Unit 1 Bonding & Water

Question 1

What is the difference between covalent and noncovalent bonding?

Answer 1

Covalent - strong, High energy covalent bonds define the BASIC molecular components of the cell.
Non cov. - weak, noncovalent bonds govern the FINAL 3D shapes of molecules and how they interact with each other.

Question 2

What are biological processes?

Answer 2

Biological processes are essentially chemical reactions and interactions between molecules inside the cell.

Question 3

True/False: Noncovalent bonds involve intimate electron sharing and contain much less energy than covalent bonds.

Answer 3

False; noncovalent bonding does NOT contain intimate electron sharing.

Question 4

What is the class, structural formula, and an example of Hydrophobic functional groups?

Answer 4

Hydrocarbon chains, R —CH3, and Alanine

Question 5

What is the class, structural formula, and an example of Hydroxyl groups?

Answer 5

Alcohol, R—OH, and Ethanol

Question 6

What is the class, structural formula, and an example of Aldehydes?

Answer 6

Aldehydes, R - C w/double bonded O - H, and Acetaldehyde.

Question 7

What is the class, structural group, and an example of Keto groups?

Answer 7

Ketones, R— C w/ double bonded O —R, Acetone.

Question 8

What is the class, structural formula, and an example of Caboxyl groups?

Answer 8

Carboxylic acids, R— C w/double bonded O—OH, Acetic Acid.

Question 9

What is the class, structural formula, and an example of Amino groups?

Answer 9

Amines, R—NH2, Alanine

Question 10

What is the class, structural formula, and an example of Phosphate groups?

Answer 10

Organic phosphates, R—O—P w/ double bonded O and 2- O, 3 - Phosphoglyceric Acid.

Question 11

What is the class, structural formula, and an example of Sulfhydryl acids?

Answer 11

Thiols, R—SH, Cysteine

Question 12

What is special about noncovalent bonds? What are the three types of noncovalent bonds?

Answer 12

Noncovalent bonds play essential roles in the faithful replication of DNA, the folding of proteins into intricate 3D forms, the specific recognition of substrates by enzymes, and the detection of molecular signals.

The three types of noncovalent bonds are Ionic Interactions (aka salt bridges), Hydrogen bonding, and Van der Waals interactions.

Question 13

What differentiates the three types of non covalent bonding?

Answer 13

They differ in geometry, strength, and their specificity. They also differ in the way they are affected in the presence of water.

Question 14

Order the following bonding from strongest to weakest: Hydrogen bonding, van der waals, covalent, ionic

Answer 14

Covalent, ionic, hydrogen bonding, van der waals

Question 15

What are Ionic interactions? Provide an example.

Answer 15

Ionic interactions are the interaction between distinct electric charges on atoms, usually between atoms bearing a completely negative charge and a completely positive charge. These are Protein - nucleic acids interactions and metal ion and protein interactions.

Example: NaCl, Na+ Cl- Or —COO- and +H3N-

Question 16

What is Coulomb’s Law? What does it tell us?

Answer 16

Coulomb’s Law: E = (kq1q2)/Dr
E = energy
K = constant
Q1q2 = the charges on the ions
D = the dielectric constant
R = the distance between two ions

Coulomb’s law tells us the energy of an electrostatic (ionic) interaction between two charges in a given compound.

Question 17

What are the properties of water?

Answer 17

Water is a solvent and it is essential to the formation of macro molecular structures and the progress of chemical reactions.

WATER IS POLAR

The shape is bent, so the distribution of charge is asymmetric - the oxygen nucleus draws electrons away from the hydrogen nuclei, thus water is an electrically polar structure.

Question 18

How does water effect hydrogen bonding?

Answer 18

Water disrupts hydrogen bonding between two molecules by competing for the hydrogen bonding capability.

Question 19

What are the two conditions of Hydrogen bonding strength?

Answer 19

The distance and bond angle.

Question 20

True/False: Water forms hydrogen bonds with each other and other biomolecules.

Answer 20

True, because of its ability to form hydrogen bonds, water is HIGHLY cohesive which accounts for its high surface tension. It is also less dense than similar size molecules.

Question 21

What are Van der Waals interactions?

Answer 21

Van der Waals interactions are transient dipole - dipole interactions between transiently charged groups.

For biomolecules that are neither polar nor charged, van der Waals interactions can occur. The basis of van der waals interactions is that the distribution of the electric charge around an atom changes with time. At ANY INSTANT the charge distribution is not perfectly symmetrical: there will be regions of partial positive charges and partial negative charges - this is a TRANSIENT ASYMMETRY: the electronic charge around an atom acting through electrostatic interactions to induce a complementary asymmetry in the electron distribution around its neighboring atoms.

