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chapter 2 water Flashcards

1
Q

Water is the medium for life
-Life evolved in
-Organisms typically contain
-Chemical reactions occur in
Water is a critical determinant of the

A

-Life evolved in water (UV protection)
-Organisms typically contain 70–90% water (human body, earth)
-Chemical reactions occur in aqueous milieu
-Water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes

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2
Q

Water is the solvent of choice for biological systems- Why?

A

-Typically constitutes 70-85% of cell weight
-Important as a solvent and a reactant in biochemical rxns
-Helps regulate temperature since it is able to absorb large amounts of heat
-Helps regulate intracellular pH
-Used for transport – delivers nutrients and removes waste from cells

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3
Q

Molecular Structure of Water
-Octet rule dictates that there are
-These electrons are in
-Water geometry is
-The electronegativity of the oxygen atom induces a
-Because of the dipole moment, water can serve as

A

-Octet rule dictates that there are four electron pairs around an oxygen atom in water
-These electrons are in four sp3 orbitals
-Two of these pairs covalently link two hydrogen atoms to a central oxygen atom
-The two remaining pairs remain nonbonding (lone pairs)
-Water geometry is a distorted tetrahedron
-The electronegativity of the oxygen atom induces a net dipole moment
-Because of the dipole moment, water can serve as both a hydrogen bond donor and acceptor

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4
Q

2 hydrogen-bonded H2O molecules

H bond
OH bond
CH bond bond dissociation energy

A

H-bonds are longer and weaker than covalent bonds

H-bond 23 kJ/mol
O-H bond 470 kJ/mol
C-H bond 348 kJ/mol

The hydrogen bond is about 10% covalent and 90% electrostatic.

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5
Q

Ice

A

4 H-bonds per H20, low S

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6
Q

Liquid water

A

H= 5.9 kJ/mol
3.4 H bonds per H20

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7
Q

Gaseous water (steam)

A

H=+44.0kJ/mol
no hydrogen bonds

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8
Q

H-bond gives water its unusual properties, such as

A

H-bond gives water its unusual properties, such as high surface tension, specific heat, and heat of vaporization, can regulate T and pH etc.

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9
Q

Water forms H-bonds with polar solutes

Water is a terrific solvent for both
The strength of the interactions between water molecules and the solutes is able to

A

Water is a terrific solvent for both polar and ionic solutes—because water is able to interact with both positively- and negatively-charged species.

The strength of the interactions between water molecules and the solutes is able to counterbalance the interactions between the solute molecules.

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10
Q

H-bond Strength and Alignment

Directionality of the H-bond

A

Directionality of the H-bond—strongest when the 3 atoms lie in a straight line. Consequence of directionality- H-bonded molecules are held in specific geometric arrangement, helping to confer precise 3-D structure as is seen in proteins and nucleic acids

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11
Q

Biology important H bonds

A

between water and alcohol
between ketone and water
between peptides groups in polypeptides
between complementary bases of DNA

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12
Q

Importance of Hydrogen Bonds

A

-Source of unique properties of water
-Structure and function of proteins
-Structure and function of DNA
-Structure and function of polysaccharides
-Binding of substrates to enzymes
-Binding of hormones to receptors
-Matching of mRNA and tRNA

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13
Q

–Linus Pauling, The Nature of the Chemical Bond, 1939

A

“I believe that as the methods of structural chemistry are further applied to physiological problems, it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature.”
–Linus Pauling, The Nature of the Chemical Bond, 1939

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14
Q

Water as a Solvent
water is a good solvent for?
water is a poor solvent for?

A

Water is a good solvent for charged and polar substances
amino acids and peptides; small alcohols; carbohydrates

Water is a poor solvent for nonpolar substances
nonpolar gases; aromatic moieties; aliphatic chains

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15
Q

Water dissolves many salts
-High dielectric constant reduces
-Strong electrostatic interactions between the solvated ions and water molecules
-Entropy ____ as ordered crystal lattice is

A

-High dielectric constant reduces attraction between oppositely charged ions in salt crystal; almost no attraction at large (> 40 nm) distances
-Strong electrostatic interactions between the solvated ions and water molecules lower the energy of the system
-Entropy increases as ordered crystal lattice is dissolved

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16
Q

Solvation and Hydration Spheres
Ionic substances such as NaCl dissolve because H2O molecules are attracted

A

Ionic substances such as NaCl dissolve because H2O molecules are attracted to the positive (Na+) or negative (Cl-) charge of each ion, forming a shield around them and weakening their ability to reform the lattice. ΔG= ΔH-TΔS; ΔH is a small positive value while TΔS is a large positive value so ΔG is negative.

