydrophobic parts
True
Explain:
How proteins get on the plasma membrane or secreted out of cell
- Endoplasmic reticulatum
- Golgi apparatus
- Plasma membrane via vesicles
Where does translation occur?
Cytoplasm
How is a protein sent to the membrane?
- A “tag” on the protein
- Cell is able to recognize this tag
- Cell transports proteins to proper places
State:
The steps of the Secretory Pathway
- RNA translated by ribosome, and a signal sequence pops out as polypeptide
- Translation stops. Signal receptor protein (SRP) binds to signal sequence
- SRP binds to a SRP receptor protein on the ER. Translation continues into the ER
- Following translation of protein to be sent to the membrane, the signal sequence is cut
True or False:
The signal sequence is not included in mRNA
False, the signal sequence is included in the mRNA
Does the signal sequence appear in the initial protein? Final/mature protein?
The signal sequence appears as a polypeptide in the initial protein, but is excised in the final/mature protein
