BCHM Exam 1

Explain compartmentalization and why it benefits the cell

• Compartmentalization is the saving of energy within cells by localizing functions to certain structures

• cells cannot afford to waste energy or time because they need to maximize efficiency

• cells use increased surface area to be more efficient

Are cells in equilibrium?

• NO, cells are NOT in equilibrium

• Equilibrium means that no changes are occurring overall, so cells can’t be in equilibrium because we know that concentrations within cells are constantly changing

Define energy

• Energy is the quantifiable property of any molecule or structure that is a force that can do work

• Energy is present everywhere, because it is inherent in mass (E=mc²)

Is energy stored in bonds?

NO, energy is NOT stored in bonds

What are the different types of energy that exist in living cells?

1) Free Energy (Δg)

• there’s +Δg and -Δg

• +Δg reactions require energy

• -Δg reactions releases energy

2) Heat Energy

• heat energy is a byproduct of chemical reactions (like ATP reactions)

• this heat energy cannot be harnessed by the cell, the only thing it can be used for is maintaining body temperature

3) Chemical Energy

4) Electrostatic Energy

Which free energy reaction REQUIRES energy?

the +Δg reactions require energy

Which free energy reaction RELEASES energy?

the -Δg reactions release energy

Which free energy reaction has energy readily available to do work?

-Δg reactions has energy available to do work

Which free energy reaction requires chemical coupling?

+Δg reactions require chemical coupling since it requires energy to take place, so it needs a -Δg to be couples with it to drive the reaction

______ reactions are exergonic

-Δg reactions are exergonic, meaning the products have a lower energy state than the reactants, therefore energy release occurred

What is ATP?

• ATP is a high energy molecule (has a high potential energy geometry) used by the cell

• adenosine triphosphate

What is ADP? How is it created?

• ADP (adenosine diphosphate) is created from ATP (adenosine triphosphate)

• to make ADP, an outer phosphate group on ATP is broken (hydrolysis)

Why are humans multicellular?

• Human cells use compartmentalization to be more efficient

• the cell utilizes volume to surface area ratio, which allows for more efficient diffusion and transfer in the cell

What is BSA? Given a mouse and an elephant, which animal would be on which point on this graph?

• BSA = Baseline Surface Area

• having higher lean muscle on average will increase metabolic rate

• mouse would be the blue point

• elephant would be the red point

What is BMR?

• BMR = Basil Metabolic Rate

• BMR is the metabolic rate of an organism at rest

Given a 100 g large brown rat and a 1 g mouse, what is the difference between their (a) total metabolisms?

(a) total metabolisms

• the rat weights 100x more than the mouse, therefore the rat’s total metabolism is about 32x higher than the mouse’s

• BMR = 100^3/4 = 32

(b) per gram metabolism

• total power (J/s) = change in energy / change in time

• the 100 g rat has more total power than the mouse (more mass), but the mouse has a higher mass-specific power per gram than the rat

• the mouse has more energy per gram of body tissue

• this is partly due to the surface area to volume ratio

What is the Second Law of Thermodynamics?

the total entropy of a system will always increase over time during a spontaneous process

Δg = ΔH - T*Δs

Define entropy

entropy (Δs) is disorder or randomness

cal/mol*K

How can enthalpy be slowed down?

the only way to slow down enthalpy is to drop the temperature (since enthalpy is the total heat in a system)

Define enthalpy

Enthalpy (H) is the total heat of a system at constant pressure

kcal/mol

Define Metabolic Coupling

the functional coordination between cells or pathways where the activity of one directly drives the activity of the other

Define Bioenergetics. Why is it important?

• Bioenergetics = the study of energy flow

• continuous energy flow in the cell is necessary so that energy can be sent to where it needs to be as quickly as possible

Describe the bioenergetic process of ATP:

bioenergetic process: how ATP (energy) moves from the mitochondria to where it is needed

• in the Mitochondria, there is an ADP/ATP carrier protein system that exchanges ATP (which leaves the mitochondria) for ADP (which enters the mitochondria to replace the ATP that’s leaving because that ADP will be turned into ATP)

• kinase enzymes in the cytosol remove a phosphate from the ATP, turning those molecules into ADP → this process of breaking off a phosphate releases energy

• transport proteins move ATP from the cytosol to the ER and can be used by proteins and ion pumps

• the Mitochondria themselves can move within the cell via microtubules to where ATP demand is high (Ex. the synapse space between two neurons located on the end of the nerve cell is where a lot of ATP is needed, so Mitochondria are constantly relocating there)

What is the cytosol?