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17
Q

Hydrophilic (water loving) Molecules

A

-Substances that dissolve readily in water
-Composed of ions or polar molecules that attract water molecules through charge effects.
-Water molecules surround each ion or polar molecule on the surface of a solid substance and carry it into solution.

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18
Q

Hydrophobic Molecules & Effects
-Molecules that contain a preponderance of nonpolar bonds are usually
-Especially true of
-H2O molecules are not
-When water is mixed with benzene or hexane, they form

Is one of the main factors behind:

A

-Molecules that contain a preponderance of nonpolar bonds are usually insoluble in water = hydrophobic
-Especially true of hydrocarbons, which contain many C-H bonds
-H2O molecules are not attracted to such molecules and so have little tendency to surround them and carry them into solution
-When water is mixed with benzene or hexane, they form two immiscible layers

-Refers to the association or folding of nonpolar molecules in the aqueous solution
-Is one of the main factors behind:
–protein folding
–protein-protein association
–formation of lipid micelles
–binding of steroid hormones to their receptors

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19
Q

symmetric=
nitrogen, oxygen, carbon dioxide, ammonia, hydrogen sulfide

A

symmetric=non-polar
nitrogen-nonpolar
oxygen-nonpolar
carbon dioxide-nonpolar
ammonia-polar
hydrogen sulfide-polar

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20
Q

Why non-polar molecules are insoluble in water:
-ΔS ? 0
-ΔH ? 0
-ΔG ? 0

A

-interfere with the “flickering cluster” structure of water
-A hydrophobic molecule creates a cavity in the water which causes the water molecules surrounding it to become more ordered (forms a “cage”).
-ΔS < 0 (reduces the entropy (disorder) of water).
-ΔH > 0 (requires energy to break H-bonds in water.
-ΔG > 0 (ΔG = ΔH-TΔS, thermodynamically unfavorable.

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21
Q

Origin of the Hydrophobic Effect (1)
-Consider amphipathic lipids in water
-Lipid molecules disperse in the solution; nonpolar tail of each lipid molecule is
-Entropy of the system
-System is now in an

A

-Consider amphipathic lipids in water
-Lipid molecules disperse in the solution; nonpolar tail of each lipid molecule is surrounded by ordered water molecules
-Entropy of the system decreases
-System is now in an unfavorable state

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22
Q

Origin of the Hydrophobic Effect (2)
-Nonpolar portions of the amphipathic molecule
-The released water molecules will be more
-All nonpolar groups are sequestered from
-Only polar “head groups” are

A

-Nonpolar portions of the amphipathic molecule aggregate so that fewer water molecules are ordered
-The released water molecules will be more random and the entropy increases
-All nonpolar groups are sequestered from water, and the released water molecules increase the entropy further
-Only polar “head groups” are exposed and make energetically favorable H-bonds

23
Q

Hydrophobic effect favors ligand binding
-Binding sites in enzymes and receptors are often
-Such sites can bind
-Many drugs are designed to take
-Substrates usually bind into

A

-Binding sites in enzymes and receptors are often hydrophobic
-Such sites can bind hydrophobic substrates and ligands such as steroid hormones
-Many drugs are designed to take advantage of the hydrophobic effect

Substrates usually bind into pockets rather than slight indents, so the waters interacting with the substrate must be pushed aside as the substrate enters the pocket (or clefts which we will do in Chapter 6 with Chymotrypsin).

24
Q

Principal types of weak noncovalent bonds that hold macromolecules together

A

-Hydrogen bonds
-van der Waals attractions
-Hydrophobic forces
-Ionic forces

25
Q

van der Waals Attractions
-van der Waals interactions have two components:

A

-van der Waals interactions have two components:
—Attractive force (London dispersion) depends on the polarizability
—Repulsive force (Steric repulsion) depends on the size of atoms
-Attraction dominates at longer distances (typically 0.4–0.7 nm)
-Repulsion dominates at very short distances
-There is a minimum energy distance (van der Waals contact distance)

26
Q

Hydrophobic Forces
Water forces
Hydrophobic groups held together in this way are sometimes said to be held together by

A

Water forces hydrophobic groups together, because doing so minimizes their disruptive effects on the H-bonded water network.

Hydrophobic groups held together in this way are sometimes said to be held together by “hydrophobic bonds”, even though the attraction is actually caused by a repulsion from the water.

27
Q

Ionic Bonds
-Ionic interactions can occur either between
-The force of attraction between the two charges
-In the absence of water, ionic forces are

A

-Ionic interactions can occur either between fully charged groups (ionic bond) or between partially charged groups.
-The force of attraction between the two charges, d+ and d-, falls off rapidly as the distance between the charges increases.
-In the absence of water, ionic forces are very strong. Responsible for the strength of minerals such as marble and agate.

