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Biochem 2 (CHEM 441B) > Ch. 2 > Flashcards

Ch. 2 Flashcards

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1
Q

What is bioenergetics?

A

Energy conversion in biological systems
- Observed in photosynthesis

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2
Q

What is the importance of chemical energy?

A
  • Used by organisms to perform work
  • Essential for cell survival
  • Usually obtained from the environment
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3
Q

What are the different types of work?

A
  • Osmotic
  • Chemical
  • Mechanical
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4
Q

What is osmotic work?

A

Maintains varying [solute] across biological membranes
- Na+/K+ pump

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5
Q

What is chemical work?

A

Biosynthesis (anabolic) and degradation (catabolic) of organic molecules

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6
Q

What is mechanical work?

A

Muscle contraction in animals

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7
Q

What are redox reactions?

A
  • Series of linked oxidation-reduction reactions
  • Transfer electrons from one compound to another in sequential fashion
  • Used in processes where chemical work is performed and energy is made
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8
Q

What is reduction vs oxidation?

A

Reduction: gain of electrons (GER)
- Increase in number of hydrogens
- Decrease in number of bonds to oxygen
- Becomes more negative

Oxidation: loss of elections (LEO)
- Decrease in number of hydrogens
- Increase in number of oxygens
- Becomes more positive

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9
Q

What is a system (thermodynamics)?

A

Collection of matter in a defined space

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10
Q

What are the surroundings (thermodynamics)?

A

All the space not included in the system

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11
Q

What are the types of systems?

A
  • Open = matter and energy are freely exchanged with the surroundings
  • Closed = only energy is exchanged with the surroundings
  • Isolated = neither matter nor energy is exchanged with the surroundings
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12
Q

What is the first law of thermodynamics?

A
  • Energy can be neither created nor destroyed
    • Can only be converted from one form to another
    • Energy has an effect on enthalpy (H)
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13
Q

What is the second law of thermodynamics?

A

All spontaneous processes in the universe tend toward disorder (entropy, S) in the absence of energy input

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14
Q

What is exothermic vs endothermic?

A
  • Exothermic: reaction releases heat (feels hot), -ΔH
  • Endothermic: reaction absorbs heat (feels cold), +ΔH
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15
Q

What is entropy?

A

Measure of disorder
- Increases when there is more dispersal of energy in a system
- Ex. protein to amino acids

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16
Q

What is Gibbs free energy?

A
  • The difference between enthlapy (H) and the entropy (S) at a given temp
    • ΔG = ΔH - TΔS
      • (Standard conditions are 298K and 1atm)
  • For biochemocal standar conditions: (pH = 7, H2O constant [55M])
    • ΔG’ = ΔH - TΔS
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17
Q

What is the Gibbs free energy equation for cellular conditions?

A

ΔG = ΔGº’ + RT(lnQ)
- If reaction is at equilibrium: ΔG’ = RT(lnQ)

18
Q

What are exergonic vs endergonic reactions?

A

Exergonic: ΔG < 0 (negative)
- Forward reactions
- Reaction is favorable and spontaneous

Endergonic (have to put energy into system): ΔG > 0 (positive)
- Reverse reactions
- Reaction is unfavorable and nonspontaneous

19
Q

What is the relationship between ΔGº and Keq?

A

ΔGº = -RT(lnKeq) (at equilibrium)
- Keq
- Keq > 1: favors formation of products
- Keq < 1: favors formation of reactants
- Keq = 1: neither reactants nor products are favored

20
Q

What are biochemical standard conditions?

A
  • pH = 7
  • [H2O] = 55.5 M
  • Mg2+ = 1 mM (when involved in reactions)
    • Usually stabilizes negative charges on ATP
21
Q

Explain coupled reactions.

A
  • Endergonic reaction can be coupled to exergonic reaction to become overall favorable as long as the exergonic reaction has an absolute value greater than the endergonic reaction
  • Ex. ATP hydrolysis
  • Must add the free energies of the separate reactions to find the overall free energy
22
Q

What is energy charge?

A

Relationship between [ATP], [ADP], and [AMP] at any given time in a cell

23
Q

What does a high vs low energy charge mean?

A
  • High EC: More ATP vs. ADP and AMP
    • Anabolic
  • Low EC: More ADP and AMP vs. ATP
    • Catabolic
24
Q

What are catabolic pathways?

A

Convert energy-rich compounds into energy-depleted compounds
- Low EC
- Generate ATP and reduced coenzymes (NADH, FADH2, NADPH) using stored fuels

25
Q

What are anabolic pathways?

A

Reactions that produce biomolecules from smaller molecules
- High EC
- Use ATP to replenish stored fuels

26
Q

Explain the polarity of water.

A

Hydrogen bonding occurs when a hydrogen atom is covalently bonded to an electronegative atom and in close proximity to another electronegative atom
- “Shared” between the 2 electronegative atoms

27
Q

What kind of stuff is water good at dissolving?

A
  • Polar
  • Partially charged
  • Fully charged
28
Q

What are the kinds of weak noncovalent interactions in biomolecules?

A
  1. Hydrogen bonds
  2. Ionic interactions
  3. Van der Waals interactions
29
Q

What are hydrogen bonds?

A

Bonds between hydrogen atoms on an electronegative donor group and another electronegative atom

30
Q

What are ionic interactions?

A

Bonds between oppositely charged atoms
- Electrostatic interactions
- Strength of bond depends on distance between the ions and the environment between them
- Salt bridges in proteins

31
Q

What are van der Waals interactions?

A

Temporarily occur between the dipoles of nearby electrically neutral molecules
- Depend strongly on the distance between the two atoms

32
Q

What are hydrophobic effects?

A
  • Occur between nonpolar molecules
  • Don’t form hydrogen bonds with water
  • Important role in protein folding reactions
  • Hydrophobic regions cluster together away from water
33
Q

What is osmosis?

A

Diffusion of solvent molecules from a region of lower solute concentration to higher solute concentration through semipermeable membrane
- Can be affected by osmotic pressure

34
Q

What is the pH equation?

A
35
Q

What is the Henderson-Hasselbach equation?

A
36
Q

What are buffers?

A

Aqueous solutions that resist small changes in pH

37
Q

Draw and label a titration curve.

A
38
Q

Explain biological membranes.

A
  • Physical barriers in living systems
  • Contain amphipathic lipid molecules that self-assemble into a bilayer
    • Majority of amphipathic lipids are phospholipids
  • Membrane fluidity depends on phospholipid composition
    • Cholesterol helps it be more semisolid (vs. fluid)
39
Q

Explain phospholipid bilayers.

A
  • Hydrophilic polar head orient toward aqueous environment
  • Hydrophobic nonpolar tails located near interior of membrane
40
Q

What is phospholipid flipping?

A
  • Proteins and lipids can move in membranes
  • Lateral mobility depends on
    • Temperature
    • Distribution of saturated and unsaturated lipids and cholesterol
    • Density and types of proteins embedded in the membrane
  • Transverse flipping is normally very slow
    • Flippases use energy from ATP hydrolysis to catalyze phospholipid flipping

Biochem 2 (CHEM 441B) (23 decks)

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