Chapter 2 + Quiz Questions

Question 1

What is the most abundant molecule in living organisms?

Answer 1

Water

Question 2

What kind of roles does water play in biochemistry?

Answer 2

It plays both active and passive roles

Question 3

What entails water’s passive role in biochemistry?

Answer 3

The structure of biomolecules form in response to interaction with water (hydrophobic/philic responses)

Question 4

What entails water’s active role in biochemistry?

Answer 4

Water is a participant in many biochemical reactions

Question 5

Why is water considered the Matrix of Life?

Answer 5

It is so critical to our understanding of the molecular basis of life. It is difficult to imagine life in the absence of water, so much so that its presence on other planets is a critical determinant of their habitability by humans

Question 6

What is the result of oxygen being more electronegative than hydrogen?

Answer 6

It gives water a permanent dipole

Question 7

Oxygen has a partial ___ charge and each hydrogen has a partial ___ charge.

Answer 7

Negative, positive

Question 8

The dipole of a water molecule influences its ability to:

Answer 8

1. Form electrostatic interactions
2. Form hydrogen bonds

Question 9

What are hydrogen bonds?

Answer 9

Electrostatic interactions between an electronegative atom with a hydrogen covalently linked to another electronegative atom with a free electron pair

Question 10

Hydrogen bonding can occur between hydrogen and four other elements, which are they an what are the most common?

Answer 10

Oxygen and Fluorine which are the most common, Nitrogen and Carbon

Question 11

True or False: oxygen and nitrogen can each serve as hydrogen bond donors and acceptors?

Answer 11

True

Question 12

What does the strength of a hydrogen bond depend on?

Answer 12

Its geometry

Question 13

Compare hydrogen bonds to covalent bonds

Answer 13

Hydrogen bonds are relatively weak, only about ~5% the strength of a covalent bond. Hydrogen bonds are also about double the length

Question 14

Within water, each water molecule has the potential to participate in ___ hydrogen bonds with four other water molecules

Answer 14

four

Question 15

Each water can donate and accept how many hydrogen bonds?

Answer 15

Two

Question 16

The hydrogen bonds between water molecules confer great internal cohesion which influences what?

Answer 16

The properties of water

Question 17

The large number of hydrogen bonds within water contributes to the high _____ and _____ of water

Answer 17

Heat of Vaporization, Specific Heat Capacity

Question 18

What is the definition of Heat of Vaporization?

Answer 18

The amount heat required to vaporize a liquid at its boiling temperature

Question 19

What is the definition of Specific Heat Capacity?

Answer 19

The amount of heat required to raise the temperature of a substance one degree

Question 20

True or False: water has a lower melting point, boiling point, and heat of vaporization than most common solvents?

Answer 20

False, it has a higher melting point, boiling point, and heat of vaporization than most common solvents

Question 21

Most living organisms are ___, and what does this mean?

Answer 21

Isothermic, they need to regulate and maintain their temperatures

Question 22

What properties of water help us stay cool?

Answer 22

The high composition of water within our bodies, coupled with the high specific heat capacity of water

Question 23

Why does ice float on water?

Answer 23

In ice, each water molecule participated in four hydrogen bonds with other water molecules. This ordered arrangement of ice has a lower density than liquid water, and so it floats

Question 24

What was polywater?

Answer 24

Polywater was a hypothesized polymerized form of water that was the subject of much scientific controversy during the late 1960s. It had a higher boiling point, a lower freezing point, and much higher viscosity

Question 25

Water molecules have great versatility in interacting with both positively and negatively charged ions by what virtue?

Answer 25

Their small size and permanent dipole

Question 26

Why are water molecules ideal hydrogen bonding partners?

Answer 26

Their small size and ability to serve as either donors or acceptors

Question 27

Biomolecules have functional groups that can form hydrogen bonds. These groups can hydrogen bond with....

Answer 27

Within the same molecule, other biomolecules, or with water

Question 28

Define Hydrophilic

Answer 28

"Water loving," molecules that are polar

Question 29

Define Hydrophobic

Answer 29

"Water fearing," molecules that are non-polar

Question 30

Define Amphipathic

Answer 30

Molecules that contain both hydrophobic and hydrophilic parts

Question 31

Many biologically important gases such as carbon dioxide and O2 have limited solubility in water which presents a challenge for their transport, how is this rectified?

