2 - WATER: THE SOLVENT FOR BIOCHEMICAL REACTIONS

Question 1

What are the levels of structural organization in the human body?

Answer 1

1. Chemical
2. Cellular
3. Tissue
4. Organ
5. Organ system
6. Organism level

Question 2

What are functional groups in a molecule?

Answer 2

are chemical motifs, or patterns of atoms, that display consistent “function” (properties and reactivity) regardless of the exact molecule they are found in.

Question 3

How do prokaryotes differ from eukaryotes?

Answer 3

Eukaryotic cells are cells containing membrane-bound organelles and are the basis for both unicellular and multicellular organisms. In contrast, prokaryotic cells do not have any membrane-bound organelles and are always part of unicellular organisms.

Question 4

What are the different organelles in a typical eukaryote? Be familiar with their functions.

Answer 4

Nucleus - the structure in a cell that contains the chromosomes.

Cell membrane (plasma membrane) - separates the interior of the cell from the outside environment.

Mitochondria - membrane-bound cell organelles that generate most of the chemical energy needed to power the cell’s biochemical reactions.

Endoplasmic reticulum - functions particularly in the synthesis, folding, modification, and transport of proteins

Ribosomes - an intercellular structure made of both RNA and protein, and it the the site of protein synthesis in the cell.

Chloroplasts (present in green plants) - contains the photosynthetic pigment chlorophyll that captures sunlight and converts it into energy, releasing oxygen from water.

Question 5

What is ATP?

Answer 5

is like a battery for cells. It stores and provides energy that cells need to do their work. When food is broken down, ATP captures the energy and then releases it to help cells perform activities, like moving muscles or thinking. All living things have ATP in their cells because it’s essential for life.

Question 6

I think my professor made a mistake in the questions and the questions for this topic is in the first lecture flashcards so please refer to those. Sorry for the confusion, future Ysa!

Question 7

the principal component of most cells

Answer 7

Water

Question 8

tendency of an atom to attract electrons to itself in a chemical bond

Answer 8

Electronegativity

Question 9

bonds in which two atoms have an unequal share in the bonding electrons

Answer 9

Polar bonds

Question 10

when the electronegativity difference is quite small (e.g. methane) and the sharing of electrons in the bond is very nearly equal; a bond in which two atoms share electrons equally

Answer 10

Nonpolar bond

Question 11

The bonds in a molecule may be polar, but the molecule itself can still be
nonpolar because of its geometry. Carbon dioxide is an example. The two C”O
bonds are polar, but because the CO2 molecule is linear, the attraction of the
oxygen for the electrons in one bond is cancelled out by the equal and opposite
attraction for the electrons by the oxygen on the other side of the molecule.

Question 12

molecules with positive and negative ends due to an uneven distribution of electrons in bonds

Answer 12

Dipoles

Question 13

Ionic compounds with full charges, such as potassium chloride (KCl; K+ and Cl− in
solution), and polar compounds with partial charges (i.e., dipoles), such as ethyl
alcohol (C2H5OH) or acetone [(CH3)2C double bond O], tend to dissolve in water, while less
polar molecules tend not to dissolve as readily in water, if at all.

Answer 13

The underlying
physical principle is electrostatic attraction between unlike charges, but there are
different types of bonds with different strengths depending on these electrostatic
attractions.

Question 14

are the strongest bonds, being many times stronger than the next weakest ones

Answer 14

Ionic and covalent bonds

Question 15

an interaction that depends on the attraction of unlike charges

Answer 15

Salt bridge

Question 16

A charged ion will interact with the corresponding opposite partial
charge on the water.

Answer 16

Ion-dipole interactions

Question 17

noncovalent associations based on the weak attraction of transient dipoles for one another

Answer 17

van der Waals forces/ van der Waals interactions/bonds

Question 18

the distance between an atom’s nucleus and its effective electronic surface

Answer 18

van der Waals radius

Question 19

These forces occur between molecules that are dipoles, with the partial positive
side of one molecule attracting the partial negative side of another molecule.

