Cycle 3 BMP Workshop

Question 1

List and Describe:

Types of energy

Answer 1

1. Kinetic: From moving particles
2. Potential: “Stored” by position or chemical structure
3. Chemical: From chemical reactions

Question 2

List and explain:

Types of systems

Answer 2

1. Open: Exchange matter AND energy (e.g. cells)
2. Closed: Exchange energy only
3. Isolated: Neither

Question 3

List and explain:

The first two laws of thermodynamics

Answer 3

Law 1: Energy CANNOT be made or destroyed, it can only be converted

Law 2: Entropy (“disorder”) of the universe ALWAYS INCREASES

Question 4

How do cells fight the 2nd Law of Thermodynamics?

Answer 4

Cells use energy to build “ordered” molecules
They are “islands” of low entropy (energy taken in to replace other things broken down)

Question 5

State:

The levels of protein structure

Answer 5

1. Primary (denatured)
2. Secondary
3. Tertiary (functional proteins)
4. Quaternary (functional proteins)

Question 6

Describe the structure and bonding of:

Primary structure protein

Answer 6

• Unfolded, 1 linear chain of amino acids
• Peptide bonds joining amino acids

Question 7

Describe the structure and bonding of:

Secondary structure protein

Answer 7

• 1 chain of amino acids (alpha-helix form or beta-barrel form)
• Peptide + Hydrogen bonds

Question 8

What are hydrogen bonds disturbed by?

Answer 8

Urea

Question 9

Describe the structure and bonding of:

Tertiary structure protein

Answer 9

• 1 fully folded 3D chain
• Peptide, Hydrogen + any other bond (dipole-dipole, disulfide bridges etc.)

Question 10

Describe the structure and bonding of:

Quaternary structure protein

Answer 10

• Multiple fully folded 3D chains
• Peptide, Hydrogen + any other bond (dipole-dipole, disulfide bridges etc.)

Question 11

Describe:

Most reduced molecules

Answer 11

• More C-H bonds
• HIGH free energy
• Electrons are easy to remove

Question 12

Describe:

Most oxidized molecules

Answer 12

• More C-O bonds
• LOW free energy
• Electrons are more tightly bound to oxygen

Question 13

Explain:

Heterotrophs

Answer 13

• “We like, we want”
• Consume: Matter and energy combine through our carbs + fats

Question 14

Explain:

Autotrophs

Answer 14

• “We hate, we expel”
• Consume matter (CO2) and energy (light)

Question 15

State the type of equation and explain:

The values in the equation:
ΔG = ΔH - TΔS

Answer 15

Thermodynamic Equation
* ΔG: Free energy, = Products - Reactants
* ΔH: Enthalpy
* ΔS: Entropy

Question 16

State the meaning of:

ΔG > 0
ΔG < 0

Answer 16

Free Energy
* ΔG > 0: Endergonic, requires energy
* ΔG < 0: Exergonic, spontaneous

Question 17

State the meaning of:

ΔH > 0
ΔH < 0

Answer 17

Enthalpy
* ΔH > 0: Endothermic
* ΔH < 0: Exothermic

Question 18

State the meaning of:

ΔS > 0
ΔS < 0

Answer 18

Entropy
* ΔS > 0: More spread out (less order)
* ΔS < 0: Less spread out (more order)

Question 19

What do enzymes do?

Answer 19

Enzymes LOWER ACTIVATION ENERGY to speed up the reaction

Question 20

True or False:

Enzymes change ΔG

Answer 20

False

Question 21

True or False:

Enzymes do not give energy

Answer 21

True

Question 22

What is required for endergonic reactions to occur?

Answer 22

Energy providers (e.g. ATP)

Question 23

True or False:

Unfolded protein (primary structure) is very stable

Answer 23

False, unfolded proteins have high ΔG, making it very unstable

Question 24

Explain:

The Energy Funneling Process

Answer 24

• 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

Question 25

# Define: Active site

Answer 25

Area on an enzyme that binds the substrate

Question 26

How is the active site found?

