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BIOCHEM 405 > Lecture 2 > Flashcards

Lecture 2 Flashcards

1
Q

“Big picture” items

A
  • Water is a structurally simple molecule with
    complicated properties
  • Water is the cause of the hydrophobic effect
  • Water can dissociate into protons and hydroxyl ions
  • The proton concentration determines the pH
  • The cell controls the pH of its content and compartments
  • Biochemists control the pH with buffers
  • pH is important in many cellular events
  • Cells store energy through a proton gradient across membranes
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2
Q

Covalent bonds

A

link atoms in molecules together and are

obviously essential

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3
Q

Non-covalent interactions

A

play also a key role in living organisms.

Examples of processes where non-covalent interactions are
important:
- The dissolution of salt in water
- The three-dimensional structure of proteins
- Base-pairing and base-stacking in the DNA double helix
- The aggregation of lipids into membrane bilayers
- The affinity of sugar molecules for taste receptors
- The binding of a medicine to its target protein

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4
Q

Non-covalent interactions between neutral molecules

A
  • interactions between permanent dipoles ( weak 1/r^3)
  • dipole-induced dipole interactions (weaker 1/r^5)
  • london dispersion forces (weakest 1/r^6)
Neutral molecules
where the center
of gravity of the
negative charges
does not coincide
with the center of
gravity of the
positive charges
are said to have a
“dipole”.
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5
Q

“van der Waals interactions”

A

While covalent bonds range typically between 300 and 500 kJ / mol,
non-covalent interactions mentioned above range from 20 (top) to 0.3 (below) kJ / mol.
The non-covalent interactions mentioned above are collectively known as:

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6
Q

water molecule

A

The water molecule is nonlinear and carries a permanent dipole moment.

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7
Q

“van der Waals envelope”

A

is the effective “surface of the molecule”. This surface is obtained by making a sphere with a “van der Waals radius” centered on each atom

Two atoms from different molecules rarely come closer together than the sum of their van der Waals
radii – with the very important exception of the “hydrogen bond”.

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8
Q

The O-O distance

A

~2.74 Å in an H-bond is smaller than the sum of :

(i) the O-H covalent bond distance of ~0.97 Å
+ (ii) the H vdW-radius of ~1.2 Å
+ (iii) the O vdW-radius of ~1.4 Å,
since this sum is: 0.97 + 1.2 + 1.4 = ~ 3.6 Å.

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9
Q

Water molecules interact with other water molecules

A

As ice, each water molecule interacts tetrahedrally with four
other water molecules

The arrangement of water molecules in
bulk liquid water is very dynamic.

Liquid water consists of a rapid fluctuating, three-dimensional network of
hydrogen-bonded H2O molecules

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10
Q

Water hydrogen bonding to other molecules

A

Biomolecules are surrounded by bulk water.

All surface-exposed hydrogen-bond donors and acceptors of biomolecules are engaged in hydrogen bonds with surrounding water molecules.

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11
Q

Hydrogen bonds in general

A

In general:
A hydrogen bond can be represented as D-H….A, where:

D-H = weakly acidic “donor” group, such as O-H, N-H

A = weakly basic “acceptor” atom such as O, N

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12
Q

Ions in solution are solvated by water molecules

A

The permanent dipoles of water molecules interact very favourably with charged ions
in solution, forming a “hydration shell”.

Several complex enthalpic and entropic factors contribute to ΔG of dissolving a salt.

Many salts, like NaCl, do dissolve very well in water.
(But not all salts! E.g. your kidney stones are made up of insoluble calcium oxalate).

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13
Q

Ions solvated by water molecules

A

The water dipoles interact favourably with positive and negatively charged ions.

In actual fact:
• There are many more waters in the first hydration shell than depicted, and
additional waters in a second shell.
• The waters in the hydration shells remain very dynamic.
• They change hydrogen bond patterns, orientation and position all the time.

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14
Q

Hydrophobic interactions

A

Hydrophobic interactions cause non-polar groups to
come together in aqueous solutions.

They are extremely important in biology. They
contribute for instance to:

  1. Folding of protein molecules into compact conformations
  2. Binding of small hydrophobic molecules to hydrophobic
    clefts on the protein surface
  3. Stacking of bases in the DNA double helix and in RNA
    tertiary structures
  4. The formation of the lipid bilayer surrounding cells
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15
Q

Hydrocarbons and water

A

Thermodynamic Changes for Transferring Hydrocarbons from Water to Nonpolar Solvents (at 18° C)

The ΔG for these processes are negative, hence the process will proceed to the right.
That means that these hydrocarbons do not like to dissolve in water.

NOTICE THAT ΔH IS ZERO (red stars).
THIS MEANS:
NO ENTHALPY DIFFERENCE FOR THIS TRANSFER PROCESS.
THESE ARE ENTROPY-DRIVEN PROCESSES!

The entropy S is smaller (thus, less favorable) for a hydrocarbon in water than
when surrounded by hydrocarbons….