Answer 19

Dipole-dipole interactions

Question 20

A permanent dipole in a molecule when it comes into close contact with any molecule, even those that have no dipoles, can induce a transient dipole in the other. As the electron cloud of the dipole pushes against the electron cloud of the other molecule, it momentarily distorts the electron cloud. This creates a brief dipole and, in that moment, the two molecules are attracted to one another

Question 21

When two molecules
lacking dipoles bump into each other, they distort each other’s electron cloud,
thereby creating a brief interaction between these induced dipoles

Answer 21

London dispersion force

Question 22

this force is the reason that all molecules are attracted to another to a very small degree, and explains why nonpolar molecules would have attractions for one another

Answer 22

London dispersion force

Question 23

When salt (like NaCl) is in solid form, the sodium (Na⁺) and chloride (Cl⁻) ions are held together by strong ionic bonds. You might think these bonds are too strong for the salt to dissolve in water. However, when salt is added to water, the water molecules surround the ions. Each water molecule forms a bond with the ions, which is known as an ion-dipole bond.

Imagine it like a tug-of-war: if the bonds between the water molecules and the ions are stronger than the bonds holding the salt crystal together, the salt will dissolve. This means the energy gained by the new bonds with water is greater than the energy needed to break the ionic bonds, leading to the salt dissolving in water.

Question 24

Ionic and polar substances tend to dissolve in water. What are they referred to as?

Answer 24

Hydrophilic

Question 25

Hydrocarbons (compounds that contain only carbon and hydrogen) are
nonpolar.

Question 26

Examples of hydrophilic substances:

Answer 26

1, Polar covalent bonds (alcohols and ketones)
2. Sugar
3. Ionic compounds
4. Amino acids, phosphate esters

Question 27

Examples of hydrophobic substances:

Answer 27

1. Nonpolar covalent compounds (hydrocarbons)
2. Fatty acids, cholesterol

Question 28

It is less favorable thermodynamically for water molecules to be associated with nonpolar molecules than with other water molecules

Question 29

Nonpolar molecules do not dissolve in water. What are these referred to as?

Answer 29

Hydrophobic

Question 30

Hydrocarbons in particular tend to sequester
themselves from an aqueous environment. A nonpolar solid leaves undissolved
material in water. A nonpolar liquid forms a two-layer system with water; an
example is an oil slick. The interactions between nonpolar molecules are called?

Answer 30

Hydrophobic interactions/bonds

Question 31

A single molecule may have both polar (hydrophilic) and nonpolar (hydrophobic) portions.

A long-chain fatty
acid having a polar carboxylic acid group and a long nonpolar hydrocarbon
portion is a prime example of an amphipathic substance.

Answer 31

Amphipathic

Question 32

special case of dipole-dipole interaction; a noncovalent association formed between a hydrogen atom covalently bonded o one electronegative atom and a lone pair of electrons on another electronegative atom

Answer 32

Hydrogen bonds

Question 33

When hydrogen is attached to a highly electronegative atom like oxygen or nitrogen, it becomes slightly positively charged because the other atom pulls electrons toward itself, making the bond polar. This doesn’t happen when hydrogen is bonded to carbon. The slight positive charge on hydrogen can attract a pair of nonbonding electrons (which are negatively charged) on another electronegative atom. All three atoms involved—the hydrogen and the two electronegative atoms—line up in a straight line, forming what’s called a hydrogen bond. This specific arrangement maximizes the positive charge on the hydrogen, resulting in the strongest interaction with the nonbonding electrons of the other electronegative atom.

Question 34

the group comprising the electronegative atom that is covalently bond to hydrogen is?

Answer 34

Hydrogen-bond donor

Question 35

the electronegative atom that contributes the unshared pair of electrons to the interaction is?

Answer 35

Hydrogen-bond acceptor

Question 36

Water molecules can form four hydrogen bonds, with each molecule acting as a donor in two bonds (due to its two hydrogen atoms) and as an acceptor in two bonds (thanks to the two lone pairs of electrons on its oxygen atom). In contrast, hydrogen fluoride (HF) has only one hydrogen atom, allowing it to form one hydrogen bond as a donor. However, the fluorine atom in HF has three lone pairs of electrons, enabling it to form up to three hydrogen bonds as an acceptor. Ammonia (NH₃) can form three hydrogen bonds as a donor, using its three hydrogen atoms, but it can only accept one hydrogen bond due to the single lone pair of electrons on the nitrogen atom.

Question 37

Ice has a lower density than liquid water because the fully hydrogen bonded
array in an ice crystal is less densely packed than that in liquid water. Liquid
water is less extensively hydrogen-bonded and thus is denser than ice. Thus, ice cubes and icebergs float.