Question 22

True/False: Van der Waal interactions have a strong dependence on distance.

Answer 22

True: E is proportional to 1/r^6.

A van der waal interaction is most attractive when the VDW spheres of two atoms touch. If they interpenetrate, repulsive forces dominate. If they move apart, attractive forces rapidly decrease.

The are weak but in abundance they can become stronger.

Question 23

True/False: The “structuring” of water around the non polar surface decreases the entropy of the system.

Answer 23

True

When water molecules come in contact with non polar molecules, they form “cages” around the nonpolar molecules, becoming more well ordered than water molecules free in solution.

When there are large amounts of nonpolar molecules are in water, they form large aggregates to minimize their contact with water molecules. THIS exclusion of non polar substances from an aqueous solution is known as hydrophobic effects.

Question 24

What are Amphiphilic molecules?

Answer 24

Molecules that have both a hydrophilic part and a hydrophobic part. These molecules in water experience both hydrophilic interactions and the hydrophobic effect.

Parts: polar head group, nonpolar tail

The polar head group = hydrophilic
Non polar tail = hydrophobic

Question 25

What structure do single tailed amphiphilic molecules form?

Answer 25

Micelle structures, they are spherical in shape. The polar groups aggregate with each other and the nonpolar tails aggregate with each other.

Question 26

What structure do double tail Amphiphilic molecules form in water?

Answer 26

Bilayer membranes

Question 27

When pH > pKa, what form predominates?

Answer 27

The conjugate base form predominates when the pH is greater than pKa.

Question 28

When pH < pKa, which form predominates?

Answer 28

The acid form predominates when the pH is less than the pKa.

Question 29

True/False: The higher the pKa, the stronger the acid.

Answer 29

False; the higher the pKa, the weaker the acid.

Question 30

True/False: the buffering ability of a weak acid ( or base) can be traced by titrations the acid (or base) with a strong base (or acid).

Answer 30

True THE HIGHER THE CONCENTRATION OF THE BUFFERING AGENT, THE HIGHER BUFFERING CAPACITY. Maximum buffering capacity is observed at pH = pKa The effective buffering range is considered to be within on pH unit of pKa. Ex: The effective buffering pH range of acetic acid is pH = 3.76 - 5.76

Question 31

What are the characteristics of covalent bonds

Answer 31

- Bonds formed by SHARING a pair of electrons - High energy covalent bonds define the basic and molecular components of the cell - high energy bonds - strong - posses bonds with about 100kj of energy,i.e. they take more energy to break - very stable also stable at room temp - determines identity for biochemical molecules - irreversible

Question 32

What are the characteristics of non - covalent bonds/interactions?

Answer 32

- less energy - weak - reversible - replace structure of biochemical molecules - These bonds are much weaker than covalent bonds - governs the final 3D shape of molecules and how they interact with each other - on the energy diagram, these bonds are at the bottom - Hover around the thermal motion at 37 degrees - Easily broken and reformed (ex: DNA and proteins) - NONCOVALENT BONDS DO NOT INVOLVE INTIMATE ELECTRON SHARING

Question 33

What do non covalent bonds/interactions play a role in?

Answer 33

- The faithful replication of DNA - The folding of proteins into intricate 3D forms - The specific recognition of substrates by enzymes - detection of moleuclar signals

Question 34

Ionic interaction (Salt bridges):

Answer 34

- least weak of the 3 non covalent bonding types - Interactions between DISTINCT electric charges on atoms - Take place between atoms bearing a completly negative charge and a completely positive charge - Typical ionic bonds are 20 KJ/mol - Example: Carboxyl group has a negative charge and the amine group has a positive charge to make a salt bridge

Question 35

What is coulombs law (equation and what does it do)? what determines energy?

Answer 35

E = kq1q2/Dr helps find the energy of an electrostatic interaction between two charges (E. - energy, K - equilibirum constant, Q - charges for ion 1 and ion 2, D - dielectric constant, R - distance between 2 ions) the more charge an ion carries, the higher the energy! If D or r gets bigger, energy will become smaller.

Question 36

What does it mean if the dielectric constant is 1 in a vacuum and 80 in water?

