Water and its properties

Question 1

Why are weak bonds beneficial for life?

Answer 1

Weak bonds permit dynamic interactions that forms the basis of biochemistry and life itself.

Question 2

What is Brownian motion a function of?

Answer 2

random motion in aqueous solution based on thermal input.

Question 3

Describe the relationship between Brownian motion and temperature.

Answer 3

The higher the temperature, the higher the Brownian motion

Question 4

What initiates many biochemical interactions?

Answer 4

Brownian motion of water (movement of molecules powered by random fluctuations of environmental energy)

Question 5

Describe the features of water? is it polar or nonpolar?

Answer 5

Water is a POLAR molecule with an e-negative oxygen atom carrying a slightly negative charge and Hydrogen atoms carry slightly positive charges (form dipoles).
water also has asymmetric distribution of e- (can be transient)

Question 6

Describe how the polarity of water provides more important properties.

Answer 6

The polarity of water allows for the formation of H-Bonds between water molecules and accounts for COHESIVENESS of water.
Polarity of water also accounts for ability to DISSOLVE many important biochemicals.

Question 7

Why does the hydrophobic effect occur?

Answer 7

Due to inability of water to dissolve nonpolar molecules.

Question 8

What are electrostatic interactions? What are other names used to describe the equation? What is the formula for energy of electrostatic equation?

Answer 8

attraction between oppositely charged ions. These interactions also called ionic bonds or salt bridges.
Formula for energy of electrostatic attraction (coulomb’s law) : E= kq1q2/Dr (E is energy, k is proportionality constant, q- charge on ions, D is dielectric constant, r is distance between 2 ions)

Question 9

What is the Dielectric constant (D) ?

Answer 9

used to determine how well a solvent can weaken or strengthen the electrostatic interaction. D =1 in vaccum. D= 2 in hexane and D=80 in water.

Question 10

How does water affect electrostatic interactions (ionic bonds)?

Answer 10

water has a high dielectric constant of 80 and therefore WEAKENS electrostatic interactions (able to dissolve ions)

Question 11

How do Hydrogen bonds form?

Answer 11

H- bonds can occur whenever hydrogen is covalently bonded to an electronegative atom. (h-bonds are not unique to water molecules)

Question 12

How does h-bonds play a role in protein strucuture?

Answer 12

H-bond puts alpha helixes together and bet sheets during secondary structure of making proteins.

Question 13

How to identify the h-bond acceptor vs H-bond donor?

Answer 13

when three atoms are linked together for instance: N-H——–N the h-bond donor is the atom on left side of H as it is pulling e-. The h-bond acceptor is the atom on right of H as it has lone pair of e that form bond with hydrogen.

Question 14

How does water affect hydrogen bonds?

Answer 14

Water disrupts hydrogen bonds between 2 molecules by competing for hydrogen bonding capability.

Question 15

how do Van Der Waals interactions occur?

Answer 15

Van Der Waals- attraction of repulsion of molecules due to unequal distribution of e- between bound atoms (intermolecular forces)
allow for nonpolar and uncharged molecules to interact electrostatically.

Question 16

Describe the interaction of molecules

In Van der waal attractions.

Answer 16

transient symmetry in one molecule will induce complementary asymmetry in nearby molecule. VDW have lower energy than H-bonds.

Question 17

How does distance of molecules affect van der waals interactions?

Answer 17

As molecules move closer to each other, steric factors push them apart, allow for more repulsion. (further they are, the higher attraction).

Question 18

What kind of forces allow for Gecko to stick to smooth surfaces?

Answer 18

Van der waals forces. The spatulae on the bottom of the gecko’s feet allow them to form van der waals with surface and foot will stick to surface.

Question 19

Compare and contrast covalent and noncovalent bonds. List examples. Which of two bonds require more energy ?

Answer 19

Covalent bonds (C-C bonds, or phosphodiester linkage in DNA) are stronger than noncovalent bonds, require more energy to break bonds.
Noncovalent bonds (ionic bonds, h-bonds, van der waals) weaker than covalent bonds. for ionic bonds- need more energy to break bonds when ion is in hexane vs, water. among noncovalent bonds, strongest to weakest: ionic, h-bonds, van der waals.

Question 20

What is the distinction between ionic bonds, hydrogen bonds and van der waals interactions?

Answer 20

the ability to break bonds.

Question 21

Why are weak bonds beneficial for life?

Answer 21

Weak bonds permit repeated interactions.
H-bonds contribute to stability of DNA double helix, But bonds are weak enough to be broken by enzymes of DNA metabolism (allowing access to genetic information)

Question 22

What is the hydrophobic effect? what is it powered by? How does it benefit bio systems?

Answer 22

Describes the clustering of hydrophobic molecules (benzene) in water. It is powered by INCREASE IN ENTROPY of water that occurs when hydrophobic molecules come together. Hydrophobic effect is powerful ORGANIZING force in bio systems.