Answer 26

Discovered by looking at enzyme's 3D shape, not primary structure

Question 27

# True or False: The active site of an enzyme is only functional as tertiary structure

Answer 27

True

Question 28

# Describe: The Catalytic Cycle

Answer 28

* The enzyme and substrate bind to form the ES complex * The complex becomes enzyme and product * The enzyme continues binding with substrate

Question 29

What does extreme temperature do to enzymes? How is this dealt with?

Answer 29

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

Question 30

What dictates an enzyme's optimum temperature?

Answer 30

The organism's environment

Question 31

What are the types of membrane-bound proteins and how are they different?

Answer 31

* Integral vs. Peripheral membrane proteins * Differences in mobility

Question 32

# State and describe: Types of membrane transport

Answer 32

* Passive: Follow their concentration gradients, spontaneous, increase in entropy * Active: Move against concentration gradients

Question 33

# Explain: Passive transporter

Answer 33

* 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

Question 34

# Explain: Active transporter

Answer 34

* 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

Question 35

What does normal lung physiology involve?

Answer 35

A delicate balance of ions and water

Question 36

What maintains the correct concentration gradient of chloride within the lungs

Answer 36

Chloride pump (CFTR), an ABC

Question 37

Why does the lung require a concentration gradient of chloride?

Answer 37

Ensures correct osmosis of water, as water is needed to keep cilia wet and mobile to prevent lung infections

Question 38

What prevents misfolded CFTR from reaching the membrane?

Answer 38

HSP90

Question 39

# True or False: HSP90 is useful

Answer 39

Conditional. HSP90 is useful in health people, but it causes problems in cystic fibrosis (infections, thick mucus, troubles breathing)

Question 40

What does the degree of lipid saturation affect?

Answer 40

The fluidity of the membrane * Increased stauration = decreased fluidity * Decreased saturation = increased fluidity

Question 41

# Define: Desaturases

Answer 41

Enzymes that can adjust membrane fluidity by increasing the degree of unsaturation in membrane fatty acids

Question 42

# True or False: Organisms cannot alter membrane fluidity

Answer 42

False, organisms can alter their membrane fluidity at different temperatures by changing the level of desaturase expression

Question 43

# State: Components of phospholipids

Answer 43

1. Glycerol head (hydrophilic) 2. Fatty acid tails (hydrophobic

Question 44

State the term for hydrophilic and hydrophobic domain together

Answer 44

Amphipathic

Question 45

# State: Membrane permeability for different molecules

Answer 45

* Passive diffusion: Nonpolar molecules (lipids), small polar molecules (water) * Facilitated diffusion: Big polar molecules (glucose), ions (Cl-, Na+...)

Question 46

# Define: Facilitated diffusion

Answer 46

Requires membrane proteins specific to the molecule

Question 47

What are integral proteins?

Answer 47

Proteins that act as channels spanning the phospholipid bilayer

Question 48

# Define: Hydropathy Plot

Answer 48

A graph where: * X-axis: Amino acid number * Y-axis: Relative hydrophobicity index * (Positive Y is hydrophobic, negative y is hydrophilic)

Question 49

# True or False: Integral membranes have hydrophobic parts

Answer 49

True

Question 50

# Explain: How proteins get on the plasma membrane or secreted out of cell

Answer 50

1. Endoplasmic reticulatum 2. Golgi apparatus 3. Plasma membrane via vesicles

Question 51

Where does translation occur?

Answer 51

Cytoplasm

Question 52

How is a protein sent to the membrane?

Answer 52

* A "tag" on the protein * Cell is able to recognize this tag * Cell transports proteins to proper places

Question 53

# State: The steps of the Secretory Pathway

Answer 53

1. RNA translated by ribosome, and a signal sequence pops out as polypeptide 2. Translation stops. Signal receptor protein (SRP) binds to signal sequence 3. SRP binds to a SRP receptor protein on the ER. Translation continues into the ER 4. Following translation of protein to be sent to the membrane, the signal sequence is cut

Question 54

# True or False: The signal sequence is not included in mRNA

Answer 54

False, the signal sequence is included in the mRNA

Question 55

Does the signal sequence appear in the initial protein? Final/mature protein?

Answer 55

The signal sequence appears as a polypeptide in the initial protein, but is excised in the final/mature protein