Lecture 2 Flashcards
T or F, macromolecules are composed of both covalent and noncovalent bonds
True; the linear sequence of DNA is maintained by covalent bonds’ but the double-helix structure is maintained by noncovalent bonds
Why are non covalent interactions very important for inter molecular interactions?
- because they’re weak so they allow for molecules to interact in a non-permanent way
T or F, noncovalent bonds allow non-permanent intereactions
True
How are noncovalent bonds stable?
– noncovalent bonds together are quite stable allowing the 3-D structure of a molecule to be maintained yet flexible
What are noncovalent bonds important for?
– structure & function for enzyme catalysis
– important 4 function as well
– intermolecular interactions
T or F, covalent bonding cannot account for complex structure biological molecules form
True
T or F, Macromolecules are responsible for cellular structure & function are made up of many thousands of atoms held together by strong covalent bonds
True
What are the different types of noncovalent interactions
- charge-charge
- charge-dipole
- dipole-dipole
- charge-induced dipole
- dipole-induced cipole
- van der Waals (dispersion)
- hydrogen bond
what are characteristics of noncovalent interactions
- all electrostatic in nature –> depend on forces electrical charges exert on one another
- exist in molecules that share electrons unequally
T or F, charge–charge interactions are stronger over large distances than van der Waals
True
Describe charge-charge interactions (w/ ex.) and its characteristics
- 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
T or F, the force of charge-charge interactions is the product of the charges over their distance of separations squared
True; neg. number signifies attraction
F= k (q1q2/r)
T or F, NaCl is an example of charge - charge interaction
True; ionic bond between an atom of Sodium and an atom Chloride
Describe dielectric constant
- 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
Why do ionic bonds tend to come apart in water?
beacuase water has a large dielectric constant (E)
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
True; the higher the dielectric constant the weaker the force
Describe dipole interactions
– 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
What is a dipole moment?
- expresses the magnitude of a molecule’s polarity
- - measures amount of polarity of a molecule
What is the relationship of energy charge and radius in charge charge interactions? What happens when the dielectric constant is higher?
– 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
What is different between dipole interactions vs charge charge interactions?
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)
What is the basis of induced dipoles and van der waals interactions?
– 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
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
Ture; (charge induced dipole interaction)/ dipole–induced dipole interaction
T or F, van der waals attractive energy is a factor only at very short range
True; when two molecules come so close together thati their electron orbitals overlap then there is mutual repulsion
T or F, two nonpolar groups can weakly attract by induced dipole (van der Waals) interaction
True; however closer than contact distance leads to repulsion
T or F, van der Waals forces are stronger if they act as a team
T; each interaction is weak on its own but collectively can make significant contributions to the stability of biomolecules
What happens to van der waals interactions in terms of energy of interaction? When is maximum energy of attraction met?
– 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
Describe Hydrogen bonding and its characteristics
– 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
T or F, the ability of an atom to function as hydrogen bond donor depends on its electronegativity
True; hydrogen forms strong bonds w/ oxygen
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)
True
Which molecules are capable of hydrogen bonding? What are the characteristics of this bond?
– 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).
T or F, Hydrogen bonds have both covalent and noncovalent features
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)
Which H bond interactions have the closest distance of interaction between donor and acceptor?
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
Why is water a very good molecule in terms of hydrogen bonding?
it is capable of forming 4 hydrogen bond interactions that give it its characteristic high boiling point. This also allows good structure when frozen
Why do ionic compounds dissolve in water?
– 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
What are hydrophobic interactions and why are they favorable?
– 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–
What is the hydrophobic effect
– 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
What is the normal physiological pH?
7.4
What are amphipathic molecules
– have both hydrophobic and hydrophilic properties
– polar head interacts with water
– nonpolar components hide from water
What can amphipathic lipds form when they are shaken in aqueous soltions?
- micelles, spherical structures, or bilayer vesicles can form
When pka is less than pH, what happens? When pka is greater than pH, what happens. When pka=pH, what happens?
pKa less than pH = deprotonation pKa more than pH = protonation
pKa = pH 50% acid base present in solution
T or F, acids with larger Ka dissociate more readily
True
T or F, higher pH indicates lower concentration of H+ and vice versa
True
As pH increases one unit above where pka=pH, what percent of compound is disassociated? How about 2?
90% and 99%
Based on Henderson-Hasselbalch equation: what happens as the pH increases? decreases?
– as pH increases = more OH present, an acid will become more dissociated
– as pH decreases, more H+ present, acids and bases become protonated
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.
True
T or F, as pH changes, so does degree of protonation or deprotonation of acidic or basic groups on amino acids, depending on pKa
True
