Lecture 2

Question 1

T or F, macromolecules are composed of both covalent and noncovalent bonds

Answer 1

True; the linear sequence of DNA is maintained by covalent bonds’ but the double-helix structure is maintained by noncovalent bonds

Question 2

Why are non covalent interactions very important for inter molecular interactions?

Answer 2

• because they’re weak so they allow for molecules to interact in a non-permanent way

Question 3

T or F, noncovalent bonds allow non-permanent intereactions

Answer 3

True

Question 4

How are noncovalent bonds stable?

Answer 4

– noncovalent bonds together are quite stable allowing the 3-D structure of a molecule to be maintained yet flexible

Question 5

What are noncovalent bonds important for?

Answer 5

– structure & function for enzyme catalysis

– important 4 function as well

– intermolecular interactions

Question 6

T or F, covalent bonding cannot account for complex structure biological molecules form

Answer 6

True

Question 7

T or F, Macromolecules are responsible for cellular structure & function are made up of many thousands of atoms held together by strong covalent bonds

Answer 7

True

Question 8

What are the different types of noncovalent interactions

Answer 8

• charge-charge
• charge-dipole
• dipole-dipole
• charge-induced dipole
• dipole-induced cipole
• van der Waals (dispersion)
• hydrogen bond

Question 9

what are characteristics of noncovalent interactions

Answer 9

• • all electrostatic in nature –> depend on forces electrical charges exert on one another
• • exist in molecules that share electrons unequally

Question 10

T or F, charge–charge interactions are stronger over large distances than van der Waals

Answer 10

True

Question 11

Describe charge-charge interactions (w/ ex.) and its characteristics

Answer 11

• • ionic bonds, salt bridges
• • ion is formed when one atom loses an electron to another atom which then gains that electron –> these ions are then charged

–> now that those atoms have a diff. number of protons and electrons they carry a net charge

–> they then have an attractive interaction based on the opposite charges between them

Question 12

T or F, the force of charge-charge interactions is the product of the charges over their distance of separations squared

Answer 12

True; neg. number signifies attraction

F= k (q1q2/r)

Question 13

T or F, NaCl is an example of charge - charge interaction

Answer 13

True; ionic bond between an atom of Sodium and an atom Chloride

Question 14

Describe dielectric constant

Answer 14

• • in a cell, charges are surrounded by water or other molecules
• • existence of this medium btwn charges has an effect of “screening” them from one another so that the actual force between two charges is always less than that

Question 15

Why do ionic bonds tend to come apart in water?

Answer 15

beacuase water has a large dielectric constant (E)

Question 16

T or F, Coulomb’s Law is an expression of force, but bond formation or cleavage involves a change in energy. Energy required to separate two charge particles

Answer 16

True; the higher the dielectric constant the weaker the force

Question 17

Describe dipole interactions

Answer 17

– carry non net charge, but have asymmetrical distribution of charge, called polar and have a dipole moment, mu, which expresses the magnitude of the polarity

– in an aqueous environment polar molecules can be attracted by nearby ions or other polar molecules –> shorter range interactions

Question 18

What is a dipole moment?

Answer 18

• • expresses the magnitude of a molecule’s polarity

- - measures amount of polarity of a molecule

Question 19

What is the relationship of energy charge and radius in charge charge interactions? What happens when the dielectric constant is higher?

Answer 19

– energy required to separate particles is proportional to both charges and inversely proportional to the dielectric constant and radius.

– A larger dielectric constant makes it easier to separate charges and thus easier for them to dissolve in solution

Question 20

What is different between dipole interactions vs charge charge interactions?

Answer 20

dipole energy depend on relative orientation of dipoles and are shorter range

– also think of a polar molecule – where it is neutral but it has regions of different charge –> also dipole means 2 (so think of two poles of diff charge)

Question 21

What is the basis of induced dipoles and van der waals interactions?

Answer 21

– result from some sudden polarization of electrons that results in partial charges.

– electron distribution is not static

– Overall it is neutral but can be used to attract substances together. More mm/size equates to more van der waal. If not charged, molecules can come close enough to induced polarization

Question 22

T or F, an anion or cation may induce a dipole in a polarizable molecule and then be attracted to it or a permanent dipole may do the same

Answer 22

Ture; (charge induced dipole interaction)/ dipole–induced dipole interaction

Question 23

T or F, van der waals attractive energy is a factor only at very short range

Answer 23

True; when two molecules come so close together thati their electron orbitals overlap then there is mutual repulsion

Question 24

T or F, two nonpolar groups can weakly attract by induced dipole (van der Waals) interaction

Answer 24

True; however closer than contact distance leads to repulsion

Question 25

T or F, van der Waals forces are stronger if they act as a team

Answer 25

T; each interaction is weak on its own but collectively can make significant contributions to the stability of biomolecules

Question 26

What happens to van der waals interactions in terms of energy of interaction? When is maximum energy of attraction met?