Question 38

If a polar solute can serve as a donor or an acceptor of hydrogen bonds, not only can it form hydrogen bonds with water but it can also be involved in nonspecific dipole−dipole interactions.

Question 39

Alcohols, amines,
carboxylic acids, and esters, as well as aldehydes and ketones, can all form hydrogen bonds with water, so they are soluble in water.

Question 40

a molecule that acts as a proton (hydrogen ior) donor

Answer 40

Acid/Bronsted acid

Question 41

proton acceptor

Answer 41

Base

Question 42

the tendency of an acid to dissociate to a hydrogen ion and its conjugate base;

Answer 42

Acid strength

Question 43

For each acid, the quantity Ka has a fixed
numerical value at a given temperature. This value is larger for more completely
dissociated acids; thus the greater the Ka, the stronger the acid.

Question 44

a number that characterizes the strength of an acid

Answer 44

Acid dissociation constant

Question 45

All solutes are extensively hydrated in aqueous solution.

Question 46

a measure of the tendency of water to dissociate to give hydrogen ion and hydroxide ion

Answer 46

Ion product constant for water

Question 47

The numerical value of Kw can be determined experimentally by measuring the hydrogen ion concentration of pure water. The hydrogen ion concentration is also equal, by definition, to the hydroxide ion concentration because water is a monoprotic acid (one that releases a single proton per molecule).

Question 48

The wide range of possible hydrogen ion and hydroxide ion concentrations
in aqueous solution makes it desirable to define a quantity for expressing these
concentrations more conveniently than by exponential notation. This quantity
is called?

Answer 48

pH

Question 49

When a solution has a pH of 7, it is said to be neutral, like pure water. Acidic
solutions have pH values lower than 7, and basic solutions have pH values
higher than 7.

Question 50

The smaller the value of pKa, the stronger the acid.

Question 51

Ka: larger values imply stronger acids

Question 52

mathematical relationship between the pKa of an acid and the pH of the solution containing the acid and its conjugate base; useful in predicting the properties of buffer solution used to control the pH of reaction mixtures.

is useful in in predicting the properties of buffer solutions used to control the pH of reaction mixtures

Answer 52

Henderson-Hasselbalch equation

Question 53

When a solution
contains equal concentrations of a weak acid and its conjugate base, the pH of that solution equals the pKa value of the weak acid

Question 54

an experiment in which a measured amount of base is added to an acid

Answer 54

Titration

Question 55

the point in a titration where an acid is exactly neutralized

Answer 55

Equivalence point

Question 56

If the pH is monitored as base is added to a sample of acetic acid in the course of a titration, an inflection point in the titration curve is reached when the pH equals the pKa of acetic acid.

Question 57

release one hydrogen ion and have a single Ka and pKa value

Answer 57

Monoprotic acids

Question 58

can release two hydrogen ions and have two Ka and pKa values

Answer 58

Diprotic acids

Question 59

can release more than two hydrogen ions (e.g. cittic acid and phosphoric acid releasing three hydrogen ions and having three pKa values.

Answer 59

Polyprotic acids

Question 60

When the pH is less than the pKa, the protonated form is dominant (Remember
that the definition of pH includes a negative logarithm.)

H+ on, substance protonated

Answer 60

pH < pKa

Question 61

When the pH is greater than the pKa, the deprotonated (conjugate base) form predominates.

H+ off, substance deprotonated

Answer 61

pH > pKa

Question 62

is something that resists change

Answer 62

Buffers

Question 63

a solution that resists a change in pH on addition of moderate amounts of strong acid or strong base; consists of a mixture of a weak acid and its conjugate base

Answer 63

Buffer solution

Question 64

Buffers work because they obey Le Chatelier’s principle. This principle states that if stress is applied to a system in equilibrium, the equilibrium will shift in the direction that relieves the stress.

Question 65

How do we choose a buffer?

note: read on this on the ebook or search on this too because I can’t understand this on the book (yt)

Answer 65

Buffers stabilize pH by using weak acids and their conjugate bases. When extra hydrogen ions (H⁺) are added, they react with the conjugate base to form the weak acid. If hydroxide ions (OH⁻) are added, they react with the weak acid to form water and the conjugate base. This process helps maintain a stable pH in the solution.