Question 23

What thermodynamic property drives the hydrophobic process? why is the property lower in solution where molecules are separted?

Answer 23

Entropy. In image A, molecules are separated, hence why entropy is low. Entropy will only increase when hydrophobic molecules cluster together in water because less ordered water molecules surround nonpolar molecules and allow for increase in disorder or entropy.

Question 24

What happens when a membrane is exposed to hexane?

Answer 24

Form compartmentalization of cell? Phospholipids have hydrophilic and hydrophobic properties (amphipathic or amphiphilic) Membrane formation powered by hydrophobic effect. Van der waals promote stability of lipid bilayer and increase in entropy.

Question 25

What important process is powered by hydrophobic effect?

Answer 25

Protein folding. The initial stages of protein folding are dependent on hydrophobic effect. hydrophobic amino acids make up anterior of protein.

Question 26

Define functional groups . List examples.

Answer 26

arrays of atoms that have distinctive chemical properties. Ex: carboxyl, amino (NH2), phosphate (R-PO4), sulfhhdryl (R-SH), aldehyde, ketone, hydroxyl (OH), hydrophobiv (R-ch3), aromatic (benzene ring,)

Question 27

What is the pH? compare it in terms of acidity and basicity.

Answer 27

measure of H+ concentration of a solution. The lower the pH, more H+ ions and acidic. The higher the pH, the less H+ ions and more basic.

Question 28

Why is controlling pH a crucial function in biological systems? What is example of disease that arises from uncontrolled pH?

Answer 28

to enable normal metabolic functions, control chemical behaviors and enzymes to work properly. controlling pH also allows substances as stomach acids to be maintained properly.
GERD- (gastric esophageal reflux disease) is a pathological condition that results when esophagus is exposed to acid of stomach.

Question 29

What ionizes to what kind of extent? What is equilibrium? where does equilibrium lie?

Answer 29

Small extent as water ionizes: H2O to H+ and OH- . Equilibrium is the condition in which concentration of reactions and products have no net charge over time.
Equilibrium lies on side of water (H2O).

Question 30

what is the equation for Keq of water ? kw? what is the pH equation?

Answer 30

keq= [H+][OH-]/[H2O] ; kw= [H+][OH-] ; pH= -log[H+] which is biochem intermediate metabolism. pH+ pOH= 14

Question 31

What is the difference between strong acid and weak acid? provide examples.

Answer 31

How easily one can let go of a proton. Strong acids like HCL are easier to dissociate (give up H+), Weak acids like acetic acid (ch3cooh) dissociate partially (CH3COOH to form CH3COO- and H+)

Question 32

differentiate between conjugate base and conjugate acid.

Answer 32

Acids ions to form proton and base.
conjugate base- chemical that forms when ionization of acid occurs (Acid forms H+and base or acid in reactant has been deprotonated)
Conjugate acid- acid formed when base is protonated.

Question 33

What is the ionization equilibrium for weak acid?

Answer 33

ionization: HA: forms H+ and A-
kd= [H+][A-]/[HA] the larger the kd (equilibrium dissociation constant) the stronger the acid. more it dissociates, stronger acid.

Question 34

what is the pka of an acid? What is the Henderson Hasselbalch equation? define relationship of pka and acidity.

Answer 34

pka= log (1/ka) tells you what pH needs to be to donate or accept H+
Henderson Hasselbalch- pH= pka+ log ([A-]/[HA])
The lower pka, the stronger the acid.

Question 35

List the relationships with pka, pH (lnverse vs non-inverse)

Answer 35

pH= pKa when [A-] = [HA], and log([A-]/[HA]) = 0. when pH greater than pka, A- dominates. when pH is less than pka, HA dominates.

Question 36

What is a buffer? When is it most effective? what is the buffering region?

Answer 36

an acid-base conjugate pair that resists changes in pH of solution. Buffer most effective at pH near its pKa. Buffering region: 3.76- 5.76 pH

Question 37

How is Buffering crucial in biological systems?

Answer 37

buffers stabilize pH of blood, maintain constant pH. pH of blood is buffered by conjugate acid-base pair of carbonic acid and bicarbonate (H2CO3/HCO3-).
CO2 (from aerobic respiration) reacts with H2O to produce weak acid called carbonic acid. Carbonic acid then ionizes to produce proton and bicarbonate
(CO2 + H2O form H2CO3-) but then H2Co3 forms H+ and HCO3-

Question 38

What is metabolic acidosis?

Answer 38

condition in which too much H+ ions accumulate in the blood (too much acid in body).

Question 39

What occurs when there is excess protons in the blood?

Answer 39

excess protons decrease the amount of HCO3- and thus reduces buffering capacity of blood. Rapid drop in pH can lead to death.