Answer 26

-- energy of repulsion is high as they approach each other but only once hit a certain mark where orbitals begin to overlap and repel. -- Maximum energy of attraction occurs at the most negative energy and occurs only when at the optimal van der wall contact distance where the radii allows close packing and favorable +/- interaction

Question 27

Describe Hydrogen bonding and its characteristics

Answer 27

-- interaction of a hydrogen (covalently bound to electronegative atone) with a pair of nonbonded electrons on another atom (typically O or N) -- fairly weak interaction -- very important for bonding of large macromolecules

Question 28

T or F, the ability of an atom to function as hydrogen bond donor depends on its electronegativity

Answer 28

True; hydrogen forms strong bonds w/ oxygen

Question 29

T or F, when bonded to an electronegative atom, hydrogen develops slight positive charge (H bond donor) and interacts with a pair of electron (H-bond acceptor)

Answer 29

True

Question 30

Which molecules are capable of hydrogen bonding? What are the characteristics of this bond?

Answer 30

-- oxygen, nitrogen, and fluorine. -- The H is covalently bonded to the electronegative atom and pairs in a non-covalent interaction with a pair of non bonded electrons of nearby electron acceptor and shares electrons (still ONF).

Question 31

T or F, Hydrogen bonds have both covalent and noncovalent features

Answer 31

True; electrons are shared between acceptors donors (similar to covalent) -- charge-charge interaction between partially-pos H and the partially-neg acceptor (non-covalent-type)

Question 32

Which H bond interactions have the closest distance of interaction between donor and acceptor?

Answer 32

oh -oh have closest followed by oh - o=c and nh - oh. This is followed by nh - o=c and nh - n= and nh -s

Question 33

Why is water a very good molecule in terms of hydrogen bonding?

Answer 33

it is capable of forming 4 hydrogen bond interactions that give it its characteristic high boiling point. This also allows good structure when frozen

Question 34

Why do ionic compounds dissolve in water?

Answer 34

-- formation of hydration shells which occurs when water replaces ionic interactions to form favorable water ion interaction. --also has high dielectric constant that decreases force of attraction in ionic interactions

Question 35

What are hydrophobic interactions and why are they favorable?

Answer 35

-- without hydration shell water forms ordered cages around hydrophobic molecules. -- when these molecules interact, this reduces the order of water molecules, making it a more energetically favorable process--

Question 36

What is the hydrophobic effect

Answer 36

-- when water is in the presence of hydrophobic elements (nonpolar) it wants to interact -- but hydrophobic (nonpolar) molecule doesn't want to interact so water ends up interact w/ itself --> cage forms -- plays a major role in protein folding

Question 37

What is the normal physiological pH?

Answer 37

7.4

Question 38

What are amphipathic molecules

Answer 38

-- have both hydrophobic and hydrophilic properties -- polar head interacts with water -- nonpolar components hide from water

Question 39

What can amphipathic lipds form when they are shaken in aqueous soltions?

Answer 39

- micelles, spherical structures, or bilayer vesicles can form

Question 40

When pka is less than pH, what happens? When pka is greater than pH, what happens. When pka=pH, what happens?

Answer 40

pKa less than pH = deprotonation pKa more than pH = protonation pKa = pH 50% acid base present in solution

Question 41

T or F, acids with larger Ka dissociate more readily

Answer 41

True

Question 42

T or F, higher pH indicates lower concentration of H+ and vice versa

Answer 42

True

Question 43

As pH increases one unit above where pka=pH, what percent of compound is disassociated? How about 2?

Answer 43

90% and 99%

Question 44

Based on Henderson-Hasselbalch equation: what happens as the pH increases? decreases?

Answer 44

-- as pH increases = more OH present, an acid will become more dissociated -- as pH decreases, more H+ present, acids and bases become protonated

Question 45

True or false. Negative or neutral charge can only exist in a basic environment and a positive or neutral charge can exist in an acidic environment.

Answer 45

True

Question 46

T or F, as pH changes, so does degree of protonation or deprotonation of acidic or basic groups on amino acids, depending on pKa

Answer 46

True