BIS102 MT1

ch2-6 Guercio UC Davis Midterm 1

What is the medium for life?

water

Organisms typically contain how much % water?

70-90%

Chemical reactions can occur where?

in aqueous environments

What three things is water a critical determinant of structure and function? (3)

• proteins

• nucleic acids

• membranes

What are 4 weak interactions

• hydrogen bonding

• electrostatic interactions/ionic interactions

• hydrophobic interactions

• Van der Waals interactions

How does water generally compare to other common solvents?

• higher melting point and boiling point

• heat of vaporization

What causes water to be different from other solvents?

hydrogen bonding

What is the bond angle in water molecule?

104.5º

attraction between adjacent water molecules results in what?

internal cohesion

Which are longer and weaker: hydrogen bonds or covalent bonds?

Hydrogen bonds

What is the length of a hydrogen bond?

0.117 nM

What is the length of a covalent bond?

0.0965 nM

Why does the oxygen atom in water molecules attract electrons more strongly than the hydrogen atoms?

Oxygen is more electronegative than hydrogen which induces a dipole

what is the cause of intermolecular interaction?

the electron structure of water

What is the result of the unequal sharing of electrons in a water molecule?

It creates two electric dipoles, one along each H-O bond

What partial charges do hydrogen atoms, and the oxygen atom in a water molecule have?

Hydrogen (δ+) and the oxygen (2𝛿−)

What type of attraction occurs between the oxygen atom of one water molecule and the hydrogen atom of another?

a hydrogen bond

Where else can hydrogen bonds form besides water?

Between electronegative atoms and hydrogen that is covalently bonded to another electronegative atom

What kind of attraction is responsible for the formation of hydrogen bonds between water molecules?

Electrostatic attraction between partial charges (δ+ and δ−)

“Flickering clusters”

Short-lived groups of water molecules interlinked by hydrogen bonds in liquid water

Is water a hydrogen donor or acceptor?

Both

In water (liquid), H2O molecules are ___

dynamic

In ice, each water molecule is fixed in ___ which is why ice is less dense than water

space

Most of the molecules in liquid water are ___

hydrogen bonded

In liquid water at room temp, how many water molecules does each molecule typically form hydrogen bonds?

~3.4 other molecules (liquid is disorganized and continuous)

How many water molecules does each water molecule form hydrogen bonds with in ice?

A full complement of four other water molecules; 4

What compounds dissolve easily

Polar and hydrophilic; can interact with water hydrogen bonds

Non-polar and hydrophobic molecules such as waxes and lipids don’t interact with what?

water

Describe the structure of ice formed by hydrogen bonds between water molecules

Lattice structure

To vaporize salt/ separate Na and Cl on air, you would need to raise the temp to ___

800ºC

Salt dissolved in water at ___ ___

room temperature

What does water shield so that they can separate?

ion’s charges

Water interacts ___ with charged solutes

electrostatically

T/F: Biologically important gases like CO2, N2, and O2 are highly soluble in water

false

What two gasses are soluble in water?

ammonia and hydrogen sulfide

What are hydrophobic effects?

scared of water

What is the hydrophobic effect driven by?

2nd Law of Thermodynamics

total ___ of the universe is continually increasing

entropy

T/F: Hydrophobic Interactions are the attraction of hydrophobic molecules to one another

False

What happens when a hydrophobic molecule enters water?

They cluster together; water “cages” them

What is the 2nd Law of Thermodynamics?

the tendency in nature toward every greater disorder in the universe

When is entropy reduced?

when a hydrophobic molecule is present

when does entropy increase?

with more disorder

What happens when hydrophobic bits cluster together (2)

• Greatest thermodynamic stability

• least amount of ordered water

What are Ionic interactions/Electrostatic Interactions?

Weak interactions between charged atoms or groups (attraction and repulsion)

What are ionic interactions often called in proteins?

salt bridges

How do Van der Waals interactions occur?

Happens when two uncharged atoms are very close

What can VDW induce?

Transient dipole(opposite) in neighboring atom

What happens to the nuclei in VDW interactions?

It gets closer but then gets repelled by their electron clouds as they get too close

What happens to the entropy of the aqueous system during the transition from ice to liquid water or from liquid water to water vapor

entropy increases

Why do both melting of ice and evaporation of water occur spontaneously at room temperature?

Increase in entropy outweighs hydrogen bonding

What must the value of ΔG be for a process to occur spontaneously?

negative

In the equation ΔG = ΔH - TΔS, what drives melting and evaporation?

The increase in entropy (ΔS)

Is ΔH positive or negative for melting and evaporation?