28
Q

Ionic Bonds in Aqueous Solution
-Charged groups are shielded by
Similarly, other ions in solution can
-Remember to factor in

A

-Charged groups are shielded by their interactions with H2O molecules. Ionic bonds are therefore quite weak in water.
-Similarly, other ions in solution can cluster around charged groups and further weaken ionic bonds.
-Remember to factor in repulsion of like charges when thinking about ionic interactions

29
Q

Role of Noncovalent Forces
-Macromolecules (proteins, DNA, etc.) contain many potential sites for
-It is the cumulative effect of
-The most stable (native) structure, or conformation, is usually the one in which
-This is the principle involved in f

A

-Macromolecules (proteins, DNA, etc.) contain many potential sites for non-covalent interactions to occur
-It is the cumulative effect of the many small binding forces that ends up being enormous.
-The most stable (native) structure, or conformation, is usually the one in which weak-binding possibilities are maximized.
-This is the principle involved in folding large molecules into 3-D shapes

30
Q

Ionic interaction bond strength

A

20

31
Q

Hydrophibic interactions bond strength

A

<40

32
Q

Water Bound in a Protein Channel
 (Cytochrome f)

A

Facilitates Proton Hopping – see later in Photosynthesis

33
Q

Solutes Affect the Colligative Properties of Aqueous Solutions
4 Colligative Properties

A

Vapor pressure
Boiling point
Melting point
Osmotic pressure

Solutes decrease vapor pressure

34
Q

Osmotic Pressure

A

Osmosis,water movement across a semipermeable membrane driven by differences in osmotic pressure,is an important factor in the life of most cells.

35
Q

Cell Response to Osmotic Pressures

isotonic
hypertonic
hypotonic

A

Plasma membranes are more permeable to water than to most other small molecules,ions,and macromolecules because protein channelsin the membrane selectively permit the passage of water.

isotonic- no net water movement
hypertonic-water moves out and cell shrinks.
hypotonic-water moves in cell swells and eventually bursts

36
Q

Key points for weak interactions in aqueous systems:
-Water is a
-Nonpolar compounds dissolve
-Weak,noncovalent interactions,in large numbers,decisively influence the
-The concentration of solutes strongly influent the

A

-Water is a highly polar molecule, can form H-bond (weak bond, <30 kJ/mol) with itself or with solutes, and is good solvent for polar solutes and for charged solutes.
-Nonpolar compounds dissolve poorly in water (no H-bond), form a particular state (e.g. micelles).
-Weak,noncovalent interactions,in large numbers,decisively influence the folding of macromolecules such as proteins and nucleic acids.
-The concentration of solutes strongly influent the physical properties of aqueous solutions (the osmotic pressure).

37
Q

Water molecules tend to undergo

A

reversible deprotonation to a small extent- promoted by H-bonding
H2O ⬄ H+ + OH-

Hydronium ions — hydration of H+ to form H3O+
Form instantaneously, so no free protons in solution
Important, because many rxns depend on [H+]

38
Q

Pure Water Is

A

Slightly Ionized
-proton hop and hydronium

hydronium ion gives up proton, proton hop, water accepts proton and becomes hydromium ion

39
Q

Ionization of Water

A

Keq = [H+][OH-] / [H2O] = 1.8 x 10-16 M (25°C)
Concentration of water - one liter = 1,000g
Mole Wt Water = 18.015
[H2O] = 55.5 M
Kw = [H+][OH-] = Keq x [H2O] = 1 x 10-14 M2
for pure water [H+] = [OH-]
so, [H+] = 10-7 M
pH is negative log [H+] , for pure water = 7.0 (look at example in pre reading questions/notes)

40
Q

pH Scale

A

pH=-log[H+]

[H+] can range from 1M ~ 1 X 10-14M
pH = -log [H+]
Neutral pH = 7.0
pH + pOH = 14
Low pH = high [H+], low [OH-]
High pH = low [H+], high [OH-]

41
Q

1MHCl
gastric juice
lemon juice
cola, vinegar
red wine
beer
black coffee
milk
saliva
human blood, tears
seawater, egg white
solution of baking soda (NaHCO3)
Household ammonia
household bleach
1MNaOH

A

1MHCl-0
gastric juice 1.5
lemon juice-2
cola, vinegar-3
red wine-3.8
beer-4.2
black coffee-5
milk,saliva-6.5
human blood, tears-7.2
seawater, egg white-7.8
solution of baking soda(NaHCO3)-9
Household ammonia-12
household bleach19.9
1MNaOH-14