Answer 31

There are specialized transport proteins and strategies required for their transport

Question 32

When an amphipathic molecule is mixed with water the hydrophilic regions interact favorably with water but what happens to the hydrophobic portions?

Answer 32

The hydrophobic regions cluster together to present the smallest surface to water

Question 33

What are hydrophobic interactions?

Answer 33

The forces that hold the non-polar regions of the molecule together

Question 34

What is a primary driving force in the formation and stabilization of biomolecular structures?

Answer 34

The hydrophobic drive

Question 35

Most biomolecules represent what?

Answer 35

Stable polymers of covalently linked building blocks

Question 36

The three dimensional structures formed by these stable polymers are largely determined through...?

Answer 36

Non-covalent interactions

Question 37

Interactions between biomolecules are largely determined by _____ interactions

Answer 37

Non-covalent interactions

Question 38

Non-covalent interactions enable:

Answer 38

1. Transient, dynamic interactions 2. Flexibility of structure and function

Question 39

What is influenced by non-covalent forces?

Answer 39

1. Formation and stabilization of structures of biomolecules 2. Recognition and interactions between biomolecules 3. Binding of reactants to enzymes

Question 40

Non-covalent interactions within biomolecules include:

Answer 40

1. Hydrogen bonds 2. Ionic (electrostatic) interactions 3. Hydrophobic interactions 4. Van der Waals interactions

Question 41

True or False: many of the functional groups with biomolecules have hydrogen bonding capacity?

Answer 41

True

Question 42

These functional groups that have hydrogen bonding capacity can form hydrogen bonds with:

Answer 42

1. Water molecules 2. Groups in the same molecule (intramolecular) 3. Groups in other molecules (intermolecular)

Question 43

Hydrogen bonds are critical for the ___ of biomolecular interactions but not for the ____ of biomolecular structures

Answer 43

Specificity, formation

Question 44

True or False: much is to be gained, from a hydrogen bonding perspective, with formation of higher order structures?

Answer 44

False, little is to be gained, from a hydrogen bonding perspective, with formation of higher order structures

Question 45

Define electrostatic interactions

Answer 45

Interactions between charged groups that can be attractive or repulsive

Question 46

How is the magnitude of the contribution of ionic interactions to biomolecular structures reduced?

Answer 46

By the shielding of these groups by water molecules

Question 47

The strength of electrostatic interactions depends on ...?

Answer 47

The distance separating the atoms and the nature of the intervening medium

Question 48

Describe van der Waals forces

Answer 48

The interaction between permanent and induced dipoles. They are short range and low magnitude

Question 49

When is the attraction maximal in van de Waals forces?

Answer 49

When two atoms are separated by the sum of the van der Waals radii

Question 50

When two surfaces of ______ _____ come together, a large number of atoms are brought into van der Waals contact

Answer 50

complementary shapes

Question 51

Where are van de Waals forces most abundant?

Answer 51

In the core of folded proteins

Question 52

What is the hydrophobic effect?

Answer 52

The drive to have polar groups interacting with water and non-polar regions shielded away from water

Question 53

The folding of a protein involves the creation of a more ordered state, which seems to be in contradiction to which law of thermodynamics?

Answer 53

The 2nd law

Question 54

The water molecules around hydrophobic molecules are more ordered than they would be in pure water. So the introduction of the non-polar molecules causes a _____ in the entropy of water

Answer 54

Decrease

Question 55

The association of non-polar molecules/regions releases some of the ordered water molecules, resulting in an ____ in the entropy of water

Answer 55

Increase

Question 56

The folding of a polypeptide ____ the entropy of the polypeptide but ____ the entropy of the associated water

Answer 56

Decreases, increases

Question 57

What was the conclusion for the question "does water have a memory?"

Answer 57

There is no substantial basis for the claim that water can be imprinted with the memory of past solutes

Question 58

Water has a limited tendency to ionize ___ and ____.