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16
Q

Two amphiphilic hydrocarbons

A

(Molecules with both polar and nonpolar segments are called “amphiphilic”)

Such molecules are at the same time hydrophilic and hydrophobic.
If the hydrophobic segments are substantial, these segments tend to cluster together.

ex: palmitate, oleate

17
Q

The hydrophobic effect and amphiphilic molecules

A

The water molecules next to the hydrophobic alkyl chains are restricted in rotational freedom – although they are still very mobile.

18
Q

Clustering of amphiphilic molecules

A

Cluster of lipid
molecules:

Only lipid portions at the edge of the cluster are in contact with water.

In the cluster, fewer water molecules are in contact with the lipid portions than in the
sum of three individual lipids.

Hence, fewer water molecules are restricted in rotational
freedom. Therefore, the entropy of the system is increased by
clustering lipids.

19
Q

Micelle formation of amphiphilic molecules

A

All hydrophobic groups are sequestered from water.

Compared to the cluster, even fewer water molecules are in
contact with the lipid portions than in the sum of individual
lipids.

Hence, fewer water molecules are restricted in rotational
freedom. Therefore, the entropy of the system is further
increased.

The principles for forming lipid bilayers by amphiphilic molecules are the same.

20
Q

Amphiphilic hydrocarbons aggregate in water

A 
Which type of aggregate
actually forms is dependent on:
• the properties and shape of
the amphiphile,
• pH,
• temperature,
• concentration of ions,
• and other factors.
21
Q

Chemical properties of water

A

The neutral water molecule has a very slight tendency to ionize:
H2O = H+ + OH-

In actual fact, the H+ ion does not exist in bulk water but is associated with a
water molecule to form a H3O+ hydronium ion.

The H+ ion is also called the “hydrogen ion” and is, of course, simply a proton.

22
Q

Ionization of water

A
  • The H-bonding within water facilitates its ionization.
  • In 1 liter of pure water (55.5 moles) there are at any time:
    1x10-7 moles of H3O+ and an equal amount of OH-
  • We often use the symbol H+ instead of H3O+

Since the concentration of bulk water is 55.5 M water, and is not changing much upon ionization:

55.5 × Keq = [H+][OH-
] = [10-7][10-7] = Kw = 1×10-14

Kw is called the “ion product of water”.
Ionization of water

Note: These numbers (that is, 55.5, 10-7 and 10-14) are
important to remember.

23
Q

pH scale

A

When dealing with numbers that can be very large and very small, it is convenient to use logarithms.

For the hydrogen ion concentration, the scale was defined as the “pH” scale by Søren Sørenson in 1909:
So, in pure water:

[H+] = 10-7, hence the pH = -log[H+] = 7

pH scale
The pH of the solutions inside and outside the cell is critical for living organisms.

24
Q

Acids and bases

A

An acid is a substance that can donate a proton

A base is a substance that can accept a proton

Many acids and bases are only partially deprotonated or protonated in aqueous solutions.

Those acids and bases are called “weak” acids and bases.

In living organisms numerous such acids and bases occur.

25
Q

[Base] = [Acid]

A

pH = pKa

26
Q

Buffering and buffers

A

Even small pH-changes in biological systems are important!

• The stability and structure of proteins can be altered dramatically by sometimes relatively small changes in pH.

  • The DNA double helix separates into individual strands due to deprotonation of the guanine base at higher pH values. At pH 9.0, half the double helix is separated into single strands.
  • The activity of enzymes can differ by one or more orders of magnitude when the pH changes by two units.

• The oxygen-binding capacity of hemoglobin is dependent on pH. This is used to enhance the efficiency of transporting oxygen from the lungs to muscles.

• Influenza virus can only infect humans because the virus senses a pH difference of about 1-2 pH units in a particular organelle which is ready to
destroy the virus.

27
Q

Proton power

A

Protons are used in biology for a wide range of processes.

For instance, protons can be used to:
• Induce a large conformational change of a protein.
• Store energy – as a proton concentration difference across a membrane

28
Q

Influenza virus

A

Influenza Virus has two main surface proteins:

haemagglutinin (H) and neuraminidase (N).

29
Q

Influenza virus infection depends on pH

A

• The pH of fluids surrounding cells, and of the cytosol inside
the cell, is around 7.

• However, in the organelles called endosomes, the pH is
lower.

• This pH difference is exploited by the influenza virus. It enters
cells via “endosomes” which have a pH of about 6.

• In this organelle with lower pH, the influenza virus cell surface
protein “haemagglutinin”
undergoes a spectacular
conformational change, enabling the flu virus to infect a cell

30
Q

Energy is stored as a proton gradient across a membrane

A

KEY point: protons cannot cross a lipid membrane

Low Proton concentration in the cytoplasm

High Proton concentration in
the periplasm

cytplasm= inside cell

periplasm= the space between the two membranes of many bacterial cells

31
Q

ATPase:

A 
A very BIG multi-protein
complex inserted into
the membrane across
which a proton gradient
has been created.

α, β, γ, δ, ε, a,
b2 and c are all different ATPase “subunits”

32
Q

Energy is stored as a proton gradient across a membrane

A 
Driven by the proton
gradient across the
membrane, part of the
enzyme rotates and
while doing so
generates ATP:

ADP + Pi ➔ ATP

BIOCHEM 405 (25 decks)

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