Answer 36

The distance must be the same

Question 37

Describe hydrogen bonds:

Answer 37

- Carries a partial positve charge - ANYTHING that is directly bonded to a hydrogen is a hydrogen bond donor - Atoms with a high affinity for hydrogens become hydrogene acceptors - Strength dependent on BOTH distance and bond angle - meaning that hydrogen bonds vary in strength and orientation - form between an electronegative atom (F, O, N) and a paritally positively charge hydrogen. - Hydrogens electron density is pulled away if covalently bonded to an electronegative atom and interacts with the atom through an electrostatic interaction. - Energy between 4 -13kj/mol (non - covalent) - Energy with C - H bond is 430Kj/mol because it is a covalent bond and holds on longer than hydrogen bonds

Question 38

Describe Van der Waals interactions:

Answer 38

- The weakest type of bond - Many molecules can interact electrostatically through Van der Waal interactions - The distribution of electic charges around an atom change with time - The charge distribution is not symmetric - There are regions of partially positive charges and negative charges - the transient asymmetry in the electronic charge acts as an electrostatic interacion to induce a complementary aymmetric electrostatic interactin to distribute around neighboring atoms - Have transient dipole - dipole interactions between transiently charged groups - very small energies: 0.4 to 4 kj/mol - Nonpolar molecules can interact through van der waal interactions.

Question 39

How do Van der waal interaction work?

Answer 39

Oscillations will produce an instantaneous dipole —> this instantaneous dipole induces dipoles in neighboring molecules through complementary electrostatic interactions **works because induced dipole attract with one another,

Question 40

What are van der waal forces very dependent on?

Answer 40

The distance; where E is proportional to 1/r^6 * r — distance

Question 41

True/False: the spheres produced in van der waal interactions are very strong when they touch?

Answer 41

True; if the spheres penetrate with one another then repulsive forces dominante which is an unstable interaction. If they move apart then attractive forces will rapidly decrease so it is optimal when they are closer, so the distance of the atoms is equal to the sum of the radii. Although weak individually, in abudance they can become very strong forces.

Question 42

True/False: some noncovalent interaction are electrostatic interactions and some are not.

Answer 42

False! All noncovalent interactions are electrostatic interaction.

Question 43

How do hydrogen bonds, van der waal interactions, and ionic bonds differ from one another (in addition to strength)?

Answer 43

They differ in geometry, strength, and specificity. They also differ in how they are affected when in the presence of water.

Question 44

What are the properties of water?

Answer 44

Water is the solvent in which most biochemical reactions take place - The properies of water are essential to the formationof macromolecular structures and the progress of chemical reactions Water is polar - its bent shape is due to the distribution of charge being asymmetrical - The oxygen nucleus draws away from the hydrogen nuclei (electron withdrawing) and has a high electron affinity, leaving the Hydrogen with a net positive charge, meaning that the O has a partial negative and H has a partial positive because of a dipole dipole moment, hence justifying the polar structure of water.

Question 45

How is water unique?

Answer 45

Water distrupts the hydrogen bonds between two molecules by competing for the hydrogen bonding capability with other molecules. It can do this because hydrogen bonds form whenever hydrogen is covalently bonded to an electronegative atom. Water can also form hydrogen bonds with other water molecules - because of this water, is highly cohesive which accounts for its high surface tension - also due to this bonding water is less dense - Water serves as both a hydrogen donor and acceptor -

Question 46

What is the hydrophobic effect?

Answer 46

Water interacting with a nonpolar molecules causes the hydrophobic effect. It is the exclusion of nonpolar substances from an aqueous solution. Water will aggregate or cluster hence rigidifying the non - polar molecules and reduces entropy (not favorable) - The structuring of water around the nonpolar surfaces decreases the entropy of the system which will result in a positive delta G (not favorable). In order to ensure that delta G is negative (favorable), the non polar molecule will spontaneously self aggregate or cluster which reduces surface area thus reducing the amount of non favorable interaction with water.

Question 47

True/False: Amphiphilic molecules in water experience both hydrophillic interactions and the hydrophobic effect?

Answer 47

True: polar groups orient towards the solvent while the nonpolar groups aggregate with each other. This unique organization leads to formation of micelle (single tail) or bilayer structures (double tail).

Question 48

How does pH affect acid and base equilibrium?

Answer 48

The optimal pH for a protein is 7 or neutral. Decreasing or increasing in pH changes the ionization charge and structures.. Molecular charge depends on pH through structure and interaction Ph has an effect in enzyme catalysis - at lower values of pH, proteins will carry more positive charges (protinated) - At higher values of pH, proteins will carry more negative charges (deprotinated)

Question 49

Which form predominates when pH > pKa?

Answer 49

The deprotinated form [A-]

Question 50

Which form dominates when the pH < pKa?

Answer 50

The protinated form dominates [HA]

Question 51

What are buffers?

Answer 51

Buffers are weak acid and conjugates base systems acting as buffers against added acid or base Weak acid/bases are preferred because a strong acid/base will completely ionize or disassociate, WA or WB reduces the impact and the proton concentration changes Maximum buffering capacity is observed at pH = pKa, buffering range is within one pH unit of pka (+/- 1) The higher the concentration of the buffering agent results in higher buffering capacity.