Most life and biochemistry is near neutral and into the acid

42
Q

Strong acids Weak Acids
Ka =
Henderson-Hasselbalch Equation Rearranges Ka
when pKa = pH
Weak acids try to hold on to the

A

Strong acids – dissociate completely
Weak acids – dissociate only partially

HA ↔ H+ + A-
Ka = [H+][A-] / [HA]

Henderson-Hasselbalch Equation Rearranges Ka
pH = pKa + log ( [A-] / [HA] )

when pKa = pH … [A-] = [HA]

Weak acids try to hold on to the proton…dependent on pH. Know this well, we will be doing problems with the Henderson Hasselbalch equation which you had in General Chemistry. What about strong acids: what happens when HCl for example is added to water? All this is review !

43
Q

Conjugate acid-base pairs

HA = Conjugate
A- = Conjugate
Ka =
Ka & pKa value describe tendency to
large Ka
small Ka
lower pka=
pKa = - log

A

HA + H2O A- + H3O+
HA A- + H+
HA = Conjugate acid ( donates H+)(Bronsted Acid)
A- = Conjugate base (accepts H+)(Bronsted Base)

Ka = ionization/dissociation constant
Ka & pKa value describe tendency to lose H+

large Ka = stronger acid
small Ka = weaker acid
Lower pKa = stronger acid, tendency to dissociate proton

Ka = [H+][A-]
[HA]

pKa = - log Ka

44
Q

What is the relationship between pKa and pH?
Henderson-Hasselbalch Equation
* H-H equation describes
the relationship between

A

HA = Conjugate acid
A- = Conjugate base

  • H-H equation describes
    the relationship between
    pH, pKa and buffer concentration

5) pH = pKa +log [A-]
[HA]

pH = pKa + log [A-]
[HA]
OR
pH = pKa + log [proton acceptor]
[proton donor]
At midpoint of titration, when [HA] = [A-],
pH = pKa + log 1.0 = pKa + 0 = pKa

45
Q

pKa values determined by titration-

A

pKa values determined by titration- pH is measured with each incremental amount of base and expressed as a fraction of the total amount of base required to convert the acetic acid to its deprotonated form.

pKa’s speak to the strength of the weak acids. Check out the difference in carboxyl pka’s. Phosphate has three pKa’s keep these in mind, we will use it later in the course.

46
Q

Weak Acids and Bases Have Characteristic Acid Dissociation Constants

A

pKa = –log Ka (strong acid → large Ka → small pKa)

47
Q

phosphate has ____ ionizable H+ and ____ pkas

A

Phosphate has three ionizable H+ and three pKas

48
Q

Acid Base Tirations: Note that acetate has two forms:

A

Associated (HA) -> pKa (half associated, half dissociated) -> Dissociated (A-).

49
Q

Buffers
-Buffers are
-A buffered system consists of
-The most effective buffering occurs at the
-Buffers are effective at pHs that are

A

-Buffers are aqueous systems that resist changes in pH when small amounts of a strong acid or base are added.
-A buffered system consists of a weak acid and its conjugate base.
-The most effective buffering occurs at the region of minimum slope on a titration curve
(i.e. around the pKa).
-Buffers are effective at pHs that are within +/-1 pH unit of the pKa

50
Q

Biological Buffers
Two important buffer systems are

A

pH is carefully controlled in multicellular organisms for the simple reason that the activity of many enzymes is sensitive to pH. (Blood plasma is pH=7.4)

Two important buffer systems are phosphate and bicarbonate

51
Q

Weak Acids or Bases Buffer Cells and Tissues against pH Changes

A

The imidazol group of the amino acid Histidine is a weak acid (one of the nitrogens, is it the imid or azole?).

52
Q

Phosphate Buffer

A

The second ionization of phosphate is especially important
pKa = 6.86, thus a decent buffer in the range of pH 5.86 to 7.86

Phosphate has three ionizable H+ and three pKas

53
Q

Bicarbonate is an important buffer in

A

blood
The pKa of carbonic acid is low (3.77), but it is still an effective buffer under physiological conditions because H2CO3 is in equilibrium with gaseous CO2 in the lungs

Any pH change (whether it’s an increase or decrease in acidity) can be re-equilibrated by the bicarb system rapidly, as the conc of dissolved CO2 can be adjusted quickly by changes in the rate of breathing

54
Q

Water as a Reactant
Addition of a molecule of water is
Removal of a molecule of water is
Most polymerizations are
and depolymerization reactions (Ex: digestive enzymes) are

A

Addition of a molecule of water is hydrolysis

Removal of a molecule of water is condensation

Most polymerizations are dehydrations and depolymerization reactions (Ex: digestive enzymes) are hydrations.

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