• Cytosol is the water-based fluid inside the cytoplasm of the cell

Describe the Maxwell Boltzmann Distribution

• gas molecules in a closed container (at equilibrium) will NOT be distributed in a bell-shaped curve

• the curve will be skewed to the right

• the cell as a whole does not follow this distribution (the cell is not at equilibrium, changes are constantly occurring)

• there are specific areas within the cell that follow Boltzmann distribution (Ex. free molecules like potassium and sodium)

Does the graph represent positive or negative free energy?

low energy molecule → high energy molecule

+Δg

work and energy are increasing

energy is being required

Does the graph represent positive or negative free energy?

high energy molecule → low energy molecule

-Δg

work and energy are decreasing

energy is released

______ reactions are endergonic

+Δg reactions are endergonic, meaning the products have a higher energy state than the reactants, therefore energy was required

Order the following molecules from highest Δg to lowest Δg:

CH₄

COOH

CO₂

highest to lowest Δg : CH₄, COOH, CO₂

CH₄ is the most reduced and least oxidized, therefore has the most energy (because the C has electrons in high-energy arrangements)

COOH is between the two

CO₂ is the least reduced and most oxidized (C has two double bonds with two O’s), therefore has the least energy available

the __________ reduced a molecule is, the MORE energy it has

MORE

more reduced = more energy

more reduced means the electrons are in a higher-energy arrangement

the __________ reduced a molecule is, the LESS energy it has

LESS

less reduced = less energy

Define electron

an electron is a finite point that has a wave function

electrons do not spin and do not orbit

Explain the Double Slit Experiment and what is showed

• Matter particles (Ex. marbles) were shot through 2 slits and onto a wall, which created a 2 slit pattern on the wall

• When wave particles were shot through the 2 slits, there were interference patterns of many bands created on the wall

• When electrons were shot through the 2 slits, they acted like the waves and created interference patterns

• But when the electrons were observed with an instrument, they acted differently and actually created the 2 slit pattern that the matter created

• Conclusion: when a wave is observed with an instrument, the wave collapses and acts as a particle, called wave-particle duality - electrons exhibit both wave-like and particle-like properties depending on how they are measured

Define wave-particle duality

when a wave is observed with an instrument, the wave collapses and acts as a particle

electrons exhibit both wave-like and particle-like properties depending on how they are measured

Define quanta

electromagnetic radiation (a beam of light) contains energy in little packets called quanta

energy is transferred in quanta steps

Label the node and antinode. Where are electrons more likely to be found and why?

orange = node

green = antinode

electrons are more likely to be found in the antinode where there is more area

Define electron orbital

regions around an atom’s nucleus where electrons are most likely to be found

electrons will go to their minimum energy state (most stable energy level), which is their orbital

What keeps an electron from collapsing into the nucleus?

• The electrons collapsing into the nucleus is prevented by the electron being confined to its orbital, which it wants to stay in because that is the electron’s most stable region with lowest energy

• this minimum energy state is created by the balance of kinetic and potential energy

• so since the lowest energy standing wave is not in the nucleus, the electron is kept away and the folding in of electrons is prevented

Define quantum tunneling

a wave particle tunnels through a potential energy barrier

during catalytic reactions, when the potential energy wall doesn’t get lowered, the electron tunnels through the barrier instead of over it

What is the buffer region when the pKa = 4.76?

buffer region is ±1 pKa

buffer region would be 3.76-5.76

Define buffer region

the range of which a solution can resist large changes in pH

buffer region is ±1 pKa

buffer region will be the flatter part of a titration cuve

When does pH = pKa during titration?

pH = pKa when 50% of the original weak acid has been converted to its conjugate base by adding base

What organ controls the pH of urine?