Question 66

a measure of the amount of acid or base that can be absorbed by a given buffer solution

Answer 66

Buffering capacity

Question 67

A buffer that contains greater amounts of
both acid and base has a higher buffering capacity.

Question 68

How do we choose a buffer?

Answer 68

We choose a buffer primarily by knowing the pH that we wish to maintain. For example, if we are performing an experiment and we want the solution to stay at pH 7.5, we look for a buffer that has a pKa of 7.5 because buffers are most effective when the pH is close to the buffer pKa.

Question 69

in vitro = outside the living body

in vivo = in living organisms

Question 70

compounds that have both a positive charge and negative charge.

Answer 70

Zwitterions

Question 71

are usually considered less likely to interfere with biochemical reactions than some of the earlier buffers

Answer 71

Zwitterions

Question 72

a condition in which blood pH drops below 7.35

Answer 72

Acidosis

Question 73

a condition in which blood pH rises above 7.45

Answer 73

Alkalosis

Question 74

How do we make buffers in the laboratory?

Answer 74

The most efficient way to make a buffer in the laboratory is to add either the weak acid form or the weak base form of the buffer compound to a container, add water, and then measure the pH with a pH meter. The pH will be either too low or too high. We then add strong acid or strong base until the pH is the desired buffer pH. Then we bring the solution up to the final volume so that concentration is correct.

Question 75

Are naturally occurring pH buffers present in living organisms?

Answer 75

Buffers are not just an artificial system used in the laboratory. Living systems are buffered by naturally occurring compounds. Naturally occurring phosphate and carbonate buffers help maintain physiological pH near 7.0.

Question 76

The favorable ion–dipole and dipole–dipole interactions responsible for the solubility of ionic and polar compounds do not occur for nonpolar compounds, so these compounds tend not to dissolve in water.

Question 77

because of the logarithms involved, a difference of one pH unit implies a tenfold difference in hydrogen ion concentration, [H+]

Question 78

In biochemistry, most of the acids encountered are weak acids. These have a Ka well below 1.

Question 79

The two examples of polyprotic acids given here, citric acid and phosphoric acid, can release three hydrogen ions and have
three Ka values and three pKa values.

Question 80

The pH of a sample being titrated changes very little in the vicinity of the inflection point of a titration curve. Also, at the inflection point, half the amount of acid originally present has been converted to the conjugate base.

Question 81

A buffer solution can maintain the pH at a relatively constant value because of the presence of appreciable amounts of both the acid and its conjugate base. This condition is met at pH values at or near the pKa of the acid. If OH− is added, an appreciable amount of the acid form of the buffer is present in solution to react with the added base. If H+ is added, an appreciable amount of the basic form of the buffer also is present to react with the added acid.

Question 82

If a buffer solution contained a suitable ratio of acid to base, but very low concentrations of both, it would take very little added acid to use up all of the base form, and vice versa.

Question 83

The buffer system based on TRIS [tris(hydroxymethyl)aminomethane] is also widely used in vitro.

Question 84

Why do some chemicals dissolve in water while others do not?

Answer 84

Water’s polar nature makes it an excellent solvent for dissolving both ionic and polar compounds. This is due to electrostatic attraction between opposite charges. The negative side of a water molecule attracts positive ions or the positive end of other polar molecules, while the positive side of water attracts negative ions or the negative end of polar molecules.

Question 85

Why do oil and water mixed together separate into layers?

Answer 85

Oil molecules are amphipathic, meaning they have both polar (hydrophilic) heads and nonpolar (hydrophobic) tails. When oil and water separate, the polar heads interact with water, while the nonpolar tails are kept away from it. Van der Waals interactions between the nonpolar tails drive this natural arrangement.

Question 86

Why does water have such interesting and unique properties?

Answer 86

Water has unusually high boiling and melting points for its size due to extensive hydrogen bonding between molecules. Each water molecule has two partial positive and two partial negative charges, enabling it to form a solid lattice and bond with multiple molecules in liquid form. These strong hydrogen bonds require significant energy to break, which is why water melts and boils at higher temperatures compared to other similarly sized molecules.

Question 87

Why do we want to know the pH?

Answer 87

It’s crucial to monitor pH because many biological processes depend on a narrow pH range. For instance, an enzyme active at pH 7.0 may lose function at pH 8.0. Scientific experiments often require precise pH control for accurate results. Although some cellular compartments may experience pH fluctuations, cells must maintain a near-neutral pH to survive.