Answer 58

Hydrogen ions, hydroxide ions

Question 59

Chemical equation for the ionization of water

Answer 59

H2O <----> H+ + OH-

Question 60

What is the equation and value for the Keq?

Answer 60

Keq = [H+][OH -] / [H2O] = 1.8 x 10^(-16) M

Question 61

What is the equation and value for the equilibrium constant for the autoionization of water (Kw)?

Answer 61

Kw = [H+][OH-] =1.0 X 10^(-14) M^2

Question 62

What is Kw more known as?

Answer 62

The ion product of water

Question 63

What is the equation for pH?

Answer 63

pH = -log [H+] = log 1/[H+]

Question 64

Example: [H+] = 1 X 10^(-5) M, what is the pH?

Answer 64

pH = -log [10^-5] = 5

Question 65

pH is a log scale such that the difference of 1 pH unit equals a ___ difference in [H+]

Answer 65

10-fold

Question 66

How can you distinguish between a strong and weak acid?

Answer 66

A strong acid will completely dissociate in water; whereas weak acids do not, and the extent of the dissociation can be quantified

Question 67

How are Ka values often expressed?

Answer 67

Ka values often expressed as pKa’s (pKa = -log Ka)

Question 68

What happens when pH = pKa?

Answer 68

Then [A-] = [HA]. And the solution is best able to resist changes in pH

Question 69

What is the buffering region?

Answer 69

A region where the pH of a solution remains constant. When a weak acid is titrated against a strong base, the pH of the solution rises, levels off through the buffer zone, and then rises quickly to reach the equivalence point.

Question 70

Where is the buffering region?

Answer 70

Extends one pH unit on either side of the pKa point. For example: a weak acid with a pKa point of 4.76 would have a buffering range of 3.76 to 5.76

Question 71

What is the relationship between the value of pKa and strength of acid?

Answer 71

The lower the pKa, the stronger the acid

Question 72

Why are buffers important to biological systems?

Answer 72

Because organisms need to be able to maintain a constant pH. Any changes to pH could alter the protonation state of biomolecules, potentially changing their structure and function

Question 73

Define protonation state

Answer 73

Protonation is the addition of a proton to an atom, molecule, or ion

Question 74

What is compensatory respiratory alkalosis?

Answer 74

It serves to maintain the ratio of H2CO3/HCO3- to maintain a constant pH

Question 75

Which relationships does the Henderson-Hasselbalch equation describe?

Answer 75

1. The pH of the solution 2. The pKa of the weak acid 3. the relative concentrations of the weak acid (HA) and conjugate base (A-)

Question 76

What is the Henderson-Hasselbalch equation?

Answer 76

pH = pKa + log( [A-] / [HA] )

Question 77

Calculate the pH of a mixture of 0.01 M acetic acid and 0.1 M sodium acetate. pKa of acetic acid is 4.76

Answer 77

pH = pKa + log [A-] / [HA] pH = 4.76 + log 0.1 / 0.01 pH = 4.76 + 1.0 = 5.76

Question 78

Calculate the pKa of lactic acid given that a mixture of 0.01 M lactic acid and 0.087 M lactate has a pH of 4.80

Answer 78

pH = pKa + log [A-] / [HA] pKa = pH – log [0.087] / [0.01] pKa = 4.80 – 0.94 = 3.86

Question 79

Which non-covalent forces contribute to the structure and stability of a biomolecule?

Answer 79

Hydrogen bonds, Electrostatic interactions, Hydrophobic interactions, Van der Waals Interactions

Question 80

The folding of a polypeptide into its biologically active conformation serves to ___ the entropy of the polypeptide and ____ the entropy of the associated water

Answer 80

decrease, increase

Question 81

What is the Henderson-Hasselbalch equation?

Answer 81

pH = pKa + log [A-]/[HA]

Question 82

Which non-covalent force is the primary driver for biomolecules to adopt their biologically active conformations?

Answer 82

Hydrophobic interactions

Question 83

Molecules with both polar and non-polar groups are called?

Answer 83

Amphipathic

Question 84

True or False: in aqueous solutions, [H+] is always equal to 10-7 M?

Answer 84

False