• kidneys filter waste and water from the blood to make urine

• the renal tubular cells of the kidneys control the pH of urine

• titratable acidity is a measure of acid excreted into urine by the kidneys (H⁺ ions secreted into urine)

Amine group’s pKa = ____

amine pKa = 9

N-R₃

carboxyl group’s pKa = ____

carboxyl pKa = 4

R-COOH

Explain how much acid and how much base would be in a buffer using a carboxyl group at each of the following pH’s:

(a) pH = 2

(b) pH = 4

(c) pH = 6

(a) pH = 2

• solution is more acidic than pKa

• more COOH than COO^-

• COO^- + H⁺ → COOH

• conjugate base + acid → acidic product

(b) pH = 4

• since we know the pKa of a carboxyl group is 4 and the pH is 4, pH=pKa, therefore there is 50% COO^- (conjugate base) and 50% COOH (carboxylic acid)

(c) pH = 6

• more basic than pKa

• more COO^- than COOH

• COOH + OH^- → COO^-

• acid + base → conjugate base

Explain how much acid and how much base would be in a buffer using an amine group at each of the following pH’s:

(a) pH = 7.5

(b) pH = 9

(c) pH = 11

(a) pH = 7.5

• more acidic than pKa

• more NH₃⁺ than NH₂

• NH₂ + H⁺ → NH₃⁺

• base + acid → conjugate acid

(b) pH = 9

• since we know the pKa of an amine group is 9 and the pH is 9, pH=pKa, and therefore there is 50% NH₂ and 50% NH₃⁺

(c) pH = 11

• more basic than pKa

• more NH₂ than NH₃⁺

• NH₃⁺ + OH^- → NH₂

• acid + base → conjugate base

Water being insulating is a __________ property

dielectric

What are the types of water organization?

1) bulk water

• tap water

• has a random/disordered arrangement

• found in open spaces in the cytosol (away from cell structures)

2) vicinal water

• layered / structured water that directly and tightly binds to surfaces of molecules or membranes

3) clathrate water

• cages of water molecules

• arranged in a highly-ordered lattice around hydrophobic molecules

How are water molecules bonded together?

• water is a polar molecule, therefore orients itself around other charged molecules, including other water molecules

• the O has a partial negative charge, and the H’s both have a partial positive charge

• the O on one water molecule hydrogen bonds to an H on another water molecule

Explain gel ↔ sol transitions in the cytoplasm

• the cytoplasm is viscous, and transitions from more gel-like to more sol-like (or vice-versa) - caused by changes in the actin cytoskeleton

• gel = more solid, more structured, less entropy

• sol = more fluid, less structured, more entropy, more bulk water needed to transition to sol

• gel-sol transitions can propel ions needed for enzymes

Define colloids

particles that are intermediate in size between a solution (not viscous) and suspension (very viscous)

the cytoplasm is a “colloidal system”

Define cytoplasm

the viscous, colloidal system inside the cell that consists of water, proteins, organelles, and other particles

Define hydration shell

a shell of ordered water molecules around an ion

Which ion has a more tightly-bound hydration shell? Why?

(a) Mg²⁺ or Na⁺

(b) K⁺ or Na⁺

*overall, a higher charge density will cause a stronger hydration shell, which is caused by a higher charge or a smaller molecule with a more concentrated charge

(a) Mg²⁺ or Na⁺

• Mg²⁺ because it has a higher charge, therefore has a stronger attraction to water

(b) K⁺ or Na⁺

• Na⁺ because it is smaller than K⁺, so the electrons are more packed together and therefore the charge is more concentrated

• atomic radius increases down the periodic table and increases to the left

Does a hydration shell have high or low entropy?

low entropy because it is organized

so when a hydration shell is ripped off, entropy increases because that caused disorder

Define hydrophobic effect

• the tendency of non-polar molecules to aggregate together in water (rather than dissolve), and water is forced to form a clathrate cage around those molecules

• the hydrophobic effect contributes to the folding of proteins

How does the presence of hydrophobic molecules impact proteins? How does this relate to the Second Law of Thermodynamics?

• proteins will fold so that hydrophobic molecules are in the middle of the protein (being shielded from the water)

• Thermodynamics: this process creates a lower-energy, more thermodynamically stable state

Define hydrophobic interaction

hydrophobic interactions occur when hydrophobic molecules are pushed together by the clathrates around each molecule, creating a lower-energy, more thermodynamically stable state

How does the presence of hydrophobic molecules within fatty acids impact the water surrounding fatty acids?

• fatty acids are made up of a hydrophilic “head” and a hydrophobic alkyl group “tail”

• the water molecules will order themselves in a clathrate cage around the hydrophobic alkyl group