ΔH is positive (endothermic) for melting and evaporation

What factor primarily makes ΔG negative for melting and evaporation?

The increase in entropy (ΔS) makes ΔG negative, driving these changes

Polar compounds such as water are hydro___, while nonpolar compounds such as lipids are hydro____

hydrophilic; hydrophobic

what biologically important gasses are nonpolar?

CO2, O2, N2

What happens to the solubility of nonpolar gases when they move from a gas phase into aqueous solution?

Their motion becomes constrained, leading to a decrease in entropy, which makes them poorly soluble in water

A reaction would happen if a reaction is ___

spontaneous

What does -ΔG mean?

-ΔG: Free energy is released; exergonic; spontaneous (forward)

What does +ΔG mean?

+ΔG: Reaction needs a net input of energy for rxn to occur; endergonic; not spontaneous (moves left)

What information does ΔG not give?

Doesn’t give info on speed, mechanism, rate

Reactions occur spontaneously only if ΔG is ____

negative

Spontaneous reaction ___ information about timing

does NOT give

If the reaction A ←→ B has a negative ΔG, the reaction will proceed to the ___.

right; forward

What is +ΔH?

Endothermic: reaction takes up heat from surroundings

What is -ΔH?

Exothermic: reaction releases heat, products have less content than reactants

What Δ’s make ΔG negative?

(-)ΔH or (+)ΔS

What does (+)ΔS do?

Entropy is increases; reaction increases randomness/disorder

What are some examples of (+)ΔS

• When rxn results in number of molecules increasing

• When there is more freedom of molecular movement: ice melting to water

Are all reactions favorable when they have both -ΔH and +ΔS

No

T/F: A reaction with a (+)ΔH is always endergonic/non-spontaneous?

False; think of ice melting where ΔH is (+) and ΔS is also (+) but a (-)ΔG

What are the three main things cells make from simpler building blocks?

• proteins

• Carbohydrates

• nucleic acids

Would ΔG be positive or negative when cells are making reactions to make proteins, carbohydrates, etc from simpler building blocks?

Positive; need energy to link monomers to create polymers and are thermodynamically unfavorable (endergonic)

How do cells make proteins, carbs, nucleic acids from simpler building blocks?

couples endergonic reactions with exergonic ones

In closed systems, chemical reactions proceed ___ until equilibrium is reached

Spontaneously

What does equilibrium mean?

The rate of product formation equals the rate of product conversion to reactants. No net change in the concentration of products or reactants

What is the energy change as system moves from initial state to equilibrium?

Free-energy change; ΔG

What is equilibrium constant?

A way to express the tendency of a reaction to go to completion

If Keq is large, are there more products or reactants at eq?

products

T/F: Up to ½ of all water molecules in pure water are ionized at any given time

F; Only 2 of every 10^9 molecules of H2O are dissociated at any given time

Acids are proton ___ and H+ ____

donors; donors

Bases are proton ___ and H+ ____

acceptors; acceptors

Strong acids and strong bases will completely ___ in H2O

dissociate

Fluid mosaic models are ___

non-covalent

Label the blanks on this titration curve (bottom up)

1. CH3COOH

2. [CH3COOH] = [CH3COO-]

3. CH3COO-

Where is the equilibrium for this titration curve?

All dotted points

At what range is [CH3COOH] greater than [CH3COO-] on this titration curve?

any pH less than 4.76

Of these weak acids, which is the strongest? Why?

CH3COOH; lower pKa = stronger acid; dissociates most readily

Which conjugate acid/conjugate base pair would you use if you were making a solution that you wanted to stay at pH=9?

pKa closest to 9 so 9.25 on [NH4+]=[NH3]

At what pH is NH4+ completely neutralized?

acid is completely dissociated ~11.5 or 12

Almost every biological process is __ dependent

pH

Why have our bodies become so good at maintaining pH?

Many proteins have ionizable groups with distinct pKa values (ionic state is determined by the pH around it)

pH in cells

• cytosolic pH=7

• biomolecules stay in optimal ionic state

• consistency of pH is kept by biological buffers

What are buffers?

aqueous system that resists changes in pH when small amounts of acid (H+) or base (OH-) are added.

What do buffers consist of?

Weak acid (HA) and its conjugate base (A-)

What are 3 important facts about lipids?

• structurally diverse biomolecules

• are NOT ‘polymers’

• insoluble in water

What are 6 main functions of lipids?

• form cellular boundaries (structural)

• chemical messengers

• ‘fats’ and store energy

• cushioning

• enzyme helpers

• help folding

• etc

what do storage lipids do?

store energy